Fixes #2 by adding the missing -D option in the help

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@595 60f365c0-8329-0410-b2a4-ec073aeeaa1d

.cproject

@@ -0,0 +1,122 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?fileVersion 4.0.0?>
+
+<cproject>
+<storageModule moduleId="org.eclipse.cdt.core.settings">
+<cconfiguration id="cdt.managedbuild.toolchain.gnu.macosx.base.985481067">
+<storageModule buildSystemId="org.eclipse.cdt.managedbuilder.core.configurationDataProvider" id="cdt.managedbuild.toolchain.gnu.macosx.base.985481067" moduleId="org.eclipse.cdt.core.settings" name="MacOSX GCC">
+<externalSettings/>
+<extensions>
+<extension id="org.eclipse.cdt.core.MachO" point="org.eclipse.cdt.core.BinaryParser"/>
+<extension id="org.eclipse.cdt.core.GASErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
+<extension id="org.eclipse.cdt.core.GLDErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
+<extension id="org.eclipse.cdt.core.GCCErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
+<extension id="org.eclipse.cdt.core.MakeErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
+</extensions>
+</storageModule>
+<storageModule moduleId="cdtBuildSystem" version="4.0.0">
+<configuration artifactName="ecoPCR" buildProperties="" id="cdt.managedbuild.toolchain.gnu.macosx.base.985481067" name="MacOSX GCC" parent="org.eclipse.cdt.build.core.emptycfg">
+<folderInfo id="cdt.managedbuild.toolchain.gnu.macosx.base.985481067.141857048" name="/" resourcePath="">
+<toolChain id="cdt.managedbuild.toolchain.gnu.macosx.base.1673936174" name="cdt.managedbuild.toolchain.gnu.macosx.base" superClass="cdt.managedbuild.toolchain.gnu.macosx.base">
+<targetPlatform archList="all" binaryParser="org.eclipse.cdt.core.MachO" id="cdt.managedbuild.target.gnu.platform.macosx.base.584997877" name="Debug Platform" osList="macosx" superClass="cdt.managedbuild.target.gnu.platform.macosx.base"/>
+<builder id="cdt.managedbuild.target.gnu.builder.macosx.base.328283627" managedBuildOn="false" name="Gnu Make Builder.MacOSX GCC" superClass="cdt.managedbuild.target.gnu.builder.macosx.base"/>
+<tool id="cdt.managedbuild.tool.macosx.c.linker.macosx.base.627652869" name="MacOS X C Linker" superClass="cdt.managedbuild.tool.macosx.c.linker.macosx.base"/>
+<tool id="cdt.managedbuild.tool.macosx.cpp.linker.macosx.base.815782479" name="MacOS X C++ Linker" superClass="cdt.managedbuild.tool.macosx.cpp.linker.macosx.base"/>
+<tool id="cdt.managedbuild.tool.gnu.assembler.macosx.base.536333148" name="GCC Assembler" superClass="cdt.managedbuild.tool.gnu.assembler.macosx.base"/>
+<tool id="cdt.managedbuild.tool.gnu.archiver.macosx.base.202459766" name="GCC Archiver" superClass="cdt.managedbuild.tool.gnu.archiver.macosx.base"/>
+<tool id="cdt.managedbuild.tool.gnu.cpp.compiler.macosx.base.1142106025" name="GCC C++ Compiler" superClass="cdt.managedbuild.tool.gnu.cpp.compiler.macosx.base"/>
+<tool id="cdt.managedbuild.tool.gnu.c.compiler.macosx.base.845498516" name="GCC C Compiler" superClass="cdt.managedbuild.tool.gnu.c.compiler.macosx.base"/>
+</toolChain>
+</folderInfo>
+</configuration>
+</storageModule>
+<storageModule moduleId="scannerConfiguration">
+<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="org.eclipse.cdt.make.core.GCCStandardMakePerProjectProfile"/>
+<profile id="org.eclipse.cdt.make.core.GCCStandardMakePerProjectProfile">
+<buildOutputProvider>
+<openAction enabled="true" filePath=""/>
+<parser enabled="true"/>
+</buildOutputProvider>
+<scannerInfoProvider id="specsFile">
+<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
+<parser enabled="true"/>
+</scannerInfoProvider>
+</profile>
+<profile id="org.eclipse.cdt.make.core.GCCStandardMakePerFileProfile">
+<buildOutputProvider>
+<openAction enabled="true" filePath=""/>
+<parser enabled="true"/>
+</buildOutputProvider>
+<scannerInfoProvider id="makefileGenerator">
+<runAction arguments="-f ${project_name}_scd.mk" command="make" useDefault="true"/>
+<parser enabled="true"/>
+</scannerInfoProvider>
+</profile>
+<profile id="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfile">
+<buildOutputProvider>
+<openAction enabled="false" filePath=""/>
+<parser enabled="false"/>
+</buildOutputProvider>
+<scannerInfoProvider id="specsFile">
+<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
+<parser enabled="true"/>
+</scannerInfoProvider>
+</profile>
+<profile id="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileCPP">
+<buildOutputProvider>
+<openAction enabled="false" filePath=""/>
+<parser enabled="false"/>
+</buildOutputProvider>
+<scannerInfoProvider id="specsFile">
+<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.cpp" command="g++" useDefault="true"/>
+<parser enabled="true"/>
+</scannerInfoProvider>
+</profile>
+<profile id="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileC">
+<buildOutputProvider>
+<openAction enabled="false" filePath=""/>
+<parser enabled="false"/>
+</buildOutputProvider>
+<scannerInfoProvider id="specsFile">
+<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.c" command="gcc" useDefault="true"/>
+<parser enabled="true"/>
+</scannerInfoProvider>
+</profile>
+<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfile">
+<buildOutputProvider>
+<openAction enabled="false" filePath=""/>
+<parser enabled="false"/>
+</buildOutputProvider>
+<scannerInfoProvider id="specsFile">
+<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
+<parser enabled="true"/>
+</scannerInfoProvider>
+</profile>
+<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfileCPP">
+<buildOutputProvider>
+<openAction enabled="false" filePath=""/>
+<parser enabled="false"/>
+</buildOutputProvider>
+<scannerInfoProvider id="specsFile">
+<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.cpp" command="g++" useDefault="true"/>
+<parser enabled="true"/>
+</scannerInfoProvider>
+</profile>
+<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfileC">
+<buildOutputProvider>
+<openAction enabled="false" filePath=""/>
+<parser enabled="false"/>
+</buildOutputProvider>
+<scannerInfoProvider id="specsFile">
+<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.c" command="gcc" useDefault="true"/>
+<parser enabled="true"/>
+</scannerInfoProvider>
+</profile>
+</storageModule>
+<storageModule moduleId="org.eclipse.cdt.core.externalSettings"/>
+</cconfiguration>
+</storageModule>
+<storageModule moduleId="cdtBuildSystem" version="4.0.0">
+<project id="ecoPCR.null.1320766773" name="ecoPCR"/>
+</storageModule>
+</cproject>

