Pseudo obihead for tests

creating a column not using indexers

LICENSE

@@ -0,0 +1,518 @@
+
+  CeCILL FREE SOFTWARE LICENSE AGREEMENT
+
+Version 2.1 dated 2013-06-21
+
+
+    Notice
+
+This Agreement is a Free Software license agreement that is the result
+of discussions between its authors in order to ensure compliance with
+the two main principles guiding its drafting:
+
+  * firstly, compliance with the principles governing the distribution
+    of Free Software: access to source code, broad rights granted to users,
+  * secondly, the election of a governing law, French law, with which it
+    is conformant, both as regards the law of torts and intellectual
+    property law, and the protection that it offers to both authors and
+    holders of the economic rights over software.
+
+The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre]) 
+license are: 
+
+Commissariat à l'énergie atomique et aux énergies alternatives - CEA, a
+public scientific, technical and industrial research establishment,
+having its principal place of business at 25 rue Leblanc, immeuble Le
+Ponant D, 75015 Paris, France.
+
+Centre National de la Recherche Scientifique - CNRS, a public scientific
+and technological establishment, having its principal place of business
+at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
+
+Institut National de Recherche en Informatique et en Automatique -
+Inria, a public scientific and technological establishment, having its
+principal place of business at Domaine de Voluceau, Rocquencourt, BP
+105, 78153 Le Chesnay cedex, France.
+
+
+    Preamble
+
+The purpose of this Free Software license agreement is to grant users
+the right to modify and redistribute the software governed by this
+license within the framework of an open source distribution model.
+
+The exercising of this right is conditional upon certain obligations for
+users so as to preserve this status for all subsequent redistributions.
+
+In consideration of access to the source code and the rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors only have limited liability.
+
+In this respect, the risks associated with loading, using, modifying
+and/or developing or reproducing the software by the user are brought to
+the user's attention, given its Free Software status, which may make it
+complicated to use, with the result that its use is reserved for
+developers and experienced professionals having in-depth computer
+knowledge. Users are therefore encouraged to load and test the
+suitability of the software as regards their requirements in conditions
+enabling the security of their systems and/or data to be ensured and,
+more generally, to use and operate it in the same conditions of
+security. This Agreement may be freely reproduced and published,
+provided it is not altered, and that no provisions are either added or
+removed herefrom.
+
+This Agreement may apply to any or all software for which the holder of
+the economic rights decides to submit the use thereof to its provisions.
+
+Frequently asked questions can be found on the official website of the
+CeCILL licenses family (http://www.cecill.info/index.en.html) for any 
+necessary clarification.
+
+
+    Article 1 - DEFINITIONS
+
+For the purpose of this Agreement, when the following expressions
+commence with a capital letter, they shall have the following meaning:
+
+Agreement: means this license agreement, and its possible subsequent
+versions and annexes.
+
+Software: means the software in its Object Code and/or Source Code form
+and, where applicable, its documentation, "as is" when the Licensee
+accepts the Agreement.
+
+Initial Software: means the Software in its Source Code and possibly its
+Object Code form and, where applicable, its documentation, "as is" when
+it is first distributed under the terms and conditions of the Agreement.
+
+Modified Software: means the Software modified by at least one
+Contribution.
+
+Source Code: means all the Software's instructions and program lines to
+which access is required so as to modify the Software.
+
+Object Code: means the binary files originating from the compilation of
+the Source Code.
+
+Holder: means the holder(s) of the economic rights over the Initial
+Software.
+
+Licensee: means the Software user(s) having accepted the Agreement.
+
+Contributor: means a Licensee having made at least one Contribution.
+
+Licensor: means the Holder, or any other individual or legal entity, who
+distributes the Software under the Agreement.
+
+Contribution: means any or all modifications, corrections, translations,
+adaptations and/or new functions integrated into the Software by any or
+all Contributors, as well as any or all Internal Modules.
+
+Module: means a set of sources files including their documentation that
+enables supplementary functions or services in addition to those offered
+by the Software.
+
+External Module: means any or all Modules, not derived from the
+Software, so that this Module and the Software run in separate address
+spaces, with one calling the other when they are run.
+
+Internal Module: means any or all Module, connected to the Software so
+that they both execute in the same address space.
+
+GNU GPL: means the GNU General Public License version 2 or any
+subsequent version, as published by the Free Software Foundation Inc.
+
+GNU Affero GPL: means the GNU Affero General Public License version 3 or
+any subsequent version, as published by the Free Software Foundation Inc.
+
+EUPL: means the European Union Public License version 1.1 or any
+subsequent version, as published by the European Commission.
+
+Parties: mean both the Licensee and the Licensor.
+
+These expressions may be used both in singular and plural form.
+
+
+    Article 2 - PURPOSE
+
+The purpose of the Agreement is the grant by the Licensor to the
+Licensee of a non-exclusive, transferable and worldwide license for the
+Software as set forth in Article 5 <#scope> hereinafter for the whole
+term of the protection granted by the rights over said Software.
+
+
+    Article 3 - ACCEPTANCE
+
+3.1 The Licensee shall be deemed as having accepted the terms and
+conditions of this Agreement upon the occurrence of the first of the
+following events:
+
+  * (i) loading the Software by any or all means, notably, by
+    downloading from a remote server, or by loading from a physical medium;
+  * (ii) the first time the Licensee exercises any of the rights granted
+    hereunder.
+
+3.2 One copy of the Agreement, containing a notice relating to the
+characteristics of the Software, to the limited warranty, and to the
+fact that its use is restricted to experienced users has been provided
+to the Licensee prior to its acceptance as set forth in Article 3.1
+<#accepting> hereinabove, and the Licensee hereby acknowledges that it
+has read and understood it.
+
+
+    Article 4 - EFFECTIVE DATE AND TERM
+
+
+      4.1 EFFECTIVE DATE
+
+The Agreement shall become effective on the date when it is accepted by
+the Licensee as set forth in Article 3.1 <#accepting>.
+
+
+      4.2 TERM
+
+The Agreement shall remain in force for the entire legal term of
+protection of the economic rights over the Software.
+
+
+    Article 5 - SCOPE OF RIGHTS GRANTED
+
+The Licensor hereby grants to the Licensee, who accepts, the following
+rights over the Software for any or all use, and for the term of the
+Agreement, on the basis of the terms and conditions set forth hereinafter.
+
+Besides, if the Licensor owns or comes to own one or more patents
+protecting all or part of the functions of the Software or of its
+components, the Licensor undertakes not to enforce the rights granted by
+these patents against successive Licensees using, exploiting or
+modifying the Software. If these patents are transferred, the Licensor
+undertakes to have the transferees subscribe to the obligations set
+forth in this paragraph.
+
+
+      5.1 RIGHT OF USE
+
+The Licensee is authorized to use the Software, without any limitation
+as to its fields of application, with it being hereinafter specified
+that this comprises:
+
+ 1. permanent or temporary reproduction of all or part of the Software
+    by any or all means and in any or all form.
+
+ 2. loading, displaying, running, or storing the Software on any or all
+    medium.
+
+ 3. entitlement to observe, study or test its operation so as to
+    determine the ideas and principles behind any or all constituent
+    elements of said Software. This shall apply when the Licensee
+    carries out any or all loading, displaying, running, transmission or
+    storage operation as regards the Software, that it is entitled to
+    carry out hereunder.
+
+
+      5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
+
+The right to make Contributions includes the right to translate, adapt,
+arrange, or make any or all modifications to the Software, and the right
+to reproduce the resulting software.
+
+The Licensee is authorized to make any or all Contributions to the
+Software provided that it includes an explicit notice that it is the
+author of said Contribution and indicates the date of the creation thereof.
+
+
+      5.3 RIGHT OF DISTRIBUTION
+
+In particular, the right of distribution includes the right to publish,
+transmit and communicate the Software to the general public on any or
+all medium, and by any or all means, and the right to market, either in
+consideration of a fee, or free of charge, one or more copies of the
+Software by any means.
+
+The Licensee is further authorized to distribute copies of the modified
+or unmodified Software to third parties according to the terms and
+conditions set forth hereinafter.
+
+
+        5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
+
+The Licensee is authorized to distribute true copies of the Software in
+Source Code or Object Code form, provided that said distribution
+complies with all the provisions of the Agreement and is accompanied by:
+
+ 1. a copy of the Agreement,
+
+ 2. a notice relating to the limitation of both the Licensor's warranty
+    and liability as set forth in Articles 8 and 9,
+
+and that, in the event that only the Object Code of the Software is
+redistributed, the Licensee allows effective access to the full Source
+Code of the Software for a period of at least three years from the
+distribution of the Software, it being understood that the additional
+acquisition cost of the Source Code shall not exceed the cost of the
+data transfer.
+
+
+        5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
+
+When the Licensee makes a Contribution to the Software, the terms and
+conditions for the distribution of the resulting Modified Software
+become subject to all the provisions of this Agreement.
+
+The Licensee is authorized to distribute the Modified Software, in
+source code or object code form, provided that said distribution
+complies with all the provisions of the Agreement and is accompanied by:
+
+ 1. a copy of the Agreement,
+
+ 2. a notice relating to the limitation of both the Licensor's warranty
+    and liability as set forth in Articles 8 and 9,
+
+and, in the event that only the object code of the Modified Software is
+redistributed,
+
+ 3. a note stating the conditions of effective access to the full source
+    code of the Modified Software for a period of at least three years
+    from the distribution of the Modified Software, it being understood
+    that the additional acquisition cost of the source code shall not
+    exceed the cost of the data transfer.
+
+
+        5.3.3 DISTRIBUTION OF EXTERNAL MODULES
+
+When the Licensee has developed an External Module, the terms and
+conditions of this Agreement do not apply to said External Module, that
+may be distributed under a separate license agreement.
+
+
+        5.3.4 COMPATIBILITY WITH OTHER LICENSES
+
+The Licensee can include a code that is subject to the provisions of one
+of the versions of the GNU GPL, GNU Affero GPL and/or EUPL in the
+Modified or unmodified Software, and distribute that entire code under
+the terms of the same version of the GNU GPL, GNU Affero GPL and/or EUPL.
+
+The Licensee can include the Modified or unmodified Software in a code
+that is subject to the provisions of one of the versions of the GNU GPL,
+GNU Affero GPL and/or EUPL and distribute that entire code under the
+terms of the same version of the GNU GPL, GNU Affero GPL and/or EUPL.
+
+
+    Article 6 - INTELLECTUAL PROPERTY
+
+
+      6.1 OVER THE INITIAL SOFTWARE
+
+The Holder owns the economic rights over the Initial Software. Any or
+all use of the Initial Software is subject to compliance with the terms
+and conditions under which the Holder has elected to distribute its work
+and no one shall be entitled to modify the terms and conditions for the
+distribution of said Initial Software.
+
+The Holder undertakes that the Initial Software will remain ruled at
+least by this Agreement, for the duration set forth in Article 4.2 <#term>.
+
+
+      6.2 OVER THE CONTRIBUTIONS
+
+The Licensee who develops a Contribution is the owner of the
+intellectual property rights over this Contribution as defined by
+applicable law.
+
+
+      6.3 OVER THE EXTERNAL MODULES
+
+The Licensee who develops an External Module is the owner of the
+intellectual property rights over this External Module as defined by
+applicable law and is free to choose the type of agreement that shall
+govern its distribution.
+
+
+      6.4 JOINT PROVISIONS
+
+The Licensee expressly undertakes:
+
+ 1. not to remove, or modify, in any manner, the intellectual property
+    notices attached to the Software;
+
+ 2. to reproduce said notices, in an identical manner, in the copies of
+    the Software modified or not.
+
+The Licensee undertakes not to directly or indirectly infringe the
+intellectual property rights on the Software of the Holder and/or
+Contributors, and to take, where applicable, vis-à-vis its staff, any
+and all measures required to ensure respect of said intellectual
+property rights of the Holder and/or Contributors.
+
+
+    Article 7 - RELATED SERVICES
+
+7.1 Under no circumstances shall the Agreement oblige the Licensor to
+provide technical assistance or maintenance services for the Software.
+
+However, the Licensor is entitled to offer this type of services. The
+terms and conditions of such technical assistance, and/or such
+maintenance, shall be set forth in a separate instrument. Only the
+Licensor offering said maintenance and/or technical assistance services
+shall incur liability therefor.
+
+7.2 Similarly, any Licensor is entitled to offer to its licensees, under
+its sole responsibility, a warranty, that shall only be binding upon
+itself, for the redistribution of the Software and/or the Modified
+Software, under terms and conditions that it is free to decide. Said
+warranty, and the financial terms and conditions of its application,
+shall be subject of a separate instrument executed between the Licensor
+and the Licensee.
+
+
+    Article 8 - LIABILITY
+
+8.1 Subject to the provisions of Article 8.2, the Licensee shall be
+entitled to claim compensation for any direct loss it may have suffered
+from the Software as a result of a fault on the part of the relevant
+Licensor, subject to providing evidence thereof.
+
+8.2 The Licensor's liability is limited to the commitments made under
+this Agreement and shall not be incurred as a result of in particular:
+(i) loss due the Licensee's total or partial failure to fulfill its
+obligations, (ii) direct or consequential loss that is suffered by the
+Licensee due to the use or performance of the Software, and (iii) more
+generally, any consequential loss. In particular the Parties expressly
+agree that any or all pecuniary or business loss (i.e. loss of data,
+loss of profits, operating loss, loss of customers or orders,
+opportunity cost, any disturbance to business activities) or any or all
+legal proceedings instituted against the Licensee by a third party,
+shall constitute consequential loss and shall not provide entitlement to
+any or all compensation from the Licensor.
+
+
+    Article 9 - WARRANTY
+
+9.1 The Licensee acknowledges that the scientific and technical
+state-of-the-art when the Software was distributed did not enable all
+possible uses to be tested and verified, nor for the presence of
+possible defects to be detected. In this respect, the Licensee's
+attention has been drawn to the risks associated with loading, using,
+modifying and/or developing and reproducing the Software which are
+reserved for experienced users.
+
+The Licensee shall be responsible for verifying, by any or all means,
+the suitability of the product for its requirements, its good working
+order, and for ensuring that it shall not cause damage to either persons
+or properties.
+
+9.2 The Licensor hereby represents, in good faith, that it is entitled
+to grant all the rights over the Software (including in particular the
+rights set forth in Article 5 <#scope>).
+
+9.3 The Licensee acknowledges that the Software is supplied "as is" by
+the Licensor without any other express or tacit warranty, other than
+that provided for in Article 9.2 <#good-faith> and, in particular,
+without any warranty as to its commercial value, its secured, safe,
+innovative or relevant nature.
+
+Specifically, the Licensor does not warrant that the Software is free
+from any error, that it will operate without interruption, that it will
+be compatible with the Licensee's own equipment and software
+configuration, nor that it will meet the Licensee's requirements.
+
+9.4 The Licensor does not either expressly or tacitly warrant that the
+Software does not infringe any third party intellectual property right
+relating to a patent, software or any other property right. Therefore,
+the Licensor disclaims any and all liability towards the Licensee
+arising out of any or all proceedings for infringement that may be
+instituted in respect of the use, modification and redistribution of the
+Software. Nevertheless, should such proceedings be instituted against
+the Licensee, the Licensor shall provide it with technical and legal
+expertise for its defense. Such technical and legal expertise shall be
+decided on a case-by-case basis between the relevant Licensor and the
+Licensee pursuant to a memorandum of understanding. The Licensor
+disclaims any and all liability as regards the Licensee's use of the
+name of the Software. No warranty is given as regards the existence of
+prior rights over the name of the Software or as regards the existence
+of a trademark.
+
+
+    Article 10 - TERMINATION
+
+10.1 In the event of a breach by the Licensee of its obligations
+hereunder, the Licensor may automatically terminate this Agreement
+thirty (30) days after notice has been sent to the Licensee and has
+remained ineffective.
+
+10.2 A Licensee whose Agreement is terminated shall no longer be
+authorized to use, modify or distribute the Software. However, any
+licenses that it may have granted prior to termination of the Agreement
+shall remain valid subject to their having been granted in compliance
+with the terms and conditions hereof.
+
+
+    Article 11 - MISCELLANEOUS
+
+
+      11.1 EXCUSABLE EVENTS
+
+Neither Party shall be liable for any or all delay, or failure to
+perform the Agreement, that may be attributable to an event of force
+majeure, an act of God or an outside cause, such as defective
+functioning or interruptions of the electricity or telecommunications
+networks, network paralysis following a virus attack, intervention by
+government authorities, natural disasters, water damage, earthquakes,
+fire, explosions, strikes and labor unrest, war, etc.
+
+11.2 Any failure by either Party, on one or more occasions, to invoke
+one or more of the provisions hereof, shall under no circumstances be
+interpreted as being a waiver by the interested Party of its right to
+invoke said provision(s) subsequently.
+
+11.3 The Agreement cancels and replaces any or all previous agreements,
+whether written or oral, between the Parties and having the same
+purpose, and constitutes the entirety of the agreement between said
+Parties concerning said purpose. No supplement or modification to the
+terms and conditions hereof shall be effective as between the Parties
+unless it is made in writing and signed by their duly authorized
+representatives.
+
+11.4 In the event that one or more of the provisions hereof were to
+conflict with a current or future applicable act or legislative text,
+said act or legislative text shall prevail, and the Parties shall make
+the necessary amendments so as to comply with said act or legislative
+text. All other provisions shall remain effective. Similarly, invalidity
+of a provision of the Agreement, for any reason whatsoever, shall not
+cause the Agreement as a whole to be invalid.
+
+
+      11.5 LANGUAGE
+
+The Agreement is drafted in both French and English and both versions
+are deemed authentic.
+
+
+    Article 12 - NEW VERSIONS OF THE AGREEMENT
+
+12.1 Any person is authorized to duplicate and distribute copies of this
+Agreement.
+
+12.2 So as to ensure coherence, the wording of this Agreement is
+protected and may only be modified by the authors of the License, who
+reserve the right to periodically publish updates or new versions of the
+Agreement, each with a separate number. These subsequent versions may
+address new issues encountered by Free Software.
+
+12.3 Any Software distributed under a given version of the Agreement may
+only be subsequently distributed under the same version of the Agreement
+or a subsequent version, subject to the provisions of Article 5.3.4
+<#compatibility>.
+
+
+    Article 13 - GOVERNING LAW AND JURISDICTION
+
+13.1 The Agreement is governed by French law. The Parties agree to
+endeavor to seek an amicable solution to any disagreements or disputes
+that may arise during the performance of the Agreement.
+
+13.2 Failing an amicable solution within two (2) months as from their
+occurrence, and unless emergency proceedings are necessary, the
+disagreements or disputes shall be referred to the Paris Courts having
+jurisdiction, by the more diligent Party.

distutils.ext/obidistutils/command/build_ext.py

@@ -7,107 +7,109 @@ Created on 13 fevr. 2014
 from distutils import log
 import os
 
-from Cython.Distutils import build_ext  as ori_build_ext  # @UnresolvedImport
-
-from Cython.Compiler import Options as cython_options  # @UnresolvedImport
 
 from distutils.errors import DistutilsSetupError
 
-class build_ext(ori_build_ext):
-
+try:
+    from Cython.Distutils import build_ext  as ori_build_ext  # @UnresolvedImport
+    from Cython.Compiler import Options as cython_options  # @UnresolvedImport
+    class build_ext(ori_build_ext):
     
-    def modifyDocScripts(self):
-        build_dir_file=open("doc/sphinx/build_dir.txt","w")
-        print(self.build_lib,file=build_dir_file)
-        build_dir_file.close()
         
-    def initialize_options(self):
-        ori_build_ext.initialize_options(self)  # @UndefinedVariable
-        self.littlebigman = None
-        self.built_files = None
-
-    
-    def finalize_options(self):
-        ori_build_ext.finalize_options(self)  # @UndefinedVariable
-
-        self.set_undefined_options('littlebigman',
-                                   ('littlebigman',  'littlebigman'))
-        
-        self.set_undefined_options('build_files',
-                                   ('files',  'built_files'))
-
-        self.cython_c_in_temp = 1
-                   
-        if self.littlebigman =='-DLITTLE_END':
-            if self.define is None:
-                self.define=[('LITTLE_END',None)]
-            else:
-                self.define.append('LITTLE_END',None)
-        
-    def substitute_sources(self,exe_name,sources):
-        """
-        Substitutes source file name starting by an @ by the actual
-        name of the built file (see --> build_files)
-        """
-        sources = list(sources)
-        for i in range(len(sources)):
-            message = "%s :-> %s" % (exe_name,sources[i])
-            if sources[i][0]=='@':
-                try:
-                    filename = self.built_files[sources[i][1:]]
-                except KeyError:
-                    tmpfilename = os.path.join(self.build_temp,sources[i][1:])
-                    if os.path.isfile       (tmpfilename):
-                        filename = tmpfilename
-                    else:
-                        raise DistutilsSetupError(
-                             'The %s filename declared in the source '
-                             'files of the program %s have not been '
-                             'built by the installation process' % (sources[i],
-                                                                     exe_name))
-                sources[i]=filename
-                log.info("%s changed to %s",message,filename)
-            else:
-                log.info("%s ok",message)
-
-        return sources
-
-    def build_extensions(self):
-        # First, sanity-check the 'extensions' list
-        
-        for ext in self.extensions:
-            ext.sources = self.substitute_sources(ext.name,ext.sources)
+        def modifyDocScripts(self):
+            build_dir_file=open("doc/sphinx/build_dir.txt","w")
+            print(self.build_lib,file=build_dir_file)
+            build_dir_file.close()
             
-        self.check_extensions_list(self.extensions)
-
-        for ext in self.extensions:
-            log.info("%s :-> %s",ext.name,ext.sources)
-            ext.sources = self.cython_sources(ext.sources, ext)
-            self.build_extension(ext)
-
-        
-    def run(self):
-        self.modifyDocScripts()
-
-        for cmd_name in self.get_sub_commands():
-            self.run_command(cmd_name)
-
-        cython_options.annotate = True
-        ori_build_ext.run(self)  # @UndefinedVariable
-        
-
-    def has_files(self):
-        return self.distribution.has_files()
-
-    def has_executables(self):
-        return self.distribution.has_executables()
+        def initialize_options(self):
+            ori_build_ext.initialize_options(self)  # @UndefinedVariable
+            self.littlebigman = None
+            self.built_files = None
     
-    sub_commands = [('build_files',has_files),
-                    ('build_cexe', has_executables)
-                    ] + \
-                   ori_build_ext.sub_commands
-
         
+        def finalize_options(self):
+            ori_build_ext.finalize_options(self)  # @UndefinedVariable
+    
+            self.set_undefined_options('littlebigman',
+                                       ('littlebigman',  'littlebigman'))
+            
+            self.set_undefined_options('build_files',
+                                       ('files',  'built_files'))
+    
+            self.cython_c_in_temp = 1
+                       
+            if self.littlebigman =='-DLITTLE_END':
+                if self.define is None:
+                    self.define=[('LITTLE_END',None)]
+                else:
+                    self.define.append('LITTLE_END',None)
+            
+        def substitute_sources(self,exe_name,sources):
+            """
+            Substitutes source file name starting by an @ by the actual
+            name of the built file (see --> build_files)
+            """
+            sources = list(sources)
+            for i in range(len(sources)):
+                message = "%s :-> %s" % (exe_name,sources[i])
+                if sources[i][0]=='@':
+                    try:
+                        filename = self.built_files[sources[i][1:]]
+                    except KeyError:
+                        tmpfilename = os.path.join(self.build_temp,sources[i][1:])
+                        if os.path.isfile       (tmpfilename):
+                            filename = tmpfilename
+                        else:
+                            raise DistutilsSetupError(
+                                 'The %s filename declared in the source '
+                                 'files of the program %s have not been '
+                                 'built by the installation process' % (sources[i],
+                                                                         exe_name))
+                    sources[i]=filename
+                    log.info("%s changed to %s",message,filename)
+                else:
+                    log.info("%s ok",message)
+    
+            return sources
+    
+        def build_extensions(self):
+            # First, sanity-check the 'extensions' list
+            
+            for ext in self.extensions:
+                ext.sources = self.substitute_sources(ext.name,ext.sources)
+                
+            self.check_extensions_list(self.extensions)
+    
+            for ext in self.extensions:
+                log.info("%s :-> %s",ext.name,ext.sources)
+                ext.sources = self.cython_sources(ext.sources, ext)
+                self.build_extension(ext)
+    
+            
+        def run(self):
+            self.modifyDocScripts()
+    
+            for cmd_name in self.get_sub_commands():
+                self.run_command(cmd_name)
+    
+            cython_options.annotate = True
+            ori_build_ext.run(self)  # @UndefinedVariable
+            
+    
+        def has_files(self):
+            return self.distribution.has_files()
+    
+        def has_executables(self):
+            return self.distribution.has_executables()
+        
+        sub_commands = [('build_files',has_files),
+                        ('build_cexe', has_executables)
+                        ] + \
+                       ori_build_ext.sub_commands
+
+except ImportError:
+    from distutils.command import build_ext  # @UnusedImport
+           
 
 
         

distutils.ext/obidistutils/serenity/bootstrappip.py

@@ -0,0 +1,36 @@
+'''
+Created on 22 janv. 2016
+
+@author: coissac
+'''
+
+import sys
+from urllib import request
+import os.path
+
+from obidistutils.serenity.util import get_serenity_dir
+from obidistutils.serenity.rerun import rerun_with_anothe_python
+from obidistutils.serenity.checkpython import is_a_virtualenv_python
+
+getpipurl="https://bootstrap.pypa.io/get-pip.py"
+
+def bootstrap():
+
+    getpipfile=os.path.join(get_serenity_dir(),"get-pip.py")
+    
+    with request.urlopen(getpipurl) as getpip:
+        with open(getpipfile,"wb") as out:
+            for l in getpip:
+                out.write(l)
+                
+    python = sys.executable
+    
+    if is_a_virtualenv_python():
+        command= "%s %s" % (python,getpipfile)        
+    else:
+        command= "%s %s --user" % (python,getpipfile)
+    
+    os.system(command)
+    
+    rerun_with_anothe_python(python)
+    

distutils.ext/obidistutils/serenity/checkpackage.py

@@ -7,8 +7,13 @@ Created on 2 oct. 2014
 import re
 import os
 
-import pip                                              # @UnresolvedImport
-from pip.utils import get_installed_distributions       # @UnresolvedImport
+try:
+    import pip                                              # @UnresolvedImport
+    from pip.utils import get_installed_distributions       # @UnresolvedImport
+except ImportError:
+    from .bootstrappip import bootstrap
+    bootstrap()
+
 from distutils.version import StrictVersion             # @UnusedImport
 from distutils.errors import DistutilsError
 from distutils import log

distutils.ext/obidistutils/serenity/virtual.py

@@ -59,7 +59,7 @@ def serenity_virtualenv(envname,package,version,minversion='3.4',maxversion=None
                     clear=True, 
                     symlinks=False, 
                     with_pip=True)
-        
+                
         # check the newly created virtualenv
         return serenity_virtualenv(envname,package,version)
     

python/obi.py

@@ -0,0 +1,50 @@
+#!/usr/local/bin/python3.4
+'''
+obi -- shortdesc
+
+obi is a description
+
+It defines classes_and_methods
+
+@author:     user_name
+
+@copyright:  2014 organization_name. All rights reserved.
+
+@license:    license
+
+@contact:    user_email
+@deffield    updated: Updated
+'''
+
+
+default_config = { 'software'       : "The OBITools",
+                   'log'            : False,
+                   'loglevel'       : 'INFO',
+                   'progress'       : True,
+                   'defaultdms'     : None
+                  }
+
+root_config_name='obi'
+
+from obitools3.apps.config import getConfiguration     # @UnresolvedImport
+from obitools3.version import version
+
+__all__     = []
+__version__ = version
+__date__    = '2014-09-28'
+__updated__ = '2014-09-28'
+
+DEBUG = 1
+TESTRUN = 0
+PROFILE = 0
+
+
+if __name__ =="__main__":
+    
+    config = getConfiguration(root_config_name,
+                              default_config)    
+                
+    config[root_config_name]['module'].run(config)
+    
+    
+    

python/obitools3/apps/arguments.pxd

@@ -0,0 +1,3 @@
+#cython: language_level=3
+
+cpdef buildArgumentParser(str configname, str softname)

python/obitools3/apps/arguments.pyx

@@ -0,0 +1,61 @@
+#cython: language_level=3
+
+'''
+Created on 27 mars 2016
+
+@author: coissac
+'''
+
+import argparse
+import sys
+
+
+from .command import getCommandsList
+
+class ObiParser(argparse.ArgumentParser): 
+    def error(self, message):
+        sys.stderr.write('error: %s\n' % message)
+        self.print_help()
+        sys.exit(2)
+
+cpdef buildArgumentParser(str configname, 
+                          str softname):
+    parser = ObiParser()
+    
+    parser.add_argument('--version',   dest='%s:version' % configname, 
+                                       action='store_true', 
+                                       default=False, 
+                        help='Print the version of %s' % softname)
+
+    parser.add_argument('--log',       dest='%s:log' % configname, 
+                                       action='store',
+                                       type=str,
+                                       default=None, 
+                        help='Create a logfile')
+
+    parser.add_argument('--no-progress', dest='%s:progress' % configname, 
+                                       action='store_false', 
+                                       default=None, 
+                        help='Do not print the progress bar during analyzes')
+
+    subparsers = parser.add_subparsers(title='subcommands',
+                                       description='valid subcommands',
+                                       help='additional help')
+    
+    commands = getCommandsList()
+    
+    for c in commands:
+        module = commands[c]
+        
+        if hasattr(module, "run"):
+            if hasattr(module, "__title__"):
+                sub = subparsers.add_parser(c,help=module.__title__)
+            else:
+                sub = subparsers.add_parser(c)
+    
+            if hasattr(module, "addOptions"):
+                module.addOptions(sub)
+            
+            sub.set_defaults(**{'%s:module'  % configname : module})
+                        
+    return parser

python/obitools3/apps/command.pxd

@@ -0,0 +1,3 @@
+#cython: language_level=3
+
+cdef object loadCommand(str name,loader)

python/obitools3/apps/command.pyx

@@ -0,0 +1,44 @@
+#cython: language_level=3
+
+'''
+Created on 27 mars 2016
+
+@author: coissac
+'''
+
+import pkgutil
+
+from obitools3 import commands
+
+cdef object loadCommand(str name,loader):
+    '''
+    Load a command module from its name and an ImpLoader
+    
+    This function is for internal use
+    
+    @param name:   name of the module
+    @type name: str 
+    @param loader: the module loader
+    @type loader: ImpLoader
+    
+    @return the loaded module
+    @rtype: module 
+    '''
+    
+    module = loader.find_module(name).load_module(name)
+    return module
+
+def getCommandsList():
+    '''
+    Returns the list of sub-commands available to the main `obi` command
+    
+    @return: a dict instance with key corresponding to each command and
+             value corresponding to the module
+             
+    @rtype: dict
+    '''
+    
+    cdef dict cmds = dict((x[1],loadCommand(x[1],x[0])) 
+                           for x in pkgutil.iter_modules(commands.__path__) 
+                           if not x[2])
+    return cmds

python/obitools3/apps/config.pxd

@@ -0,0 +1,10 @@
+#cython: language_level=3
+
+cpdef str setRootConfigName(str rootname)
+cpdef str getRootConfigName()
+
+cdef dict buildDefaultConfiguration(str root_config_name,
+                                    dict  config)
+
+cpdef dict getConfiguration(str root_config_name=?,
+                                    dict  config=?)

