updated documentation

doc/source/formats.rst

@@ -3,6 +3,66 @@ Formats
 #######
 
 
+********
+OBITypes
+********
+
+.. note::
+    All OBITypes have an associated NA (Not Available) value.
+
+
+Atomic types
+============
+
+=========   =========   ============   ==============================
+ Type        C type      OBIType        Definition
+=========   =========   ============   ==============================
+ integer     int32_t     OBIInt_t       a signed integer value
+ float       double      OBIFloat_t     a floating value
+ boolean     ?           OBIBool_t      a boolean true/false value
+ char        char        OBIChar_t      a character
+ index       size_t      OBIIdx_t       an index in a data structure
+=========   =========   ============   ==============================
+
+
+Character string type
+=====================
+
+================   ======   ========   ==================
+Type               C type   OBIType    Definition
+================   ======   ========   ==================
+Character string   char*    OBIStr_t   a character string
+================   ======   ========   ==================
+
+
+Container types
+===============
+
+Lists
+-----
+
+Lists of values with an atomic OBIType.
+
+
+Ensembles
+---------
+
+Ensembles of values with an atomic OBIType.
+
+
+Dictionaries
+------------
+
+* Dictionaries of *OBIIdx_t* values indexed by *OBIStr_t* values, typically used for the storage of DNA sequences.
+* Bit arrays for data presence/absence informations in the above dictionaries.
+
+
+The taxid type
+--------------
+
+A couple of (*OBIInt_t* value, *OBIStr_t* value) corresponding to the taxid and a reference to a taxonomic database.
+
+
 *********************************************
 The OBItools3 Data Management System (OBIDMS)
 *********************************************
@@ -10,7 +70,8 @@ The OBItools3 Data Management System (OBIDMS)
 An OBIDMS directory consists of : 
 	* OBIDMS column files
 	* OBIDMS release files
-	* an OBIDMS history file
+	* OBIDMS dictionary files
+	* one OBIDMS history file
 
 
 OBIDMS column files
@@ -19,9 +80,37 @@ OBIDMS column files
 Each OBIDMS column file contains :
 	* a header of a size equal to a multiple of PAGESIZE (PAGESIZE being equal to 4096 bytes 
 	  on most systems) containing metadata
-	* one column of data of the same type
+	* one column of data with the same OBIType
 
-OBIDMS column files are read-only.
+
+Header
+------
+
+The header of an OBIDMS column contains :
+	
+	* Endian byte order
+	* Header size (PAGESIZE multiple)
+	*
+	* File status : Open/Closed
+	* Owner : PID of the process that created the file and is the only one allowed to modify it if it is open
+	* Number of lines (total or without the header?)
+	* OBIType
+	* Date of creation
+	* Version of the file
+	* Eventual comments
+
+
+Data
+----
+
+A column of data with the same OBIType.
+
+
+Mandatory columns
+-----------------
+
+Some columns must exist in an OBIDMS directory :
+    * sequence identifiers column (type *OBIStr_t*)
 
 
 File name
@@ -33,47 +122,30 @@ its version, separated by an ``@``, and with the extension ``.odc``.
 Example : ``count@3.odc``
 
 
-Header
+Modifications
-------
+-------------
 
-The header of an OBIDMS column contains :
+An OBIDMS column file can only be modified by the process that created it, if its status is set to Open. Those informations are
+contained in the `header <#header>`_.
 
-	* Endian byte order
+When a process wants to modify an OBIDMS column file that is closed, it must first clone it. Cloning creates a new version of the 
-	* PAGESIZE value / Size of the header
+file that belongs to the process, i.e., only that process can modify that file, as long as its status is set to Open. Once the process 
+has finished writing the new version of the column file, it sets the column file's status to Closed, and the file can never be modified 
+again.
 
-	* Number of lines (total or without the header?)
+That means that one column is stored in one file (if there is only one version) 
-	* Data type (int, str...)
+or more (if there are several versions), and that there is one file per version. 
-	* Date of creation
-	* Version of the file
-	* Eventual comments
-
-
-Data
-----
-
-A column of data of the same type.
 
 
 Versioning
 ----------
 
-OBIDMS column files are read-only, and any modification leads to the creation of a new version 
-of the column file. That means that one column is stored in one file (if there is only one version) 
-or more (if there are several versions), and that there is one file per version. 
-
 The first version of a column file is numbered 1, and each new version increments that 
 number by 1.
 
 The number of the latest version of an OBIDMS column is stored in an `OBIDMS release file <formats.html#obidms-release-files>`_.
 
 
-Mandatory columns
------------------
-
-Some columns must exist in an OBIDMS directory :
-	* sequence identifiers column
-
-
 OBIDMS release files
 ====================
  
@@ -89,21 +161,28 @@ have the extension ``.odr``.
 Example : ``count.odr``
 
 
-OBIDMS history file
-===================
-
-An OBIDMS history file consists of data that can be represented in the form of a directed acyclic 
-graph presenting the history of all the operations ever done in the OBIDMS directory.
-
-
 OBIDMS views
 ============
 
-An OBIDMS view corresponds to a list of OBIDMS columns and lines. A view includes one version 
+An OBIDMS view consists of a list of OBIDMS columns and lines. A view includes one version 
 of each mandatory column. Only one version of each column is included. All the columns of 
 one view contain the same number of lines in the same order.
 
 
+OBIDMS history file
+===================
+
+An OBIDMS history file consists of an ordered list of views and commands, those commands leading 
+from one view to the next one.
+
+This history can be represented in the form of a --- showing all the 
+operations ever done in the OBIDMS directory and the views in between them :
+
+.. image:: ./images/history.png
+    :width: 150 px
+    :align: center
+
+
 OBIDMS UML
 ==========
 

doc/source/guidelines.rst

@@ -100,12 +100,12 @@ Naming conventions
 ******************
 
 .. todo::
-	Look for usual naming conventions
+	Look for common naming conventions
 
 
 *****************
 Programming rules
 *****************
 
-* The *int* type should never be used
+    * 
 

doc/source/index.rst

@@ -11,6 +11,7 @@ OBITools3 documentation
    
    Programming guidelines <guidelines>
    Formats <formats>
+   Pistes de reflexion <pistes>
 
 
 Indices and tables

doc/source/pistes.rst

@@ -0,0 +1,20 @@
+###################
+Pistes de reflexion
+###################
+
+
+******************************
+Ce que l'on veut pouvoir faire
+******************************
+
+    * Gerer les valeurs manquantes
+    * Modifier une colonne en cours d'ecriture (mmap)
+    * Ajouter des valeurs a la fin d'une colonne en cours d'ecriture (mmap)
+
+
+******
+Divers
+******
+
+* Si l'ordre d'une colonne est change, elle est reecrite (pas d'index).
+* Truc pour verrouiller l'acces en lecture a un programme a la fois...