.gitignore

@@ -0,0 +1,16 @@
+
+# /src/
+/src/ecoPCR
+/src/ecofind
+/src/*.P
+/src/ecogrep
+
+# /src/libapat/
+/src/libapat/libapat.a
+/src/libapat/*.P
+
+# /src/libecoPCR/
+/src/libecoPCR/*.P
+
+# /src/libthermo/
+/src/libthermo/*.P

.project

@@ -0,0 +1,83 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>ecoPCR</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.python.pydev.PyDevBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.cdt.managedbuilder.core.genmakebuilder</name>
+			<triggers>clean,full,incremental,</triggers>
+			<arguments>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.fullBuildTarget</key>
+					<value>all</value>
+				</dictionary>
+				<dictionary>
+					<key>?name?</key>
+					<value></value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.enableAutoBuild</key>
+					<value>false</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.enableFullBuild</key>
+					<value>true</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.enableCleanBuild</key>
+					<value>true</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.cleanBuildTarget</key>
+					<value>clean</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.append_environment</key>
+					<value>true</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.contents</key>
+					<value>org.eclipse.cdt.make.core.activeConfigSettings</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.useDefaultBuildCmd</key>
+					<value>true</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.buildArguments</key>
+					<value></value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.buildCommand</key>
+					<value>make</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.autoBuildTarget</key>
+					<value>all</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.stopOnError</key>
+					<value>true</value>
+				</dictionary>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.cdt.managedbuilder.core.ScannerConfigBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.cdt.core.cnature</nature>
+		<nature>org.eclipse.cdt.managedbuilder.core.ScannerConfigNature</nature>
+		<nature>org.eclipse.cdt.managedbuilder.core.managedBuildNature</nature>
+		<nature>org.python.pydev.pythonNature</nature>
+	</natures>
+</projectDescription>

.pydevproject

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?eclipse-pydev version="1.0"?>
+
+<pydev_project>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.4</pydev_property>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Default</pydev_property>
+</pydev_project>