python/obitools3/apps/config.pyx

@@ -0,0 +1,103 @@
+#cython: language_level=3
+
+'''
+Created on 27 mars 2016
+
+@author: coissac
+'''
+
+import sys
+
+from .command   import  getCommandsList
+from .logging   cimport getLogger
+from .arguments cimport buildArgumentParser
+
+from ..version import version
+from _curses import version
+
+cdef dict __default_config__ = {}
+
+
+cpdef str setRootConfigName(str rootname):
+    global __default_config__
+    if '__root_config__' in __default_config__:
+        if __default_config__["__root_config__"] in __default_config__:
+            __default_config__[rootname]=__default_config__[__default_config__["__root_config__"]]
+            del __default_config__[__default_config__["__root_config__"]]
+    __default_config__['__root_config__']=rootname
+    return rootname
+
+cpdef str getRootConfigName():
+    global __default_config__
+    return __default_config__.get('__root_config__',None)
+
+cdef dict buildDefaultConfiguration(str root_config_name,
+                                    dict  config):
+    global __default_config__
+    
+    __default_config__.clear()
+    setRootConfigName(root_config_name)    
+
+    __default_config__[root_config_name]=config
+    
+    config['version']=version
+    
+    commands = getCommandsList()
+    
+    for c in commands:
+        module = commands[c]
+    
+        assert hasattr(module, "run")
+        
+        if hasattr(module, 'default_config'):
+            __default_config__[c]=module.default_config
+        else:
+            __default_config__[c]={}
+                        
+    return __default_config__
+        
+
+cpdef dict getConfiguration(str root_config_name="__default__",
+                            dict  config={}):
+    global __default_config__
+
+    if '__done__' in __default_config__:
+        return __default_config__
+    
+    if root_config_name=="__default__":
+        raise RuntimeError("No root_config_name specified")
+    
+    if not config:
+        raise RuntimeError("Base configuration is empty")
+    
+    
+    
+    config =  buildDefaultConfiguration(root_config_name,
+                                        config)
+    
+    parser = buildArgumentParser(root_config_name,
+                                 config[root_config_name]['software'])
+    
+    options = vars(parser.parse_args())
+
+    if options['%s:version' % root_config_name]:
+        print("%s - Version %s" % (config[root_config_name]['software'],
+                                   config[root_config_name]['version']))
+        sys.exit(0)
+    
+    for k in options:
+        section,key = k.split(':')
+        s = config[section]
+        if options[k] is not None:
+            s[key]=options[k]
+            
+    if not 'module' in config[root_config_name]:
+        print('\nError: No command specified',file=sys.stderr)
+        parser.print_help()
+        sys.exit(2)
+                
+    getLogger(config)
+    
+    config['__done__']=True
+            
+    return config

python/obitools3/apps/logging.pxd

@@ -0,0 +1,3 @@
+#cython: language_level=3
+
+cpdef getLogger(dict config)

python/obitools3/apps/logging.pyx

@@ -0,0 +1,46 @@
+#cython: language_level=3
+
+'''
+Created on 27 mars 2016
+
+@author: coissac
+'''
+
+import logging
+import sys
+
+cpdef getLogger(dict config):
+    '''
+    Returns the logger as defined by the command line option
+    or by the config file
+    :param config:
+    '''
+    
+    root = config["__root_config__"]
+ 
+    level  = config[root]['loglevel'] 
+    logfile= config[root]['log'] 
+    
+    rootlogger   = logging.getLogger()
+    logFormatter = logging.Formatter("%(asctime)s [%(levelname)-5.5s]  %(message)s")
+
+    stderrHandler = logging.StreamHandler(sys.stderr)
+    stderrHandler.setFormatter(logFormatter)
+
+    rootlogger.addHandler(stderrHandler)
+    
+    if logfile:
+        fileHandler = logging.FileHandler(logfile)
+        fileHandler.setFormatter(logFormatter)
+        rootlogger.addHandler(fileHandler)
+    
+    try:
+        loglevel = getattr(logging, level) 
+    except:
+        loglevel = logging.INFO
+        
+    rootlogger.setLevel(loglevel)
+    
+    config[root]['logger']=rootlogger
+    
+    return rootlogger

python/obitools3/apps/progress.pxd

@@ -0,0 +1,65 @@
+#cython: language_level=3
+
+from ..utils cimport str2bytes
+
+cdef extern from "stdio.h":
+    struct FILE
+    int fprintf(FILE *stream, char *format, ...)
+    FILE* stderr
+    ctypedef unsigned int off_t "unsigned long long"
+    
+cdef extern from "unistd.h":
+    int fsync(int fd);
+
+cdef extern from "time.h":
+    struct tm :
+        int tm_yday 
+        int tm_hour
+        int tm_min
+        int tm_sec
+
+    enum: CLOCKS_PER_SEC
+    
+    ctypedef int time_t
+    ctypedef int clock_t
+    ctypedef int suseconds_t
+    
+    struct timeval:
+        time_t      tv_sec     #  seconds */
+        suseconds_t tv_usec    #  microseconds */
+
+
+    struct timezone :
+        int tz_minuteswest;    # minutes west of Greenwich
+        int tz_dsttime;        # type of DST correction 
+
+        
+    int gettimeofday(timeval *tv, timezone *tz)
+
+
+    tm *gmtime_r(time_t *clock, tm *result)
+    time_t time(time_t *tloc)
+    clock_t clock()
+
+cdef class ProgressBar:
+    cdef off_t   maxi
+    cdef clock_t starttime
+    cdef clock_t lasttime
+    cdef clock_t tickcount
+    cdef int freq
+    cdef int cycle
+    cdef int arrow
+    cdef int lastlog
+    cdef bint ontty
+    cdef int fd
+    
+    cdef bytes head
+    cdef char *chead
+    
+    cdef object logger
+
+    cdef char  *wheel
+    cdef char  *spaces
+    cdef char*  diese 
+    
+    cdef clock_t clock(self)

python/obitools3/apps/progress.pyx

@@ -0,0 +1,138 @@
+#cython: language_level=3
+
+'''
+Created on 27 mars 2016
+
+@author: coissac
+'''
+
+import sys
+from ..utils cimport bytes2str
+
+cdef class ProgressBar:
+    cdef clock_t clock(self):
+        cdef clock_t t
+        cdef timeval tp
+        cdef clock_t s
+        
+        <void> gettimeofday(&tp,NULL)
+        s = <clock_t> (<double> tp.tv_usec * 1.e-6 * <double> CLOCKS_PER_SEC)
+        t = tp.tv_sec * CLOCKS_PER_SEC + s 
+        
+        return t
+
+    def __init__(self,
+                 off_t maxi,
+                 dict  config,
+                 str head="",
+                 double seconde=0.1):
+        self.starttime = self.clock()
+        self.lasttime  = self.starttime
+        self.tickcount = <clock_t> (seconde * CLOCKS_PER_SEC)
+        self.freq      = 1
+        self.cycle     = 0
+        self.arrow     = 0
+        self.lastlog   = 0
+        
+        self.ontty = sys.stderr.isatty()
+        
+        if (maxi<=0):
+            maxi=1
+            
+        self.maxi = maxi
+        self.head = str2bytes(head)
+        self.chead= self.head 
+        
+        
+        self.logger=config[config["__root_config__"]]["logger"]
+        self.wheel =  '|/-\\'
+        self.spaces='          ' \
+                    '          ' \
+                    '          ' \
+                    '          ' \
+                    '          '
+        self.diese ='##########' \
+                    '##########' \
+                    '##########' \
+                    '##########' \
+                    '##########'  
+                           
+    def __call__(self,object pos):
+        cdef off_t    ipos
+        cdef clock_t  elapsed
+        cdef clock_t  newtime
+        cdef clock_t  delta
+        cdef clock_t  more 
+        cdef double   percent 
+        cdef tm remain
+        cdef int days,hour,minu,sec
+        cdef off_t fraction
+        cdef int twentyth
+        
+        self.cycle+=1
+    
+        if self.cycle % self.freq == 0:
+            self.cycle=1
+            newtime  = self.clock()
+            delta         = newtime - self.lasttime
+            self.lasttime = newtime
+            elapsed       = newtime - self.starttime
+#            print(" ",delta,elapsed,elapsed/CLOCKS_PER_SEC,self.tickcount)
+            
+            if   delta < self.tickcount / 5 :
+                self.freq*=2
+            elif delta > self.tickcount * 5 and self.freq>1:
+                self.freq/=2
+                
+            
+            if callable(pos):
+                ipos=pos()
+            else:
+                ipos=pos
+                
+            if ipos==0:
+                ipos=1                
+
+            percent = <double>ipos/<double>self.maxi
+            more = <time_t>((<double>elapsed / percent * (1. - percent))/CLOCKS_PER_SEC)
+            <void>gmtime_r(&more, &remain)
+            days  = remain.tm_yday 
+            hour  = remain.tm_hour
+            minu  = remain.tm_min
+            sec   = remain.tm_sec
+                
+            if self.ontty:
+                fraction=<int>(percent * 50.)
+                self.arrow=(self.arrow+1) % 4
+                self.diese[fraction]=0
+                self.spaces[50 - fraction]=0
+            
+                if days:
+                    <void>fprintf(stderr,b'\r%s %5.1f %% |%s%c%s] remain : %d days %02d:%02d:%02d',
+                                    self.chead,
+                                    percent*100,
+                                    self.diese,self.wheel[self.arrow],self.spaces,
+                                    days,hour,minu,sec)
+                else:
+                    <void>fprintf(stderr,b'\r%s %5.1f %% |%s%c%s] remain : %02d:%02d:%02d',
+                                    self.chead,
+                                    percent*100.,
+                                    self.diese,self.wheel[self.arrow],self.spaces,
+                                    hour,minu,sec)
+                self.diese[fraction]=b'#'
+                self.spaces[50 - fraction]=b' '
+
+            twentyth = int(percent * 20)
+            if twentyth != self.lastlog:
+                
+                if self.ontty:
+                    <void>fprintf(stderr,b'\n')
+                    
+                self.logger.info('%s %5.1f %% remain : %02d:%02d:%02d' % (
+                                        bytes2str(self.head),
+                                        percent*100.,
+                                        hour,minu,sec))
+                self.lastlog=twentyth
+        else:
+            self.cycle+=1
+

python/obitools3/commands/count.py

@@ -0,0 +1,44 @@
+'''
+Created on 8 mars 2016
+
+@author: coissac
+'''
+
+from obitools3.apps.progress import ProgressBar  # @UnresolvedImport
+import time
+
+__title__="Counts sequences in a sequence set"
+
+
+default_config = {   'countmode'       : None
+                 }
+
+def addOptions(parser):
+    parser.add_argument(dest='obi:input',     metavar='obi:input', 
+                                              nargs='?', 
+                                              default=None,
+                        help='input data set' )
+
+    group=parser.add_argument_group('Obicount specific options')
+    group.add_argument('-s','--sequence',
+                             action="store_true", dest="count:sequence",
+                             default=False,
+                             help="Prints only the number of sequence records."
+                             )
+ 
+    group.add_argument('-a','--all',
+                             action="store_true", dest="count:all",
+                             default=False,
+                             help="Prints only the total count of sequence records (if a sequence has no `count` attribute, its default count is 1) (default: False)."
+                             )
+
+    
+    
+def run(config):
+    # The code of my command
+    pb = ProgressBar(1000,config,seconde=1)
+    
+    for i in range(1,1001):
+        pb(i)
+        time.sleep(0.01)
+        

python/obitools3/commands/import.pyx

@@ -0,0 +1,136 @@
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.files.universalopener cimport uopen
+from obitools3.parsers.fasta import fastaIterator
+from obitools3.parsers.fastq import fastqIterator
+from obitools3.obidms._obidms import OBIDMS
+
+
+import time
+
+__title__="Counts sequences in a sequence set"
+
+
+default_config = {   'destview'     : None,
+                     'skip'         : 0,
+                     'only'         : None,
+                     'skiperror'    : False,
+                     'seqinformat'  : None,
+                     'moltype'      : 'nuc',
+                     'filename'     : None
+                 }
+
+def addOptions(parser):
+    parser.add_argument(dest='import:filename',     
+                        metavar='<FILENAME>', 
+                        nargs='?', 
+                        default=None,
+                        help='sequence file name to be imported' )
+
+    group=parser.add_argument_group('obi import specific options')
+
+    group.add_argument('--default-dms','-d',
+                     action="store", dest="obi:defaultdms",
+                     metavar='<DMS NAME>',
+                     default=None,
+                     type=str,
+                     help="Name of the default DMS for reading and writing data")
+    
+    
+    group.add_argument('--destination-view','-v',
+                     action="store", dest="import:destview",
+                     metavar='<VIEW NAME>',
+                     default=None,
+                     type=str,
+                     required=True,
+                     help="Name of the default DMS for reading and writing data")
+
+    group=parser.add_argument_group('obi import specific options')
+    
+    group.add_argument('--skip',
+                     action="store", dest="import:skip",
+                     metavar='<N>',
+                     default=None,
+                     type=int,
+                     help="skip the N first sequences")
+
+    group.add_argument('--only',
+                     action="store", dest="import:only",
+                     metavar='<N>',
+                     default=None,
+                     type=int,
+                     help="treat only N sequences")
+
+    group.add_argument('--skip-on-error',
+                     action="store_true", dest="import:skiperror",
+                     default=None,
+                     help="Skip sequence entries with parse error")
+    
+    group.add_argument('--fasta',
+                     action="store_const", dest="import:seqinformat",
+                     default=None,
+                     const='fasta',
+                     help="Input file is in fasta nucleic format (including obitools fasta extentions)")
+
+    group.add_argument('--fastq',
+                     action="store_const", dest="import:seqinformat",
+                     default=None,
+                     const='fastq',
+                     help="Input file is in sanger fastq nucleic format (standard fastq)")
+
+    group.add_argument('--nuc',
+                     action="store_const", dest="import:moltype",
+                     default=None,
+                     const='nuc',
+                     help="Input file contains nucleic sequences")
+    
+    group.add_argument('--prot',
+                     action="store_const", dest="import:moltype",
+                     default=None,
+                     const='pep',
+                     help="Input file contains protein sequences")
+
+    
+    
+def run(config):
+    pb = ProgressBar(35000000,config,seconde=5)
+      
+    inputs = uopen(config['import']['filename'])
+    
+    if config['import']['seqinformat']=='fasta':
+        iseq = fastaIterator(inputs)
+        view_type="NUC_SEQS_VIEW"
+    elif config['import']['seqinformat']=='fastq':
+        iseq = fastqIterator(inputs)
+        view_type="NUC_SEQS_VIEW"
+    else:
+        raise RuntimeError('No file format specified')
+    
+    # Temporary way to handle NA values
+    #NA_list = ["nan"]
+    
+    # Create DMS
+    d = OBIDMS(config['obi']['defaultdms'])
+    
+    # Create view
+    view = d.new_view(config['import']['destview'], view_type=view_type)
+    
+    i = 0
+    for seq in iseq:
+        pb(i)
+        view[i].set_id(seq['id'])
+        view[i].set_definition(seq['definition'])
+        view[i].set_sequence(seq['sequence'])
+        for tag in seq['tags'] :
+            #print(tag, seq['tags'][tag])
+            #if seq['tags'][tag] not in NA_list :
+            view[i][tag] = seq['tags'][tag]
+        i+=1
+
+   #print(view)
+    print(view.__repr__())
+
+    view.save_and_close()
+    d.close()
+    
+    print("Done.")
+        

python/obitools3/files/linebuffer.pxd

@@ -0,0 +1,6 @@
+#cython: language_level=3
+
+
+cdef class LineBuffer:
+    cdef object fileobj
+    cdef int    size

python/obitools3/files/linebuffer.pyx

@@ -0,0 +1,23 @@
+#cython: language_level=3
+
+'''
+Created on 30 mars 2016
+
+@author: coissac
+'''
+
+cdef class LineBuffer:
+
+    def __init__(self,object fileobj,int size=100000000):
+        self.fileobj=fileobj 
+        self.size=size
+    
+    def __iter__(self):
+        cdef list buff = self.fileobj.readlines(self.size)
+        cdef str  l
+        
+        while buff:
+            for l in buff:
+                yield l
+            buff = self.fileobj.readlines(self.size)
+    

python/obitools3/files/uncompress.pxd

@@ -0,0 +1,17 @@
+#cython: language_level=3
+
+cdef class MagicKeyFile:
+    cdef object stream
+    cdef str    stream_mode
+    cdef object binary
+    cdef bytes  key 
+    cdef int    keylength 
+    cdef int    pos
+    
+    cpdef bytes read(self,int size=?)
+    cpdef int tell(self)
+
+    
+cdef class CompressedFile:
+    cdef object accessor
+    

python/obitools3/files/uncompress.pyx

@@ -0,0 +1,114 @@
+#cython: language_level=3
+
+'''
+Created on 28 mars 2016
+
+@author: coissac
+'''
+
+import zipfile
+import bz2
+import gzip
+
+import io
+
+cdef class MagicKeyFile:
+    def __init__(self,stream,length=2):
+        
+        binary=stream
+        self.stream = stream
+        self.stream_mode = None 
+        if hasattr(stream, "mode"):
+            self.stream_mode = stream.mode
+            if (not 'b' in stream.mode and 
+                hasattr(stream, "buffer") and 
+                'b' in stream.buffer.mode):
+                binary=stream.buffer
+
+        if (self.stream_mode is None and 
+            not (hasattr(stream, 'headers') and 
+                 hasattr(stream.headers, "keys") and
+                 'Content-type' in stream.headers)):
+            raise TypeError("stream does not present the good interface")
+        
+        self.binary=binary
+        self.key=binary.read(length)
+        self.keylength=length
+        self.pos=0
+        
+    cpdef bytes read(self,int size=-1):
+        cdef bytes r
+        
+        if self.pos < self.keylength:
+            if size > (self.keylength - self.pos):
+                size = size - self.keylength + self.pos
+                r = self.key[self.pos:] + self.binary.read(size)
+                self.pos=self.keylength + 1
+            elif size >=0 :
+                r = self.key[self.pos:(self.pos+size)]
+                self.pos+=size
+            else:
+                r = self.key[self.pos:] + self.binary.read(size)
+                self.pos=self.keylength + 1
+        else:
+            r = self.binary.read(size)
+            
+        return r
+    
+    cpdef int tell(self):
+        cdef int p
+        
+        if self.pos < self.keylength:
+            p = self.pos 
+        else:
+            p = self.tell()
+        
+        return p
+    
+    def __getattr__(self,name):
+        return getattr(self.binary, name)
+        
+
+    
+cdef class CompressedFile:
+    
+    
+    def __init__(self,stream):
+        cdef int            keylength
+        cdef MagicKeyFile   magic
+        cdef str            compressor
+        cdef bytes          k 
+        cdef object         c
+        
+        cdef dict compress = { 'zip' : (b'\x50\x4b\x03\x04',zipfile.ZipFile),
+                               'bz2' : (b'\x42\x5a\x68',bz2.BZ2File),
+                               'gz'  : (b'\x1f\x8b\x08',gzip.open)
+                   }
+        
+        keylength = max([len(x[0]) for x in compress.values()])
+        magic=MagicKeyFile(stream,keylength)
+        
+        self.accessor = None
+        
+        for compressor in compress:
+            k,c = compress[compressor]
+            if magic.key.startswith(k):
+                self.accessor = c(magic)
+        
+        if self.accessor is None:
+            self.accessor = magic
+        
+        if ((hasattr(stream, 'headers') and 
+             hasattr(stream.headers, "keys") and
+             'Content-type' in stream.headers and
+             stream.headers['Content-type'].startswith('text/')) or
+            'b' not in magic.stream_mode):
+            self.accessor = io.TextIOWrapper(self.accessor)
+        
+    
+    def __getattr__(self,name):
+        return getattr(self.accessor, name)
+    
+    def __iter__(self):
+        for x in self.accessor:
+            yield x 

python/obitools3/files/universalopener.pxd

@@ -0,0 +1,5 @@
+#cython: language_level=3
+
+from .uncompress cimport CompressedFile
+
+cpdef CompressedFile uopen(str name, mode=?)

python/obitools3/files/universalopener.pyx

@@ -0,0 +1,23 @@
+#cython: language_level=3
+
+'''
+Created on 25 mars 2016
+
+@author: coissac
+'''
+
+from urllib.request import urlopen
+
+
+cpdef CompressedFile uopen(str name, mode='r'):
+    cdef CompressedFile c
+    
+    try:
+        f = urlopen(name)
+    except:
+        f = open(name,mode) 
+        
+    c = CompressedFile(f)
+    
+    return c
+    

python/obitools3/obidms/_obidms.cfiles

@@ -1,5 +1,28 @@
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.h
+../../../src/encode.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/obidebug.h
+../../../src/obidms_taxonomy.h
+../../../src/obidms_taxonomy.c
 ../../../src/obidms.h
 ../../../src/obidms.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
 ../../../src/obidmscolumn.h
 ../../../src/obidmscolumn.c
 ../../../src/obidmscolumndir.h
@@ -10,7 +33,19 @@
 ../../../src/obilittlebigman.c
 ../../../src/obitypes.h
 ../../../src/obitypes.c
-../../../src/private_at_functions.h
-../../../src/private_at_functions.c
-../../../src/obiarray.h
-../../../src/obiarray.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_str.c
+../../../src/obidmscolumn_str.h

python/obitools3/obidms/_obidms.pxd

@@ -2,46 +2,93 @@
 
 from .capi.obidms       cimport OBIDMS_p
 from .capi.obidmscolumn cimport OBIDMS_column_p
+from .capi.obiview      cimport Obiview_p
 from .capi.obitypes     cimport obiversion_t, OBIType_t, index_t
+from ._obitaxo          cimport OBI_Taxonomy
+
+cdef class OBIDMS_column:
+
+    cdef  OBIDMS_column_p*   pointer
+    cdef  OBIDMS             dms
+    cdef  Obiview_p          view
+    cdef  str                data_type
+    cdef  str                dms_name
+    cdef  str                column_name
+    cdef  index_t            nb_elements_per_line
+    cdef  list               elements_names
+        
+    cpdef         update_pointer(self)
+    cpdef list    get_elements_names(self)
+    cpdef str     get_data_type(self)
+    cpdef index_t get_nb_lines_used(self)
+    cpdef str     get_creation_date(self)
+    cpdef str     get_comments(self)
+    cpdef         close(self)
+    @staticmethod
+    cdef  object  get_subclass_type(OBIDMS_column_p column_p)
 
 
-cdef class OBIDMS_column
+cdef class OBIDMS_column_multi_elts(OBIDMS_column):
+    
+    cpdef set_line(self, index_t line_nb, dict values)
+
+
+cdef class OBIDMS_column_line:
+
+    cdef OBIDMS_column column
+    cdef index_t index
+
+
+cdef class OBIView:
+    
+    cdef Obiview_p pointer
+    cdef str       name
+    cdef str       comments
+    cdef dict      columns
+    cdef dict      columns_pp    # TODO this dict might be unnecessary
+    cdef OBIDMS    dms
+    
+    cpdef delete_column(self, str column_name)
+    cpdef add_column(self, 
+                     str column_name, 
+                     obiversion_t version_number=*, 
+                     str type=*,
+                     index_t nb_lines=*, 
+                     index_t nb_elements_per_line=*,
+                     list elements_names=*,
+                     str indexer_name=*,
+                     str comments=*,
+                     bint create=*
+                    )
+    cpdef select_line(self, index_t line_nb)
+    cpdef select_lines(self, list line_selection)
+    cpdef save_and_close(self)
+
+
+cdef class OBIView_NUC_SEQS(OBIView):
+
+    cdef OBIDMS_column ids
+    cdef OBIDMS_column sequences
+    cdef OBIDMS_column definitions
+    
+    cpdef delete_column(self, str column_name)
+    
+
+cdef class OBIView_line :
+
+    cdef index_t index
+    cdef OBIView view
+
 
-            
 cdef class OBIDMS:
 
     cdef OBIDMS_p pointer
     cdef str dms_name
     
-    cpdef dict list(self)
     cpdef close(self)
-    cpdef OBIDMS_column open_column(self,
-                                    str column_name,
-                                    bint create=*, 
-                                    bint clone=*, bint clone_data=*,
-                                    obiversion_t version_number=*, 
-                                    OBIType_t data_type=*,
-                                    index_t nb_lines=*, 
-                                    index_t nb_elements_per_line=*, 
-                                    list elements_names=*,
-                                    str array_name=*)
-
-
-cdef class OBIDMS_column:
-
-    cdef OBIDMS_column_p    pointer
-    cdef OBIDMS             dms
-    cdef str                data_type   # TODO keep as OBIType_t? both?
-    cdef str                dms_name
-    cdef str                column_name
-    cdef index_t             nb_elements_per_line
-    cdef list               elements_names
-
-#    cpdef object get_item(self, index_t line_nb, str element_name)                  TODO can't declare because not the same in all subclasses
-#    cpdef        set_item(self, index_t line_nb, str element_name, object value)    TODO can't declare because object value
-    cpdef list    get_elements_names(self)
-    cpdef str     get_data_type(self)
-    cpdef index_t get_nb_lines_used(self)
-    cpdef str     get_creation_date(self)
-    cpdef         close(self)
+    cpdef OBI_Taxonomy open_taxonomy(self, str taxo_name)
+    cpdef OBIView open_view(self, str view_name)
+    cpdef OBIView new_view(self, str view_name, object view_to_clone=*, list line_selection=*, str view_type=*, str comments=*)
+    cpdef dict read_view_infos(self, str view_name)
+    cpdef dict read_views(self)
 

python/obitools3/obidms/_obidmscolumn_bool.cfiles

@@ -1,18 +1,51 @@
-../../../src/obidmscolumn_bool.c
-../../../src/obidmscolumn_bool.h
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.h
+../../../src/encode.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/obidebug.h
+../../../src/obidms_taxonomy.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
 ../../../src/obidmscolumn.h
 ../../../src/obidmscolumn.c
 ../../../src/obidmscolumndir.h
 ../../../src/obidmscolumndir.c
-../../../src/obidms.h
-../../../src/obidms.c
 ../../../src/obierrno.h
 ../../../src/obierrno.c
 ../../../src/obilittlebigman.h
 ../../../src/obilittlebigman.c
 ../../../src/obitypes.h
 ../../../src/obitypes.c
-../../../src/private_at_functions.h
-../../../src/private_at_functions.c
-../../../src/obiarray.h
-../../../src/obiarray.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_str.c
+../../../src/obidmscolumn_str.h

python/obitools3/obidms/_obidmscolumn_bool.pxd

@@ -1,25 +1,14 @@
 #cython: language_level=3
 
-from .capi.obitypes cimport obibool_t, index_t
-from ._obidms       cimport OBIDMS_column
+from .capi.obitypes cimport index_t
+from ._obidms       cimport OBIDMS_column, OBIDMS_column_multi_elts
 
 
 cdef class OBIDMS_column_bool(OBIDMS_column):
     cpdef object get_line(self, index_t line_nb)
     cpdef set_line(self, index_t line_nb, object value)
-    cpdef close(self)
 
-cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):     
-    cpdef set_line(self, index_t line_nb, object value)
-    cpdef close(self)
-
-cdef class OBIDMS_column_bool_multi_elts(OBIDMS_column_bool):
+cdef class OBIDMS_column_multi_elts_bool(OBIDMS_column_multi_elts):
     cpdef object get_item(self, index_t line_nb, str element_name)
     cpdef object get_line(self, index_t line_nb)
-    cpdef set_item(self, index_t line_nb, str element_name, obibool_t value)
-    cpdef set_line(self, index_t line_nb, object values)
-
-cdef class OBIDMS_column_bool_multi_elts_writable(OBIDMS_column_bool_multi_elts):
-    cpdef set_item(self, index_t line_nb, str element_name, obibool_t value)
-    cpdef set_line(self, index_t line_nb, object values)
-    cpdef close(self)
+    cpdef set_item(self, index_t line_nb, str element_name, object value)

python/obitools3/obidms/_obidmscolumn_bool.pyx

@@ -1,13 +1,11 @@
 #cython: language_level=3
  
-from .capi.obidmscolumn cimport obi_close_column,\
-                                obi_truncate_and_close_column, \
-                                obi_column_get_obibool_with_elt_name, \
-                                obi_column_get_obibool_with_elt_idx, \
-                                obi_column_set_obibool_with_elt_name, \
-                                obi_column_set_obibool_with_elt_idx
+from .capi.obiview      cimport obi_column_get_obibool_with_elt_name_in_view, \
+                                obi_column_get_obibool_with_elt_idx_in_view, \
+                                obi_column_set_obibool_with_elt_name_in_view, \
+                                obi_column_set_obibool_with_elt_idx_in_view
 from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIBool_NA
+from .capi.obitypes     cimport OBIBool_NA, obibool_t
 
 from obitools3.utils cimport str2bytes
 
@@ -19,7 +17,7 @@ cdef class OBIDMS_column_bool(OBIDMS_column):
     cpdef object get_line(self, index_t line_nb):
         cdef obibool_t value
         cdef object result
-        value = obi_column_get_obibool_with_elt_idx(self.pointer, line_nb, 0)
+        value = obi_column_get_obibool_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
         if obi_errno > 0 :
             raise IndexError(line_nb)
         if value == OBIBool_NA :
@@ -27,32 +25,20 @@ cdef class OBIDMS_column_bool(OBIDMS_column):
         else :
             result = PyBool_FromLong(value)
         return result
-
-    cpdef set_line(self, index_t line_nb, object value):
-        raise Exception("Column is read-only")
     
-    cpdef close(self):
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-
-
-cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):     
-
     cpdef set_line(self, index_t line_nb, object value):
-        if obi_column_set_obibool_with_elt_idx(self.pointer, line_nb, 0, <obibool_t> value) < 0:
+        if value is None :
+            value = OBIBool_NA
+        if obi_column_set_obibool_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, <obibool_t> value) < 0:
             raise Exception("Problem setting a value in a column")
 
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
 
-
-cdef class OBIDMS_column_bool_multi_elts(OBIDMS_column_bool):
+cdef class OBIDMS_column_multi_elts_bool(OBIDMS_column_multi_elts):
 
     cpdef object get_item(self, index_t line_nb, str element_name):
         cdef obibool_t value
         cdef object result
-        value = obi_column_get_obibool_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
+        value = obi_column_get_obibool_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
         if obi_errno > 0 :
             raise IndexError(line_nb, element_name)
         if value == OBIBool_NA :
@@ -63,42 +49,29 @@ cdef class OBIDMS_column_bool_multi_elts(OBIDMS_column_bool):
     
     cpdef object get_line(self, index_t line_nb) :
         cdef obibool_t value
-        cdef object result
+        cdef object value_in_result
+        cdef dict result
         cdef index_t i
         cdef bint all_NA
         result = {}
         all_NA = True
         for i in range(self.nb_elements_per_line) :
-            value = obi_column_get_obibool_with_elt_idx(self.pointer, line_nb, i)
+            value = obi_column_get_obibool_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
             if obi_errno > 0 :
-                raise IndexError(line_nb)           
-            result[self.elements_names[i]] = PyBool_FromLong(value)
-            if all_NA and (value != OBIBool_NA) :
+                raise IndexError(line_nb)
+            if value == OBIBool_NA :
+                value_in_result = None
+            else :
+                value_in_result = PyBool_FromLong(value)   
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
                 all_NA = False
         if all_NA :
             result = None
         return result
 
-    cpdef set_item(self, index_t line_nb, str element_name, obibool_t value):
-        raise Exception("Column is read-only")
-
-    cpdef set_line(self, index_t line_nb, object values):
-        raise Exception("Column is read-only")
-
-
-cdef class OBIDMS_column_bool_multi_elts_writable(OBIDMS_column_bool_multi_elts):     
-
-    cpdef set_item(self, index_t line_nb, str element_name, obibool_t value):
-        if obi_column_set_obibool_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
+    cpdef set_item(self, index_t line_nb, str element_name, object value):
+        if value is None :
+            value = OBIBool_NA
+        if obi_column_set_obibool_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), <obibool_t> value) < 0:
             raise Exception("Problem setting a value in a column")
-    
-    cpdef set_line(self, index_t line_nb, object values):
-        cdef obibool_t value
-        for element_name in values :
-            value = <obibool_t> values[element_name]
-            self.set_item(line_nb, element_name, value)
-
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-

python/obitools3/obidms/_obidmscolumn_char.cfiles

@@ -1,18 +1,51 @@
-../../../src/obidmscolumn_char.c
-../../../src/obidmscolumn_char.h
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.h
+../../../src/encode.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/obidebug.h
+../../../src/obidms_taxonomy.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
 ../../../src/obidmscolumn.h
 ../../../src/obidmscolumn.c
 ../../../src/obidmscolumndir.h
 ../../../src/obidmscolumndir.c
-../../../src/obidms.h
-../../../src/obidms.c
 ../../../src/obierrno.h
 ../../../src/obierrno.c
 ../../../src/obilittlebigman.h
 ../../../src/obilittlebigman.c
 ../../../src/obitypes.h
 ../../../src/obitypes.c
-../../../src/private_at_functions.h
-../../../src/private_at_functions.c
-../../../src/obiarray.h
-../../../src/obiarray.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_str.c
+../../../src/obidmscolumn_str.h

python/obitools3/obidms/_obidmscolumn_char.pxd

@@ -1,25 +1,14 @@
 #cython: language_level=3
 
-from .capi.obitypes cimport obichar_t, index_t
-from ._obidms       cimport OBIDMS_column
+from .capi.obitypes cimport index_t
+from ._obidms       cimport OBIDMS_column, OBIDMS_column_multi_elts
 
 
 cdef class OBIDMS_column_char(OBIDMS_column):
     cpdef object get_line(self, index_t line_nb)
     cpdef set_line(self, index_t line_nb, object value)
-    cpdef close(self)
 
-cdef class OBIDMS_column_char_writable(OBIDMS_column_char):     
-    cpdef set_line(self, index_t line_nb, object value)
-    cpdef close(self)
-
-cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
+cdef class OBIDMS_column_multi_elts_char(OBIDMS_column_multi_elts):
     cpdef object get_item(self, index_t line_nb, str element_name)
     cpdef object get_line(self, index_t line_nb)
-    cpdef set_item(self, index_t line_nb, str element_name, bytes value)
-    cpdef set_line(self, index_t line_nb, object values)
-
-cdef class OBIDMS_column_char_multi_elts_writable(OBIDMS_column_char_multi_elts):
-    cpdef set_item(self, index_t line_nb, str element_name, bytes value)
-    cpdef set_line(self, index_t line_nb, object values)
-    cpdef close(self)
+    cpdef set_item(self, index_t line_nb, str element_name, object value)

python/obitools3/obidms/_obidmscolumn_char.pyx

@@ -1,15 +1,13 @@
 #cython: language_level=3
  
-from .capi.obidmscolumn cimport obi_close_column,\
-                                obi_truncate_and_close_column, \
-                                obi_column_get_obichar_with_elt_name, \
-                                obi_column_get_obichar_with_elt_idx, \
-                                obi_column_set_obichar_with_elt_name, \
-                                obi_column_set_obichar_with_elt_idx
+from .capi.obiview      cimport obi_column_get_obichar_with_elt_name_in_view, \
+                                obi_column_get_obichar_with_elt_idx_in_view, \
+                                obi_column_set_obichar_with_elt_name_in_view, \
+                                obi_column_set_obichar_with_elt_idx_in_view
 from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIChar_NA
+from .capi.obitypes     cimport OBIChar_NA, obichar_t
 
-from obitools3.utils cimport str2bytes
+from obitools3.utils cimport str2bytes, bytes2str
 
 
 cdef class OBIDMS_column_char(OBIDMS_column):
@@ -17,122 +15,62 @@ cdef class OBIDMS_column_char(OBIDMS_column):
     cpdef object get_line(self, index_t line_nb):
         cdef obichar_t value
         cdef object result
-        value = obi_column_get_obichar_with_elt_idx(self.pointer, line_nb, 0)
+        value = obi_column_get_obichar_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
         if obi_errno > 0 :
             raise IndexError(line_nb)
         if value == OBIChar_NA :
             result = None
         else :
-            result = <bytes> value
+            result = bytes2str(value)
         return result
 
     cpdef set_line(self, index_t line_nb, object value):
-        raise Exception("Column is read-only")
-    
-    cpdef close(self):
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-
-
-cdef class OBIDMS_column_char_writable(OBIDMS_column_char):     
-
-    cpdef set_line(self, index_t line_nb, object value):
-        if obi_column_set_obichar_with_elt_idx(self.pointer, line_nb, 0, <bytes> value[0]) < 0:
+        if value is None :
+            value = OBIChar_NA
+        if obi_column_set_obichar_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, str2bytes(value)[0]) < 0:
             raise Exception("Problem setting a value in a column")
 
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
 
-
-cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
+cdef class OBIDMS_column_multi_elts_char(OBIDMS_column_multi_elts):
 
     cpdef object get_item(self, index_t line_nb, str element_name):
         cdef obichar_t value
         cdef object result
-        value = obi_column_get_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
+        value = obi_column_get_obichar_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
         if obi_errno > 0 :
             raise IndexError(line_nb, element_name)
         if value == OBIChar_NA :
             result = None
         else :
-            result = <bytes> value
+            result = bytes2str(value)
         return result
-    
+
     cpdef object get_line(self, index_t line_nb) :
         cdef obichar_t value
-        cdef object result
+        cdef object value_in_result
+        cdef dict result
         cdef index_t i
         cdef bint all_NA
         result = {}
         all_NA = True
         for i in range(self.nb_elements_per_line) :
-            value = obi_column_get_obichar_with_elt_idx(self.pointer, line_nb, i)
+            value = obi_column_get_obichar_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
             if obi_errno > 0 :
-                raise IndexError(line_nb)           
-            result[self.elements_names[i]] = <bytes> value
-            if all_NA and (value != OBIChar_NA) :
+                raise IndexError(line_nb)
+            if value == OBIChar_NA :
+                value_in_result = None
+            else :
+                value_in_result = bytes2str(value)   
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
                 all_NA = False
         if all_NA :
             result = None
         return result
 
-    cpdef set_item(self, index_t line_nb, str element_name, bytes value):
-        raise Exception("Column is read-only")
-
-    cpdef set_line(self, index_t line_nb, object values):
-        raise Exception("Column is read-only")
-
-
-cdef class OBIDMS_column_char_multi_elts_writable(OBIDMS_column_char_multi_elts):     
-
-    cpdef set_item(self, index_t line_nb, str element_name, bytes value):
-        if obi_column_set_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value[0]) < 0:
+    cpdef set_item(self, index_t line_nb, str element_name, object value):
+        if value is None :
+            value = OBIChar_NA
+        if obi_column_set_obichar_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), str2bytes(value)[0]) < 0:
             raise Exception("Problem setting a value in a column")
-    
-    cpdef set_line(self, index_t line_nb, object values):
-        cdef bytes value
-        for element_name in values :
-            value = <bytes> values[element_name]
-            self.set_item(line_nb, element_name, value)
 
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-
-
-
-
-
-# cdef class OBIDMS_column_char(OBIDMS_column) :
-#  
-#     cpdef object get_item(self, index_t line_nb, str element_name):
-#         cdef char value
-#         cdef object result
-#         value = obi_column_get_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
-#         if obi_errno > 0 :
-#             raise IndexError(line_nb, element_name)
-#         if value == OBIChar_NA :
-#             result = None
-#         else :
-#             result = <bytes> value
-#         return result
-# 
-#     cpdef set_item(self, index_t line_nb, str element_name, bytes value):
-#         raise Exception("Column is read-only")
-#  
-#     cpdef close(self):
-#         if obi_close_column(self.pointer) < 0 :
-#             raise Exception("Problem closing a column")
-#  
-#          
-# cdef class OBIDMS_column_char_writable(OBIDMS_column_char) :     
-#  
-#     cpdef set_item(self, index_t line_nb, str element_name, bytes value):
-#         if obi_column_set_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value[0]) < 0:
-#             raise Exception("Problem setting a value in a column")
-#  
-#     cpdef close(self):
-#         if obi_truncate_and_close_column(self.pointer) < 0 :
-#             raise Exception("Problem closing a column")
-#       

python/obitools3/obidms/_obidmscolumn_float.cfiles

@@ -1,18 +1,51 @@
-../../../src/obidmscolumn_float.c
-../../../src/obidmscolumn_float.h
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.h
+../../../src/encode.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/obidebug.h
+../../../src/obidms_taxonomy.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
 ../../../src/obidmscolumn.h
 ../../../src/obidmscolumn.c
 ../../../src/obidmscolumndir.h
 ../../../src/obidmscolumndir.c
-../../../src/obidms.h
-../../../src/obidms.c
 ../../../src/obierrno.h
 ../../../src/obierrno.c
 ../../../src/obilittlebigman.h
 ../../../src/obilittlebigman.c
 ../../../src/obitypes.h
 ../../../src/obitypes.c
-../../../src/private_at_functions.h
-../../../src/private_at_functions.c
-../../../src/obiarray.h
-../../../src/obiarray.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_str.c
+../../../src/obidmscolumn_str.h

python/obitools3/obidms/_obidmscolumn_float.pxd

@@ -1,25 +1,14 @@
 #cython: language_level=3
 
-from .capi.obitypes cimport obifloat_t, index_t
-from ._obidms       cimport OBIDMS_column
+from .capi.obitypes cimport index_t
+from ._obidms       cimport OBIDMS_column, OBIDMS_column_multi_elts
 
 
 cdef class OBIDMS_column_float(OBIDMS_column):
     cpdef object get_line(self, index_t line_nb)
     cpdef set_line(self, index_t line_nb, object value)
-    cpdef close(self)
 
-cdef class OBIDMS_column_float_writable(OBIDMS_column_float):     
-    cpdef set_line(self, index_t line_nb, object value)
-    cpdef close(self)
-
-cdef class OBIDMS_column_float_multi_elts(OBIDMS_column_float):
+cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts):
     cpdef object get_item(self, index_t line_nb, str element_name)
     cpdef object get_line(self, index_t line_nb)
-    cpdef set_item(self, index_t line_nb, str element_name, obifloat_t value)
-    cpdef set_line(self, index_t line_nb, object values)
-
-cdef class OBIDMS_column_float_multi_elts_writable(OBIDMS_column_float_multi_elts):
-    cpdef set_item(self, index_t line_nb, str element_name, obifloat_t value)
-    cpdef set_line(self, index_t line_nb, object values)
-    cpdef close(self)
+    cpdef set_item(self, index_t line_nb, str element_name, object value)

python/obitools3/obidms/_obidmscolumn_float.pyx

@@ -1,13 +1,11 @@
 #cython: language_level=3
 
-from .capi.obidmscolumn cimport obi_close_column,\
-                                obi_truncate_and_close_column, \
-                                obi_column_get_obifloat_with_elt_name, \
-                                obi_column_get_obifloat_with_elt_idx, \
-                                obi_column_set_obifloat_with_elt_name, \
-                                obi_column_set_obifloat_with_elt_idx
+from .capi.obiview      cimport obi_column_get_obifloat_with_elt_name_in_view, \
+                                obi_column_get_obifloat_with_elt_idx_in_view, \
+                                obi_column_set_obifloat_with_elt_name_in_view, \
+                                obi_column_set_obifloat_with_elt_idx_in_view
 from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIFloat_NA
+from .capi.obitypes     cimport OBIFloat_NA, obifloat_t
 
 from obitools3.utils cimport str2bytes
 
@@ -17,7 +15,7 @@ cdef class OBIDMS_column_float(OBIDMS_column):
     cpdef object get_line(self, index_t line_nb):
         cdef obifloat_t value
         cdef object result
-        value = obi_column_get_obifloat_with_elt_idx(self.pointer, line_nb, 0)
+        value = obi_column_get_obifloat_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
         if obi_errno > 0 :
             raise IndexError(line_nb)
         if value == OBIFloat_NA :
@@ -27,30 +25,18 @@ cdef class OBIDMS_column_float(OBIDMS_column):
         return result
 
     cpdef set_line(self, index_t line_nb, object value):
-        raise Exception("Column is read-only")
-    
-    cpdef close(self):
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-
-
-cdef class OBIDMS_column_float_writable(OBIDMS_column_float):     
-
-    cpdef set_line(self, index_t line_nb, object value):
-        if obi_column_set_obifloat_with_elt_idx(self.pointer, line_nb, 0, <obifloat_t> value) < 0:
+        if value is None :
+            value = OBIFloat_NA
+        if obi_column_set_obifloat_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, <obifloat_t> value) < 0:
             raise Exception("Problem setting a value in a column")
 
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
 
-
-cdef class OBIDMS_column_float_multi_elts(OBIDMS_column_float):
+cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts):
 
     cpdef object get_item(self, index_t line_nb, str element_name):
         cdef obifloat_t value
         cdef object result
-        value = obi_column_get_obifloat_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
+        value = obi_column_get_obifloat_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
         if obi_errno > 0 :
             raise IndexError(line_nb, element_name)
         if value == OBIFloat_NA :
@@ -58,46 +44,33 @@ cdef class OBIDMS_column_float_multi_elts(OBIDMS_column_float):
         else :
             result = <double> value
         return result
-    
+
     cpdef object get_line(self, index_t line_nb) :
         cdef obifloat_t value
-        cdef object result
+        cdef object value_in_result
+        cdef dict result
         cdef index_t i
         cdef bint all_NA
         result = {}
         all_NA = True
         for i in range(self.nb_elements_per_line) :
-            value = obi_column_get_obifloat_with_elt_idx(self.pointer, line_nb, i)
+            value = obi_column_get_obifloat_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
             if obi_errno > 0 :
-                raise IndexError(line_nb)           
-            result[self.elements_names[i]] = <double> value
-            if all_NA and (value != OBIFloat_NA) :
+                raise IndexError(line_nb)
+            if value == OBIFloat_NA :
+                value_in_result = None
+            else :
+                value_in_result = <double> value
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
                 all_NA = False
         if all_NA :
             result = None
         return result
-
-    cpdef set_item(self, index_t line_nb, str element_name, obifloat_t value):
-        raise Exception("Column is read-only")
-
-    cpdef set_line(self, index_t line_nb, object values):
-        raise Exception("Column is read-only")
-
-
-cdef class OBIDMS_column_float_multi_elts_writable(OBIDMS_column_float_multi_elts):     
-
-    cpdef set_item(self, index_t line_nb, str element_name, obifloat_t value):
-        if obi_column_set_obifloat_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
+   
+    cpdef set_item(self, index_t line_nb, str element_name, object value):
+        if value is None :
+            value = OBIFloat_NA
+        if obi_column_set_obifloat_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), <obifloat_t> value) < 0:
             raise Exception("Problem setting a value in a column")
-    
-    cpdef set_line(self, index_t line_nb, object values):
-        cdef obifloat_t value
-        for element_name in values :
-            value = <obifloat_t> values[element_name]
-            self.set_item(line_nb, element_name, value)
-
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-
  

python/obitools3/obidms/_obidmscolumn_int.cfiles

@@ -1,18 +1,51 @@
-../../../src/obidmscolumn_int.c
-../../../src/obidmscolumn_int.h
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.h
+../../../src/encode.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/obidebug.h
+../../../src/obidms_taxonomy.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
 ../../../src/obidmscolumn.h
 ../../../src/obidmscolumn.c
 ../../../src/obidmscolumndir.h
 ../../../src/obidmscolumndir.c
-../../../src/obidms.h
-../../../src/obidms.c
 ../../../src/obierrno.h
 ../../../src/obierrno.c
 ../../../src/obilittlebigman.h
 ../../../src/obilittlebigman.c
 ../../../src/obitypes.h
 ../../../src/obitypes.c
-../../../src/private_at_functions.h
-../../../src/private_at_functions.c
-../../../src/obiarray.h
-../../../src/obiarray.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_str.c
+../../../src/obidmscolumn_str.h

python/obitools3/obidms/_obidmscolumn_int.pxd

@@ -1,25 +1,14 @@
 #cython: language_level=3
 
-from .capi.obitypes cimport obiint_t, index_t
-from ._obidms       cimport OBIDMS_column
+from .capi.obitypes cimport index_t
+from ._obidms       cimport OBIDMS_column, OBIDMS_column_multi_elts
 
 
 cdef class OBIDMS_column_int(OBIDMS_column):
     cpdef object get_line(self, index_t line_nb)
     cpdef set_line(self, index_t line_nb, object value)
-    cpdef close(self)
 
-cdef class OBIDMS_column_int_writable(OBIDMS_column_int):     
-    cpdef set_line(self, index_t line_nb, object value)
-    cpdef close(self)
-
-cdef class OBIDMS_column_int_multi_elts(OBIDMS_column_int):
+cdef class OBIDMS_column_multi_elts_int(OBIDMS_column_multi_elts):
     cpdef object get_item(self, index_t line_nb, str element_name)
     cpdef object get_line(self, index_t line_nb)
-    cpdef set_item(self, index_t line_nb, str element_name, obiint_t value)
-    cpdef set_line(self, index_t line_nb, object values)
-
-cdef class OBIDMS_column_int_multi_elts_writable(OBIDMS_column_int_multi_elts):
-    cpdef set_item(self, index_t line_nb, str element_name, obiint_t value)
-    cpdef set_line(self, index_t line_nb, object values)
-    cpdef close(self)
+    cpdef set_item(self, index_t line_nb, str element_name, object value)

python/obitools3/obidms/_obidmscolumn_int.pyx

@@ -1,13 +1,11 @@
 #cython: language_level=3
 
-from .capi.obidmscolumn cimport obi_close_column,\
-                                obi_truncate_and_close_column, \
-                                obi_column_get_obiint_with_elt_name, \
-                                obi_column_get_obiint_with_elt_idx, \
-                                obi_column_set_obiint_with_elt_name, \
-                                obi_column_set_obiint_with_elt_idx
+from .capi.obiview      cimport obi_column_get_obiint_with_elt_name_in_view, \
+                                obi_column_get_obiint_with_elt_idx_in_view, \
+                                obi_column_set_obiint_with_elt_name_in_view, \
+                                obi_column_set_obiint_with_elt_idx_in_view
 from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIInt_NA
+from .capi.obitypes     cimport OBIInt_NA, obiint_t
 
 from obitools3.utils cimport str2bytes
 
@@ -19,7 +17,7 @@ cdef class OBIDMS_column_int(OBIDMS_column):
     cpdef object get_line(self, index_t line_nb):
         cdef obiint_t value
         cdef object result
-        value = obi_column_get_obiint_with_elt_idx(self.pointer, line_nb, 0)
+        value = obi_column_get_obiint_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
         if obi_errno > 0 :
             raise IndexError(line_nb)
         if value == OBIInt_NA :
@@ -27,32 +25,20 @@ cdef class OBIDMS_column_int(OBIDMS_column):
         else :
             result = PyInt_FromLong(value)
         return result
-
+            
     cpdef set_line(self, index_t line_nb, object value):
-        raise Exception("Column is read-only")
-    
-    cpdef close(self):
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-
-
-cdef class OBIDMS_column_int_writable(OBIDMS_column_int):     
-
-    cpdef set_line(self, index_t line_nb, object value):
-        if obi_column_set_obiint_with_elt_idx(self.pointer, line_nb, 0, <obiint_t> value) < 0:
+        if value is None :
+            value = OBIInt_NA
+        if obi_column_set_obiint_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, <obiint_t> value) < 0:
             raise Exception("Problem setting a value in a column")
 
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
 
-
-cdef class OBIDMS_column_int_multi_elts(OBIDMS_column_int):
+cdef class OBIDMS_column_multi_elts_int(OBIDMS_column_multi_elts):
 
     cpdef object get_item(self, index_t line_nb, str element_name):
         cdef obiint_t value
         cdef object result
-        value = obi_column_get_obiint_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
+        value = obi_column_get_obiint_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
         if obi_errno > 0 :
             raise IndexError(line_nb, element_name)
         if value == OBIInt_NA :
@@ -63,42 +49,30 @@ cdef class OBIDMS_column_int_multi_elts(OBIDMS_column_int):
     
     cpdef object get_line(self, index_t line_nb) :
         cdef obiint_t value
-        cdef object result
+        cdef object value_in_result
+        cdef dict result
         cdef index_t i
         cdef bint all_NA
         result = {}
         all_NA = True
         for i in range(self.nb_elements_per_line) :
-            value = obi_column_get_obiint_with_elt_idx(self.pointer, line_nb, i)
+            value = obi_column_get_obiint_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
             if obi_errno > 0 :
-                raise IndexError(line_nb)           
-            result[self.elements_names[i]] = PyInt_FromLong(value)
-            if all_NA and (value != OBIInt_NA) :
+                raise IndexError(line_nb)
+            if value == OBIInt_NA :
+                value_in_result = None
+            else :
+                value_in_result = PyInt_FromLong(value)
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
                 all_NA = False
         if all_NA :
-            result = None
+            result = None   # TODO discuss
         return result
 
-    cpdef set_item(self, index_t line_nb, str element_name, obiint_t value):
-        raise Exception("Column is read-only")
-
-    cpdef set_line(self, index_t line_nb, object values):
-        raise Exception("Column is read-only")
-
-
-cdef class OBIDMS_column_int_multi_elts_writable(OBIDMS_column_int_multi_elts):     
-
-    cpdef set_item(self, index_t line_nb, str element_name, obiint_t value):
-        if obi_column_set_obiint_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
+    cpdef set_item(self, index_t line_nb, str element_name, object value):
+        if value is None :
+            value = OBIInt_NA
+        if obi_column_set_obiint_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), <obiint_t> value) < 0:
             raise Exception("Problem setting a value in a column")
-    
-    cpdef set_line(self, index_t line_nb, object values):
-        cdef obiint_t value
-        for element_name in values :
-            value = <obiint_t> values[element_name]
-            self.set_item(line_nb, element_name, value)
-
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
 

python/obitools3/obidms/_obidmscolumn_seq.cfiles

@@ -0,0 +1,51 @@
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.h
+../../../src/encode.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/obidebug.h
+../../../src/obidms_taxonomy.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/obilittlebigman.h
+../../../src/obilittlebigman.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_str.c
+../../../src/obidmscolumn_str.h

python/obitools3/obidms/_obidmscolumn_seq.pxd

@@ -0,0 +1,14 @@
+#cython: language_level=3
+
+from .capi.obitypes cimport index_t
+from ._obidms       cimport OBIDMS_column, OBIDMS_column_multi_elts
+
+
+cdef class OBIDMS_column_seq(OBIDMS_column):
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_line(self, index_t line_nb, object value)
+
+cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
+    cpdef object get_item(self, index_t line_nb, str element_name)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_item(self, index_t line_nb, str element_name, object value)

python/obitools3/obidms/_obidmscolumn_seq.pyx

@@ -0,0 +1,88 @@
+#cython: language_level=3
+ 
+from .capi.obiview      cimport obi_column_get_obiseq_with_elt_name_in_view, \
+                                obi_column_get_obiseq_with_elt_idx_in_view, \
+                                obi_column_set_obiseq_with_elt_name_in_view, \
+                                obi_column_set_obiseq_with_elt_idx_in_view
+from .capi.obierrno     cimport obi_errno
+from .capi.obitypes     cimport OBISeq_NA, const_char_p
+
+from obitools3.utils cimport str2bytes, bytes2str
+
+from libc.stdlib cimport free
+from libc.string cimport strcmp
+
+
+cdef class OBIDMS_column_seq(OBIDMS_column):
+
+    cpdef object get_line(self, index_t line_nb):
+        cdef char*  value
+        cdef object result
+        value = obi_column_get_obiseq_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
+        if obi_errno > 0 :
+            raise IndexError(line_nb)
+        if strcmp(value, OBISeq_NA) == 0 :
+            result = None
+        else :
+            result = bytes2str(value)
+            free(value)
+        return result
+
+    cpdef set_line(self, index_t line_nb, object value):
+        cdef bytes value_b
+        if value is None :
+            value_b = OBISeq_NA
+        else :
+            value_b = str2bytes(value)
+        if obi_column_set_obiseq_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, value_b) < 0:
+            raise Exception("Problem setting a value in a column")
+
+
+cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
+
+    cpdef object get_item(self, index_t line_nb, str element_name):
+        cdef char*  value
+        cdef object result
+        value = obi_column_get_obiseq_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
+        if obi_errno > 0 :
+            raise IndexError(line_nb, element_name)
+        if strcmp(value, OBISeq_NA) == 0 :
+            result = None
+        else :
+            result = bytes2str(value)
+            free(value)
+        return result
+
+    cpdef object get_line(self, index_t line_nb) :
+        cdef char*   value
+        cdef object  value_in_result
+        cdef dict    result
+        cdef index_t i
+        cdef bint    all_NA
+        result = {}
+        all_NA = True
+        for i in range(self.nb_elements_per_line) :
+            value = obi_column_get_obiseq_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
+            if obi_errno > 0 :
+                raise IndexError(line_nb)
+            if strcmp(value, OBISeq_NA) == 0 :
+                value_in_result = None
+            else :
+                value_in_result = bytes2str(value)
+                free(value)    
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
+                all_NA = False
+        if all_NA :
+            result = None
+        return result
+
+    cpdef set_item(self, index_t line_nb, str element_name, object value):
+        cdef bytes value_b
+        if value is None :
+            value_b = OBISeq_NA
+        else :
+            value_b = str2bytes(value)
+        if obi_column_set_obiseq_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
+            raise Exception("Problem setting a value in a column")
+    

python/obitools3/obidms/_obidmscolumn_str.cfiles

@@ -1,18 +1,51 @@
-../../../src/obidmscolumn_str.c
-../../../src/obidmscolumn_str.h
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.h
+../../../src/encode.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/obidebug.h
+../../../src/obidms_taxonomy.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
 ../../../src/obidmscolumn.h
 ../../../src/obidmscolumn.c
 ../../../src/obidmscolumndir.h
 ../../../src/obidmscolumndir.c
-../../../src/obidms.h
-../../../src/obidms.c
 ../../../src/obierrno.h
 ../../../src/obierrno.c
 ../../../src/obilittlebigman.h
 ../../../src/obilittlebigman.c
 ../../../src/obitypes.h
 ../../../src/obitypes.c
-../../../src/private_at_functions.h
-../../../src/private_at_functions.c
-../../../src/obiarray.h
-../../../src/obiarray.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_str.c
+../../../src/obidmscolumn_str.h

python/obitools3/obidms/_obidmscolumn_str.pxd

@@ -1,25 +1,14 @@
 #cython: language_level=3
 
 from .capi.obitypes cimport index_t
-from ._obidms       cimport OBIDMS_column
+from ._obidms       cimport OBIDMS_column, OBIDMS_column_multi_elts
 
 
 cdef class OBIDMS_column_str(OBIDMS_column):
     cpdef object get_line(self, index_t line_nb)
     cpdef set_line(self, index_t line_nb, object value)
-    cpdef close(self)
 
-cdef class OBIDMS_column_str_writable(OBIDMS_column_str):     
-    cpdef set_line(self, index_t line_nb, object value)
-    cpdef close(self)
-
-cdef class OBIDMS_column_str_multi_elts(OBIDMS_column_str):
+cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
     cpdef object get_item(self, index_t line_nb, str element_name)
     cpdef object get_line(self, index_t line_nb)
-    cpdef set_item(self, index_t line_nb, str element_name, str value)
-    cpdef set_line(self, index_t line_nb, object values)
-
-cdef class OBIDMS_column_str_multi_elts_writable(OBIDMS_column_str_multi_elts):
-    cpdef set_item(self, index_t line_nb, str element_name, str value)
-    cpdef set_line(self, index_t line_nb, object values)
-    cpdef close(self)
+    cpdef set_item(self, index_t line_nb, str element_name, object value)

python/obitools3/obidms/_obidmscolumn_str.pyx

@@ -1,103 +1,87 @@
 #cython: language_level=3
  
-from .capi.obidmscolumn cimport obi_close_column,\
-                                obi_truncate_and_close_column, \
-                                obi_column_get_obistr_with_elt_name, \
-                                obi_column_get_obistr_with_elt_idx, \
-                                obi_column_set_obistr_with_elt_name, \
-                                obi_column_set_obistr_with_elt_idx
+from .capi.obiview      cimport obi_column_get_obistr_with_elt_name_in_view, \
+                                obi_column_get_obistr_with_elt_idx_in_view, \
+                                obi_column_set_obistr_with_elt_name_in_view, \
+                                obi_column_set_obistr_with_elt_idx_in_view
 from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIIdx_NA, const_char_p
+from .capi.obitypes     cimport OBIStr_NA, const_char_p
 
 from obitools3.utils cimport str2bytes, bytes2str
 
+from libc.string cimport strcmp
+
 
 cdef class OBIDMS_column_str(OBIDMS_column):
 
     cpdef object get_line(self, index_t line_nb):
-        cdef bytes value
-        cdef object result
-        value = <bytes> obi_column_get_obistr_with_elt_idx(self.pointer, line_nb, 0)
+        cdef const_char_p value
+        cdef object       result
+        value = obi_column_get_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
         if obi_errno > 0 :
             raise IndexError(line_nb)
-        if value == OBIIdx_NA :
+        if strcmp(value, OBIStr_NA) == 0 :
             result = None
         else :
             result = bytes2str(value)
+        # NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. (TODO discuss)
         return result
 
     cpdef set_line(self, index_t line_nb, object value):
-        raise Exception("Column is read-only")
-    
-    cpdef close(self):
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-
-
-cdef class OBIDMS_column_str_writable(OBIDMS_column_str):     
-
-    cpdef set_line(self, index_t line_nb, object value):
-        if obi_column_set_obistr_with_elt_idx(self.pointer, line_nb, 0, str2bytes(value)) < 0:
+        cdef bytes value_b
+        if value is None :
+            value_b = OBIStr_NA
+        else :
+            value_b = str2bytes(value)
+        if obi_column_set_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, value_b) < 0:
             raise Exception("Problem setting a value in a column")
 
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
 
-
-cdef class OBIDMS_column_str_multi_elts(OBIDMS_column_str):
+cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
 
     cpdef object get_item(self, index_t line_nb, str element_name):
-        cdef bytes value
-        cdef object result
-        value = <bytes> obi_column_get_obistr_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
+        cdef const_char_p value
+        cdef object       result
+        value = obi_column_get_obistr_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
         if obi_errno > 0 :
             raise IndexError(line_nb, element_name)
-        if value == OBIIdx_NA :
+        if strcmp(value, OBIStr_NA) == 0 :
             result = None
         else :
             result = bytes2str(value)
+        # NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. (TODO discuss)
         return result
-    
+
     cpdef object get_line(self, index_t line_nb) :
-        cdef bytes value
-        cdef object result
-        cdef index_t i
-        cdef bint all_NA
+        cdef const_char_p value
+        cdef object       value_in_result
+        cdef dict         result
+        cdef index_t      i
+        cdef bint         all_NA
         result = {}
         all_NA = True
         for i in range(self.nb_elements_per_line) :
-            value = <bytes> obi_column_get_obistr_with_elt_idx(self.pointer, line_nb, i)
+            value = obi_column_get_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
             if obi_errno > 0 :
-                raise IndexError(line_nb)           
-            result[self.elements_names[i]] = bytes2str(value)
-            if all_NA and (value != OBIIdx_NA) :
+                raise IndexError(line_nb)
+            if strcmp(value, OBIStr_NA) == 0 :
+                value_in_result = None
+            else :
+                value_in_result = bytes2str(value)
+            # NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. (TODO discuss)
+            result[self.elements_names[i]] = value_in_result
+            if all_NA and (value_in_result is not None) :
                 all_NA = False
         if all_NA :
             result = None
         return result
 
-    cpdef set_item(self, index_t line_nb, str element_name, str value):
-        raise Exception("Column is read-only")
-
-    cpdef set_line(self, index_t line_nb, object values):
-        raise Exception("Column is read-only")
-
-
-cdef class OBIDMS_column_str_multi_elts_writable(OBIDMS_column_str_multi_elts):     
-
-    cpdef set_item(self, index_t line_nb, str element_name, str value):
-        if obi_column_set_obistr_with_elt_name(self.pointer, line_nb, str2bytes(element_name), str2bytes(value)) < 0:
+    cpdef set_item(self, index_t line_nb, str element_name, object value):
+        cdef bytes value_b
+        if value is None :
+            value_b = OBIStr_NA
+        else :
+            value_b = str2bytes(value)
+        if obi_column_set_obistr_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
             raise Exception("Problem setting a value in a column")
     
-    cpdef set_line(self, index_t line_nb, object values):
-        cdef str value
-        for element_name in values :
-            value = values[element_name]
-            self.set_item(line_nb, element_name, value)
-
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-
- 

python/obitools3/obidms/_obiseq.cfiles

@@ -0,0 +1,51 @@
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.h
+../../../src/encode.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/obidebug.h
+../../../src/obidms_taxonomy.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/obilittlebigman.h
+../../../src/obilittlebigman.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_str.c
+../../../src/obidmscolumn_str.h

python/obitools3/obidms/_obiseq.pxd

@@ -0,0 +1,30 @@
+#cython: language_level=3
+
+from ._obidms cimport OBIView_line
+
+
+cdef class OBI_Seq(dict) :
+    cdef str id
+    cdef str definition
+    cdef str sequence
+
+    cpdef set_id(self, str id)
+    cpdef get_id(self)
+    cpdef set_definition(self, str definition)
+    cpdef get_definition(self)
+    cpdef get_sequence(self)
+
+
+cdef class OBI_Nuc_Seq(OBI_Seq) :
+    #cpdef str reverse_complement(self)    
+    cpdef set_sequence(self, str sequence)
+
+
+cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
+    cpdef set_id(self, str id)
+    cpdef get_id(self)
+    cpdef set_definition(self, str definition)
+    cpdef get_definition(self)
+    cpdef set_sequence(self, str sequence)
+    cpdef get_sequence(self)
+   # cpdef str reverse_complement(self)

python/obitools3/obidms/_obiseq.pyx

@@ -0,0 +1,75 @@
+#cython: language_level=3
+
+from obitools3.utils cimport bytes2str, str2bytes
+
+from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \
+                           ID_COLUMN, \
+                           DEFINITION_COLUMN
+
+cdef class OBI_Seq(dict) :
+
+    def __init__(self, str id, str seq, str definition=None) :
+        self.set_id(id)
+        self.set_sequence(seq)
+        if definition is not None :
+            self.set_definition(definition)
+        
+    cpdef set_id(self, str id) :
+        self.id = id
+        self[bytes2str(ID_COLUMN)] = id
+        
+    cpdef get_id(self) :
+        return self.id
+            
+    cpdef set_definition(self, str definition) :
+        self.definition = definition
+        self[bytes2str(DEFINITION_COLUMN)] = definition
+        
+    cpdef get_definition(self) :
+        return self.definition
+        
+    cpdef get_sequence(self) :
+        return self.sequence
+
+    def __str__(self) :
+        return self.sequence    # or not
+
+
+cdef class OBI_Nuc_Seq(OBI_Seq) :
+    
+    cpdef set_sequence(self, str sequence) :
+        self.sequence = sequence
+        self[bytes2str(NUC_SEQUENCE_COLUMN)] = sequence
+
+#    cpdef str reverse_complement(self) :    TODO in C ?
+#        pass
+
+
+cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
+
+    cpdef set_id(self, str id) :
+        self[bytes2str(ID_COLUMN)] = id
+        
+    cpdef get_id(self) :
+        return self[bytes2str(ID_COLUMN)]
+            
+    cpdef set_definition(self, str definition) :
+        self[bytes2str(DEFINITION_COLUMN)] = definition
+
+    cpdef get_definition(self) :
+        return self[bytes2str(DEFINITION_COLUMN)]
+
+    cpdef set_sequence(self, str sequence) :
+        self[bytes2str(NUC_SEQUENCE_COLUMN)] = sequence
+
+    cpdef get_sequence(self) :
+        return self[bytes2str(NUC_SEQUENCE_COLUMN)]
+    
+#    def __str__(self) :
+#        return self[bytes2str(NUC_SEQUENCE_COLUMN)]    # or not
+    
+#    cpdef str reverse_complement(self) :    TODO in C ?
+#        pass
+
+    # TODO static method to import?
+    

python/obitools3/obidms/_obitaxo.cfiles

@@ -0,0 +1,51 @@
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.h
+../../../src/encode.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/obidebug.h
+../../../src/obidms_taxonomy.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/obilittlebigman.h
+../../../src/obilittlebigman.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_str.c
+../../../src/obidmscolumn_str.h

python/obitools3/obidms/_obitaxo.pxd

@@ -0,0 +1,31 @@
+#cython: language_level=3
+
+from .capi.obitaxonomy cimport ecotx_t, OBIDMS_taxonomy_p
+
+from libc.stdint   cimport int32_t
+
+
+cdef class OBI_Taxonomy :
+
+    cdef str name
+    cdef OBIDMS_taxonomy_p pointer
+    
+    cpdef close(self)
+
+ 
+cdef class OBI_Taxon :
+
+    cdef ecotx_t* pointer
+    cdef int32_t  taxid
+    cdef int32_t  rank
+    cdef int32_t  farest
+    cdef ecotx_t* parent
+    cdef str name
+        
+    cpdef int32_t taxid(self)
+    
+    cpdef int32_t rank(self)
+    
+    cpdef int32_t farest(self)
+    
+    cpdef OBI_Taxon parent(self)

python/obitools3/obidms/_obitaxo.pyx

@@ -0,0 +1,65 @@
+#cython: language_level=3
+
+from obitools3.utils   cimport bytes2str, str2bytes
+
+from .capi.obitaxonomy cimport obi_read_taxonomy, \
+                               obi_close_taxonomy, \
+                               obi_taxo_get_taxon_with_taxid
+
+from ._obidms cimport OBIDMS
+
+from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
+
+
+cdef class OBI_Taxonomy :
+
+    def __init__(self, OBIDMS dms, str name) :
+        
+        self.name = name
+        self.pointer = obi_read_taxonomy(dms.pointer, str2bytes(name), True)    # TODO discuss
+    
+    
+    def __getitem__(self, object ref):
+        
+        cdef ecotx_t* taxon_p
+        cdef object taxon_capsule
+        
+        if type(ref) == int :
+            taxon_p = obi_taxo_get_taxon_with_taxid(self.pointer, ref)
+            taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL)
+            return OBI_Taxon(taxon_capsule)
+    
+         
+    cpdef close(self) :
+        if (obi_close_taxonomy(self.pointer) < 0) :
+            raise Exception("Error closing the taxonomy")
+        
+
+cdef class OBI_Taxon :    # dict subclass?
+
+    def __init__(self, object taxon_capsule) :
+        
+        cdef ecotx_t* taxon
+        
+        taxon = <ecotx_t*> PyCapsule_GetPointer(taxon_capsule, NULL)   
+        self.pointer = taxon
+        self.taxid = taxon.taxid
+        self.rank = taxon.rank
+        self.farest = taxon.farest
+        self.parent = taxon.parent
+        self.name = bytes2str(taxon.name)
+        
+    cpdef int32_t taxid(self):
+        return self.taxid
+    
+    cpdef int32_t rank(self):
+        return self.rank
+    
+    cpdef int32_t farest(self):
+        return self.farest
+    
+    cpdef OBI_Taxon parent(self):
+        cdef object parent_capsule
+        parent_capsule = PyCapsule_New(self.parent, NULL, NULL)
+        return OBI_Taxon(parent_capsule)
+    

python/obitools3/obidms/capi/obidmscolumn.pxd

@@ -15,25 +15,28 @@ from ..capi.obitypes cimport const_char_p, \
 cdef extern from "obidmscolumn.h" nogil:
     
     struct OBIDMS_column_header_t:
-        bint            little_endian
-        int             header_size
+        size_t          header_size
+        size_t          data_size
         index_t         line_count
         index_t         lines_used
         index_t         nb_elements_per_line
         const_char_p    elements_names
-        OBIType_t       data_type
+        OBIType_t       returned_data_type
+        OBIType_t       stored_data_type
         time_t          creation_date
         obiversion_t    version
         obiversion_t    cloned_from
         const_char_p    name
-        const_char_p    array_name
+        const_char_p    indexer_name
         const_char_p    comments
     
     ctypedef OBIDMS_column_header_t* OBIDMS_column_header_p
 
     struct OBIDMS_column_t:
+        OBIDMS_p               dms
         OBIDMS_column_header_p header
-
+        bint                   writable
+        
     ctypedef OBIDMS_column_t* OBIDMS_column_p
 
     OBIDMS_column_p obi_create_column(OBIDMS_p dms, 
@@ -42,7 +45,8 @@ cdef extern from "obidmscolumn.h" nogil:
                                       index_t nb_lines, 
                                       index_t nb_elements_per_line, 
                                       const_char_p elements_names,
-                                      const_char_p array_name)
+                                      const_char_p indexer_name,
+                                      const_char_p comments)
                 
     OBIDMS_column_p obi_open_column(OBIDMS_p dms, 
                                     const_char_p column_name, 
@@ -51,24 +55,27 @@ cdef extern from "obidmscolumn.h" nogil:
     int obi_close_column(OBIDMS_column_p column)
         
     OBIDMS_column_p obi_clone_column(OBIDMS_p dms, 
+                                     OBIDMS_column_p line_selection,
                                      const_char_p column_name, 
                                      obiversion_t version_number, 
                                      bint clone_data)
     
-    int obi_truncate_and_close_column(OBIDMS_column_p column)
+    int obi_close_column(OBIDMS_column_p column)
     
     obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, 
                                                          const_char_p column_name)
         
     OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, 
-                                                           const_char_p column_name)
+                                                           const_char_p column_name,
+                                                           obiversion_t version_number)
     
-    int obi_unmap_header(OBIDMS_column_header_p header)
-        
-    char* obi_column_format_date(time_t date)
+    int obi_close_header(OBIDMS_column_header_p header)
+
+    int obi_select(OBIDMS_column_p line_selection_column, index_t line_to_grep)
+
 
-    
 cdef extern from "obidmscolumn_int.h" nogil:
+
     int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, 
                                             index_t line_nb, 
                                             const_char_p element_name, 
@@ -77,7 +84,7 @@ cdef extern from "obidmscolumn_int.h" nogil:
     int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, 
                                            index_t line_nb, 
                                            index_t element_idx, 
-                                        obiint_t value)
+                                           obiint_t value)
     
     obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, 
                                                  index_t line_nb, 
@@ -87,14 +94,13 @@ cdef extern from "obidmscolumn_int.h" nogil:
                                                 index_t line_nb, 
                                                 index_t element_idx)
 
-
 cdef extern from "obidmscolumn_bool.h" nogil:
 
     int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, 
                                              index_t line_nb, 
                                              const_char_p element_name, 
                                              obibool_t value)
-    
+
     int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, 
                                             index_t line_nb, 
                                             index_t element_idx, 
@@ -114,7 +120,7 @@ cdef extern from "obidmscolumn_char.h" nogil:
                                              index_t line_nb, 
                                              const_char_p element_name, 
                                              obichar_t value)
-    
+
     int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, 
                                             index_t line_nb, 
                                             index_t element_idx, 
@@ -134,7 +140,7 @@ cdef extern from "obidmscolumn_float.h" nogil:
                                               index_t line_nb, 
                                               const_char_p element_name, 
                                               obifloat_t value)
-    
+
     int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, 
                                              index_t line_nb, 
                                              index_t element_idx, 
@@ -153,18 +159,38 @@ cdef extern from "obidmscolumn_str.h" nogil:
     int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, 
                                             index_t line_nb, 
                                             const_char_p element_name, 
-                                            char* value)
-    
+                                            const_char_p value)
+
     int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, 
                                            index_t line_nb, 
                                            index_t element_idx, 
-                                           char* value)
+                                           const_char_p value)
     
     const_char_p obi_column_get_obistr_with_elt_name(OBIDMS_column_p column, 
+                                                     index_t line_nb, 
+                                                     const_char_p element_name)
+    
+    const_char_p obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, 
+                                                    index_t line_nb, 
+                                                    index_t element_idx)
+
+cdef extern from "obidmscolumn_seq.h" nogil:
+
+    int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column, 
+                                            index_t line_nb, 
+                                            const_char_p element_name, 
+                                            const_char_p value)
+
+    int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, 
+                                           index_t line_nb, 
+                                           index_t element_idx, 
+                                           const_char_p value)
+    
+    char* obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column, 
                                               index_t line_nb, 
                                               const_char_p element_name)
     