Debug/.gdb_history

@@ -1,62 +0,0 @@
-r  -1acghtgd -2gctcagctagcta /Users/coissac/encours/ecoPCR/tools/ecodb 
-print put
-print out
-f ecoPCR
-r  -1GGGCAATCCTGAGCCAA -2CCATTGAGTCTCTGCACCTATC -l5 -L200 -e2 /Users/coissac/encours/ecoPCR/tools/ecodb
-bt
-print label1
-up
-print label1
-print (char*)label1
-r  -1GGGCAATCCTGAGCCAA -2CCATTGAGTCTCTGCACCTATC -l5 -L200 -e2 /Users/coissac/encours/ecoPCR/tools/ecodb
-bt
-up 3
-l
-b 38
-r
-r  -1GGGCAATCCTGAGCCAA -2CCATTGAGTCTCTGCACCTATC -l5 -L200 -e2 /Users/coissac/encours/ecoPCR/tools/ecodb
-print label
-print ranks
-print *ranks
-print ranks->label +1
-print *ranks->label +1
-print *(ranks->label +1)
-print *(ranks->label +2)
-b ecotax.c:147
-r  -1GGGCAATCCTGAGCCAA -2CCATTGAGTCTCTGCACCTATC -l5 -L200 -e2 /Users/coissac/encours/ecoPCR/tools/ecodb
-print current_taxon ;
-print current_taxon 
-n
-print current_taxon ;
-print current_taxon 
-print *current_taxon 
-print taxonomy->taxons[11]
-print taxonomy->taxons[2952]
-print taxonomy->taxons->taxon[2952]
-print taxonomy->ranks->rank[11]
-print taxonomy->ranks->label[11]
-print taxonomy->ranks->label[3]
-b ecotax.c:147
-r  -1GGGCAATCCTGAGCCAA -2CCATTGAGTCTCTGCACCTATC -l5 -L200 -e2 /Users/coissac/encours/ecoPCR/tools/ecodb
-print current_taxon 
-print *current_taxon 
-n
-print *current_taxon 
-b ecotax.c:147
-r  -1GGGCAATCCTGAGCCAA -2CCATTGAGTCTCTGCACCTATC -l5 -L200 -e2 /Users/coissac/encours/ecoPCR/tools/ecodb
-n
-print *current_taxon 
-r  -1GGGCAATCCTGAGCCAA -2CCATTGAGTCTCTGCACCTATC -l5 -L200 -e2 /Users/coissac/encours/ecoPCR/tools/ecodb
-n
-print *current_taxon 
-b ecodna.c:70
-r  -1GGGCAATCCTGAGCC#A#A# -2CCATTGAGTCTCTGCACCTA#T#C# -l5 -L200 -e2 /Users/coissac/encours/ecoPCR/tools/ecodb
-*sb
-print *sb
-print sb
-print str
-b 52
-r  -1GGGCAATCCTGAGCC#A#A# -2CCATTGAGTCTCTGCACCTA#T#C# -l5 -L200 -e2 /Users/coissac/encours/ecoPCR/tools/ecodb
-print str
-r  -1GGGCAATCCTGAGCC#A#A# -2CCATTGAGTCTCTGCACCTA#T#C# -l5 -L200 -e2 /Users/coissac/encours/ecoPCR/tools/ecodb
-bt

Debug/makefile

@@ -1,46 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
--include ../makefile.init
-
-RM := rm -rf
-
-# All of the sources participating in the build are defined here
--include sources.mk
--include subdir.mk
--include src/libecoPCR/subdir.mk
--include src/libapat/subdir.mk
--include src/subdir.mk
--include objects.mk
-
-ifneq ($(MAKECMDGOALS),clean)
-ifneq ($(strip $(C_DEPS)),)
--include $(C_DEPS)
-endif
-endif
-
--include ../makefile.defs
-
-# Add inputs and outputs from these tool invocations to the build variables 
-
-# All Target
-all: ecoPCR
-
-# Tool invocations
-ecoPCR: $(OBJS) $(USER_OBJS)
-	@echo 'Building target: $@'
-	@echo 'Invoking: MacOS X C Linker'
-	gcc  -o "ecoPCR" $(OBJS) $(USER_OBJS) $(LIBS)
-	@echo 'Finished building target: $@'
-	@echo ' '
-
-# Other Targets
-clean:
-	-$(RM) $(OBJS)$(EXECUTABLES)$(C_DEPS) ecoPCR
-	-@echo ' '
-
-.PHONY: all clean dependents
-.SECONDARY:
-
--include ../makefile.targets

Debug/objects.mk

@@ -1,7 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-LIBS := -lz
-
-USER_OBJS :=