-    const_char_p obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, 
+    char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, 
                                              index_t line_nb, 
                                              index_t element_idx)
 

python/obitools3/obidms/capi/obitaxonomy.pxd

@@ -0,0 +1,42 @@
+#cython: language_level=3
+
+from .obitypes     cimport const_char_p
+from .obidms       cimport OBIDMS_p
+from libc.stdint   cimport int32_t
+
+
+cdef extern from "obidms_taxonomy.h" nogil:
+
+    struct OBIDMS_taxonomy_t
+    ctypedef OBIDMS_taxonomy_t* OBIDMS_taxonomy_p
+    
+    struct ecotxnode :
+        int32_t           taxid
+        int32_t           rank
+        int32_t           farest
+        ecotxnode*        parent
+        char*             name
+    
+    ctypedef ecotxnode ecotx_t
+
+
+    OBIDMS_taxonomy_p obi_read_taxonomy(OBIDMS_p dms, const_char_p taxonomy_name, bint read_alternative_names)
+    
+    int obi_close_taxonomy(OBIDMS_taxonomy_p taxonomy)
+    
+    ecotx_t* obi_taxo_get_parent_at_rank(ecotx_t* taxon, int32_t rankidx)
+    
+    ecotx_t* obi_taxo_get_taxon_with_taxid(OBIDMS_taxonomy_p taxonomy, int32_t taxid)
+    
+    bint obi_taxo_is_taxon_under_taxid(ecotx_t* taxon, int32_t other_taxid)
+    
+    ecotx_t* obi_taxo_get_species(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
+    
+    ecotx_t* obi_taxo_get_genus(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
+    
+    ecotx_t* obi_taxo_get_family(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
+    
+    ecotx_t* obi_taxo_get_kingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
+    
+    ecotx_t* obi_taxo_get_superkingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
+    

python/obitools3/obidms/capi/obitypes.pxd

@@ -9,20 +9,22 @@ cdef extern from *:
     ctypedef char* const_char_p "const char*"
 
 
-cdef extern from "obidmscolumn.h" nogil:
-
-    ctypedef int32_t obiversion_t
+cdef extern from "encode.h" nogil:
+    bint only_ATGC(const_char_p seq)
 
 
 cdef extern from "obitypes.h" nogil:
 
-    enum OBIType:       # TODO je sais pas si ça sert de declarer le contenu de l'enum
-        OBI_VOID = 0,
+    enum OBIType:
+        OBI_VOID,
         OBI_INT,
         OBI_FLOAT,
         OBI_BOOL,
         OBI_CHAR,
+        OBI_STR,
+        OBI_SEQ,
         OBI_IDX
+
     
     ctypedef OBIType OBIType_t
     
@@ -31,14 +33,18 @@ cdef extern from "obitypes.h" nogil:
     
     ctypedef OBIBool obibool_t
     ctypedef int32_t obiint_t
-    ctypedef double obifloat_t
-    ctypedef char obichar_t  
+    ctypedef double  obifloat_t
+    ctypedef char    obichar_t  
     ctypedef int64_t index_t
 
-    extern obiint_t   OBIInt_NA
-    extern index_t    OBIIdx_NA
-    extern obifloat_t OBIFloat_NA
-    extern obichar_t  OBIChar_NA
-    extern obibool_t  OBIBool_NA
+    ctypedef int32_t obiversion_t
 
-    char* name_data_type(int data_type)
+    extern obiint_t      OBIInt_NA
+    extern index_t       OBIIdx_NA
+    extern obifloat_t    OBIFloat_NA
+    extern obichar_t     OBIChar_NA
+    extern obibool_t     OBIBool_NA
+    extern const_char_p  OBISeq_NA
+    extern const_char_p  OBIStr_NA
+
+    const_char_p name_data_type(int data_type)

python/obitools3/obidms/capi/obiutils.pxd

@@ -0,0 +1,12 @@
+#cython: language_level=3
+
+
+from posix.types cimport time_t
+
+from ..capi.obitypes cimport const_char_p
+
+
+cdef extern from "utils.h" nogil:
+
+    const_char_p obi_format_date(time_t date)
+

python/obitools3/obidms/capi/obiview.pxd

@@ -0,0 +1,249 @@
+#cython: language_level=3
+
+from .obitypes           cimport const_char_p, \
+                                 OBIType_t, \
+                                 obiversion_t, \
+                                 obiint_t, \
+                                 obibool_t, \
+                                 obichar_t, \
+                                 obifloat_t, \
+                                 index_t, \
+                                 time_t
+from ..capi.obidms       cimport OBIDMS_p
+from ..capi.obidmscolumn cimport OBIDMS_column_p
+
+
+cdef extern from "obiview.h" nogil:
+
+    extern const_char_p VIEW_TYPE_NUC_SEQS
+    extern const_char_p NUC_SEQUENCE_COLUMN
+    extern const_char_p ID_COLUMN
+    extern const_char_p DEFINITION_COLUMN
+
+    struct Obiview_t :
+        OBIDMS_p            dms
+        const_char_p        name
+        const_char_p        created_from
+        const_char_p        view_type
+        bint                read_only
+        OBIDMS_column_p     line_selection
+        OBIDMS_column_p     new_line_selection
+        index_t             line_count
+        int                 column_count
+        OBIDMS_column_p     columns
+        const_char_p        comments
+
+    ctypedef Obiview_t* Obiview_p
+
+
+    struct Column_reference_t :
+        const_char_p  column_name
+        obiversion_t  version
+    
+    ctypedef Column_reference_t* Column_reference_p
+
+
+    struct Obiview_infos_t :
+        int                 view_number
+        time_t              creation_date
+        const_char_p        name
+        const_char_p        created_from
+        const_char_p        view_type
+        bint                all_lines
+        Column_reference_t  line_selection
+        index_t             line_count
+        int                 column_count
+        Column_reference_p  column_references
+        const_char_p        comments
+
+    ctypedef Obiview_infos_t* Obiview_infos_p
+
+
+    struct Obiviews_header_t :
+        size_t header_size
+        size_t views_size
+        int    view_count
+    
+    ctypedef Obiviews_header_t* Obiviews_header_p
+
+
+    struct Obiviews_infos_all_t :
+        Obiviews_header_p    header
+        Obiview_infos_p      view_infos
+
+    ctypedef Obiviews_infos_all_t* Obiviews_infos_all_p
+
+
+    Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const_char_p view_name, Obiview_p view_to_clone, index_t* line_selection, const_char_p comments)
+
+    Obiview_p obi_new_view(OBIDMS_p dms, const_char_p view_name, Obiview_p view_to_clone, index_t* line_selection, const_char_p comments)
+    
+    Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const_char_p view_name, const_char_p view_to_clone_name, index_t* line_selection, const_char_p comments)
+
+    Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const_char_p view_name, const_char_p view_to_clone_name, index_t* line_selection, const_char_p comments)
+              
+    Obiview_p obi_open_view(OBIDMS_p dms, const_char_p view_name)
+    
+    int obi_view_add_column(Obiview_p view,
+                            const_char_p column_name,
+                            obiversion_t version_number,
+                            OBIType_t data_type,
+                            index_t nb_lines,
+                            index_t nb_elements_per_line,
+                            const_char_p elements_names,
+                            const_char_p indexer_name,
+                            const_char_p comments,
+                            bint create)
+
+    int obi_view_delete_column(Obiview_p view, const_char_p column_name)
+    
+    int obi_select_line(Obiview_p view, index_t line_nb)
+
+    int obi_select_lines(Obiview_p view, index_t* line_nbs)
+        
+    OBIDMS_column_p obi_view_get_column(Obiview_p view, const_char_p column_name)
+
+    OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const_char_p column_name)
+
+    int obi_save_view(Obiview_p view)
+    
+    int obi_close_view(Obiview_p view)
+    
+    int obi_save_and_close_view(Obiview_p view)
+    
+    Obiviews_infos_all_p obi_read_view_infos(OBIDMS_p dms)
+
+    int obi_close_view_infos(Obiviews_infos_all_p views)
+
+    int obi_column_set_obiint_with_elt_name_in_view(Obiview_p view,
+                                                    OBIDMS_column_p column, 
+                                                    index_t line_nb, 
+                                                    const_char_p element_name, 
+                                                    obiint_t value)
+
+    int obi_column_set_obiint_with_elt_idx_in_view(Obiview_p view,
+                                                   OBIDMS_column_p column, 
+                                                   index_t line_nb, 
+                                                   index_t element_idx, 
+                                                   obiint_t value)
+    
+    obiint_t obi_column_get_obiint_with_elt_name_in_view(Obiview_p view,
+                                                         OBIDMS_column_p column, 
+                                                         index_t line_nb, 
+                                                         const_char_p element_name)
+    
+    obiint_t obi_column_get_obiint_with_elt_idx_in_view(Obiview_p view,
+                                                        OBIDMS_column_p column, 
+                                                        index_t line_nb, 
+                                                        index_t element_idx)
+
+    int obi_column_set_obibool_with_elt_name_in_view(Obiview_p view,
+                                                     OBIDMS_column_p column, 
+                                                     index_t line_nb, 
+                                                     const_char_p element_name, 
+                                                     obibool_t value)
+
+    int obi_column_set_obibool_with_elt_idx_in_view(Obiview_p view,
+                                                    OBIDMS_column_p column, 
+                                                    index_t line_nb, 
+                                                    index_t element_idx, 
+                                                    obibool_t value)
+    
+    obibool_t obi_column_get_obibool_with_elt_name_in_view(Obiview_p view,
+                                                           OBIDMS_column_p column, 
+                                                           index_t line_nb, 
+                                                           const_char_p element_name)
+    
+    obibool_t obi_column_get_obibool_with_elt_idx_in_view(Obiview_p view,
+                                                          OBIDMS_column_p column, 
+                                                          index_t line_nb, 
+                                                          index_t element_idx)
+
+    int obi_column_set_obichar_with_elt_name_in_view(Obiview_p view,
+                                                     OBIDMS_column_p column, 
+                                                     index_t line_nb, 
+                                                     const_char_p element_name, 
+                                                     obichar_t value)
+
+    int obi_column_set_obichar_with_elt_idx_in_view(Obiview_p view,
+                                                    OBIDMS_column_p column, 
+                                                    index_t line_nb, 
+                                                    index_t element_idx, 
+                                                    obichar_t value)
+    
+    obichar_t obi_column_get_obichar_with_elt_name_in_view(Obiview_p view,
+                                                           OBIDMS_column_p column, 
+                                                           index_t line_nb, 
+                                                           const_char_p element_name)
+    
+    obichar_t obi_column_get_obichar_with_elt_idx_in_view(Obiview_p view,
+                                                          OBIDMS_column_p column, 
+                                                          index_t line_nb, 
+                                                          index_t element_idx)
+
+    int obi_column_set_obifloat_with_elt_name_in_view(Obiview_p view,
+                                                      OBIDMS_column_p column, 
+                                                      index_t line_nb, 
+                                                      const_char_p element_name, 
+                                                      obifloat_t value)
+
+    int obi_column_set_obifloat_with_elt_idx_in_view(Obiview_p view,
+                                                     OBIDMS_column_p column, 
+                                                     index_t line_nb, 
+                                                     index_t element_idx, 
+                                                     obifloat_t value)
+    
+    obifloat_t obi_column_get_obifloat_with_elt_name_in_view(Obiview_p view,
+                                                             OBIDMS_column_p column, 
+                                                             index_t line_nb, 
+                                                             const_char_p element_name)
+    
+    obifloat_t obi_column_get_obifloat_with_elt_idx_in_view(Obiview_p view,
+                                                            OBIDMS_column_p column, 
+                                                            index_t line_nb, 
+                                                            index_t element_idx)
+
+    int obi_column_set_obistr_with_elt_name_in_view(Obiview_p view,
+                                                    OBIDMS_column_p column, 
+                                                    index_t line_nb, 
+                                                    const_char_p element_name, 
+                                                    const_char_p value)
+
+    int obi_column_set_obistr_with_elt_idx_in_view(Obiview_p view,
+                                                   OBIDMS_column_p column, 
+                                                   index_t line_nb, 
+                                                   index_t element_idx, 
+                                                   const_char_p value)
+    
+    const_char_p obi_column_get_obistr_with_elt_name_in_view(Obiview_p view,
+                                                           OBIDMS_column_p column, 
+                                                           index_t line_nb, 
+                                                           const_char_p element_name)
+    
+    const_char_p obi_column_get_obistr_with_elt_idx_in_view(Obiview_p view,
+                                                            OBIDMS_column_p column, 
+                                                            index_t line_nb, 
+                                                            index_t element_idx)
+
+    int obi_column_set_obiseq_with_elt_name_in_view(Obiview_p view,
+                                                    OBIDMS_column_p column, 
+                                                    index_t line_nb, 
+                                                    const_char_p element_name, 
+                                                    const_char_p value)
+
+    int obi_column_set_obiseq_with_elt_idx_in_view(Obiview_p view,
+                                                   OBIDMS_column_p column, 
+                                                   index_t line_nb, 
+                                                   index_t element_idx, 
+                                                   const_char_p value)
+    
+    char* obi_column_get_obiseq_with_elt_name_in_view(Obiview_p view,
+                                                      OBIDMS_column_p column, 
+                                                      index_t line_nb, 
+                                                      const_char_p element_name)
+    
+    char* obi_column_get_obiseq_with_elt_idx_in_view(Obiview_p view,
+                                                     OBIDMS_column_p column, 
+                                                     index_t line_nb, 
+                                                     index_t element_idx)
+

python/obitools3/obigrep.py

@@ -0,0 +1,51 @@
+import sys
+import argparse
+
+from obitools3.obidms._obidms import OBIDMS
+
+if __name__ == '__main__': 
+    
+    parser = argparse.ArgumentParser(description='Pseudo obigrep.')
+    
+    parser.add_argument('-V', '--view', dest='view', type=str,
+                       help='Name of the view that should be considered')    
+
+    parser.add_argument('-N', '--new_view', dest='new_view', type=str,
+                       help='Name of the new view that should be created')    
+    
+#     parser.add_argument('-k', '--key', dest='key', type=str,
+#                        help='Name of the key that should be considered')
+# 
+#     parser.add_argument('-c', '--comp', dest='comparison', type=int,
+#                        help='Comparison to be made: -1:< ; 0:== ; 1:>')
+# 
+#     parser.add_argument('-v', '--value', dest='value', type=object,
+#                        help='Value to be compared')
+
+    args = parser.parse_args()
+    
+    d = OBIDMS('tdms')
+    
+    #condition = 1
+    line_selec = []
+    
+    v = d.open_view(args.view)
+    
+    i = 0
+    for l in v :
+        if l['score'] > 350 : 
+            line_selec.append(i)
+        i+=1
+        
+    new_v = d.new_view(args.new_view, view_to_clone=v, line_selection=line_selec, view_type="NUC_SEQS_VIEW", comments="obigrep "+args.view+" to "+args.new_view) #args.key+" "+str(args.comparison)+" "+str(args.value)+" "+)
+
+    print("\n")
+    print(new_v.__repr__())
+
+    v.save_and_close()
+    new_v.save_and_close()
+    
+    d.close()
+
+    print("\nDone.")
+    

python/obitools3/obihead.py

@@ -0,0 +1,43 @@
+import sys
+import argparse
+
+from obitools3.obidms._obidms import OBIDMS
+
+if __name__ == '__main__': 
+    
+    parser = argparse.ArgumentParser(description='Pseudo obihead.')
+    
+    parser.add_argument('-V', '--view', dest='view', type=str,
+                       help='Name of the view that should be considered')    
+
+    parser.add_argument('-N', '--new_view', dest='new_view', type=str,
+                       help='Name of the new view that should be created')    
+    
+    parser.add_argument('-n', '--nb', dest='nb_lines', type=int,
+                       help='Number of lines that should be taken')    
+    
+
+    args = parser.parse_args()
+    
+    d = OBIDMS('tdms')
+    
+    #condition = 1
+    line_selec = []
+    
+    v = d.open_view(args.view)
+    
+    for i in range(0, args.nb_lines) :
+        line_selec.append(i)
+        
+    new_v = d.new_view(args.new_view, view_to_clone=v, line_selection=line_selec, view_type="NUC_SEQS_VIEW", comments="obihead "+str(args.nb_lines)+", "+args.view+" to "+args.new_view) #args.key+" "+str(args.comparison)+" "+str(args.value)+" "+)
+
+    print("\n")
+    print(new_v.__repr__())
+
+    v.save_and_close()
+    new_v.save_and_close()
+    
+    d.close()
+
+    print("\nDone.")
+    

python/obitools3/obiimport.py

@@ -0,0 +1,199 @@
+import sys
+import argparse
+import time
+
+from obitools3.obidms._obidms import OBIDMS
+
+
+def bufferedRead(fileobj,size=209715200):   ## 200 MB
+   buffer = fileobj.readlines(size)
+   while buffer:
+       for l in buffer:
+           yield l
+       buffer = fileobj.readlines(size)
+
+
+if __name__ == '__main__': 
+    
+    parser = argparse.ArgumentParser(description='Convert a fasta file in an OBIDMS.')
+    
+    parser.add_argument('-i', '--input', dest='input_file', type=str,
+                       help='Name of the file containing the sequences')
+
+    args = parser.parse_args()
+
+    d = OBIDMS('tdms')
+    
+    view = d.new_view('uniq view', view_type="NUC_SEQS_VIEW")
+
+#    for i in range(35000000) :
+#        if (not (i%500000)) :
+#            print(str(time.time())+'\t'+str(i))
+#        id = "@HWI-D00405:142:C71BAANXX:4:1101:1234:2234_CONS_SUB_SUB_"+str(i)
+#        view[i].set_id(id)
+#        if id != view[i]["ID"] :
+#            print("nope", id, view[i]["ID"])
+    
+    input_file = open(args.input_file, 'r')
+    input_file_buffered = bufferedRead(input_file)
+    
+#         
+#     if args.input_file[-1:] == "a" :
+#     
+#         i = 0
+#         next = False
+#         first = True
+#         
+#         for line in input_file :
+#             
+#             if line[0] == ">" :
+#                 
+#                 if not first :
+#                     # save seq
+#                     #print(i, id, seq)
+#                     view[i].set_sequence(seq)
+#                     i+=1
+#                 
+#                 first = False
+#                     
+#                 #id = line.split(" ", 1)[0][1:]
+#                 #rest = (line[:-1].split(" ", 1)[1]).split(";")
+#                 #view[i].set_id(id)
+#                 
+# #                 description = ""
+# #                 for j in range(len(rest)) :
+# #                     if "=" in rest[j] :
+# #                         rest[j] = rest[j].strip()
+# #                         rest[j] = rest[j].split("=", 1)
+# #                         column_name = rest[j][0]
+# #                         v = rest[j][1]
+# #                         if ((not v.isalpha()) and (v.isalnum())) :
+# #                             conv_v = int(v)
+# #                         elif (v == "True") or (v == "False") :
+# #                             conv_v = bool(v)
+# #                         else :
+# #                             f = True
+# #                             for letter in v :
+# #                                 if ((not letter.isalnum()) or (letter != ".")) :
+# #                                     f = False
+# #                             if f :
+# #                                 conv_v = float(v)
+# #                             else : 
+# #                                 conv_v = v
+# #                         view[i][column_name] = conv_v
+# #                     else :
+# #                         description+=rest[j]
+# #                 
+# #                 if description != "" :
+# #                     description = description.strip()
+# #                     view[i].set_description(description)
+#                     
+#                 #print(id)
+#                 #print(rest)
+#                 #print(description)
+#                 
+#                 next = True
+#                 
+#             elif next == True :
+#                 
+#      #           if not (i % 1E5) :
+#      #               print(i)
+#                 
+#                 seq = line[:-1]
+#                 next = False
+#             
+#             elif not next :
+#                 
+#                 seq += line[:-1]
+# 
+# 
+#     elif args.input_file[-1:] == "q" :
+#         
+#         i = 0
+#         l = 0
+#         next = False
+#
+    l=0
+    i=0
+#     while (True):
+#         l+=1
+#         line = input_file.readline()
+#         if line=="":
+#             break
+    for line in input_file_buffered :
+# 
+             #if i > 1E7 :
+#             #    print('hmm?')
+#                         
+#        if i == 6000000 :
+#            break
+#             
+        if l%4 == 0 :
+#                
+            if (not (i%500000)) :
+                print(str(time.time())+'\t'+str(i))
+# # 
+# #                 #print("header", line)
+# # 
+            id = line.split(" ", 1)[0][1:]
+#            print(id)
+# #                 #rest = (line[:-1].split(" ", 1)[1]).split(";")
+            view[i].set_id(id)
+#            print(view[i]["ID"])
+# 
+#            i+=1
+        
+#        l+=1
+#                 
+# #                 description = ""
+# #                 for j in range(len(rest)) :
+# #                     if "=" in rest[j] :
+# #                         rest[j] = rest[j].strip()
+# #                         rest[j] = rest[j].split("=", 1)
+# #                         column_name = rest[j][0]
+# #                         #print("COLUMN", column_name)
+# #                         v = rest[j][1]
+# #                         if (v == "") and (column_name in view) and (view[column_name].get_data_type() == "OBI_SEQ") :
+# #                             #print(">>>>>>YUP")
+# #                             conv_v = "aa"
+# #                         else :
+# #                             if ((not v.isalpha()) and (v.isalnum())) :
+# #                                 conv_v = int(v)
+# #                             elif (v == "True") or (v == "False") :
+# #                                 conv_v = bool(v)
+# #                             else :
+# #                                 f = True
+# #                                 for letter in v :
+# #                                     if ((not letter.isalnum()) or (letter != ".")) :
+# #                                         f = False
+# #                                 if f :
+# #                                     conv_v = float(v)
+# #                                 else :
+# #                                     conv_v = v
+# #                         view[i][column_name] = conv_v
+# #                     else :
+# #                         description+=rest[j]
+# #                 
+# #                 if description != "" :
+# #                     description = description.strip()
+# #                     view[i].set_description(description)
+#                 
+        elif l%4 == 1 :
+# #                
+            seq = line[:-1]
+#                 #print("seq", seq)
+            view[i].set_sequence(seq)
+            i+=1
+#                         
+        l+=1
+#     
+#     
+    input_file.close()
+
+    #print(view)
+    print(view.__repr__())
+
+    view.save_and_close()
+    d.close()
+
+    print("Done.")

python/obitools3/parsers/fasta.pxd

@@ -0,0 +1,8 @@
+#cython: language_level=3
+
+from .header cimport parseHeader
+from ..files.universalopener cimport uopen
+from ..files.linebuffer cimport LineBuffer
+
+
+    

python/obitools3/parsers/fasta.pyx

@@ -0,0 +1,46 @@
+#cython: language_level=3
+
+'''
+Created on 30 mars 2016
+
+@author: coissac
+'''
+
+def fastaIterator(lineiterator, int buffersize=100000000):
+    cdef LineBuffer lb
+    cdef str        ident
+    cdef str        definition
+    cdef dict       tags
+    cdef list       s
+    
+    if isinstance(lineiterator,(str,bytes)):
+        lineiterator=uopen(lineiterator)
+    
+    if isinstance(lineiterator, LineBuffer):
+        lb=lineiterator
+    else:
+        lb=LineBuffer(lineiterator,buffersize)
+        
+    i = iter(lb)
+    line = next(i)
+    
+    while True:
+        ident,tags,definition = parseHeader(line)
+        s = []
+        line = next(i)
+        while line[0]!='>':
+            s.append(line[0:-1])
+            line = next(i)
+        sequence  = "".join(s)
+        quality   = None
+
+        yield { "id"         : ident,
+                "definition" : definition,
+                "sequence"   : sequence,
+                "quality"    : quality,
+                "tags"       : tags,
+                "annotation" : {}
+              }
+        
+        
+        

python/obitools3/parsers/fastq.pxd

@@ -0,0 +1,8 @@
+#cython: language_level=3
+
+from .header cimport parseHeader
+from ..files.universalopener cimport uopen
+from ..files.linebuffer cimport LineBuffer
+
+
+    

python/obitools3/parsers/fastq.pyx

@@ -0,0 +1,41 @@
+#cython: language_level=3
+
+'''
+Created on 30 mars 2016
+
+@author: coissac
+'''
+
+
+
+def fastqIterator(lineiterator, int buffersize=100000000):
+    cdef LineBuffer lb
+    cdef str        ident
+    cdef str        definition
+    cdef dict       tags
+    
+    if isinstance(lineiterator,(str,bytes)):
+        lineiterator=uopen(lineiterator)
+    
+    if isinstance(lineiterator, LineBuffer):
+        lb=lineiterator
+    else:
+        lb=LineBuffer(lineiterator,buffersize)
+        
+    i = iter(lb)
+    for line in i:
+        ident,tags,definition = parseHeader(line)
+        sequence  = next(i)[0:-1]
+        next(i)
+        quality   = next(i)[0:-1]
+
+        yield { "id"         : ident,
+                "definition" : definition,
+                "sequence"   : sequence,
+                "quality"    : quality,
+                "tags"       : tags,
+                "annotation" : {}
+              }
+        
+        
+        

python/obitools3/parsers/header.pxd

@@ -0,0 +1,5 @@
+#cython: language_level=3
+
+cdef object __etag__(str x)
+
+cpdef tuple parseHeader(str header)

python/obitools3/parsers/header.pyx

@@ -0,0 +1,78 @@
+#cython: language_level=3
+
+'''
+Created on 25 mars 2016
+
+@author: coissac
+'''
+
+import re
+
+__ret__         = re.compile('''(([^ ]+)=('[^']*'|"[^"]*"|[^;]+); *)+?''')
+__re_int__      = re.compile("^[+-]?[0-9]+$")
+__re_float__    = re.compile("^[+-]?[0-9]+(\.[0-9]*)?([eE][+-]?[0-9]+)?$")
+__re_str__      = re.compile("""^"[^"]*"|'[^']*'$""")
+__re_dict__     = re.compile("""^\{\ *
+                                   (
+                                       ("[^"]*"|'[^']*')
+                                        \ *:\ *
+                                       ([^,}]+|
+                                        "[^"]*"|
+                                        '[^']*'
+                                       )
+                                   )?
+                                   (\ *,\ *
+                                       ("[^"]*"|'[^']*')
+                                        \ *:\ *
+                                       ([^,}]+|
+                                        "[^"]*"|
+                                        '[^']*'
+                                       )
+                                    )*\ *\}$""", re.VERBOSE)
+
+
+cdef object __etag__(str x):
+    if __re_int__.match(x):
+        v=int(x)
+    elif __re_float__.match(x):
+        v=float(x)
+    elif __re_str__.match(x):
+        v=x[1:-1]
+    elif x=='False':
+        v=False
+    elif x=='True':
+        v=True
+    elif __re_dict__.match(x):
+        v=eval(x)
+    else:
+        v=x
+    return v
+
+cpdef tuple parseHeader(str header):
+    cdef list m 
+    cdef dict tags 
+    cdef str definition
+    cdef str ident
+    cdef str second
+    
+    m=header[1:-1].split(maxsplit=1)
+
+    ident=m[0]
+    
+    if len(m)==1:
+        tags={}
+        definition='' 
+    else:
+        second=m[1]
+        m = __ret__.findall(second)
+        
+        if m:
+            tags = dict([(a[1],__etag__(a[2])) for a in m])
+            definition = second.split(m[-1][0],1)[1].strip()
+        else:
+            tags = {}
+            definition = second.strip() 
+        
+    return ident,tags,definition
+    
+    

python/obitools3/unit_tests.py

@@ -10,9 +10,8 @@ from obitools3.obidms._obidms import OBIDMS
 
 LINE_COUNT_FOR_TEST_COLUMN = 10000         # TODO randomize?
 SMALLER_LINE_COUNT_FOR_TEST_COLUMN = 1000  # TODO randomize?
-NB_ELEMENTS_PER_LINE = 20                  # TODO randomize?
+NB_ELEMENTS_PER_LINE = 10                  # TODO randomize?
 DMS_NAME = "unit_test_dms"
-DATA_TYPES = ['OBI_INT', 'OBI_FLOAT', 'OBI_BOOL', 'OBI_CHAR', 'OBI_IDX']
 
 
 def create_test_obidms():
@@ -22,26 +21,24 @@ def create_test_obidms():
     return (dms, dms_name, dms_dir_name)
 
 
-def create_test_column(dms, data_type_code, multiple_elements_per_line=False):
-    data_types = DATA_TYPES
-    data_type_code = data_type_code
-    data_type_str = data_types[data_type_code-1]
-    col_name = "unit_test_"+data_type_str
-        
+def create_test_column(dms, data_type, multiple_elements_per_line=False):
+    
+    col_name = "unit_test_"+data_type
+
     if multiple_elements_per_line :
         elts_names = elements_names()
         col = dms.open_column(col_name, 
                               create=True, 
-                              data_type=data_type_code, 
+                              type=data_type, 
                               nb_elements_per_line=NB_ELEMENTS_PER_LINE,
                               elements_names=elts_names)
-        return (col, col_name, elts_names, data_type_str)
+        return (col, col_name, elts_names)
 
     else :
         col = dms.open_column(col_name, 
                               create=True, 
-                              data_type=data_type_code)
-        return (col, col_name, data_type_str)
+                              type=data_type)
+        return (col, col_name)
 
 
 def elements_names():
@@ -58,12 +55,15 @@ def random_obivalue(data_type):
     elif data_type == "OBI_BOOL" :
         return randint(0,1)
     elif data_type == "OBI_CHAR" :
-        nucs = 'atgc'
-        return bytes(nucs[randint(0,3)], 'utf-8')
-    elif data_type == "OBI_IDX" :
-        length = randint(1,500)
+        return choice(string.ascii_lowercase)
+    elif data_type == "OBI_STR" :
+        length = randint(1,200)
         randoms = ''.join(choice(string.ascii_lowercase) for i in range(length))
         return randoms
+    elif data_type == "OBI_SEQ" :
+        length = randint(1,200)
+        randoms = ''.join(choice("atgcryswkmdbhvn") for i in range(length))
+        return randoms
 
 class OBIDMS_Column_TestCase(unittest.TestCase):
     def tearDown(self):
@@ -71,10 +71,10 @@ class OBIDMS_Column_TestCase(unittest.TestCase):
         self.dms.close()
         shutil.rmtree(self.dms_dir_name, ignore_errors=True)
     def test_OBIDMS_column_type(self):
-        assert self.col.get_data_type() == self.data_type_str, 'Wrong data type associated with column'
+        assert self.col.get_data_type() == self.data_type, 'Wrong data type associated with column'
     def test_OBIDMS_column_cloning(self):
         for i in range(LINE_COUNT_FOR_TEST_COLUMN):
-            self.col[i]= random_obivalue(self.data_type_str)
+            self.col[i]= random_obivalue(self.data_type)
         self.col.close()
         clone = self.dms.open_column(self.col_name, clone=True)
         self.col = self.dms.open_column(self.col_name)
@@ -86,10 +86,21 @@ class OBIDMS_Column_TestCase(unittest.TestCase):
         clone.close()
     def test_OBIDMS_column_set_and_get(self):
         for i in range(LINE_COUNT_FOR_TEST_COLUMN):
-            v = random_obivalue(self.data_type_str)
+            v = random_obivalue(self.data_type)
             self.col[i] = v
             assert self.col[i] == v, "Different value than the set value"
             assert self.col[i] is not None, "None value"
+    def test_OBIDMS_referring_column(self):
+        for i in range(LINE_COUNT_FOR_TEST_COLUMN):
+            self.col[i] = random_obivalue(self.data_type)
+        ref_col = self.dms.open_column(self.col_name, referring=True)
+        j = 0
+        for i in range(LINE_COUNT_FOR_TEST_COLUMN):
+            if i%2 :    # TODO randomize
+                ref_col.grep_line(i)
+                assert ref_col[j] == self.col[i], "Different value in original column and returned by referring column"
+                assert ref_col[j] is not None, "None value"
+                j+=1
 
 
 class OBIDMS_Column_multiple_elements_TestCase(OBIDMS_Column_TestCase):
@@ -98,7 +109,7 @@ class OBIDMS_Column_multiple_elements_TestCase(OBIDMS_Column_TestCase):
         for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
             v = {}
             for e in self.elts_names :
-                v[e] = random_obivalue(self.data_type_str)
+                v[e] = random_obivalue(self.data_type)
             self.col[i] = v
         self.col.close()
         clone = self.dms.open_column(self.col_name, clone=True)
@@ -112,7 +123,7 @@ class OBIDMS_Column_multiple_elements_TestCase(OBIDMS_Column_TestCase):
     def test_OBIDMS_column_set_and_get_with_elements_names(self):
         for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
             for e in range(NB_ELEMENTS_PER_LINE) :
-                v = random_obivalue(self.data_type_str)
+                v = random_obivalue(self.data_type)
                 self.col.set_item(i, self.elts_names[e], v)
                 assert self.col.get_item(i, self.elts_names[e]) == v, "Different value than the set value"
                 assert self.col.get_item(i, self.elts_names[e]) is not None, "None value"
@@ -120,141 +131,168 @@ class OBIDMS_Column_multiple_elements_TestCase(OBIDMS_Column_TestCase):
         for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
             v = {}
             for e in self.elts_names :
-                v[e] = random_obivalue(self.data_type_str)
+                v[e] = random_obivalue(self.data_type)
             self.col[i] = v
             assert self.col[i] == v, "Different value than the set value"
             assert self.col[i] is not None, "None value"
+    def test_OBIDMS_referring_column(self):
+        for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
+            v = {}
+            for e in self.elts_names :
+                v[e] = random_obivalue(self.data_type)
+            self.col[i] = v
+        ref_col = self.dms.open_column(self.col_name, referring=True)
+        j = 0
+        for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
+            if i%2 :    # TODO randomize
+                ref_col.grep_line(i)
+                assert ref_col[j] == self.col[i], "Different value in original column and returned by referring column"
+                assert ref_col[j] is not None, "None value"
+                j+=1
+        ref_col.close()
 
 
 class OBIDMS_Column_OBI_INT_TestCase(OBIDMS_Column_TestCase):
     def setUp(self):
-        self.data_type_code = 1
+        self.data_type = 'OBI_INT'
         self.dms, \
         self.dms_name, \
         self.dms_dir_name = create_test_obidms()
         self.col, \
-        self.col_name, \
-        self.data_type_str = create_test_column(self.dms, 
-                                                self.data_type_code)
+        self.col_name = create_test_column(self.dms, 
+                                           self.data_type)
        
 
 class OBIDMS_Column_OBI_INT_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
     def setUp(self):
-        self.data_type_code = 1
+        self.data_type = 'OBI_INT'
         self.dms, \
         self.dms_name, \
         self.dms_dir_name = create_test_obidms()
         self.col, \
         self.col_name, \
-        self.elts_names, \
-        self.data_type_str = create_test_column(self.dms, 
-                                                self.data_type_code,
-                                                multiple_elements_per_line=True)
+        self.elts_names = create_test_column(self.dms, 
+                                             self.data_type,
+                                             multiple_elements_per_line=True)
 
 
 class OBIDMS_Column_OBI_FLOAT_TestCase(OBIDMS_Column_TestCase):
     def setUp(self):
-        self.data_type_code = 2
+        self.data_type = 'OBI_FLOAT'
         self.dms, \
         self.dms_name, \
         self.dms_dir_name = create_test_obidms()
         self.col, \
-        self.col_name, \
-        self.data_type_str = create_test_column(self.dms, 
-                                                self.data_type_code)
+        self.col_name = create_test_column(self.dms, 
+                                           self.data_type)
        
 
 class OBIDMS_Column_OBI_FLOAT_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
     def setUp(self):
-        self.data_type_code = 2
+        self.data_type = 'OBI_FLOAT'
         self.dms, \
         self.dms_name, \
         self.dms_dir_name = create_test_obidms()
         self.col, \
         self.col_name, \
-        self.elts_names, \
-        self.data_type_str = create_test_column(self.dms, 
-                                                self.data_type_code,
-                                                multiple_elements_per_line=True)
+        self.elts_names = create_test_column(self.dms, 
+                                             self.data_type,
+                                             multiple_elements_per_line=True)
 
 
 class OBIDMS_Column_OBI_BOOL_TestCase(OBIDMS_Column_TestCase):
     def setUp(self):
-        self.data_type_code = 3
+        self.data_type = 'OBI_BOOL'
         self.dms, \
         self.dms_name, \
         self.dms_dir_name = create_test_obidms()
         self.col, \
-        self.col_name, \
-        self.data_type_str = create_test_column(self.dms, 
-                                                self.data_type_code)
+        self.col_name = create_test_column(self.dms, 
+                                           self.data_type)
        
 
 class OBIDMS_Column_OBI_BOOL_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
     def setUp(self):
-        self.data_type_code = 3
+        self.data_type = 'OBI_BOOL'
         self.dms, \
         self.dms_name, \
         self.dms_dir_name = create_test_obidms()
         self.col, \
         self.col_name, \
-        self.elts_names, \
-        self.data_type_str = create_test_column(self.dms, 
-                                                self.data_type_code,
-                                                multiple_elements_per_line=True)
+        self.elts_names = create_test_column(self.dms, 
+                                             self.data_type,
+                                             multiple_elements_per_line=True)
 
 
 class OBIDMS_Column_OBI_CHAR_TestCase(OBIDMS_Column_TestCase):
     def setUp(self):
-        self.data_type_code = 4
+        self.data_type = 'OBI_CHAR'
         self.dms, \
         self.dms_name, \
         self.dms_dir_name = create_test_obidms()
         self.col, \
-        self.col_name, \
-        self.data_type_str = create_test_column(self.dms, 
-                                                self.data_type_code)
+        self.col_name = create_test_column(self.dms, 
+                                                self.data_type)
        
 
 class OBIDMS_Column_OBI_CHAR_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
     def setUp(self):
-        self.data_type_code = 4
+        self.data_type = 'OBI_CHAR'
         self.dms, \
         self.dms_name, \
         self.dms_dir_name = create_test_obidms()
         self.col, \
         self.col_name, \
-        self.elts_names, \
-        self.data_type_str = create_test_column(self.dms, 
-                                                self.data_type_code,
-                                                multiple_elements_per_line=True)
+        self.elts_names = create_test_column(self.dms, 
+                                             self.data_type,
+                                             multiple_elements_per_line=True)
 
 
 class OBIDMS_Column_OBI_STR_TestCase(OBIDMS_Column_TestCase):
     def setUp(self):
-        self.data_type_code = 5
+        self.data_type = 'OBI_STR'
         self.dms, \
         self.dms_name, \
         self.dms_dir_name = create_test_obidms()
         self.col, \
-        self.col_name, \
-        self.data_type_str = create_test_column(self.dms, 
-                                                self.data_type_code)
+        self.col_name = create_test_column(self.dms, 
+                                           self.data_type)
        
 
 class OBIDMS_Column_OBI_STR_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
     def setUp(self):
-        self.data_type_code = 5
+        self.data_type = 'OBI_STR'
         self.dms, \
         self.dms_name, \
         self.dms_dir_name = create_test_obidms()
         self.col, \
         self.col_name, \
-        self.elts_names, \
-        self.data_type_str = create_test_column(self.dms, 
-                                                self.data_type_code,
-                                                multiple_elements_per_line=True)
+        self.elts_names = create_test_column(self.dms, 
+                                             self.data_type,
+                                             multiple_elements_per_line=True)
 
+class OBIDMS_Column_OBI_SEQ_TestCase(OBIDMS_Column_TestCase):
+    def setUp(self):
+        self.data_type = 'OBI_SEQ'
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name = create_test_column(self.dms, 
+                                           self.data_type)
+       
+
+class OBIDMS_Column_OBI_SEQ_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
+    def setUp(self):
+        self.data_type = 'OBI_SEQ'
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name, \
+        self.elts_names = create_test_column(self.dms, 
+                                             self.data_type,
+                                             multiple_elements_per_line=True)
 
 if __name__ == '__main__': 
      unittest.main(verbosity=2, defaultTest=["OBIDMS_Column_OBI_INT_TestCase",
@@ -266,6 +304,8 @@ if __name__ == '__main__':
                                              "OBIDMS_Column_OBI_CHAR_TestCase",
                                              "OBIDMS_Column_OBI_CHAR_multiple_elements_TestCase",
                                              "OBIDMS_Column_OBI_STR_TestCase",
-                                             "OBIDMS_Column_OBI_STR_multiple_elements_TestCase"])
+                                             "OBIDMS_Column_OBI_STR_multiple_elements_TestCase",
+                                             "OBIDMS_Column_OBI_SEQ_TestCase",
+                                             "OBIDMS_Column_OBI_SEQ_multiple_elements_TestCase"])
 
 

python/obitools3/utils.pxd

@@ -1,5 +1,6 @@
 #cython: language_level=3
 
+
 cdef bytes str2bytes(str string)
 
 cdef str bytes2str(bytes string)

python/obitools3/utils.pyx

@@ -1,7 +1,28 @@
 #cython: language_level=3
 
+import sys
+import io
+
 cdef bytes str2bytes(str string):
+    """
+    Short cut to convert ascii encoded python string (str) to bytes 
+    which can be easily converted to C-strings. 
+    
+        @param string: the python string to be converted.
+        @type string: str
+        @return a transcoded string
+        @rtype: bytes 
+    """
     return string.encode('ascii')
 
 cdef str bytes2str(bytes string):
-    return string.decode('ascii')
+    """
+    Short cut to convert bytes (C-strings) to ascii encoded python string (str).
+    
+        @param string: the binary (C-string) string to be converted.
+        @type string: bytes
+        @return an ascii transcoded string
+        @rtype: str 
+    """
+    return string.decode('ascii')
+

python/obitools3/version.py

@@ -1,5 +1,5 @@
-major = 1
-minor = 1
-serial= '16'
+major = 0
+minor = 0
+serial= '0'
 
 version ="%d.%02d.%s" % (major,minor,serial)

requirements.txt

@@ -1,5 +1,5 @@
 --extra-index-url https://pypi.python.org/simple/
-Cython>=0.21
+Cython==0.23.5
 Sphinx>=1.2.0
 ipython>=3.0.0
 breathe>=4.0.0

src/bloom.c

@@ -0,0 +1,248 @@
+/*
+ *  Copyright (c) 2012-2015, Jyri J. Virkki
+ *  All rights reserved.
+ *
+ *  This file is under BSD license. See LICENSE file.
+ */
+
+/*
+ * Refer to bloom.h for documentation on the public interfaces.
+ */
+
+#include <assert.h>
+#include <fcntl.h>
+#include <math.h>
+#include <stdint.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <unistd.h>
+
+#include "bloom.h"
+#include "murmurhash2.h"
+
+#define MAKESTRING(n) STRING(n)
+#define STRING(n) #n
+
+//#ifdef __linux__										// TODO commented because triggers error on luke21
+//unsigned detect_bucket_size(unsigned fallback_size);
+//#endif
+
+
+static int test_bit_set_bit(unsigned char * buf, unsigned int x, int set_bit)
+{
+  register uint32_t * word_buf = (uint32_t *)buf;
+  register unsigned int offset = x >> 5;
+  register uint32_t word = word_buf[offset];
+  register unsigned int mask = 1 << (x % 32);
+
+  if (word & mask) {
+    return 1;
+  } else {
+    if (set_bit) {
+      word_buf[offset] = word | mask;
+    }
+    return 0;
+  }
+}
+
+
+static int bloom_check_add(struct bloom * bloom,
+                           const void * buffer, int len, int add)
+{
+  if (bloom->ready == 0) {
+    (void)printf("bloom at %p not initialized!\n", (void *)bloom);
+    return -1;
+  }
+
+  int hits = 0;
+  register unsigned int a = murmurhash2(buffer, len, 0x9747b28c);
+  register unsigned int b = murmurhash2(buffer, len, a);
+  register unsigned int x;
+  register int i;	// TODO why was it unsigned?
+
+  unsigned bucket_index = (a % bloom->buckets);
+
+  unsigned char * bucket_ptr =
+    (bloom->bf + (bucket_index << bloom->bucket_bytes_exponent));
+
+  for (i = 0; i < bloom->hashes; i++) {
+    x = (a + i*b) & bloom->bucket_bits_fast_mod_operand;
+    if (test_bit_set_bit(bucket_ptr, x, add)) {
+      hits++;
+    }
+  }
+
+  if (hits == bloom->hashes) {
+    return 1;                // 1 == element already in (or collision)
+  }
+
+  return 0;
+}
+
+
+static void setup_buckets(struct bloom * bloom, unsigned int cache_size)
+{
+  // If caller passed a non-zero cache_size, use it as given, otherwise
+  // either compute it or use built-in default
+
+  if (cache_size == 0) {
+//#ifdef __linux__													// TODO commented because triggers error on luke21
+//    cache_size = detect_bucket_size(BLOOM_BUCKET_SIZE_FALLBACK);
+//#else
+    cache_size = BLOOM_BUCKET_SIZE_FALLBACK;
+//#endif
+  }
+
+  bloom->buckets = (bloom->bytes / cache_size);
+  bloom->bucket_bytes = cache_size;
+
+  // make sure bloom buffer bytes and bucket_bytes are even
+  int not_even_by = (bloom->bytes % bloom->bucket_bytes);
+
+  if (not_even_by) {
+    // adjust bytes
+    bloom->bytes += (bloom->bucket_bytes - not_even_by);
+    assert((bloom->bytes % bloom->bucket_bytes) == 0); // Should get even
+
+    // adjust bits
+    bloom->bits = bloom->bytes * 8;
+
+    // adjust bits per element
+    bloom->bpe = bloom->bits*1. / bloom->entries;
+
+    // adjust buckets
+    bloom->buckets++;
+  }
+
+  bloom->bucket_bytes_exponent = __builtin_ctz(cache_size);
+  bloom->bucket_bits_fast_mod_operand = (cache_size * 8 - 1);
+}
+
+
+int bloom_filter_size(int entries, double error)
+{
+	int bytes;
+	double num;
+	double denom;
+	double bpe;
+	int bits;
+	unsigned bucket_bytes;
+	int not_even_by;
+
+	num = log(error);
+	denom = 0.480453013918201; // ln(2)^2
+	bpe = -(num / denom);
+	bits = (int)(((double)entries) * bpe);
+
+	if (bits % 8) {
+		bytes = (bits / 8) + 1;
+	}
+	else {
+		bytes = bits / 8;
+	}
+
+	bucket_bytes = BLOOM_BUCKET_SIZE_FALLBACK;
+	not_even_by = bytes % bucket_bytes;
+	if (not_even_by) {
+	  // adjust bytes
+		bytes += (bucket_bytes - not_even_by);
+	}
+
+	return bytes;
+}
+
+
+int bloom_init_size(struct bloom * bloom, int entries, double error,
+                    unsigned int cache_size)
+{
+  bloom->ready = 0;
+
+  if (entries < 1 || error == 0) {
+    return 1;
+  }
+
+  bloom->entries = entries;
+  bloom->error = error;
+
+  double num = log(bloom->error);
+  double denom = 0.480453013918201; // ln(2)^2
+  bloom->bpe = -(num / denom);
+
+  double dentries = (double)entries;
+  bloom->bits = (int)(dentries * bloom->bpe);
+
+  if (bloom->bits % 8) {
+    bloom->bytes = (bloom->bits / 8) + 1;
+  } else {
+    bloom->bytes = bloom->bits / 8;
+  }
+
+  bloom->hashes = (int)ceil(0.693147180559945 * bloom->bpe);  // ln(2)
+
+  setup_buckets(bloom, cache_size);
+
+  // celine.mercier@metabarcoding.org :
+  // Replaced the calloc with a memset, as the memory for the bloom filter is mapped in our data structure
+  memset(bloom->bf, 0, bloom->bytes);
+  //bloom->bf = (unsigned char *)calloc(bloom->bytes, sizeof(unsigned char));
+  //if (bloom->bf == NULL) {
+  //  return 1;
+  //}
+
+  bloom->ready = 1;
+  return 0;
+}
+
+
+int bloom_init(struct bloom * bloom, int entries)  //, double error)
+{
+  return bloom_init_size(bloom, entries, BLOOM_FILTER_ERROR_RATE, 0);
+}
+
+
+int bloom_check(struct bloom * bloom, const void * buffer, int len)
+{
+  return bloom_check_add(bloom, buffer, len, 0);
+}
+
+
+int bloom_add(struct bloom * bloom, const void * buffer, int len)
+{
+  return bloom_check_add(bloom, buffer, len, 1);
+}
+
+
+void bloom_print(struct bloom * bloom)
+{
+  (void)printf("bloom at %p\n", (void *)bloom);
+  (void)printf(" ->entries = %d\n", bloom->entries);
+  (void)printf(" ->error = %f\n", bloom->error);
+  (void)printf(" ->bits = %d\n", bloom->bits);
+  (void)printf(" ->bits per elem = %f\n", bloom->bpe);
+  (void)printf(" ->bytes = %d\n", bloom->bytes);
+  (void)printf(" ->buckets = %u\n", bloom->buckets);
+  (void)printf(" ->bucket_bytes = %u\n", bloom->bucket_bytes);
+  (void)printf(" ->bucket_bytes_exponent = %u\n",
+               bloom->bucket_bytes_exponent);
+  (void)printf(" ->bucket_bits_fast_mod_operand = 0%o\n",
+               bloom->bucket_bits_fast_mod_operand);
+  (void)printf(" ->hash functions = %d\n", bloom->hashes);
+}
+
+
+void bloom_free(struct bloom * bloom)
+{
+  if (bloom->ready) {
+    free(bloom->bf);
+  }
+  bloom->ready = 0;
+}
+
+
+const char * bloom_version()
+{
+  return MAKESTRING(BLOOM_VERSION);
+}

src/bloom.h

@@ -0,0 +1,210 @@
+/*
+ *  Copyright (c) 2012-2015, Jyri J. Virkki
+ *  All rights reserved.
+ *
+ *  This file is under BSD license. See LICENSE file.
+ */
+
+#ifndef _BLOOM_H
+#define _BLOOM_H
+
+
+/** ***************************************************************************
+ * Added by celine.mercier@metabarcoding.org
+ *
+ * Bloom filter error rate wanted.
+ *
+ */
+#define BLOOM_FILTER_ERROR_RATE (0.001)
+
+
+/** ***************************************************************************
+ * On Linux, the code attempts to compute a bucket size based on CPU cache
+ * size info, if available. If that fails for any reason, this fallback size
+ * is used instead.
+ *
+ * On non-Linux systems, this is the bucket size always used unless the
+ * caller overrides it (see bloom_init_size()).
+ *
+ */
+#define BLOOM_BUCKET_SIZE_FALLBACK (32 * 1024)
+
+
+/** ***************************************************************************
+ * It was found that using multiplier x0.5 for CPU L1 cache size is
+ * more effective in terms of CPU usage and, surprisingly, collisions
+ * number.
+ *
+ * Feel free to tune this constant the way it will work for you.
+ *
+ */
+#define BLOOM_L1_CACHE_SIZE_DIV 1
+
+
+/** ***************************************************************************
+ * Structure to keep track of one bloom filter.  Caller needs to
+ * allocate this and pass it to the functions below. First call for
+ * every struct must be to bloom_init().
+ *
+ */
+struct bloom
+{
+  // These fields are part of the public interface of this structure.
+  // Client code may read these values if desired. Client code MUST NOT
+  // modify any of these.
+  int entries;
+  double error;
+  int bits;
+  int bytes;
+  int hashes;
+
+  // Fields below are private to the implementation. These may go away or
+  // change incompatibly at any moment. Client code MUST NOT access or rely
+  // on these.
+  unsigned buckets;
+  unsigned bucket_bytes;
+
+  // x86 CPU divide by/multiply by operation optimization helpers
+  unsigned bucket_bytes_exponent;
+  unsigned bucket_bits_fast_mod_operand;
+
+  double bpe;
+  int ready;
+
+  unsigned char bf[];
+};
+
+typedef struct bloom bloom_t;
+
+
+/** ***************************************************************************
+ * Added by celine.mercier@metabarcoding.org
+ *
+ * This function computes the size needed by the bloom filter
+ * depending on the number of entries and the error rate.
+ *
+ */
+int bloom_filter_size(int entries, double error);
+
+
+/** ***************************************************************************
+ * Initialize the bloom filter for use.
+ *
+ * The filter is initialized with a bit field and number of hash functions
+ * according to the computations from the wikipedia entry:
+ *     http://en.wikipedia.org/wiki/Bloom_filter
+ *
+ * Optimal number of bits is:
+ *     bits = (entries * ln(error)) / ln(2)^2
+ *
+ * Optimal number of hash functions is:
+ *     hashes = bpe * ln(2)
+ *
+ * Parameters:
+ * -----------
+ *     bloom   - Pointer to an allocated struct bloom (see above).
+ *     entries - The expected number of entries which will be inserted.
+ *     error   - Probability of collision (as long as entries are not
+ *               exceeded).
+ *
+ * Return:
+ * -------
+ *     0 - on success
+ *     1 - on failure
+ *
+ */
+int bloom_init(struct bloom * bloom, int entries); //, double error);
+
+
+/** ***************************************************************************
+ * Initialize the bloom filter for use.
+ *
+ * See comments above for general information.
+ *
+ * This is the same as bloom_init() but allows the caller to pass in a
+ * cache_size to override the internal value (which is either computed
+ * or the default of BLOOM_BUCKET_SIZE_FALLBACK). Mostly useful for
+ * experimenting.
+ *
+ * See misc/bucketsize for a script which can help identify a good value
+ * for cache_size.
+ *
+ */
+int bloom_init_size(struct bloom * bloom, int entries, double error,
+                    unsigned int cache_size);
+
+
+/** ***************************************************************************
+ * Check if the given element is in the bloom filter. Remember this may
+ * return false positive if a collision occured.
+ *
+ * Parameters:
+ * -----------
+ *     bloom  - Pointer to an allocated struct bloom (see above).
+ *     buffer - Pointer to buffer containing element to check.
+ *     len    - Size of 'buffer'.
+ *
+ * Return:
+ * -------
+ *     0 - element is not present
+ *     1 - element is present (or false positive due to collision)
+ *    -1 - bloom not initialized
+ *
+ */
+int bloom_check(struct bloom * bloom, const void * buffer, int len);
+
+
+/** ***************************************************************************
+ * Add the given element to the bloom filter.
+ * The return code indicates if the element (or a collision) was already in,
+ * so for the common check+add use case, no need to call check separately.
+ *
+ * Parameters:
+ * -----------
+ *     bloom  - Pointer to an allocated struct bloom (see above).
+ *     buffer - Pointer to buffer containing element to add.
+ *     len    - Size of 'buffer'.
+ *
+ * Return:
+ * -------
+ *     0 - element was not present and was added
+ *     1 - element (or a collision) had already been added previously
+ *    -1 - bloom not initialized
+ *
+ */
+int bloom_add(struct bloom * bloom, const void * buffer, int len);
+
+
+/** ***************************************************************************
+ * Print (to stdout) info about this bloom filter. Debugging aid.
+ *
+ */
+void bloom_print(struct bloom * bloom);
+
+
+/** ***************************************************************************
+ * Deallocate internal storage.
+ *
+ * Upon return, the bloom struct is no longer usable. You may call bloom_init
+ * again on the same struct to reinitialize it again.
+ *
+ * Parameters:
+ * -----------
+ *     bloom  - Pointer to an allocated struct bloom (see above).
+ *
+ * Return: none
+ *
+ */
+void bloom_free(struct bloom * bloom);
+
+
+/** ***************************************************************************
+ * Returns version string compiled into library.
+ *
+ * Return: version string
+ *
+ */
+const char * bloom_version();
+
+
+#endif

src/char_str_indexer.c

@@ -0,0 +1,80 @@
+/****************************************************************************
+ * Character string indexing functions                                      *
+ ****************************************************************************/
+
+/**
+ * @file char_str_indexer.c
+ * @author Celine Mercier
+ * @date April 12th 2016
+ * @brief Functions handling the indexing and retrieval of character strings.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <math.h>
+
+#include "obiblob.h"
+#include "obiblob_indexer.h"
+#include "obidebug.h"
+#include "obitypes.h"
+
+
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
+
+
+Obi_blob_p obi_str_to_blob(const char* value)
+{
+	Obi_blob_p 		 value_b;
+	int32_t 		 length;
+
+	// Compute the number of bytes on which the value will be encoded
+	length = strlen(value) + 1;		// +1 to store \0 at the end (makes retrieving faster)
+
+	value_b = obi_blob((byte_t*)value, ELEMENT_SIZE_STR, length, length);
+	if (value_b == NULL)
+	{
+		obidebug(1, "\nError encoding a character string in a blob");
+		return NULL;
+	}
+
+	return value_b;
+}
+
+
+char* obi_blob_to_str(Obi_blob_p value_b)
+{
+	return value_b->value;
+}
+
+
+index_t obi_index_char_str(Obi_indexer_p indexer, const char* value)
+{
+	Obi_blob_p  value_b;
+	index_t 	idx;
+
+	// Encode value
+	value_b = obi_str_to_blob(value);
+	if (value_b == NULL)
+		return -1;
+
+	// Add in the indexer
+	idx = obi_indexer_add(indexer, value_b);
+
+	free(value_b);
+
+	return idx;
+}
+
+
+char* obi_retrieve_char_str(Obi_indexer_p indexer, index_t idx)
+{
+	Obi_blob_p  value_b;
+
+	// Get encoded value
+	value_b = obi_indexer_get(indexer, idx);
+
+	// Return decoded character string
+	return obi_blob_to_str(value_b);
+}
+

src/char_str_indexer.h

@@ -0,0 +1,87 @@
+/****************************************************************************
+ * DNA sequence indexer header file	                                        *
+ ****************************************************************************/
+
+/**
+ * @file dna_seq_indexer.h
+ * @author Celine Mercier
+ * @date April 12th 2016
+ * @brief Header file for the functions handling the indexing of DNA sequences.
+ */
+
+
+#ifndef CHAR_STR_INDEXER_H_
+#define CHAR_STR_INDEXER_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "obitypes.h"
+#include "obiblob.h"
+#include "obiblob_indexer.h"
+
+
+/**
+ * @brief Converts a character string to a blob.
+ *
+ * @warning The blob must be freed by the caller.
+ *
+ * @param value The character string to convert.
+ *
+ * @returns A pointer to the blob created.
+ * @retval NULL if an error occurred.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+Obi_blob_p obi_str_to_blob(char* value);
+
+
+/**
+ * @brief Converts a blob to a character string.
+ *
+ * @warning The character string returned is mapped.
+ *
+ * @param value_b The blob to convert.
+ *
+ * @returns A pointer on the character string contained in the blob.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_blob_to_str(Obi_blob_p value_b);
+
+
+/**
+ * @brief Stores a character string in an indexer and returns the index.
+ *
+ * @param indexer The indexer structure.
+ * @param value The character string to index.
+ *
+ * @returns The index referring to the stored character string in the indexer.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+index_t obi_index_char_str(Obi_indexer_p indexer, const char* value);
+
+
+/**
+ * @brief Retrieves a character string from an indexer.
+ *
+ * @warning The character string returned is mapped.
+ *
+ * @param indexer The indexer structure.
+ * @param idx The index referring to the character string to retrieve in the indexer.
+ *
+ * @returns A pointer on the character string.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_retrieve_char_str(Obi_indexer_p indexer, index_t idx);
+
+
+#endif /* CHAR_STR_INDEXER_H_ */
+

src/crc64.c

@@ -0,0 +1,198 @@
+/* Redis uses the CRC64 variant with "Jones" coefficients and init value of 0.
+ *
+ * Specification of this CRC64 variant follows:
+ * Name: crc-64-jones
+ * Width: 64 bites
+ * Poly: 0xad93d23594c935a9
+ * Reflected In: True
+ * Xor_In: 0xffffffffffffffff
+ * Reflected_Out: True
+ * Xor_Out: 0x0
+ * Check("123456789"): 0xe9c6d914c4b8d9ca
+ *
+ * Copyright (c) 2012, Salvatore Sanfilippo <antirez at gmail dot com>
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ *   * Redistributions of source code must retain the above copyright notice,
+ *     this list of conditions and the following disclaimer.
+ *   * Redistributions in binary form must reproduce the above copyright
+ *     notice, this list of conditions and the following disclaimer in the
+ *     documentation and/or other materials provided with the distribution.
+ *   * Neither the name of Redis nor the names of its contributors may be used
+ *     to endorse or promote products derived from this software without
+ *     specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE. */
+
+#include <stdint.h>
+
+static const uint64_t crc64_tab[256] = {
+    UINT64_C(0x0000000000000000), UINT64_C(0x7ad870c830358979),
+    UINT64_C(0xf5b0e190606b12f2), UINT64_C(0x8f689158505e9b8b),
+    UINT64_C(0xc038e5739841b68f), UINT64_C(0xbae095bba8743ff6),
+    UINT64_C(0x358804e3f82aa47d), UINT64_C(0x4f50742bc81f2d04),
+    UINT64_C(0xab28ecb46814fe75), UINT64_C(0xd1f09c7c5821770c),
+    UINT64_C(0x5e980d24087fec87), UINT64_C(0x24407dec384a65fe),
+    UINT64_C(0x6b1009c7f05548fa), UINT64_C(0x11c8790fc060c183),
+    UINT64_C(0x9ea0e857903e5a08), UINT64_C(0xe478989fa00bd371),
+    UINT64_C(0x7d08ff3b88be6f81), UINT64_C(0x07d08ff3b88be6f8),
+    UINT64_C(0x88b81eabe8d57d73), UINT64_C(0xf2606e63d8e0f40a),
+    UINT64_C(0xbd301a4810ffd90e), UINT64_C(0xc7e86a8020ca5077),
+    UINT64_C(0x4880fbd87094cbfc), UINT64_C(0x32588b1040a14285),
+    UINT64_C(0xd620138fe0aa91f4), UINT64_C(0xacf86347d09f188d),
+    UINT64_C(0x2390f21f80c18306), UINT64_C(0x594882d7b0f40a7f),
+    UINT64_C(0x1618f6fc78eb277b), UINT64_C(0x6cc0863448deae02),
+    UINT64_C(0xe3a8176c18803589), UINT64_C(0x997067a428b5bcf0),
+    UINT64_C(0xfa11fe77117cdf02), UINT64_C(0x80c98ebf2149567b),
+    UINT64_C(0x0fa11fe77117cdf0), UINT64_C(0x75796f2f41224489),
+    UINT64_C(0x3a291b04893d698d), UINT64_C(0x40f16bccb908e0f4),
+    UINT64_C(0xcf99fa94e9567b7f), UINT64_C(0xb5418a5cd963f206),
+    UINT64_C(0x513912c379682177), UINT64_C(0x2be1620b495da80e),
+    UINT64_C(0xa489f35319033385), UINT64_C(0xde51839b2936bafc),
+    UINT64_C(0x9101f7b0e12997f8), UINT64_C(0xebd98778d11c1e81),
+    UINT64_C(0x64b116208142850a), UINT64_C(0x1e6966e8b1770c73),
+    UINT64_C(0x8719014c99c2b083), UINT64_C(0xfdc17184a9f739fa),
+    UINT64_C(0x72a9e0dcf9a9a271), UINT64_C(0x08719014c99c2b08),
+    UINT64_C(0x4721e43f0183060c), UINT64_C(0x3df994f731b68f75),
+    UINT64_C(0xb29105af61e814fe), UINT64_C(0xc849756751dd9d87),
+    UINT64_C(0x2c31edf8f1d64ef6), UINT64_C(0x56e99d30c1e3c78f),
+    UINT64_C(0xd9810c6891bd5c04), UINT64_C(0xa3597ca0a188d57d),
+    UINT64_C(0xec09088b6997f879), UINT64_C(0x96d1784359a27100),
+    UINT64_C(0x19b9e91b09fcea8b), UINT64_C(0x636199d339c963f2),
+    UINT64_C(0xdf7adabd7a6e2d6f), UINT64_C(0xa5a2aa754a5ba416),
+    UINT64_C(0x2aca3b2d1a053f9d), UINT64_C(0x50124be52a30b6e4),
+    UINT64_C(0x1f423fcee22f9be0), UINT64_C(0x659a4f06d21a1299),
+    UINT64_C(0xeaf2de5e82448912), UINT64_C(0x902aae96b271006b),
+    UINT64_C(0x74523609127ad31a), UINT64_C(0x0e8a46c1224f5a63),
+    UINT64_C(0x81e2d7997211c1e8), UINT64_C(0xfb3aa75142244891),
+    UINT64_C(0xb46ad37a8a3b6595), UINT64_C(0xceb2a3b2ba0eecec),
+    UINT64_C(0x41da32eaea507767), UINT64_C(0x3b024222da65fe1e),
+    UINT64_C(0xa2722586f2d042ee), UINT64_C(0xd8aa554ec2e5cb97),
+    UINT64_C(0x57c2c41692bb501c), UINT64_C(0x2d1ab4dea28ed965),
+    UINT64_C(0x624ac0f56a91f461), UINT64_C(0x1892b03d5aa47d18),
+    UINT64_C(0x97fa21650afae693), UINT64_C(0xed2251ad3acf6fea),
+    UINT64_C(0x095ac9329ac4bc9b), UINT64_C(0x7382b9faaaf135e2),
+    UINT64_C(0xfcea28a2faafae69), UINT64_C(0x8632586aca9a2710),
+    UINT64_C(0xc9622c4102850a14), UINT64_C(0xb3ba5c8932b0836d),
+    UINT64_C(0x3cd2cdd162ee18e6), UINT64_C(0x460abd1952db919f),
+    UINT64_C(0x256b24ca6b12f26d), UINT64_C(0x5fb354025b277b14),
+    UINT64_C(0xd0dbc55a0b79e09f), UINT64_C(0xaa03b5923b4c69e6),
+    UINT64_C(0xe553c1b9f35344e2), UINT64_C(0x9f8bb171c366cd9b),
+    UINT64_C(0x10e3202993385610), UINT64_C(0x6a3b50e1a30ddf69),
+    UINT64_C(0x8e43c87e03060c18), UINT64_C(0xf49bb8b633338561),
+    UINT64_C(0x7bf329ee636d1eea), UINT64_C(0x012b592653589793),
+    UINT64_C(0x4e7b2d0d9b47ba97), UINT64_C(0x34a35dc5ab7233ee),
+    UINT64_C(0xbbcbcc9dfb2ca865), UINT64_C(0xc113bc55cb19211c),
+    UINT64_C(0x5863dbf1e3ac9dec), UINT64_C(0x22bbab39d3991495),
+    UINT64_C(0xadd33a6183c78f1e), UINT64_C(0xd70b4aa9b3f20667),
+    UINT64_C(0x985b3e827bed2b63), UINT64_C(0xe2834e4a4bd8a21a),
+    UINT64_C(0x6debdf121b863991), UINT64_C(0x1733afda2bb3b0e8),
+    UINT64_C(0xf34b37458bb86399), UINT64_C(0x8993478dbb8deae0),
+    UINT64_C(0x06fbd6d5ebd3716b), UINT64_C(0x7c23a61ddbe6f812),
+    UINT64_C(0x3373d23613f9d516), UINT64_C(0x49aba2fe23cc5c6f),
+    UINT64_C(0xc6c333a67392c7e4), UINT64_C(0xbc1b436e43a74e9d),
+    UINT64_C(0x95ac9329ac4bc9b5), UINT64_C(0xef74e3e19c7e40cc),
+    UINT64_C(0x601c72b9cc20db47), UINT64_C(0x1ac40271fc15523e),
+    UINT64_C(0x5594765a340a7f3a), UINT64_C(0x2f4c0692043ff643),
+    UINT64_C(0xa02497ca54616dc8), UINT64_C(0xdafce7026454e4b1),
+    UINT64_C(0x3e847f9dc45f37c0), UINT64_C(0x445c0f55f46abeb9),
+    UINT64_C(0xcb349e0da4342532), UINT64_C(0xb1eceec59401ac4b),
+    UINT64_C(0xfebc9aee5c1e814f), UINT64_C(0x8464ea266c2b0836),
+    UINT64_C(0x0b0c7b7e3c7593bd), UINT64_C(0x71d40bb60c401ac4),
+    UINT64_C(0xe8a46c1224f5a634), UINT64_C(0x927c1cda14c02f4d),
+    UINT64_C(0x1d148d82449eb4c6), UINT64_C(0x67ccfd4a74ab3dbf),
+    UINT64_C(0x289c8961bcb410bb), UINT64_C(0x5244f9a98c8199c2),
+    UINT64_C(0xdd2c68f1dcdf0249), UINT64_C(0xa7f41839ecea8b30),
+    UINT64_C(0x438c80a64ce15841), UINT64_C(0x3954f06e7cd4d138),
+    UINT64_C(0xb63c61362c8a4ab3), UINT64_C(0xcce411fe1cbfc3ca),
+    UINT64_C(0x83b465d5d4a0eece), UINT64_C(0xf96c151de49567b7),
+    UINT64_C(0x76048445b4cbfc3c), UINT64_C(0x0cdcf48d84fe7545),
+    UINT64_C(0x6fbd6d5ebd3716b7), UINT64_C(0x15651d968d029fce),
+    UINT64_C(0x9a0d8ccedd5c0445), UINT64_C(0xe0d5fc06ed698d3c),
+    UINT64_C(0xaf85882d2576a038), UINT64_C(0xd55df8e515432941),
+    UINT64_C(0x5a3569bd451db2ca), UINT64_C(0x20ed197575283bb3),
+    UINT64_C(0xc49581ead523e8c2), UINT64_C(0xbe4df122e51661bb),
+    UINT64_C(0x3125607ab548fa30), UINT64_C(0x4bfd10b2857d7349),
+    UINT64_C(0x04ad64994d625e4d), UINT64_C(0x7e7514517d57d734),
+    UINT64_C(0xf11d85092d094cbf), UINT64_C(0x8bc5f5c11d3cc5c6),
+    UINT64_C(0x12b5926535897936), UINT64_C(0x686de2ad05bcf04f),
+    UINT64_C(0xe70573f555e26bc4), UINT64_C(0x9ddd033d65d7e2bd),
+    UINT64_C(0xd28d7716adc8cfb9), UINT64_C(0xa85507de9dfd46c0),
+    UINT64_C(0x273d9686cda3dd4b), UINT64_C(0x5de5e64efd965432),
+    UINT64_C(0xb99d7ed15d9d8743), UINT64_C(0xc3450e196da80e3a),
+    UINT64_C(0x4c2d9f413df695b1), UINT64_C(0x36f5ef890dc31cc8),
+    UINT64_C(0x79a59ba2c5dc31cc), UINT64_C(0x037deb6af5e9b8b5),
+    UINT64_C(0x8c157a32a5b7233e), UINT64_C(0xf6cd0afa9582aa47),
+    UINT64_C(0x4ad64994d625e4da), UINT64_C(0x300e395ce6106da3),
+    UINT64_C(0xbf66a804b64ef628), UINT64_C(0xc5bed8cc867b7f51),
+    UINT64_C(0x8aeeace74e645255), UINT64_C(0xf036dc2f7e51db2c),
+    UINT64_C(0x7f5e4d772e0f40a7), UINT64_C(0x05863dbf1e3ac9de),
+    UINT64_C(0xe1fea520be311aaf), UINT64_C(0x9b26d5e88e0493d6),
+    UINT64_C(0x144e44b0de5a085d), UINT64_C(0x6e963478ee6f8124),
+    UINT64_C(0x21c640532670ac20), UINT64_C(0x5b1e309b16452559),
+    UINT64_C(0xd476a1c3461bbed2), UINT64_C(0xaeaed10b762e37ab),
+    UINT64_C(0x37deb6af5e9b8b5b), UINT64_C(0x4d06c6676eae0222),
+    UINT64_C(0xc26e573f3ef099a9), UINT64_C(0xb8b627f70ec510d0),
+    UINT64_C(0xf7e653dcc6da3dd4), UINT64_C(0x8d3e2314f6efb4ad),
+    UINT64_C(0x0256b24ca6b12f26), UINT64_C(0x788ec2849684a65f),
+    UINT64_C(0x9cf65a1b368f752e), UINT64_C(0xe62e2ad306bafc57),
+    UINT64_C(0x6946bb8b56e467dc), UINT64_C(0x139ecb4366d1eea5),
+    UINT64_C(0x5ccebf68aecec3a1), UINT64_C(0x2616cfa09efb4ad8),
+    UINT64_C(0xa97e5ef8cea5d153), UINT64_C(0xd3a62e30fe90582a),
+    UINT64_C(0xb0c7b7e3c7593bd8), UINT64_C(0xca1fc72bf76cb2a1),
+    UINT64_C(0x45775673a732292a), UINT64_C(0x3faf26bb9707a053),
+    UINT64_C(0x70ff52905f188d57), UINT64_C(0x0a2722586f2d042e),
+    UINT64_C(0x854fb3003f739fa5), UINT64_C(0xff97c3c80f4616dc),
+    UINT64_C(0x1bef5b57af4dc5ad), UINT64_C(0x61372b9f9f784cd4),
+    UINT64_C(0xee5fbac7cf26d75f), UINT64_C(0x9487ca0fff135e26),
+    UINT64_C(0xdbd7be24370c7322), UINT64_C(0xa10fceec0739fa5b),
+    UINT64_C(0x2e675fb4576761d0), UINT64_C(0x54bf2f7c6752e8a9),
+    UINT64_C(0xcdcf48d84fe75459), UINT64_C(0xb71738107fd2dd20),
+    UINT64_C(0x387fa9482f8c46ab), UINT64_C(0x42a7d9801fb9cfd2),
+    UINT64_C(0x0df7adabd7a6e2d6), UINT64_C(0x772fdd63e7936baf),
+    UINT64_C(0xf8474c3bb7cdf024), UINT64_C(0x829f3cf387f8795d),
+    UINT64_C(0x66e7a46c27f3aa2c), UINT64_C(0x1c3fd4a417c62355),
+    UINT64_C(0x935745fc4798b8de), UINT64_C(0xe98f353477ad31a7),
+    UINT64_C(0xa6df411fbfb21ca3), UINT64_C(0xdc0731d78f8795da),
+    UINT64_C(0x536fa08fdfd90e51), UINT64_C(0x29b7d047efec8728),
+};
+
+
+uint64_t crc64(const char* s, uint64_t l)
+{
+	uint64_t j;
+    uint64_t crc = 0;
+
+    for (j = 0; j < l; j++)
+    {
+        uint8_t byte = s[j];
+        crc = crc64_tab[(uint8_t)crc ^ byte] ^ (crc >> 8);
+    }
+    return crc;
+}
+
+
+/* Test main */
+//#ifdef TEST_MAIN
+//#include <stdio.h>
+//int main(void) {
+//    printf("e9c6d914c4b8d9ca == %016llx\n",
+//        (unsigned long long) crc64(0,(unsigned char*)"123456789",9));
+//    return 0;
+//}
+//#endif
+
+

src/crc64.h

@@ -0,0 +1,14 @@
+/**
+ * @file crc64.h
+ * @date March 24th 2016
+ * @brief Header file for CRC64 function.
+ */
+
+#include <stdint.h>
+
+
+/**
+ * @brief Generates and returns a 64-bit Cyclic Redundancy Check from a
+ *        character string s of length l.
+ */
+uint64_t crc64(const char* s, uint64_t l);

src/dna_seq_indexer.c

@@ -0,0 +1,102 @@
+/****************************************************************************
+ * DNA sequence indexing functions                                          *
+ ****************************************************************************/
+
+/**
+ * @file dna_seq_indexer.c
+ * @author Celine Mercier
+ * @date April 12th 2016
+ * @brief Functions handling the indexing and retrieval of DNA sequences.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <math.h>
+
+#include "obiblob.h"
+#include "obiblob_indexer.h"
+#include "obidebug.h"
+#include "obitypes.h"
+
+
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
+
+
+Obi_blob_p obi_seq_to_blob(const char* seq)
+{
+	Obi_blob_p 		 value_b;
+	int32_t          length_encoded_seq;	// length of the encoded sequence in bytes
+	int32_t          seq_length;
+	byte_t*          encoded_seq;
+
+	seq_length = strlen(seq);
+
+	// Check if just ATGC and encode accordingly
+	if (only_ATGC(seq))
+	{
+		// Compute the length (in bytes) of the encoded sequence
+		length_encoded_seq = ceil((double) seq_length / (double) 4.0);
+		// Encode
+		encoded_seq = encode_seq_on_2_bits(seq, seq_length);
+		if (encoded_seq == NULL)
+			return NULL;
+		value_b = obi_blob(encoded_seq, ELEMENT_SIZE_SEQ_2, length_encoded_seq, seq_length);
+	}
+	else
+	{
+		// Compute the length (in bytes) of the encoded sequence
+		length_encoded_seq = ceil((double) seq_length / (double) 2.0);
+		// Encode
+		encoded_seq = encode_seq_on_4_bits(seq, seq_length);
+		if (encoded_seq == NULL)
+			return NULL;
+		value_b = obi_blob(encoded_seq, ELEMENT_SIZE_SEQ_4, length_encoded_seq, seq_length);
+	}
+
+	free(encoded_seq);
+
+	return value_b;
+}
+
+
+char* obi_blob_to_seq(Obi_blob_p value_b)
+{
+	// Decode
+	if (value_b->element_size == 2)
+		return decode_seq_on_2_bits(value_b->value, value_b->length_decoded_value);
+	else
+		return decode_seq_on_4_bits(value_b->value, value_b->length_decoded_value);
+}
+
+
+index_t obi_index_dna_seq(Obi_indexer_p indexer, const char* value)
+{
+	Obi_blob_p  value_b;
+	index_t 	idx;
+
+	// Encode value
+	value_b = obi_seq_to_blob(value);
+	if (value_b == NULL)
+		return -1;
+
+	// Add in the indexer
+	idx = obi_indexer_add(indexer, value_b);
+
+	free(value_b);
+
+	return idx;
+}
+
+
+char* obi_retrieve_dna_seq(Obi_indexer_p indexer, index_t idx)
+{
+	Obi_blob_p  value_b;
+
+	// Get encoded value
+	value_b = obi_indexer_get(indexer, idx);
+
+	// Return decoded sequence
+	return obi_blob_to_seq(value_b);
+}
+

src/dna_seq_indexer.h

@@ -0,0 +1,87 @@
+/****************************************************************************
+ * DNA sequence indexer header file	                                        *
+ ****************************************************************************/
+
+/**
+ * @file dna_seq_indexer.h
+ * @author Celine Mercier
+ * @date April 12th 2016
+ * @brief Header file for the functions handling the indexing of DNA sequences.
+ */
+
+
+#ifndef DNA_SEQ_INDEXER_H_
+#define DNA_SEQ_INDEXER_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "obidms.h"
+#include "obitypes.h"
+#include "obiblob.h"
+#include "obiblob_indexer.h"
+
+
+/**
+ * @brief Converts a DNA sequence to a blob.
+ *
+ * @warning The blob must be freed by the caller.
+ *
+ * @param value The DNA sequence to convert.
+ *
+ * @returns A pointer to the blob created.
+ * @retval NULL if an error occurred.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+Obi_blob_p obi_seq_to_blob(const char* seq);
+
+
+/**
+ * @brief Converts a blob to a DNA sequence.
+ *
+ * @param value_b The blob to convert.
+ *
+ * @returns A pointer to the DNA sequence contained in the blob.
+ * @retval NULL if an error occurred.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_blob_to_seq(Obi_blob_p value_b);
+
+
+/**
+ * @brief Stores a DNA sequence in an indexer and returns the index.
+ *
+ * @param indexer The indexer structure.
+ * @param value The DNA sequence to index.
+ *
+ * @returns The index referring to the stored DNA sequence in the indexer.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+index_t obi_index_dna_seq(Obi_indexer_p indexer, const char* value);
+
+
+/**
+ * @brief Retrieves a DNA sequence from an indexer.
+ *
+ * @warning The DNA sequence returned must be freed by the caller.
+ *
+ * @param indexer The indexer structure.
+ * @param idx The index referring to the DNA sequence to retrieve in the indexer.
+ *
+ * @returns A pointer on the DNA sequence.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_retrieve_dna_seq(Obi_indexer_p indexer, index_t idx);
+
+
+#endif /* DNA_SEQ_INDEXER_H_ */
+

src/encode.c

@@ -0,0 +1,367 @@
+/****************************************************************************
+ * Encoding functions                                                       *
+ ****************************************************************************/
+
+/**
+ * @file encode.c
+ * @author Celine Mercier
+ * @date November 18th 2015
+ * @brief Functions encoding DNA sequences.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+#include <math.h>
+
+#include "encode.h"
+#include "obierrno.h"
+#include "obitypes.h"	// For byte_t type
+#include "obidebug.h"
+
+
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
+
+
+// TODO: endianness problem?
+
+
+
+bool only_ATGC(const char* seq)
+{
+	const char* c = seq;
+
+	while (*c)
+	{
+		if (!((*c == 'A') || \
+			  (*c == 'T') || \
+			  (*c == 'G') || \
+			  (*c == 'C') || \
+			  (*c == 'a') || \
+			  (*c == 't') || \
+			  (*c == 'g') || \
+			  (*c == 'c')))
+		{
+			return 0;
+		}
+		else
+		{
+			c++;
+		}
+	}
+	return 1;
+}
+
+
+byte_t* encode_seq_on_2_bits(const char* seq, int32_t length)
+{
+	byte_t*  seq_b;
+	uint8_t  modulo;
+	int32_t  length_b;
+	int32_t  i;
+
+	length_b = ceil((double) length / (double) 4.0);
+
+	seq_b = (byte_t*) calloc(length_b, sizeof(byte_t));
+	if (seq_b == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for an encoded DNA sequence");
+		return NULL;
+	}
+
+	for (i=0; i<length; i++)
+	{
+		// Shift of 2 to make place for new nucleotide
+		seq_b[i/4] <<= 2;
+
+		// Add new nucleotide
+		switch (seq[i])
+		{
+		case 'a':
+		case 'A':
+			seq_b[i/4] |= NUC_A_2b;
+			break;
+		case 'c':
+		case 'C':
+			seq_b[i/4] |= NUC_C_2b;
+			break;
+		case 'g':
+		case 'G':
+			seq_b[i/4] |= NUC_G_2b;
+			break;
+		case 't':
+		case 'T':
+			seq_b[i/4] |= NUC_T_2b;
+			break;
+		default:
+			obi_set_errno(OBI_ENCODE_ERROR);
+			obidebug(1, "\nInvalid nucleotide base when encoding (not [atgcATGC])");
+			return NULL;
+		}
+	}
+
+	// Final shift for the last byte if needed
+	modulo = (length % 4);
+	if (modulo)
+		seq_b[(i-1)/4] <<= (2*(4 - modulo));
+
+	return seq_b;
+}
+
+
+char* decode_seq_on_2_bits(byte_t* seq_b, int32_t length_seq)
+{
+	char*   seq;
+	int32_t i;
+	uint8_t shift;
+	uint8_t mask;
+	uint8_t nuc;
+
+	seq = (char*) malloc((length_seq+1) * sizeof(char));
+	if (seq == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for a decoded DNA sequence");
+		return NULL;
+	}
+
+	for (i=0; i<length_seq; i++)
+	{
+		shift = 6 - 2*(i % 4);
+		mask = NUC_MASK_2B << shift;
+		nuc = (seq_b[i/4] & mask) >> shift;
+
+		switch (nuc)
+		{
+		case NUC_A_2b:
+			seq[i] = 'a';
+			break;
+		case NUC_C_2b:
+			seq[i] = 'c';
+			break;
+		case NUC_G_2b:
+			seq[i] = 'g';
+			break;
+		case NUC_T_2b:
+			seq[i] = 't';
+			break;
+		default:
+			obi_set_errno(OBI_DECODE_ERROR);
+			obidebug(1, "\nInvalid nucleotide base when decoding");
+			return NULL;
+		}
+	}
+
+	seq[length_seq] = '\0';
+
+	return seq;
+}
+
+
+byte_t* encode_seq_on_4_bits(const char* seq, int32_t length)
+{
+	byte_t*  seq_b;
+	uint8_t  modulo;
+	int32_t  length_b;
+	int32_t  i;
+
+	length_b = ceil((double) length / (double) 2.0);
+
+	seq_b = (byte_t*) calloc(length_b, sizeof(byte_t));
+	if (seq_b == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for an encoded DNA sequence");
+		return NULL;
+	}
+
+	for (i=0; i<length; i++)
+	{
+		// Shift of 4 to make place for new nucleotide
+		seq_b[i/2] <<= 4;
+
+		// Add new nucleotide
+		switch (seq[i])
+		{
+		case 'a':
+		case 'A':
+			seq_b[i/2] |= NUC_A_4b;
+			break;
+		case 'c':
+		case 'C':
+			seq_b[i/2] |= NUC_C_4b;
+			break;
+		case 'g':
+		case 'G':
+			seq_b[i/2] |= NUC_G_4b;
+			break;
+		case 't':
+		case 'T':
+			seq_b[i/2] |= NUC_T_4b;
+			break;
+		case 'r':
+		case 'R':
+			seq_b[i/2] |= NUC_R_4b;
+			break;
+		case 'y':
+		case 'Y':
+			seq_b[i/2] |= NUC_Y_4b;
+			break;
+		case 's':
+		case 'S':
+			seq_b[i/2] |= NUC_S_4b;
+			break;
+		case 'w':
+		case 'W':
+			seq_b[i/2] |= NUC_W_4b;
+			break;
+		case 'k':
+		case 'K':
+			seq_b[i/2] |= NUC_K_4b;
+			break;
+		case 'm':
+		case 'M':
+			seq_b[i/2] |= NUC_M_4b;
+			break;
+		case 'b':
+		case 'B':
+			seq_b[i/2] |= NUC_B_4b;
+			break;
+		case 'd':
+		case 'D':
+			seq_b[i/2] |= NUC_D_4b;
+			break;
+		case 'h':
+		case 'H':
+			seq_b[i/2] |= NUC_H_4b;
+			break;
+		case 'v':
+		case 'V':
+			seq_b[i/2] |= NUC_V_4b;
+			break;
+		case 'n':
+		case 'N':
+			seq_b[i/2] |= NUC_N_4b;
+			break;
+		default:
+			obi_set_errno(OBI_ENCODE_ERROR);
+			obidebug(1, "\nInvalid nucleotide base when encoding (not IUPAC)");
+			return NULL;
+		}
+	}
+
+	// Final shift for the last byte if needed
+	modulo = (length % 2);
+	if (modulo)
+		seq_b[(i-1)/2] <<= (4*modulo);
+
+	return seq_b;
+}
+
+
+char* decode_seq_on_4_bits(byte_t* seq_b, int32_t length_seq)
+{
+	char*   seq;
+	int32_t i;
+	uint8_t shift;
+	uint8_t mask;
+	uint8_t nuc;
+
+	seq = (char*) malloc((length_seq+1) * sizeof(char));
+	if (seq == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for a decoded DNA sequence");
+		return NULL;
+	}
+
+	for (i=0; i<length_seq; i++)
+	{
+		shift = 4 - 4*(i % 2);
+		mask = NUC_MASK_4B << shift;
+		nuc = (seq_b[i/2] & mask) >> shift;
+
+		switch (nuc)
+		{
+		case NUC_A_4b:
+			seq[i] = 'a';
+			break;
+		case NUC_C_4b:
+			seq[i] = 'c';
+			break;
+		case NUC_G_4b:
+			seq[i] = 'g';
+			break;
+		case NUC_T_4b:
+			seq[i] = 't';
+			break;
+		case NUC_R_4b:
+			seq[i] = 'r';
+			break;
+		case NUC_Y_4b:
+			seq[i] = 'y';
+			break;
+		case NUC_S_4b:
+			seq[i] = 's';
+			break;
+		case NUC_W_4b:
+			seq[i] = 'w';
+			break;
+		case NUC_K_4b:
+			seq[i] = 'k';
+			break;
+		case NUC_M_4b:
+			seq[i] = 'm';
+			break;
+		case NUC_B_4b:
+			seq[i] = 'b';
+			break;
+		case NUC_D_4b:
+			seq[i] = 'd';
+			break;
+		case NUC_H_4b:
+			seq[i] = 'h';
+			break;
+		case NUC_V_4b:
+			seq[i] = 'v';
+			break;
+		case NUC_N_4b:
+			seq[i] = 'n';
+			break;
+		default:
+			obi_set_errno(OBI_DECODE_ERROR);
+			obidebug(1, "\nInvalid nucleotide base when decoding");
+			return NULL;
+		}
+	}
+
+	seq[length_seq] = '\0';
+
+	return seq;
+}
+
+
+///////////////////// FOR DEBUGGING ///////////////////////////
+//NOTE: The first byte is printed the first (at the left-most).
+
+void print_bits(void* ptr, int32_t size)
+{
+	uint8_t* b = (uint8_t*) ptr;
+	uint8_t byte;
+    int32_t i, j;
+
+    fprintf(stderr, "\n");
+    for (i=0;i<size;i++)
+    {
+        for (j=7;j>=0;j--)
+        {
+            byte = b[i] & (1<<j);
+            byte >>= j;
+            fprintf(stderr, "%u", byte);
+        }
+        fprintf(stderr, " ");
+    }
+    fprintf(stderr, "\n");
+}

src/encode.h

@@ -0,0 +1,190 @@
+/****************************************************************************
+ * Encoding header file	                                                    *
+ ****************************************************************************/
+
+/**
+ * @file encode.h
+ * @author Celine Mercier
+ * @date November 18th 2015
+ * @brief Header file for encoding DNA sequences.
+ */
+
+
+#ifndef ENCODE_H_
+#define ENCODE_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+#include <stdbool.h>
+
+#include "obitypes.h"
+
+
+#define NUC_MASK_2B 0x3   	/**< Binary: 11 to use when decoding 2 bits sequences
+ 	 	 	 	 	 	 	 */
+#define NUC_MASK_4B 0xF  	/**< Binary: 1111 to use when decoding 4 bits sequences
+ 	 	 	 	 	 	 	 */
+
+
+/**
+ * @brief enum for the 2-bits codes for each of the 4 nucleotides.
+ */
+enum
+{
+    NUC_A_2b = 0x0,   /* binary: 00 */
+    NUC_C_2b = 0x1,   /* binary: 01 */
+    NUC_G_2b = 0x2,   /* binary: 10 */
+    NUC_T_2b = 0x3,   /* binary: 11 */
+};
+
+
+/**
+ * @brief enum for the 4-bits codes for each of the 15 IUPAC nucleotides.
+ */
+enum
+{
+    NUC_A_4b = 0x1,   /* binary: 0001 */
+    NUC_C_4b = 0x2,   /* binary: 0010 */
+    NUC_G_4b = 0x3,   /* binary: 0011 */
+    NUC_T_4b = 0x4,   /* binary: 0100 */
+	NUC_R_4b = 0x5,   /* binary: 0101 */
+	NUC_Y_4b = 0x6,   /* binary: 0110 */
+	NUC_S_4b = 0x7,   /* binary: 0111 */
+	NUC_W_4b = 0x8,   /* binary: 1000 */
+	NUC_K_4b = 0x9,   /* binary: 1001 */
+	NUC_M_4b = 0xA,   /* binary: 1010 */
+	NUC_B_4b = 0xB,   /* binary: 1011 */
+	NUC_D_4b = 0xC,   /* binary: 1100 */
+	NUC_H_4b = 0xD,   /* binary: 1101 */
+	NUC_V_4b = 0xE,   /* binary: 1110 */
+	NUC_N_4b = 0xF,   /* binary: 1111 */
+};
+
+
+/**
+ * @brief Checks if there are only 'atgcATGC' characters in a
+ *        character string.
+ *
+ * @param seq The sequence to check.
+ *
+ * @returns A boolean value indicating if there are only
+ *          'atgcATGC' characters in a character string.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+bool only_ATGC(const char* seq);
+
+
+/**
+ * @brief Encodes a DNA sequence with each nucleotide coded on 2 bits.
+ *
+ *    A or a : 00
+ *    C or c : 01
+ *    T or t : 10
+ *    G or g : 11
+ *
+ * @warning The DNA sequence must contain only 'atgcATGC' characters.
+ *
+ * @param seq The sequence to encode.
+ * @param length The length of the sequence to encode.
+ *
+ * @returns The encoded sequence.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+byte_t* encode_seq_on_2_bits(const char* seq, int32_t length);
+
+
+/**
+ * @brief Decodes a DNA sequence that is coded with each nucleotide on 2 bits.
+ *
+ *    00 -> a
+ *    01 -> c
+ *    10 -> t
+ *    11 -> g
+ *
+ * @param seq_b The sequence to decode.
+ * @param length_seq The initial length of the sequence before it was encoded.
+ *
+ * @returns The decoded sequence ended with '\0'.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* decode_seq_on_2_bits(byte_t* seq_b, int32_t length_seq);
+
+
+/**
+ * @brief Encodes a DNA sequence with each nucleotide coded on 4 bits.
+ *
+ *		A or a : 0001
+ *      C or c : 0010
+ *      G or g : 0011
+ *      T or t : 0100
+ *      R or r : 0101
+ *      Y or y : 0110
+ *      S or s : 0111
+ *      W or w : 1000
+ *      K or k : 1001
+ *      M or m : 1010
+ *      B or b : 1011
+ *      D or d : 1100
+ *      H or h : 1101
+ *      V or v : 1110
+ *      N or n : 1111
+ *
+ * @warning The DNA sequence must contain only IUPAC characters.
+ *
+ * @param seq The sequence to encode.
+ * @param length The length of the sequence to encode.
+ *
+ * @returns The encoded sequence.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+byte_t* encode_seq_on_4_bits(const char* seq, int32_t length);
+
+
+/**
+ * @brief Decodes a DNA sequence that is coded with each nucleotide on 4 bits.
+ *
+ *		A or a : 0001
+ *      C or c : 0010
+ *      G or g : 0011
+ *      T or t : 0100
+ *      R or r : 0101
+ *      Y or y : 0110
+ *      S or s : 0111
+ *      W or w : 1000
+ *      K or k : 1001
+ *      M or m : 1010
+ *      B or b : 1011
+ *      D or d : 1100
+ *      H or h : 1101
+ *      V or v : 1110
+ *      N or n : 1111
+ *
+ * @param seq_b The sequence to decode.
+ * @param length_seq The initial length of the sequence before it was encoded.
+ *
+ * @returns The decoded sequence ended with '\0'.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* decode_seq_on_4_bits(byte_t* seq_b, int32_t length_seq);
+
+
+////////// FOR DEBUGGING ///////////
+
+// little endian
+void print_bits(void* ptr, int32_t length);
+
+
+#endif /* ENCODE_H_ */
+

src/murmurhash2.c

@@ -0,0 +1,64 @@
+//-----------------------------------------------------------------------------
+// MurmurHash2, by Austin Appleby
+
+// Note - This code makes a few assumptions about how your machine behaves -
+
+// 1. We can read a 4-byte value from any address without crashing
+// 2. sizeof(int) == 4
+
+// And it has a few limitations -
+
+// 1. It will not work incrementally.
+// 2. It will not produce the same results on little-endian and big-endian
+//    machines.	->TODO
+
+unsigned int murmurhash2(const void * key, int len, const unsigned int seed)
+{
+	// 'm' and 'r' are mixing constants generated offline.
+	// They're not really 'magic', they just happen to work well.
+
+	const unsigned int m = 0x5bd1e995;
+	const int r = 24;
+
+	// Initialize the hash to a 'random' value
+
+	unsigned int h = seed ^ len;
+
+	// Mix 4 bytes at a time into the hash
+
+	const unsigned char * data = (const unsigned char *)key;
+
+	while(len >= 4)
+	{
+		unsigned int k = *(unsigned int *)data;
+
+		k *= m;
+		k ^= k >> r;
+		k *= m;
+
+		h *= m;
+		h ^= k;
+
+		data += 4;
+		len -= 4;
+	}
+
+	// Handle the last few bytes of the input array
+
+	switch(len)
+	{
+	case 3: h ^= data[2] << 16;
+	case 2: h ^= data[1] << 8;
+	case 1: h ^= data[0];
+	        h *= m;
+	};
+
+	// Do a few final mixes of the hash to ensure the last few
+	// bytes are well-incorporated.
+
+	h ^= h >> 13;
+	h *= m;
+	h ^= h >> 15;
+
+	return h;
+}

src/murmurhash2.h

@@ -0,0 +1,11 @@
+
+#ifndef _BLOOM_MURMURHASH2
+#define _BLOOM_MURMURHASH2
+
+
+/**
+ * @brief Generates and returns a hash code from a byte array.
+ */
+unsigned int murmurhash2(const void * key, int len, const unsigned int seed);
+
+#endif

src/obiarray.h

@@ -1,285 +0,0 @@
-/****************************************************************************
- * OBIDMS array header file	                                                *
- ****************************************************************************/
-
-/**
- * @file obiarray.h
- * @author Celine Mercier
- * @date October 19th 2015
- * @brief Header file for handling arrays for storing and retrieving byte arrays (i.e. coding for character strings).
- */
-
-
-#ifndef OBIARRAY_H_
-#define OBIARRAY_H_
-
-
-#include <stdlib.h>
-#include <stdio.h>
-#include <stdint.h>
-#include <time.h>
-#include <sys/types.h>
-#include <dirent.h>
-
-#include "obidms.h"
-#include "obitypes.h"
-
-
-#define ARRAY_MAX_NAME (2048) 		/**< The maximum length of an array name.
-                              	  	 */
-#define ARRAY_GROWTH_FACTOR (2)		/**< The growth factor when an array is enlarged.
-                                	 */
-#define BYTE_ARRAY_HEADER_SIZE (5)  /**< The size of the header of a byte array.
-                              	  	 */
-
-
-typedef char byte_t;		/**< Defining byte type since data is stored in bits
-							 *	 and char (stored on one byte) is the smallest addressable unit.
- 	 	 	 	 	 	 	 */
-
-
-/**
- * @brief OBIDMS array data header structure.
- */
-typedef struct OBIDMS_array_data_header {
-	int			header_size;						/**< Size of the header in bytes.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	index_t		data_size_used;						/**< Size of the data used in bytes.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	index_t		data_size_max;						/**< Max size of the data in bytes.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	index_t		nb_items;							/**< Number of items.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	char    	array_name[ARRAY_MAX_NAME+1];		/**< The array name as a NULL terminated string.
-													 */
-	time_t		creation_date;			    	    /**< Date of creation of the file.
-												     */
-} OBIDMS_array_data_header_t, *OBIDMS_array_data_header_p;
-
-
-/**
- * @brief OBIDMS array data structure.
- */
-typedef struct OBIDMS_array_data {
-	OBIDMS_array_data_header_p	header; 		 	/**< A pointer to the header of the array data.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	byte_t*                   	data;   		 	/**< A pointer to the beginning of the data.
-													 */
-} OBIDMS_array_data_t, *OBIDMS_array_data_p;
-
-
-/**
- * @brief OBIDMS array header structure.
- */
-typedef struct OBIDMS_array_header {
-	int			header_size;						/**< Size of the header in bytes.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	size_t		array_size;							/**< Size of the array in bytes.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	index_t		nb_items;							/**< Number of items in the array.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	index_t		nb_items_max;						/**< Maximum number of items in the array before it has to be enlarged.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	char    	array_name[ARRAY_MAX_NAME+1];		/**< The array name as a NULL terminated string.
-													 */
-	time_t		creation_date;			    	    /**< Date of creation of the file.
-												     */
-} OBIDMS_array_header_t, *OBIDMS_array_header_p;
-
-
-/**
- * @brief OBIDMS array structure.
- */
-typedef struct OBIDMS_array {
-	OBIDMS_array_header_p		header; 		 	/**< A pointer to the header of the array.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	index_t*                 	first;   		 	/**< A pointer to the beginning of the array itself.
-													 */
-	OBIDMS_array_data_p			data;				/**< A pointer to the structure containing the data
-													 *   that the array references.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	DIR*						directory;			/**< A directory entry usable to
-										 	 	 	 *    refer and scan the array directory.
-										 	 	 	 */
-} OBIDMS_array_t, *OBIDMS_array_p;
-
-
-/**
- * @brief Checks if an obiarray already exists or not.
- *
- * @param dms The OBIDMS to which the obiarray belongs.
- * @param array_name The name of the obiarray.
- *
- * @returns A value indicating whether the obiarray exists or not.
- * @retval 1 if the obiarray exists.
- * @retval 0 if the obiarray does not exist.
- * @retval -1 if an error occurred.
- *
- * @since October 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-int obi_array_exists(OBIDMS_p dms, const char* array_name);
-
-
-/**
- * @brief Opens an obiarray and creates it if it does not already exist.
- *
- * Note: An obiarray is made of two files (referred to by two structures).
- * 		 One file contains the indices referring to the data, and the other
- * 		 file contains the data itself. The obiarray as a whole is referred
- * 		 to via the OBIDMS_array structure.
- *
- * @param dms The OBIDMS to which the obiarray belongs.
- * @param array_name The name of the obiarray.
- *
- * @returns A pointer to the obiarray structure.
- * @retval NULL if an error occurred.
- *
- * @since October 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-OBIDMS_array_p obi_array(OBIDMS_p dms, const char* array_name);
-
-
-/**
- * @brief Creates an obiarray. Fails if it already exists.
- *
- * Note: An obiarray is made of two files (referred to by two structures).
- * 		 One file contains the indices referring to the data, and the other
- * 		 file contains the data itself. The obiarray as a whole is referred
- * 		 to via the OBIDMS_array structure.
- *
- * @param dms The OBIDMS to which the obiarray belongs.
- * @param array_name The name of the obiarray.
- *
- * @returns A pointer to the newly created obiarray structure.
- * @retval NULL if an error occurred.
- *
- * @since October 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-OBIDMS_array_p obi_create_array(OBIDMS_p dms, const char* array_name);
-
-
-/**
- * @brief Opens an obiarray. Fails if it does not already exist.
- *
- * Note: An obiarray is made of two files (referred to by two structures).
- * 		 One file contains the indices referring to the data, and the other
- * 		 file contains the data itself. The obiarray as a whole is referred
- * 		 to via the OBIDMS_array structure.
- *
- * @param dms The OBIDMS to which the obiarray belongs.
- * @param array_name The name of the obiarray.
- *
- * @returns A pointer to the obiarray structure.
- * @retval NULL if an error occurred.
- *
- * @since October 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-OBIDMS_array_p obi_open_array(OBIDMS_p dms, const char* array_name);
-
-
-/**
- * @brief Closes an obiarray.
- *
- * Note: An obiarray is made of two files (referred to by two structures).
- * 		 One file contains the indices referring to the data, and the other
- * 		 file contains the data itself. The obiarray as a whole is referred
- * 		 to via the OBIDMS_array structure.
- *
- * @param array A pointer to the obiarray structure to close and free.
- *
- * @retval 0 if the operation was successfully completed.
- * @retval -1 if an error occurred.
- *
- * @since October 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-int obi_close_array(OBIDMS_array_p array);
-
-
-/**
- * @brief Adds a value (byte array) in an obiarray, checking first if it is already in it.
- *
- * @warning The byte array to add must already be encoded and contain its header.
- *
- * @param array A pointer to the obiarray.
- * @param value The byte array to add in the obiarray.
- *
- * @returns The index of the value, whether it was added or already in the obiarray.
- * @retval -1 if an error occurred.
- *
- * @since October 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-index_t obi_array_add(OBIDMS_array_p array, byte_t* value);
-
-
-/**
- * @brief Recovers a value (byte array) in an obiarray.
- *
- * @warning The byte array recovered is encoded and contains its header.
- *
- * @param array A pointer to the obiarray.
- * @param index The index of the value in the data array.
- *
- * @returns A pointer to the byte array recovered.
- *
- * @since October 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-byte_t* obi_array_get(OBIDMS_array_p array, index_t index);
-
-
-/**
- * @brief Searches a value (byte array) in an obiarray performing a binary search.
- *
- * @warning The byte array to search must already be encoded and contain its header.
- *
- * @param array A pointer to the obiarray.
- * @param value The byte array to add in the obiarray.
- *
- * @returns If the value is found, its data index is returned.
- * 			If the value is not found, the array index indicating where the value's data index
- * 			should be in the array is returned in the form (- (index + 1)), as data indices in an
- * 			obiarray are sorted according to the ascending order of the values (byte arrays) themselves.
- *
- * @since October 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-index_t obi_array_search(OBIDMS_array_p array, byte_t* value);
-
-
-/**
- * @brief Converts a character string to a byte array with a header.
- *
- * @warning The byte array must be freed by the caller.
- *
- * @param value The character string to convert.
- *
- * @returns A pointer to the byte array created.
- * @retval NULL if an error occurred.
- *
- * @since October 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-byte_t* obi_str_to_obibytes(char* value);
-
-
-/**
- * @brief Converts a byte array to a character string.
- *
- * @param value_b The byte array to convert.
- *
- * @returns A pointer to the character string contained in the byte array.
- *
- * @since October 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-const char* obi_obibytes_to_str(byte_t* value_b);
-
-
-#endif /* OBIARRAY_H_ */
-

src/obiavl.h

@@ -0,0 +1,414 @@
+/****************************************************************************
+ * OBIDMS AVL tree header file	                                            *
+ ****************************************************************************/
+
+/**
+ * @file obiavl.h
+ * @author Celine Mercier
+ * @date December 3rd 2015
+ * @brief Header file for handling AVL trees for storing and retrieving blobs.
+ */
+
+
+#ifndef OBIAVL_H_
+#define OBIAVL_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+#include <time.h>
+#include <sys/types.h>
+#include <dirent.h>
+#include <stdbool.h>
+
+#include "obidms.h"
+#include "obiblob.h"
+#include "obitypes.h"
+#include "bloom.h"
+#include "utils.h"
+#include "encode.h"
+
+
+#define MAX_NB_OF_AVLS_IN_GROUP (100)						/**< The maximum number of AVL trees in a group.	// TODO discuss
+                              	  	 	 	 	 	 	 	 */
+#define MAX_NODE_COUNT_PER_AVL (10000000)					/**< The maximum number of nodes in an AVL tree.
+															 *   Only used to decide when to create a new AVL in a group, and to initialize the bloom filter // TODO discuss.
+                              	  	 	 	 	 	 	 	 */
+#define MAX_DATA_SIZE_PER_AVL (1073741824)		            /**< The maximum size of the data referred to by an AVL tree in a group.
+ 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   Only used to decide when to create a new AVL in a group.
+ 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   Should not be greater than int32_t max (2,147,483,647), as indexes will have to be stored on 32 bits.
+ 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   Here 1073741824 B = 1 GB
+ 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+#define AVL_MAX_DEPTH (1024)								/**< The maximum depth of an AVL tree. Used to save paths through the tree.
+                              	  	 	 	 	 	 	 	 */
+#define AVL_MAX_NAME (1024) 								/**< The maximum length of an AVL tree name.
+                              	  	 	 	 	 	 	 	 */
+#define AVL_GROWTH_FACTOR (2)								/**< The growth factor when an AVL tree is enlarged.
+                                	 	 	 	 	 	 	 */
+#define LEFT_CHILD(node)	(avl->tree)+(node->left_child)  /**< Pointer to the left child of a node in an AVL tree.
+															 */
+#define RIGHT_CHILD(node)	(avl->tree)+(node->right_child) /**< Pointer to the right child of a node in an AVL tree.
+															 */
+
+
+/**
+ * @brief AVL tree node structure.
+ */
+typedef struct AVL_node {
+	index_t  left_child;	  /**< Index of left less child node.
+	  	 	 	 	 	 	   */
+	index_t  right_child; 	  /**< Index of right greater child node.
+	 	 	 	 	 	 	   */
+	int8_t   balance_factor;  /**< Balance factor of the node.
+							   */
+	index_t  value;			  /**< Index of the value associated with the node in the data array.
+							   */
+	uint64_t crc64;			  /**< Cyclic Redundancy Check code on 64 bits associated with the value.
+	 	 	 	 	 	 	   */
+} AVL_node_t, *AVL_node_p;
+
+
+/**
+ * @brief OBIDMS AVL tree data header structure.
+ */
+typedef struct OBIDMS_avl_data_header {
+	int			header_size;						/**< Size of the header in bytes.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t		data_size_used;						/**< Size of the data used in bytes.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t		data_size_max;						/**< Max size of the data in bytes.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t		nb_items;							/**< Number of items.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	char    	avl_name[AVL_MAX_NAME+1];			/**< The AVL tree name as a NULL terminated string.
+													 */
+	time_t		creation_date;			    	    /**< Date of creation of the file.
+												     */
+} OBIDMS_avl_data_header_t, *OBIDMS_avl_data_header_p;
+
+
+/**
+ * @brief OBIDMS AVL tree data structure.
+ */
+typedef struct OBIDMS_avl_data {
+	OBIDMS_avl_data_header_p	header; 		 	/**< A pointer to the header of the AVL tree data.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	byte_t*                 	data;   		 	/**< A pointer to the beginning of the data.
+													 */
+	int							data_fd;	        /**< File descriptor of the file containing the data.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+} OBIDMS_avl_data_t, *OBIDMS_avl_data_p;
+
+
+/**
+ * @brief OBIDMS AVL tree header structure.
+ */
+typedef struct OBIDMS_avl_header {
+	int			header_size;						/**< Size of the header in bytes.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	size_t		avl_size;							/**< Size of the AVL tree in bytes.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t		nb_items;							/**< Number of items in the AVL tree.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t		nb_items_max;						/**< Maximum number of items in the AVL tree before it has to be enlarged.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t		root_idx;							/**< Index of the root of the AVL tree.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	char    	avl_name[AVL_MAX_NAME+1];			/**< The AVL tree name as a NULL terminated string.
+													 */
+	time_t		creation_date;			    	    /**< Date of creation of the file.
+												     */
+	bloom_t 	bloom_filter;			    	    /**< Bloom filter associated with the AVL tree, enabling to know if a value
+													 *   might already be stored in the data referred to by the tree.
+     	 	 	 	 	 	 	 	 	 	 	 	 */
+} OBIDMS_avl_header_t, *OBIDMS_avl_header_p;
+
+
+/**
+ * @brief OBIDMS AVL tree structure.
+ */
+typedef struct OBIDMS_avl {
+	OBIDMS_p                	dms;			 			/**< A pointer to the OBIDMS structure to which the AVL tree belongs.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	OBIDMS_avl_header_p			header; 	 				/**< A pointer to the header of the AVL tree.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	struct AVL_node*           	tree;   		 			/**< A pointer to the root of the AVL tree.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t                     path_idx[AVL_MAX_DEPTH];	/**< The path taken to a node from the root as an array of node indices.
+													 	     */
+	int8_t                      path_dir[AVL_MAX_DEPTH];	/**< The path taken to a node from the root as an array of directions
+															 *   (0 for left, -1 for right).
+															 */
+	OBIDMS_avl_data_p			data;						/**< A pointer to the structure containing the data
+													 	 	 *   that the AVL tree references.
+													 	 	 */
+	DIR*						directory;					/**< A directory entry usable to
+										 	 	 	 	 	 *    refer and scan the AVL tree directory.
+										 	 	 	 	 	 */
+	int							dir_fd;						/**< The file descriptor of the directory entry
+													 	 	 *    usable to refer and scan the AVL tree directory.
+													 	 	 */
+	int							avl_fd;						/**< The file descriptor of the file containing the AVL tree.
+													 	 	 */
+} OBIDMS_avl_t, *OBIDMS_avl_p;
+
+
+/**
+ * @brief OBIDMS AVL tree group structure.
+ */
+typedef struct OBIDMS_avl_group {
+	OBIDMS_avl_p 	sub_avls[MAX_NB_OF_AVLS_IN_GROUP];		/**< Array containing the pointers to the AVL trees of the group.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	int 			current_avl_idx;						/**< Index in the sub_avls array of the AVL tree currently being filled.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	char			name[AVL_MAX_NAME+1];				 	/**< Base name of the AVL group. The AVL trees in it have names of the form basename_idx.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	OBIDMS_p        dms;									/**< Pointer to the OBIDMS structure to which the AVL group belongs.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	bool			writable;								/**< Indicates whether the AVL group is read-only or not.
+															 */
+	size_t			counter;								/**< Indicates by how many threads/programs (TODO) the AVL group is used.
+													 	 	 */
+} OBIDMS_avl_group_t, *OBIDMS_avl_group_p;
+
+
+/**
+ * @brief Checks if an AVL tree or AVL tree group already exists or not.
+ *
+ * @param dms The OBIDMS to which the AVL tree or AVL tree group belongs.
+ * @param avl_name The name of the AVL treeor the base name of the AVL tree group.
+ *
+ * @returns A value indicating whether the AVL tree or AVL tree group exists or not.
+ * @retval 1 if the AVL tree or AVL tree group exists.
+ * @retval 0 if the AVL tree or AVL tree group does not exist.
+ * @retval -1 if an error occurred.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_avl_exists(OBIDMS_p dms, const char* avl_name);
+
+
+/**
+ * @brief Creates an AVL tree. Fails if it already exists.
+ *
+ * Note: An AVL tree is made of two files (referred to by two structures).
+ * 		 One file contains the tree referring to the data, and the other
+ * 		 file contains the data itself. The AVL tree as a whole is referred
+ * 		 to via the OBIDMS_avl structure. An AVL tree is stored in a directory
+ * 		 with the same name, or with the base name of the AVL group if it is
+ * 		 part of an AVL group.
+ *
+ * @param dms The OBIDMS to which the AVL tree belongs.
+ * @param avl_name The name of the AVL tree.
+ * @param avl_idx The index of the AVL tree if it is part of an AVL group,
+ *        or -1 if it is not part of an AVL group.
+ *
+ * @returns A pointer to the newly created AVL tree structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+OBIDMS_avl_p obi_create_avl(OBIDMS_p dms, const char* avl_name, int avl_idx);
+
+
+/**
+ * @brief Opens an AVL tree in read-only mode. Fails if it does not already exist.
+ *
+ * Note: An AVL tree is made of two files (referred to by two structures).
+ * 		 One file contains the tree referring to the data, and the other
+ * 		 file contains the data itself. The AVL tree as a whole is referred
+ * 		 to via the OBIDMS_avl structure.
+ *
+ * @param dms The OBIDMS to which the AVL tree belongs.
+ * @param avl_name The name of the AVL tree.
+ * @param avl_idx The index of the AVL tree if it is part of an AVL group,
+ *        or -1 if it is not part of an AVL group.
+ *
+ * @returns A pointer to the AVL tree structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name, int avl_idx);
+
+
+/**
+ * @brief Opens an AVL tree group and creates it if it does not already exist.
+ *
+ * Note: An AVL tree group is composed of multiple AVL trees that all have the
+ *       same base name, and an index differentiating them.
+ *
+ * @param dms The OBIDMS to which the AVL tree belongs.
+ * @param avl_name The base name of the AVL tree group.
+ *
+ * @returns A pointer to the AVL tree group structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+OBIDMS_avl_group_p obi_avl_group(OBIDMS_p dms, const char* avl_name);
+
+
+/**
+ * @brief Creates an AVL tree group.
+ *
+ * Note: An AVL tree group is composed of multiple AVL trees that all have the
+ *       same base name, and an index differentiating them.
+ *
+ * @param dms The OBIDMS to which the AVL tree belongs.
+ * @param avl_name The base name of the AVL tree group.
+ *
+ * @returns A pointer to the AVL tree group structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+OBIDMS_avl_group_p obi_create_avl_group(OBIDMS_p dms, const char* avl_name);
+
+
+/**
+ * @brief Opens an AVL tree group in read-only mode.
+ *
+ * Note: An AVL tree group is composed of multiple AVL trees that all have the
+ *       same base name, and an index differentiating them.
+ *
+ * @param dms The OBIDMS to which the AVL tree belongs.
+ * @param avl_name The base name of the AVL tree group.
+ *
+ * @returns A pointer to the AVL tree group structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+OBIDMS_avl_group_p obi_open_avl_group(OBIDMS_p dms, const char* avl_name);
+
+
+/**
+ * @brief Closes an AVL tree.
+ *
+ * @param avl A pointer to the AVL tree structure to close and free.
+ *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_close_avl(OBIDMS_avl_p avl);
+
+
+/**
+ * @brief Closes an AVL tree group.
+ *
+ * @param avl_group A pointer to the AVL tree group structure to close and free.
+ *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_close_avl_group(OBIDMS_avl_group_p avl_group);
+
+
+/**
+ * @brief Recovers a value (blob) in an AVL tree.
+ *
+ * @warning The blob recovered must be decoded to get the original value.
+ * @warning The blob recovered is mapped in memory.
+ *
+ * @param avl A pointer to the AVL tree.
+ * @param index The index of the value in the data array.
+ *
+ * @returns A pointer to the blob recovered.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+Obi_blob_p obi_avl_get(OBIDMS_avl_p avl, index_t index);
+
+
+/**
+ * @brief Adds a value (blob) in an AVL tree.
+ *
+ * @warning The value given must be already be encoded into a blob structure (Obi_blob_t).
+ * @warning If the value is already in the AVL tree, an error will be triggered.		// TODO to discuss
+ *
+ * @param avl A pointer to the AVL tree.
+ * @param value The blob to add in the AVL tree.
+ *
+ * @returns The index of the value newly added in the AVL tree.
+ * @retval -1 if an error occurred.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+index_t obi_avl_add(OBIDMS_avl_p avl, Obi_blob_p value);
+
+
+/**
+ * @brief Finds a value (blob) in an AVL tree.
+ *
+ * @warning The value given must be already be encoded into a blob structure (Obi_blob_t).
+ *
+ * @param avl A pointer to the AVL tree.
+ * @param value The blob to add in the AVL tree.
+ *
+ * @returns The data index of the value.
+ * @retval -1 if the value is not in the tree.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+index_t obi_avl_find(OBIDMS_avl_p avl, Obi_blob_p value);
+
+
+/**
+ * @brief Recovers a value (blob) in an AVL tree.
+ *
+ * @warning The blob recovered must be decoded to get the original value.
+ * @warning The blob recovered is mapped in memory.
+ *
+ * @param avl_group A pointer to the AVL tree.
+ * @param index The index of the value in the form of a 64-bit integer
+ *              with the 32 left-most bits coding for the index of the tree of
+ *              the group in which the value is stored, and the 32 right-most bits
+ *              coding for the index at which the value is stored in that AVL tree.
+ *
+ * @returns A pointer to the blob recovered.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+Obi_blob_p obi_avl_group_get(OBIDMS_avl_group_p avl_group, index_t idx);
+
+
+/**
+ * @brief Adds a value (blob) in an AVL tree group, checking if it is already in it.
+ *
+ * @warning The value given must be already be encoded into a blob structure (Obi_blob_t).
+ *
+ * @param avl_group A pointer to the AVL tree group.
+ * @param value The blob to add in the AVL tree group.
+ *
+ * @returns The index of the value newly added in the AVL tree group, in the form of a
+ *          64-bit integer with the 32 left-most bits coding for the index of the tree
+ *          of the group in which the value is stored, and the 32 right-most bits
+ *          coding for the index at which the value is stored in that AVL tree.
+ * @retval -1 if an error occurred.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+index_t obi_avl_group_add(OBIDMS_avl_group_p avl_group, Obi_blob_p value);
+
+
+#endif /* OBIAVL_H_ */
+

src/obiblob.c

@@ -0,0 +1,91 @@
+/****************************************************************************
+ * Obiblob functions                                                       *
+ ****************************************************************************/
+
+/**
+ * @file obiblob.c
+ * @author Celine Mercier
+ * @date April 11th 2016
+ * @brief Functions handling Obiblob structures.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+#include <math.h>
+
+#include "obiblob.h"
+#include "obierrno.h"
+#include "obitypes.h"	// For byte_t type
+#include "obidebug.h"
+
+
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
+
+
+// TODO: endianness problem?
+
+
+Obi_blob_p obi_blob(byte_t* encoded_value, uint8_t element_size, int32_t length_encoded_value, int32_t length_decoded_value)
+{
+	Obi_blob_p blob;
+
+	// Allocate the memory for the blob structure
+	blob = (Obi_blob_p) malloc(sizeof(Obi_blob_t) + length_encoded_value);
+	if (blob == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for a blob");
+		return NULL;
+	}
+
+	// Store the number of bits on which each element is encoded
+	blob->element_size = element_size;
+
+	// Store the length (in bytes) of the encoded value
+	blob->length_encoded_value = length_encoded_value;
+
+	// Store the initial length (in bytes) of the decoded value
+	blob->length_decoded_value = length_decoded_value;
+
+	// Store the encoded value
+	memcpy(blob->value, encoded_value, length_encoded_value);
+
+	return blob;
+}
+
+
+int obi_blob_compare(Obi_blob_p value_1, Obi_blob_p value_2)
+{
+	int 	comp;
+	int32_t b;
+
+	if (value_1->element_size != value_2->element_size)
+		return (value_1->element_size - value_2->element_size);
+
+	if (value_1->length_encoded_value != value_2->length_encoded_value)
+		return (value_1->length_encoded_value - value_2->length_encoded_value);
+
+	if (value_1->element_size != ELEMENT_SIZE_STR) // because if so, length_decoded_value == length_encoded_value
+	{
+		if (value_1->length_decoded_value != value_2->length_decoded_value)
+			return (value_1->length_decoded_value - value_2->length_decoded_value);
+	}
+
+	b = 0;
+	comp = 0;
+	while (!comp && (b < value_1->length_encoded_value))
+	{
+		comp = *((value_1->value)+b) - *((value_2->value)+b);
+		b++;
+	}
+	return comp;
+}
+
+
+int obi_blob_sizeof(Obi_blob_p value)
+{
+	return (sizeof(Obi_blob_t) + (value->length_encoded_value));
+}
+

src/obiblob.h

@@ -0,0 +1,98 @@
+/****************************************************************************
+ * Obiblob header file	                                                    *
+ ****************************************************************************/
+
+/**
+ * @file obiblob.h
+ * @author Celine Mercier
+ * @date November 18th 2015
+ * @brief Header file for handling Obi_blob structures.
+ */
+
+
+#ifndef OBIBLOB_H_
+#define OBIBLOB_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+
+#include "obitypes.h"
+
+
+#define ELEMENT_SIZE_STR (8)		/**< The size of an element from a value of type character string.
+                              	  	 */
+#define ELEMENT_SIZE_SEQ_2 (2)		/**< The size of an element from a value of type DNA sequence encoded on 2 bits.
+                              	  	 */
+#define ELEMENT_SIZE_SEQ_4 (4)		/**< The size of an element from a value of type DNA sequence encoded on 4 bits.
+                              	  	 */
+
+
+/**
+ * @brief Blob structure, for handling encoded values.
+ */
+typedef struct Obi_blob {
+	uint8_t  element_size;		 	/**< Size in bits of one element from the encoded value.
+	 	 	 	 	 	 	 	 	 */
+	int32_t  length_encoded_value;	/**< Length in bytes of the encoded value.
+	 	 	 	 	 	 	 	 	 */
+	int32_t  length_decoded_value;	/**< Length in bytes of the decoded value.
+	 	 	 	 	 	 	 	 	 */
+	byte_t   value[];				/**< Encoded value.
+	 	 	 	 	 	 	 	 	 */
+} Obi_blob_t, *Obi_blob_p;
+
+
+
+/**
+ * @brief Function building a blob structure.
+ *
+ * @param encoded_value A pointer to the encoded value that will be stored in the blob.
+ * @param element_size The size in bits of one element from the encoded value.
+ * @param length_encoded_value The length in bytes of the encoded value.
+ * @param length_decoded_value The length in bytes of the decoded value.
+ *
+ * @returns A pointer to the created blob structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+Obi_blob_p obi_blob(byte_t* encoded_value, uint8_t element_size, int32_t length_encoded_value, int32_t length_decoded_value);
+
+
+/**
+ * @brief Function comparing two blobs.
+ *
+ * The encoding is compared first, then the length of the
+ * values, then the values themselves.
+ *
+ * @param value_1 A pointer to the first blob structure.
+ * @param value_2 A pointer to the second blob structure.
+ *
+ * @returns A value < 0 if value_1 < value_2,
+ * 			a value > 0 if value_1 > value_2,
+ * 			and 0 if value_1 == value_2.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_blob_compare(Obi_blob_p value_1, Obi_blob_p value_2);
+
+
+/**
+ * @brief Function calculating the size in bytes of a blob.
+ *
+ * @param value A pointer to the blob structure.
+ *
+ * @returns The size of the blob in bytes.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_blob_sizeof(Obi_blob_p value);
+
+
+#endif /* OBIBLOB_H_ */
+

src/obiblob_indexer.c

@@ -0,0 +1,57 @@
+/****************************************************************************
+ * Obiblob functions                                                       *
+ ****************************************************************************/
+
+/**
+ * @file obiblob_indexer.c
+ * @author Celine Mercier
+ * @date April 12th 2016
+ * @brief Functions handling the indexing and retrieval of blob structures.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "obiblob_indexer.h"
+#include "obidms.h"
+#include "obierrno.h"
+#include "obidebug.h"
+
+
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
+
+
+//inline int obi_indexer_exists(OBIDMS_p dms, const char* name);
+
+//inline Obi_indexer_p obi_indexer(OBIDMS_p dms, const char* name);
+
+//inline Obi_indexer_p obi_create_indexer(OBIDMS_p dms, const char* name);
+
+//inline Obi_indexer_p obi_open_indexer(OBIDMS_p dms, const char* name);
+
+//inline int obi_close_indexer(Obi_indexer_p indexer);
+
+//inline index_t obi_indexer_add(Obi_indexer_p indexer, Obi_blob_p value);
+
+//inline Obi_blob_p obi_indexer_get(Obi_indexer_p indexer, index_t idx);
+
+
+char* obi_build_indexer_name(const char* column_name, obiversion_t column_version)
+{
+	char* indexer_name;
+
+	indexer_name = (char*) malloc(INDEXER_MAX_NAME * sizeof(char));
+	if (indexer_name == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating the memory for an indexer name");
+		return NULL;
+	}
+
+	strcpy(indexer_name, column_name);
+	sprintf(indexer_name+strlen(column_name), "_%d_indexer", column_version);
+
+	return indexer_name;
+}
+

src/obiblob_indexer.h

@@ -0,0 +1,159 @@
+/****************************************************************************
+ * Blob indexer header file	                                                    *
+ ****************************************************************************/
+
+/**
+ * @file obiblob_indexer.h
+ * @author Celine Mercier
+ * @date April 12th 2016
+ * @brief Header file for the functions handling the indexing of values.
+ */
+
+
+#ifndef OBIBLOB_INDEXER_H_
+#define OBIBLOB_INDEXER_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "obidms.h"
+#include "obiavl.h"
+#include "obitypes.h"
+#include "obiblob.h"
+
+
+#define INDEXER_MAX_NAME AVL_MAX_NAME 			/**< Macro to refer to the maximum size of the name of an indexer structure.
+ 	 	 	 	 	 	 	 	 	 	 	 	 */
+
+
+typedef struct OBIDMS_avl_group Obi_indexer;	/**< Typedef to refer to the used indexer structure.
+ 	 	 	 	 	 	 	 	 	 	 	 	 */
+typedef OBIDMS_avl_group_p Obi_indexer_p; 		/**< Typedef to refer to the pointer of the used indexer structure.
+ 	 	 	 	 	 	 	 	 	 	 	 	 */
+
+
+/**
+ * @brief Checks if an indexer already exists or not.
+ *
+ * @param dms The OBIDMS to which the indexer belongs.
+ * @param name The name of the indexer.
+ *
+ * @returns A value indicating whether the indexer exists or not.
+ * @retval 1 if the indexer exists.
+ * @retval 0 if the indexer does not exist.
+ * @retval -1 if an error occurred.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+#define obi_indexer_exists obi_avl_exists
+
+
+/**
+ * @brief Opens an indexer and creates it if it does not already exist.
+ *
+ * @param dms The OBIDMS to which the indexer belongs.
+ * @param name The name of the indexer.
+ *
+ * @returns A pointer to the indexer structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+#define obi_indexer obi_avl_group
+
+
+/**
+ * @brief Creates an indexer.
+ *
+ * @param dms The OBIDMS to which the indexer belongs.
+ * @param name The name of the indexer.
+ *
+ * @returns A pointer to the AVL tree group structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+#define obi_create_indexer obi_create_avl_group
+
+
+/**
+ * @brief Opens an indexer.
+ *
+ * @param dms The OBIDMS to which the indexer belongs.
+ * @param name The name of the indexer.
+ *
+ * @returns A pointer to the indexer structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+#define obi_open_indexer obi_open_avl_group
+
+
+/**
+ * @brief Closes an indexer.
+ *
+ * @param indexer A pointer to the indexer structure to close and free.
+ *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+#define obi_close_indexer obi_close_avl_group
+
+
+/**
+ * @brief Indexes a blob in an indexer and returns the index referring to the blob.
+ *
+ * @param indexer A pointer to the indexer.
+ * @param value The blob to index.
+ *
+ * @returns The index of the blob newly added in the indexer.
+ * @retval -1 if an error occurred.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+#define obi_indexer_add obi_avl_group_add
+
+
+/**
+ * @brief Recovers a blob from an indexer.
+ *
+ * @param indexer A pointer to the indexer.
+ * @param index The index of the blob in the indexer.
+ *
+ * @returns A pointer to the blob recovered.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+#define obi_indexer_get obi_avl_group_get
+
+
+/**
+ * @brief Builds an indexer name in the form columnname_columnversion_indexer.
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param column_name The name of the column associated with the indexer.
+ * @param column_version The version of the column associated with the indexer.
+ *
+ * @returns A pointer on the indexer name built.
+ * @retval NULL if an error occurred.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_build_indexer_name(const char* column_name, obiversion_t column_version);
+
+
+#endif /* OBIBLOB_INDEXER_H_ */
+

src/obidms.c

@@ -13,6 +13,7 @@
 #include <stdlib.h>
 #include <stdio.h>
 #include <string.h>
+#include <stdbool.h>
 #include <sys/stat.h>
 #include <fcntl.h>
 #include <sys/types.h>
@@ -22,7 +23,9 @@
 #include "obierrno.h"
 #include "obidebug.h"
 #include "obidmscolumn.h"
-#include "private_at_functions.h"
+#include "obiblob_indexer.h"
+#include "utils.h"
+#include "obilittlebigman.h"
 
 
 #define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
@@ -54,6 +57,44 @@
 static char* build_directory_name(const char* dms_name);
 
 
+/**
+ * Internal function building the informations file name from an OBIDMS name.
+ *
+ * The function builds the file name for the informations file of an OBIDMS.
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param dms_name The name of the OBIDMS.
+ *
+ * @returns A pointer to the file name.
+ * @retval NULL if an error occurred.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+static char* build_infos_file_name(const char* dms_name);
+
+
+/**
+ * Internal function creating the file containing basic informations on the OBIDMS.
+ *
+ * This file contains:
+ * 		- The endianness of the platform
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param dms_file_descriptor The file descriptor for the OBIDMS directory.
+ * @param dms_name The name of the OBIDMS.
+ *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int create_dms_infos_file(int dms_file_descriptor, const char* dms_name);
+
+
 /************************************************************************
  *
  * D E F I N I T I O N   O F   T H E   P R I V A T E   F U N C T I O N S
@@ -65,7 +106,8 @@ static char* build_directory_name(const char* dms_name)
 	char* directory_name;
 
 	// Build the database directory name
-	if (asprintf(&directory_name, "%s.obidms", dms_name) < 0)
+	directory_name = (char*) malloc((strlen(dms_name) + 8)*sizeof(char));
+	if (sprintf(directory_name, "%s.obidms", dms_name) < 0)
 	{
 		obi_set_errno(OBIDMS_MEMORY_ERROR);
 		obidebug(1, "\nProblem building an OBIDMS directory name");
@@ -85,6 +127,75 @@ static char* build_directory_name(const char* dms_name)
 }
 
 
+static char* build_infos_file_name(const char* dms_name)
+{
+	char* file_name;
+
+	// Build file name
+	file_name = (char*) malloc((strlen(dms_name) + 7)*sizeof(char));
+	if (sprintf(file_name, "%s_infos", dms_name) < 0)
+	{
+		obi_set_errno(OBIDMS_MEMORY_ERROR);
+		obidebug(1, "\nProblem building an informations file name");
+		return NULL;
+	}
+
+	return file_name;
+}
+
+
+int create_dms_infos_file(int dms_file_descriptor, const char* dms_name)
+{
+	char* 	file_name;
+	int 	infos_file_descriptor;
+	off_t 	file_size;
+	bool	little_endian;
+
+	file_size = sizeof(bool);
+
+	// Create file name
+	file_name = build_infos_file_name(dms_name);
+	if (file_name == NULL)
+		return -1;
+
+    // Create file
+	infos_file_descriptor = openat(dms_file_descriptor, file_name, O_RDWR | O_CREAT | O_EXCL, 0777);
+	if (infos_file_descriptor < 0)
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError creating an informations file");
+		free(file_name);
+		return -1;
+	}
+
+	free(file_name);
+
+	// Truncate the infos file to the right size
+	if (ftruncate(infos_file_descriptor, file_size) < 0)
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError truncating an informations file");
+		close(infos_file_descriptor);
+		return -1;
+	}
+
+	// Write endianness
+	little_endian = obi_is_little_endian();
+	if (write(infos_file_descriptor, &little_endian, sizeof(bool)) < ((ssize_t) sizeof(bool)))
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError writing the endianness in an informations file");
+		close(infos_file_descriptor);
+		return -1;
+	}
+
+	// Close file
+	close(infos_file_descriptor);
+
+	return 0;
+}
+
+
 /**********************************************************************
  *
  * D E F I N I T I O N   O F   T H E   P U B L I C   F U N C T I O N S
@@ -94,8 +205,8 @@ static char* build_directory_name(const char* dms_name)
 int obi_dms_exists(const char* dms_name)
 {
     struct stat buffer;
-	char *directory_name;
-    int check_dir;
+	char*       directory_name;
+    int 		check_dir;
 
 	// Build and check the directory name
     directory_name = build_directory_name(dms_name);
@@ -116,8 +227,8 @@ int obi_dms_exists(const char* dms_name)
 OBIDMS_p obi_create_dms(const char* dms_name)
 {
 	char* directory_name;
-	DIR* dms_dir;
-	int dms_file_descriptor;
+	DIR*  dms_dir;
+	int   dms_file_descriptor;
 
 	// Build and check the directory name
 	directory_name = build_directory_name(dms_name);
@@ -128,7 +239,10 @@ OBIDMS_p obi_create_dms(const char* dms_name)
 	if (mkdir(directory_name, 00777) < 0)
 	{
 		if (errno == EEXIST)
+		{
 			obi_set_errno(OBIDMS_EXIST_ERROR);
+			obidebug(1, "\nAn OBIDMS directory with the same name already exists in this directory.");
+		}
 		else
 			obi_set_errno(OBIDMS_UNKNOWN_ERROR);
 		obidebug(1, "\nProblem creating an OBIDMS directory");
@@ -136,7 +250,7 @@ OBIDMS_p obi_create_dms(const char* dms_name)
 		return NULL;
 	}
 
-	// Get file descriptor of DMS directory to create the arrays directory
+	// Get file descriptor of DMS directory to create the indexer directory
 	dms_dir = opendir(directory_name);
 	if (dms_dir == NULL)
 	{
@@ -145,25 +259,28 @@ OBIDMS_p obi_create_dms(const char* dms_name)
 		free(directory_name);
 		return NULL;
 	}
+
+	free(directory_name);
+
 	dms_file_descriptor = dirfd(dms_dir);
 	if (dms_file_descriptor < 0)
 	{
 		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
 		obidebug(1, "\nProblem getting the file descriptor of a newly created OBIDMS directory");
-		free(directory_name);
 		return NULL;
 	}
 
-	// Create the arrays directory
-	if (mkdirat(dms_file_descriptor, ARRAY_DIR_NAME, 00777) < 0)
+	// Create the indexer directory
+	if (mkdirat(dms_file_descriptor, INDEXER_DIR_NAME, 00777) < 0)
 	{
-		obi_set_errno(OBI_ARRAY_ERROR);
-		obidebug(1, "\nProblem creating an arrays directory");
-		free(directory_name);
+		obi_set_errno(OBI_INDEXER_ERROR);
+		obidebug(1, "\nProblem creating an indexer directory");
 		return NULL;
 	}
 
-	free(directory_name);
+	// Create the informations file
+	if (create_dms_infos_file(dms_file_descriptor, dms_name) < 0)
+		return NULL;
 
 	return obi_open_dms(dms_name);
 }
@@ -173,19 +290,36 @@ OBIDMS_p obi_open_dms(const char* dms_name)
 {
 	OBIDMS_p	dms;
 	char*	 	directory_name;
-	DIR*		directory;
-	int			dms_file_descriptor;
+	char* 		infos_file_name;
+	int			infos_file_descriptor;
+	bool		little_endian_dms;
+	bool 		little_endian_platform;
 
 	dms = NULL;
 
+	// Allocate the data structure
+	dms = (OBIDMS_p) malloc(sizeof(OBIDMS_t));
+	if (dms == NULL)
+	{
+		obi_set_errno(OBIDMS_MEMORY_ERROR);
+		obidebug(1, "\nError allocating the memory for the OBIDMS structure");
+		return NULL;
+	}
+
 	// Build and check the directory name
 	directory_name = build_directory_name(dms_name);
 	if (directory_name == NULL)
+	{
+		free(dms);
 		return NULL;
+	}
+
+	strncpy(dms->directory_name, directory_name, OBIDMS_MAX_NAME);
+	free(directory_name);
 
 	// Try to open the directory
-	directory = opendir(directory_name);
-	if (directory == NULL)
+	dms->directory = opendir(dms->directory_name);
+	if (dms->directory == NULL)
 	{
 		switch (errno)
 		{
@@ -205,45 +339,90 @@ OBIDMS_p obi_open_dms(const char* dms_name)
 				obi_set_errno(OBIDMS_UNKNOWN_ERROR);
 		}
 		obidebug(1, "\nCan't open OBIDMS directory");
-		free(directory_name);
+		free(dms);
 		return NULL;
 	}
 
-	// Allocate the data structure
-	dms = (OBIDMS_p) malloc(sizeof(OBIDMS_t));
-	if (dms == NULL)
-	{
-		obi_set_errno(OBIDMS_MEMORY_ERROR);
-		obidebug(1, "\nError allocating the memory for the OBIDMS structure");
-		free(directory_name);
-		return NULL;
-	}
-
-	// Initialize the data structure
-	strcpy(dms->directory_name, directory_name);
-	dms->directory = directory;
-
-	// Get file descriptor of DMS directory to open the arrays directory
-	dms_file_descriptor = dirfd(directory);
-	if (dms_file_descriptor < 0)
+	// Get and store file descriptor of DMS directory to open the informations file
+	dms->dir_fd = dirfd(dms->directory);
+	if (dms->dir_fd < 0)
 	{
 		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
 		obidebug(1, "\nError getting the file descriptor for a newly created OBIDMS directory");
-		free(directory_name);
+		closedir(dms->directory);
+		free(dms);
 		return NULL;
 	}
 
-	// Open the arrays directory
-	dms->array_directory = private_opendirat(dms_file_descriptor, ARRAY_DIR_NAME);
-	if (dms->array_directory == NULL)
+	// Open informations file to check endianness
+	infos_file_name = build_infos_file_name(dms_name);
+	infos_file_descriptor = openat(dms->dir_fd, infos_file_name, O_RDONLY, 0777);
+	if (infos_file_descriptor < 0)
 	{
 		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
-		obidebug(1, "\nError opening the arrays directory");
-		free(directory_name);
+		obidebug(1, "\nError opening an informations file");
+		closedir(dms->directory);
+		free(dms);
 		return NULL;
 	}
 
-	free(directory_name);
+	free(infos_file_name);
+
+	// Check endianness of the platform and DMS
+	little_endian_platform = obi_is_little_endian();
+	if (read(infos_file_descriptor, &little_endian_dms, sizeof(bool)) < ((ssize_t) sizeof(bool)))
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError reading the endianness in an informations file");
+		close(infos_file_descriptor);
+		closedir(dms->directory);
+		free(dms);
+		return NULL;
+	}
+	if (little_endian_platform != little_endian_dms)
+	{
+		obi_set_errno(OBIDMS_BAD_ENDIAN_ERROR);
+		obidebug(1, "\nError: The DMS and the platform have different endianness");
+		close(infos_file_descriptor);
+		closedir(dms->directory);
+		free(dms);
+		return NULL;
+	}
+
+	close(infos_file_descriptor);
+
+	dms->little_endian = little_endian_dms;
+
+	// Open the indexer directory
+	dms->indexer_directory = opendir_in_dms(dms, INDEXER_DIR_NAME);
+	if (dms->indexer_directory == NULL)
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError opening the indexer directory");
+		closedir(dms->directory);
+		free(dms);
+		return NULL;
+	}
+
+	// Store the indexer directory's file descriptor
+	dms->indexer_dir_fd = dirfd(dms->indexer_directory);
+	if (dms->indexer_dir_fd < 0)
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError getting the file descriptor of the indexer directory");
+		closedir(dms->indexer_directory);
+		closedir(dms->directory);
+		free(dms);
+		return NULL;
+	}
+
+	// Initialize the list of opened columns
+	dms->opened_columns = (Opened_columns_list_p) malloc(sizeof(Opened_columns_list_t));
+	(dms->opened_columns)->nb_opened_columns = 0;
+
+	// Initialize the list of opened indexers
+	dms->opened_indexers = (Opened_indexers_list_p) malloc(sizeof(Opened_indexers_list_t));
+	(dms->opened_indexers)->nb_opened_indexers = 0;
 
 	return dms;
 }
@@ -272,6 +451,11 @@ int obi_close_dms(OBIDMS_p dms)
 {
 	if (dms != NULL)
 	{
+		// Close all columns
+		while ((dms->opened_columns)->nb_opened_columns > 0)
+			obi_close_column(*((dms->opened_columns)->columns));
+
+		// Close dms and indexer directories
 		if (closedir(dms->directory) < 0)
 		{
 			obi_set_errno(OBIDMS_MEMORY_ERROR);
@@ -279,10 +463,10 @@ int obi_close_dms(OBIDMS_p dms)
 			free(dms);
 			return -1;
 		}
-		if (closedir(dms->array_directory) < 0)
+		if (closedir(dms->indexer_directory) < 0)
 		{
-			obi_set_errno(OBI_ARRAY_ERROR);
-			obidebug(1, "\nError closing an array directory");
+			obi_set_errno(OBI_INDEXER_ERROR);
+			obidebug(1, "\nError closing an indexer directory");
 			free(dms);
 			return -1;
 		}
@@ -292,3 +476,175 @@ int obi_close_dms(OBIDMS_p dms)
 	return 0;
 }
 
+
+int obi_dms_is_column_name_in_list(OBIDMS_p dms, const char* column_name)
+{
+	int i;
+	Opened_columns_list_p columns_list;
+
+	columns_list = dms->opened_columns;
+
+	for (i=0; i < (columns_list->nb_opened_columns); i++)
+	{
+		if (!strcmp(((*((columns_list->columns)+i))->header)->name, column_name))
+		{	// Found it
+			return 1;
+		}
+	}
+	return 0;
+}
+
+
+OBIDMS_column_p obi_dms_get_column_from_list(OBIDMS_p dms, const char* column_name, obiversion_t version)
+{
+	int i;
+
+	for (i=0; i < ((dms->opened_columns)->nb_opened_columns); i++)
+	{
+		if (!strcmp(((*(((dms->opened_columns)->columns)+i))->header)->name, column_name)
+				&& (((*(((dms->opened_columns)->columns)+i))->header)->version == version))
+		{	// Found the column already opened, return it
+			return *(((dms->opened_columns)->columns)+i);
+		}
+	}
+	// Didn't find the column
+	return NULL;
+}
+
+
+void obi_dms_list_column(OBIDMS_p dms, OBIDMS_column_p column)	// TODO add check if column already in list?
+{
+	*(((dms->opened_columns)->columns)+((dms->opened_columns)->nb_opened_columns)) = column;
+	((dms->opened_columns)->nb_opened_columns)++;
+}
+
+
+int obi_dms_unlist_column(OBIDMS_p dms, OBIDMS_column_p column)
+{
+	int i;
+	Opened_columns_list_p columns_list;
+
+	columns_list = dms->opened_columns;
+
+	for (i=0; i < columns_list->nb_opened_columns; i++)
+	{
+		if (!strcmp(((*((columns_list->columns)+i))->header)->name, (column->header)->name)
+				&& (((*((columns_list->columns)+i))->header)->version == (column->header)->version))
+		{	// Found the column. Rearrange list
+			(columns_list->nb_opened_columns)--;
+			(columns_list->columns)[i] = (columns_list->columns)[columns_list->nb_opened_columns];
+			return 0;
+		}
+	}
+
+	obidebug(1, "\nCould not find the column to delete from list of open columns");
+	return -1;
+}
+
+
+Obi_indexer_p obi_dms_get_indexer_from_list(OBIDMS_p dms, const char* indexer_name)
+{
+	int i;
+	Opened_indexers_list_p indexers_list;
+
+	indexers_list = dms->opened_indexers;
+
+	for (i=0; i < (indexers_list->nb_opened_indexers); i++)
+	{
+		if (!strcmp(((indexers_list->indexers)[i])->name, indexer_name))	// TODO get_name function indexer
+		{	// Found the indexer already opened, return it
+			return (indexers_list->indexers)[i];
+		}
+	}
+	// Didn't find the indexer
+	return NULL;
+}
+
+
+void obi_dms_list_indexer(OBIDMS_p dms, Obi_indexer_p indexer)
+{
+	*(((dms->opened_indexers)->indexers)+((dms->opened_indexers)->nb_opened_indexers)) = indexer;
+	((dms->opened_indexers)->nb_opened_indexers)++;
+}
+
+
+int obi_dms_unlist_indexer(OBIDMS_p dms, Obi_indexer_p indexer)
+{
+	int i;
+	Opened_indexers_list_p indexers_list;
+
+	indexers_list = dms->opened_indexers;
+
+	for (i=0; i < indexers_list->nb_opened_indexers; i++)
+	{
+		if (!strcmp(((indexers_list->indexers)[i])->name, indexer->name))	// TODO get_name function indexer
+		{	// Found the indexer. Rearrange list
+			(indexers_list->nb_opened_indexers)--;
+			(indexers_list->indexers)[i] = (indexers_list->indexers)[indexers_list->nb_opened_indexers];
+			return 0;
+		}
+	}
+
+	obidebug(1, "\nCould not find the indexer to delete from list of open indexers");
+	return -1;
+}
+
+
+char* obi_dms_get_dms_path(OBIDMS_p dms)
+{
+	char* full_path;
+
+	full_path = (char*) malloc((MAX_PATH_LEN)*sizeof(char));
+	if (full_path == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for the char* path to a file or directory");
+		return NULL;
+	}
+
+	if (getcwd(full_path, MAX_PATH_LEN) == NULL)	// TODO store when opening
+	{
+		obi_set_errno(OBI_UTILS_ERROR);
+		obidebug(1, "\nError getting the path to a file or directory");
+		return NULL;
+	}
+
+	strcat(full_path, "/");
+	strcat(full_path, dms->directory_name);
+
+	return full_path;
+}
+
+
+char* obi_dms_get_full_path(OBIDMS_p dms, const char* path_name)
+{
+	char* full_path;
+
+	full_path = obi_dms_get_dms_path(dms);
+	strcat(full_path, "/");
+	strcat(full_path, path_name);
+
+	return full_path;
+}
+
+
+DIR* opendir_in_dms(OBIDMS_p dms, const char* path_name)
+{
+	char* full_path;
+	DIR* directory;
+
+	full_path = obi_dms_get_full_path(dms, path_name);
+	if (full_path == NULL)
+		return NULL;
+
+	directory = opendir(full_path);
+	if (directory == NULL)
+	{
+		obi_set_errno(OBI_UTILS_ERROR);
+		obidebug(1, "\nError opening a directory");
+	}
+
+	free(full_path);
+
+	return directory;
+}

src/obidms.h

@@ -20,14 +20,55 @@
 #include <dirent.h>
 #include <string.h>
 #include <stdio.h>
+#include <stdbool.h>
 
 #include "obierrno.h"
+#include "obitypes.h"
 
 
-#define OBIDMS_MAX_NAME (2048) 	   /**< The maximum length of an OBIDMS name.
-                                	*/
-#define ARRAY_DIR_NAME "arrays"	   /**< The name of the arrays directory.
-                                	*/
+#define OBIDMS_MAX_NAME (2048) 	    			/**< The maximum length of an OBIDMS name.
+ 	 	 	 	 	 	 	 	 	 	 	 	 */
+#define INDEXER_DIR_NAME "OBIBLOB_INDEXERS"  	/**< The name of the Obiblob indexer directory.
+                                	 	 	 	 */
+#define TAXONOMY_DIR_NAME "TAXONOMY"    		/**< The name of the taxonomy directory.
+                                	 	 	 	 */
+#define MAX_NB_OPENED_COLUMNS (100) 			/**< The maximum number of columns open at the same time.
+                                	 	 	 	 */
+#define MAX_NB_OPENED_INDEXERS (1000) 			/**< The maximum number of indexers open at the same time.
+                                	 	 	 	 */
+#define MAX_PATH_LEN 4096						/**< Maximum length for the character string defining a
+ 	 	 	 	 	 	 	 	 	 	 	 	 *	 file or directory path.
+ 	 	 	 	 	 	 	 	 	 	 	 	 */
+
+
+struct OBIDMS_column;							/**< Declarations to avoid circular dependencies. */
+typedef struct OBIDMS_column* OBIDMS_column_p;  /**< Declarations to avoid circular dependencies. */
+
+/**
+ * @brief Structure listing the columns opened in a DMS, identified by their name and version number.
+ */
+typedef struct Opened_columns_list {
+	int	 		 			nb_opened_columns;	  				/**< Number of opened columns.
+	 	   	   	   	   	   	   	   	   	   	   	   	   	   	   	 */
+	OBIDMS_column_p		 	columns[MAX_NB_OPENED_COLUMNS];	  	/**< Array of pointers on the opened columns.
+ 	   	   	   	   	   	   	 	 	 	 	 	 	 	 	 	 */
+} Opened_columns_list_t, *Opened_columns_list_p;
+
+
+// TODO Need to find a way to not refer to AVLs specifically
+struct OBIDMS_avl_group;								/**< Declarations to avoid circular dependencies. */
+typedef struct OBIDMS_avl_group* OBIDMS_avl_group_p;	/**< Declarations to avoid circular dependencies. */
+typedef OBIDMS_avl_group_p Obi_indexer_p;				/**< Declarations to avoid circular dependencies. */
+
+/**
+ * @brief Structure listing the indexers opened in a DMS, identified by their name.
+ */
+typedef struct Opened_indexers_list {
+	int		 		 		nb_opened_indexers;					/**< Number of opened indexers.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	Obi_indexer_p		    indexers[MAX_NB_OPENED_INDEXERS];	/**< Array of pointers on the opened indexers.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+} Opened_indexers_list_t, *Opened_indexers_list_p;
 
 
 /**
@@ -37,15 +78,27 @@
  * and opening of an OBITools Data Management System (DMS)
  */
 typedef struct OBIDMS {
-	char	directory_name[OBIDMS_MAX_NAME+1];	/**< The name of the directory
-	                                     	 	 *   containing the DMS.
-	                                     	 	 */
-	DIR*	directory;							/**< A directory entry usable to
-										 	 	 *   refer and scan the database directory.
-										 	 	 */
-	DIR*	array_directory;					/**< A directory entry usable to
-										 	 	 *   refer and scan the array directory.
-										 	 	 */
+	char					directory_name[OBIDMS_MAX_NAME+1];	/**< The name of the directory
+																 *   containing the DMS.
+																 */
+	DIR*					directory;							/**< A directory entry usable to
+																 *   refer and scan the database directory.
+																 */
+	int     				dir_fd;								/**< The file descriptor of the directory entry
+																 *   usable to refer and scan the database directory.
+																 */
+	DIR*					indexer_directory;					/**< A directory entry usable to
+																 *   refer and scan the indexer directory.
+																 */
+	int						indexer_dir_fd;						/**< The file descriptor of the directory entry
+																 *   usable to refer and scan the indexer directory.
+																 */
+	bool					little_endian;						/**< Endianness of the database.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	Opened_columns_list_p 	opened_columns;						/**< List of opened columns.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	Opened_indexers_list_p 	opened_indexers;					/**< List of opened indexers.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 } OBIDMS_t, *OBIDMS_p;
 
 
@@ -54,7 +107,7 @@ typedef struct OBIDMS {
  *
  * @param dms_name A pointer to a C string containing the name of the database.
  *
- * @returns An integer value indicating the status of the database
+ * @returns An integer value indicating the status of the database.
  * @retval 1 if the database exists.
  * @retval 0 if the database does not exist.
  * @retval -1 if an error occurred.
@@ -72,7 +125,7 @@ int obi_dms_exists(const char* dms_name);
  * if a directory with this name does not already exist
  * before creating the new database.
  *
- * A directory to store obiarrays is also created.
+ * A directory to store Obiblob indexers is also created.
  *
  * @param dms_name A pointer to a C string containing the name of the database.
  *                 The actual directory name used to store the DMS will be
@@ -139,4 +192,141 @@ OBIDMS_p obi_dms(const char* dms_name);
 int obi_close_dms(OBIDMS_p dms);
 
 
+/**
+ * @brief Checks if a column with a given name is in the list of opened columns.
+ *
+ * @warning: Checking only the name means that the column can be of any version.
+ *
+ * @param dms The OBIDMS.
+ * @param column_name The column name that should be looked for.
+ *
+ * @returns An integer value indicating whether there is at least one column with that name
+ * 			in the list of opened columns.
+ * @retval 0 if there is at least one column with that name in the list of opened columns.
+ * @retval 1 if there is no column with that name in the list of opened columns.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_dms_is_column_name_in_list(OBIDMS_p dms, const char* column_name);
+
+
+/**
+ * @brief Returns a column identified by its name and its version number from the list of opened columns.
+ *
+ * @param dms The OBIDMS.
+ * @param column_name The column name that should be looked for.
+ * @param version The version number of the column that should be looked for.
+ *
+ * @returns A pointer on the column if it was found in the list of opened columns.
+ * @retval NULL if the column was not found in the list of opened columns.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+OBIDMS_column_p obi_dms_get_column_from_list(OBIDMS_p dms, const char* column_name, obiversion_t version);
+
+
+/**
+ * @brief Adds a column identified by its name and its version number in the list of opened columns.
+ *
+ * @param dms The OBIDMS.
+ * @param column A pointer on the column that should be added in the list of opened columns.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+void obi_dms_list_column(OBIDMS_p dms, OBIDMS_column_p column);
+
+
+/**
+ * @brief Removes a column identified by its name and its version number from the list of opened columns.
+ *
+ * @param dms The OBIDMS.
+ * @param column A pointer on the column that should be removed from the list of opened columns.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_dms_unlist_column(OBIDMS_p dms, OBIDMS_column_p column);
+
+
+/**
+ * @brief Returns an indexer identified by its name from the list of opened indexers.
+ *
+ * @param dms The OBIDMS.
+ * @param indexer_name The indexer name that should be looked for.
+ *
+ * @returns A pointer on the indexer if it was found in the list of opened indexers.
+ * @retval NULL if the indexer was not found in the list of opened indexers.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+Obi_indexer_p obi_dms_get_indexer_from_list(OBIDMS_p dms, const char* indexer_name);
+
+
+/**
+ * @brief Adds an indexer identified by its name in the list of opened indexers.
+ *
+ * @param dms The OBIDMS.
+ * @param indexer A pointer on the indexer that should be added in the list of opened indexers.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+void obi_dms_list_indexer(OBIDMS_p dms, Obi_indexer_p indexer);
+
+
+/**
+ * @brief Removes an indexer identified by its name from the list of opened indexers.
+ *
+ * @param dms The OBIDMS.
+ * @param column A pointer on the indexer that should be removed from the list of opened indexers.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_dms_unlist_indexer(OBIDMS_p dms, Obi_indexer_p indexer);
+
+
+/**
+ * Function meant to disappear soon
+ */
+char* obi_dms_get_path(OBIDMS_p dms);
+
+
+/**
+ * @brief Gets the full path of a file or a directory from its
+ *        path relative to the DMS.
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param dms The DMS to which path_name is relative.
+ * @param path_name The path name for the file or directory, relative to the DMS.
+ *
+ * @returns A pointer to the full path.
+ * @retval NULL if an error occurred.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_dms_get_full_path(OBIDMS_p dms, const char* path_name);
+
+
+/**
+ * @brief Opens a directory relative to the DMS.
+ *
+ * @param dms The DMS to which path_name is relative.
+ * @param path_name The path name for the directory to be opened, relative to the DMS.
+ *
+ * @returns The directory stream of the opened directory.
+ * @retval NULL if an error occurred.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+DIR* opendir_in_dms(OBIDMS_p dms, const char* path_name);
+
+
 #endif /* OBIDMS_H_ */

src/obidms_taxonomy.c

@@ -0,0 +1,682 @@
+/********************************************************************
+ * OBIDMS taxonomy functions                                        *
+ ********************************************************************/
+
+/**
+ * @file obidms_taxonomy.c
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ * @date March 2nd 2016
+ * @brief Functions for reading binary taxonomy files.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <stdbool.h>
+#include <fcntl.h>
+
+#include "obidms_taxonomy.h"
+#include "obidms.h"
+#include "obidebug.h"
+#include "obierrno.h"
+#include "utils.h"
+
+
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
+
+// TODO : the malloc aren't checked but won't exist for long because mapping instead
+
+
+int compareRankLabel(const void *label1, const void *label2)
+{
+	return strcmp((const char*)label1,*(const char**)label2);
+}
+
+
+int32_t rank_index(const char* label, ecorankidx_t* ranks)
+{
+	char **rep;
+
+	rep = bsearch(label, ranks->label, ranks->count, sizeof(char*), compareRankLabel);
+
+	if (rep)
+		return rep-ranks->label;	// TODO what???
+
+	return -1;
+}
+
+
+void* read_ecorecord(FILE* f, int32_t* record_size)
+{
+	static void* buffer = NULL;
+	int32_t      buffer_size = 0;
+	int32_t      read;
+
+	if (!record_size)
+	{
+ 		obi_set_errno(OBI_TAXONOMY_ERROR);
+ 		obidebug(1, "\nError reading a taxonomy file: record_size can not be NULL");
+ 		return NULL;
+	}
+
+	read = fread(record_size,
+	      		 1,
+	      		 sizeof(int32_t),
+	             f);
+
+	if (feof(f))
+		return NULL;
+
+	if (read != sizeof(int32_t))
+	{
+ 		obi_set_errno(OBI_TAXONOMY_ERROR);
+ 		obidebug(1, "\nError reading a taxonomy file: error reading record size");
+ 		return NULL;
+	}
+
+//	if (is_big_endian())						// TODO
+//		*recordSize=swap_int32_t(*recordSize);
+
+	if (buffer_size < *record_size)
+	{
+		if (buffer)
+			buffer = realloc(buffer, *record_size);
+		else
+			buffer = malloc(*record_size);
+		if (buffer == NULL)
+		{
+	 		obi_set_errno(OBI_TAXONOMY_ERROR);
+	 		obidebug(1, "\nError reading a taxonomy file: error allocating memory");
+	 		return NULL;
+		}
+	}
+
+	read = fread(buffer,
+	             1,
+				 *record_size,
+				 f);
+
+	if (read != *record_size)
+	{
+ 		obi_set_errno(OBI_TAXONOMY_ERROR);
+ 		obidebug(1, "\nError reading a taxonomy file: error reading a record %d, %d", read, *record_size);
+ 		return NULL;
+	}
+
+	return buffer;
+};
+
+
+ecotx_t* readnext_ecotaxon(FILE* f, ecotx_t* taxon)
+{
+	ecotxformat_t* raw;
+	int32_t        record_length;
+
+	raw = read_ecorecord(f, &record_length);
+
+	if (!raw)
+		return NULL;
+
+//	if (is_big_endian())		// TODO
+//	{
+//		raw->namelength = swap_int32_t(raw->namelength);
+//		raw->parent     = swap_int32_t(raw->parent);
+//		raw->rank       = swap_int32_t(raw->rank);
+//		raw->taxid      = swap_int32_t(raw->taxid);
+//	}
+
+	taxon->parent = (ecotx_t*) ((size_t) raw->parent);
+	taxon->taxid  = raw->taxid;
+	taxon->rank   = raw->rank;
+	taxon->farest = -1;
+
+	taxon->name   = malloc((raw->name_length+1) * sizeof(char));
+
+	strncpy(taxon->name, raw->name, raw->name_length);
+
+	return taxon;
+}
+
+
+FILE* open_ecorecorddb(const char* file_name,
+                       int32_t*    count,
+                       int32_t     abort_on_open_error)
+{
+    FILE*		f;
+	int32_t     read;
+
+	fprintf(stderr, "\n%s\n", file_name);
+
+	f = fopen(file_name, "rb");
+
+	if (!f)
+	{
+		if (abort_on_open_error)
+		{
+	 		obi_set_errno(OBI_TAXONOMY_ERROR);
+	 		obidebug(1, "\nCouldn't open a taxonomy file");
+	 		return NULL;
+		}
+	 	else
+	 	{
+	 		*count = 0;
+	 		return NULL;
+	 	}
+	}
+
+	read = fread(count,
+	      		 1,
+	      		 sizeof(int32_t),
+	      		 f);
+
+	if (read != sizeof(int32_t))
+	{
+ 		obi_set_errno(OBI_TAXONOMY_ERROR);
+ 		obidebug(1, "\nError reading taxonomy record size");
+ 		return NULL;
+	}
+
+//	if (!obi_is_little_endian())		// TODO
+//		*count = swap_int32_t(*count);
+
+	return f;
+}
+
+
+ecorankidx_t* read_rankidx(const char* ranks_file_name)
+{
+	int32_t      			count;
+	FILE*        			ranks_file;
+	ecorankidx_t*           ranks_index;
+	int32_t      			i;
+	int32_t      			rank_length;
+	char*					buffer;
+
+	ranks_file = open_ecorecorddb(ranks_file_name, &count, 0);
+
+	if (ranks_file==NULL)
+		return NULL;
+
+	ranks_index = (ecorankidx_t*) malloc(sizeof(ecorankidx_t) + sizeof(char*) * (count-1));
+
+	ranks_index->count = count;
+
+	for (i=0; i < count; i++)
+	{
+		buffer = read_ecorecord(ranks_file, &rank_length);
+		ranks_index->label[i] = (char*) malloc(rank_length+1);
+		strncpy(ranks_index->label[i], buffer, rank_length);
+	}
+
+	return ranks_index;
+}
+
+
+ecotxidx_t* read_taxonomyidx(const char* taxa_file_name, const char* local_taxa_file_name)
+{
+	int32_t      	  count_taxa;
+	int32_t      	  count_local_taxa;
+	FILE*			  f_taxa;
+	FILE* 			  f_local_taxa;
+	ecotxidx_t*		  taxa_index;
+	struct ecotxnode* t;
+	int32_t      	  i;
+	int32_t      	  j;
+
+	f_taxa = open_ecorecorddb(taxa_file_name, &count_taxa,0);
+
+	if (f_taxa == NULL)
+	{
+ 		obidebug(1, "\nError reading taxonomy taxa file");
+ 		return NULL;
+	}
+
+	f_local_taxa = open_ecorecorddb(local_taxa_file_name, &count_local_taxa, 0);
+
+	taxa_index = (ecotxidx_t*) malloc(sizeof(ecotxidx_t) + sizeof(ecotx_t) * (count_taxa + count_local_taxa - 1));
+
+	taxa_index->count = count_taxa + count_local_taxa;
+	taxa_index->buffer_size = taxa_index->count;
+
+	taxa_index->max_taxid = 0;
+	printf("Reading %d taxa...\n", count_taxa);
+	for (i=0; i<count_taxa; i++)
+	{
+		readnext_ecotaxon(f_taxa, &(taxa_index->taxon[i]));
+		taxa_index->taxon[i].parent = taxa_index->taxon + (size_t) taxa_index->taxon[i].parent;
+		taxa_index->taxon[i].parent->farest = 0;
+		if (taxa_index->taxon[i].taxid > taxa_index->max_taxid)
+			taxa_index->max_taxid = taxa_index->taxon[i].taxid;
+	}
+
+	if (count_local_taxa > 0)
+		printf("Reading %d local taxa...\n", count_local_taxa);
+	else
+		printf("No local taxa\n");
+
+	count_taxa = taxa_index->count;
+
+	for (; i < count_taxa; i++){
+		readnext_ecotaxon(f_local_taxa, &(taxa_index->taxon[i]));
+		taxa_index->taxon[i].parent = taxa_index->taxon + (size_t) taxa_index->taxon[i].parent;
+		taxa_index->taxon[i].parent->farest=0;
+		if (taxa_index->taxon[i].taxid > taxa_index->max_taxid)
+			taxa_index->max_taxid = taxa_index->taxon[i].taxid;
+	}
+
+	printf("Computing longest branches...\n");
+
+	for (i=0; i < count_taxa; i++)
+	{
+		t = taxa_index->taxon+i;
+		if (t->farest == -1)
+		{
+			t->farest=0;
+            while (t->parent != t)
+            {
+            	j = t->farest + 1;
+            	if (j > t->parent->farest)
+            	{
+            		t->parent->farest = j;
+            		t=t->parent;
+            	}
+            	else
+            		t = taxa_index->taxon;
+            }
+		}
+	}
+
+	return taxa_index;
+}
+
+
+econame_t* readnext_econame(FILE* f, econame_t* name, OBIDMS_taxonomy_p taxonomy)
+{
+
+	econameformat_t* raw;
+	int32_t record_length;
+
+	raw = read_ecorecord(f, &record_length);
+
+	if (!raw)
+		return NULL;
+
+//	if (is_big_endian())		// TODO
+//	{
+//		raw->is_scientificname 	= swap_int32_t(raw->is_scientificname);
+//		raw->namelength 	    = swap_int32_t(raw->namelength);
+//		raw->classlength        = swap_int32_t(raw->classlength);
+//		raw->taxid  	        = swap_int32_t(raw->taxid);
+//	}
+
+	name->is_scientific_name = raw->is_scientific_name;
+
+	name->name = malloc((raw->name_length + 1) * sizeof(char));
+	strncpy(name->name, raw->names, raw->name_length);
+	name->name[raw->name_length] = 0;
+
+	name->class_name = malloc((raw->class_length+1) * sizeof(char));
+	strncpy(name->class_name,(raw->names + raw->name_length), raw->class_length);
+	name->class_name[raw->class_length] = 0;
+
+	name->taxon = taxonomy->taxa->taxon + raw->taxid;
+
+	return name;
+}
+
+
+econameidx_t* read_nameidx(const char *file_name, OBIDMS_taxonomy_p taxonomy)
+{
+	int32_t      		count;
+	FILE*				f;
+	econameidx_t*		index_names;
+	int32_t      		i;
+
+	f = open_ecorecorddb(file_name, &count, 0);
+
+	if (f == NULL)
+		return NULL;
+
+	index_names = (econameidx_t*) malloc(sizeof(econameidx_t) + sizeof(econame_t) * (count-1));
+
+	index_names->count = count;
+
+	for (i=0; i < count; i++)
+		readnext_econame(f, (index_names->names)+i, taxonomy);
+
+	return index_names;
+}
+
+
+static int bcomptaxon (const void* ptaxid, const void* ptaxon)
+{
+  ecotx_t* current_taxon = (ecotx_t*) ptaxon;
+  int32_t  taxid = (int32_t) ((size_t) ptaxid);
+  return taxid - current_taxon->taxid;
+}
+
+
+/////// PUBLIC /////////
+
+
+OBIDMS_taxonomy_p obi_read_taxonomy(OBIDMS_p dms, const char* taxonomy_name, bool read_alternative_names)
+{
+	OBIDMS_taxonomy_p  tax;
+	char*			   main_taxonomy_dir_path;
+	char*			   taxonomy_path;
+	char*  			   ranks_file_name;
+	char*              taxa_file_name;
+	char*			   local_taxa_file_name;
+	char*			   alter_names_file_name;
+	int                buffer_size;
+
+	tax = (OBIDMS_taxonomy_p) malloc(sizeof(OBIDMS_taxonomy_t));
+
+	tax->ranks = NULL;
+	tax->taxa  = NULL;
+	tax->names = NULL;
+
+	buffer_size = 2048;		// TODO
+
+	main_taxonomy_dir_path = obi_dms_get_full_path(dms, TAXONOMY_DIR_NAME);
+	taxonomy_path = (char*) malloc((strlen(main_taxonomy_dir_path) + strlen(taxonomy_name) + strlen(taxonomy_name) + 3)*sizeof(char));
+	if (sprintf(taxonomy_path, "%s/%s/%s", main_taxonomy_dir_path, taxonomy_name, taxonomy_name) < 0)
+	{
+		free(main_taxonomy_dir_path);
+		obi_close_taxonomy(tax);
+		return NULL;
+	}
+
+	free(main_taxonomy_dir_path);
+
+	// Read ranks
+	ranks_file_name = (char*) malloc(buffer_size*sizeof(char));
+	if (ranks_file_name == NULL)
+	{
+		free(taxonomy_path);
+		obi_close_taxonomy(tax);
+		return NULL;
+	}
+	if (snprintf(ranks_file_name, buffer_size, "%s.rdx", taxonomy_path) < 0)
+	{
+		free(taxonomy_path);
+		free(ranks_file_name);
+		obi_close_taxonomy(tax);
+		return NULL;
+	}
+	tax->ranks = read_rankidx(ranks_file_name);
+	if (tax->ranks == NULL)
+	{
+		free(ranks_file_name);
+		obi_close_taxonomy(tax);
+		return NULL;
+	}
+	free(ranks_file_name);
+
+	// Read taxa
+	taxa_file_name = (char*) malloc(buffer_size*sizeof(char));
+	if (taxa_file_name == NULL)
+	{
+		free(taxonomy_path);
+		obi_close_taxonomy(tax);
+		return NULL;
+	}
+	if (snprintf(taxa_file_name, buffer_size,"%s.tdx", taxonomy_path) < 0)
+	{
+		free(taxonomy_path);
+		free(taxa_file_name);
+		obi_close_taxonomy(tax);
+		return NULL;
+	}
+	local_taxa_file_name = (char*) malloc(buffer_size*sizeof(char));
+	if (local_taxa_file_name == NULL)
+	{
+		free(taxonomy_path);
+		free(taxa_file_name);
+		obi_close_taxonomy(tax);
+		return NULL;
+	}
+	if (snprintf(local_taxa_file_name, buffer_size,"%s.ldx", taxonomy_path) < 0)
+	{
+		free(taxonomy_path);
+		free(taxa_file_name);
+		free(local_taxa_file_name);
+		obi_close_taxonomy(tax);
+		return NULL;
+	}
+	tax->taxa = read_taxonomyidx(taxa_file_name, local_taxa_file_name);
+	if (tax->taxa == NULL)
+	{
+		free(taxonomy_path);
+		free(taxa_file_name);
+		free(local_taxa_file_name);
+		obi_close_taxonomy(tax);
+		return NULL;
+	}
+	free(taxa_file_name);
+	free(local_taxa_file_name);
+
+	// Read alternative names
+	if (read_alternative_names)
+	{
+		alter_names_file_name = (char*) malloc(buffer_size*sizeof(char));
+		if (alter_names_file_name == NULL)
+		{
+			free(taxonomy_path);
+			obi_close_taxonomy(tax);
+			return NULL;
+		}
+		if (snprintf(alter_names_file_name, buffer_size,"%s.ndx", taxonomy_path) < 0)
+		{
+			free(taxonomy_path);
+			free(alter_names_file_name);
+			obi_close_taxonomy(tax);
+			return NULL;
+		}
+        tax->names = read_nameidx(alter_names_file_name, tax);
+    	if (tax->names == NULL)
+    	{
+    		free(alter_names_file_name);
+    		obi_close_taxonomy(tax);
+    		return NULL;
+    	}
+        free(alter_names_file_name);
+	}
+
+	free(taxonomy_path);
+
+	return tax;
+}
+
+
+int obi_close_taxonomy(OBIDMS_taxonomy_p taxonomy)
+{
+	if (taxonomy)
+	{
+		if (taxonomy->ranks)
+			free(taxonomy->ranks);	// TODO those don't free everything but mapping will replace anyway
+
+		if (taxonomy->names)
+			free(taxonomy->names);
+
+		if (taxonomy->taxa)
+			free(taxonomy->taxa);
+
+		free(taxonomy);
+
+		return 0;
+	}
+
+	// TODO no closing files?
+
+	return 1;
+}
+
+
+//////////////////////////////////////////////////////////////////////////
+
+
+ecotx_t* obi_taxo_get_parent_at_rank(ecotx_t* taxon, int32_t rankidx)
+{
+	ecotx_t* current_taxon;
+	ecotx_t* next_taxon;
+
+	current_taxon = taxon;
+	next_taxon    = current_taxon->parent;
+
+	while ((current_taxon != next_taxon) &&  // root node
+		   (current_taxon->rank != rankidx))
+	{
+		current_taxon = next_taxon;
+		next_taxon    = current_taxon->parent;
+	}
+
+	if (current_taxon->rank == rankidx)
+		return current_taxon;
+	else
+		return NULL;
+}
+
+
+ecotx_t* obi_taxo_get_taxon_with_taxid(OBIDMS_taxonomy_p taxonomy, int32_t taxid)
+{
+	ecotx_t    *current_taxon;
+	int32_t     count;
+
+	count = taxonomy->taxa->count;
+
+	current_taxon = (ecotx_t*) bsearch((const void *) ((size_t) taxid),
+                                       (const void *) taxonomy->taxa->taxon,
+                                       count,
+                                       sizeof(ecotx_t),
+                                       bcomptaxon);
+	return current_taxon;
+}
+
+
+bool obi_taxo_is_taxon_under_taxid(ecotx_t* taxon, int32_t other_taxid)
+{
+	ecotx_t* next_parent;
+
+	next_parent = taxon->parent;
+
+	while ((other_taxid != next_parent->taxid) && (strcmp(next_parent->name, "root")))
+		next_parent = next_parent->parent;
+
+	if (other_taxid == next_parent->taxid)
+		return 1;
+	else
+		return 0;
+}
+
+
+ecotx_t* obi_taxo_get_species(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
+{
+	static OBIDMS_taxonomy_p tax = NULL;
+	static int32_t		  rankindex = -1;
+
+	if (taxonomy && (tax != taxonomy))
+	{
+		rankindex = rank_index("species", taxonomy->ranks);
+		tax = taxonomy;
+	}
+
+	if (!tax || (rankindex < 0))
+	{
+		obi_set_errno(OBI_TAXONOMY_ERROR);
+		obidebug(1, "\nError trying to get the species associated with a taxon: No taxonomy defined");
+		return NULL;
+	}
+
+	return obi_taxo_get_parent_at_rank(taxon, rankindex);
+}
+
+
+ecotx_t* obi_taxo_get_genus(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
+{
+	static OBIDMS_taxonomy_p tax = NULL;
+	static int32_t		  rankindex = -1;
+
+	if (taxonomy && (tax != taxonomy))
+	{
+		rankindex = rank_index("genus", taxonomy->ranks);
+		tax = taxonomy;
+	}
+
+	if (!tax || (rankindex < 0))
+	{
+		obi_set_errno(OBI_TAXONOMY_ERROR);
+		obidebug(1, "\nError trying to get the genus associated with a taxon: No taxonomy defined");
+		return NULL;
+	}
+
+	return obi_taxo_get_parent_at_rank(taxon, rankindex);
+}
+
+
+ecotx_t* obi_taxo_get_family(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
+{
+	static OBIDMS_taxonomy_p tax = NULL;
+	static int32_t		  rankindex = -1;
+
+	if (taxonomy && (tax != taxonomy))
+	{
+		rankindex = rank_index("family", taxonomy->ranks);
+		tax = taxonomy;
+	}
+
+	if (!tax || (rankindex < 0))
+	{
+		obi_set_errno(OBI_TAXONOMY_ERROR);
+		obidebug(1, "\nError trying to get the family associated with a taxon: No taxonomy defined");
+		return NULL;
+	}
+
+	return obi_taxo_get_parent_at_rank(taxon, rankindex);
+}
+
+
+ecotx_t* obi_taxo_get_kingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
+{
+	static OBIDMS_taxonomy_p tax = NULL;
+	static int32_t		  rankindex = -1;
+
+	if (taxonomy && (tax != taxonomy))
+	{
+		rankindex = rank_index("kingdom", taxonomy->ranks);
+		tax = taxonomy;
+	}
+
+	if (!tax || (rankindex < 0))
+	{
+		obi_set_errno(OBI_TAXONOMY_ERROR);
+		obidebug(1, "\nError trying to get the kingdom associated with a taxon: No taxonomy defined");
+		return NULL;
+	}
+
+	return obi_taxo_get_parent_at_rank(taxon, rankindex);
+}
+
+
+ecotx_t* obi_taxo_get_superkingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
+{
+	static OBIDMS_taxonomy_p tax = NULL;
+	static int32_t		  rankindex = -1;
+
+	if (taxonomy && (tax != taxonomy))
+	{
+		rankindex = rank_index("superkingdom", taxonomy->ranks);
+		tax = taxonomy;
+	}
+
+	if (!tax || (rankindex < 0))
+	{
+		obi_set_errno(OBI_TAXONOMY_ERROR);
+		obidebug(1, "\nError trying to get the superkingdom associated with a taxon: No taxonomy defined");
+		return NULL;
+	}
+
+	return obi_taxo_get_parent_at_rank(taxon, rankindex);
+}
+

src/obidms_taxonomy.h

@@ -0,0 +1,101 @@
+/********************************************************************
+ * OBIDMS taxonomy headeer file                                     *
+ ********************************************************************/
+
+/**
+ * @file obidms_taxonomy.h
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ * @date March 2nd 2016
+ * @brief Header file for the functions handling the reading of binary taxonomy files.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdbool.h>
+
+#include "obidms.h"
+
+
+typedef struct {
+	int32_t  taxid;
+	int32_t  rank;
+	int32_t	 parent;
+	int32_t  name_length;
+	char     name[1];
+} ecotxformat_t;
+
+
+typedef struct ecotxnode {
+	int32_t           taxid;
+	int32_t           rank;
+	int32_t  		  farest;
+	struct ecotxnode* parent;
+	char*			  name;
+} ecotx_t;
+
+
+typedef struct {
+	int32_t count;
+	int32_t max_taxid;
+	int32_t buffer_size;
+	ecotx_t taxon[1];
+} ecotxidx_t;
+
+
+typedef struct {
+	int32_t count;
+	char*   label[1];
+} ecorankidx_t;
+
+
+typedef struct {
+ 	int32_t is_scientific_name;
+	int32_t  name_length;
+	int32_t  class_length;
+	int32_t  taxid;
+	char     names[1];
+} econameformat_t;
+
+
+typedef struct {
+	char*   		  name;
+	char*   		  class_name;
+	int32_t 		  is_scientific_name;
+	struct ecotxnode* taxon;
+} econame_t;
+
+
+typedef struct {
+	int32_t 	count;
+	econame_t   names[1];
+} econameidx_t;
+
+
+typedef struct OBIDMS_taxonomy_t {
+	ecorankidx_t* ranks;
+	econameidx_t* names;
+	ecotxidx_t*   taxa;
+} OBIDMS_taxonomy_t, *OBIDMS_taxonomy_p;
+
+
+OBIDMS_taxonomy_p obi_read_taxonomy(OBIDMS_p dms, const char* taxonomy_name, bool read_alternative_names);
+
+int obi_close_taxonomy(OBIDMS_taxonomy_p taxonomy);
+
+ecotx_t* obi_taxo_get_parent_at_rank(ecotx_t* taxon, int32_t rankidx);
+
+ecotx_t* obi_taxo_get_taxon_with_taxid(OBIDMS_taxonomy_p taxonomy, int32_t taxid);
+
+bool obi_taxo_is_taxon_under_taxid(ecotx_t* taxon, int32_t other_taxid);
+
+ecotx_t* obi_taxo_get_species(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
+
+ecotx_t* obi_taxo_get_genus(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
+
+ecotx_t* obi_taxo_get_family(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
+
+ecotx_t* obi_taxo_get_kingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
+
+ecotx_t* obi_taxo_get_superkingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
+