Debug/sources.mk

@@ -1,19 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-C_SRCS := 
-O_SRCS := 
-ASM_SRCS := 
-S_SRCS := 
-OBJ_SRCS := 
-OBJS := 
-EXECUTABLES := 
-C_DEPS := 
-
-# Every subdirectory with source files must be described here
-SUBDIRS := \
-src/libecoPCR \
-src/libapat \
-src \
-

Debug/src/libapat/CODES/subdir.mk

@@ -1,24 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-# Add inputs and outputs from these tool invocations to the build variables 
-C_SRCS += \
-../src/libapat/CODES/gendual.c 
-
-OBJS += \
-./src/libapat/CODES/gendual.o 
-
-C_DEPS += \
-./src/libapat/CODES/gendual.d 
-
-
-# Each subdirectory must supply rules for building sources it contributes
-src/libapat/CODES/%.o: ../src/libapat/CODES/%.c
-	@echo 'Building file: $<'
-	@echo 'Invoking: GCC C Compiler'
-	gcc -DMAC_OS_X -O0 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o"$@" "$<"
-	@echo 'Finished building: $<'
-	@echo ' '
-
-

Debug/src/libapat/subdir.mk

@@ -1,30 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-# Add inputs and outputs from these tool invocations to the build variables 
-C_SRCS += \
-../src/libapat/apat_parse.c \
-../src/libapat/apat_search.c \
-../src/libapat/libstki.c 
-
-OBJS += \
-./src/libapat/apat_parse.o \
-./src/libapat/apat_search.o \
-./src/libapat/libstki.o 
-
-C_DEPS += \
-./src/libapat/apat_parse.d \
-./src/libapat/apat_search.d \
-./src/libapat/libstki.d 
-
-
-# Each subdirectory must supply rules for building sources it contributes
-src/libapat/%.o: ../src/libapat/%.c
-	@echo 'Building file: $<'
-	@echo 'Invoking: GCC C Compiler'
-	gcc -DMAC_OS_X -O0 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o"$@" "$<"
-	@echo 'Finished building: $<'
-	@echo ' '
-
-

Debug/src/libecoPCR/subdir.mk

@@ -1,45 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-# Add inputs and outputs from these tool invocations to the build variables 
-C_SRCS += \
-../src/libecoPCR/ecoError.c \
-../src/libecoPCR/ecoIOUtils.c \
-../src/libecoPCR/ecoMalloc.c \
-../src/libecoPCR/ecoapat.c \
-../src/libecoPCR/ecodna.c \
-../src/libecoPCR/ecorank.c \
-../src/libecoPCR/ecoseq.c \
-../src/libecoPCR/ecotax.c 
-
-OBJS += \
-./src/libecoPCR/ecoError.o \
-./src/libecoPCR/ecoIOUtils.o \
-./src/libecoPCR/ecoMalloc.o \
-./src/libecoPCR/ecoapat.o \
-./src/libecoPCR/ecodna.o \
-./src/libecoPCR/ecorank.o \
-./src/libecoPCR/ecoseq.o \
-./src/libecoPCR/ecotax.o 
-
-C_DEPS += \
-./src/libecoPCR/ecoError.d \
-./src/libecoPCR/ecoIOUtils.d \
-./src/libecoPCR/ecoMalloc.d \
-./src/libecoPCR/ecoapat.d \
-./src/libecoPCR/ecodna.d \
-./src/libecoPCR/ecorank.d \
-./src/libecoPCR/ecoseq.d \
-./src/libecoPCR/ecotax.d 
-
-
-# Each subdirectory must supply rules for building sources it contributes
-src/libecoPCR/%.o: ../src/libecoPCR/%.c
-	@echo 'Building file: $<'
-	@echo 'Invoking: GCC C Compiler'
-	gcc -DMAC_OS_X -O0 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o"$@" "$<"
-	@echo 'Finished building: $<'
-	@echo ' '
-
-

Debug/src/subdir.mk

@@ -1,24 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-# Add inputs and outputs from these tool invocations to the build variables 
-C_SRCS += \
-../src/ecopcr.c 
-
-OBJS += \
-./src/ecopcr.o 
-
-C_DEPS += \
-./src/ecopcr.d 
-
-
-# Each subdirectory must supply rules for building sources it contributes
-src/%.o: ../src/%.c
-	@echo 'Building file: $<'
-	@echo 'Invoking: GCC C Compiler'
-	gcc -DMAC_OS_X -O0 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o"$@" "$<"
-	@echo 'Finished building: $<'
-	@echo ' '
-
-

Release/makefile

@@ -1,46 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
--include ../makefile.init
-
-RM := rm -rf
-
-# All of the sources participating in the build are defined here
--include sources.mk
--include subdir.mk
--include src/libecoPCR/subdir.mk
--include src/libapat/subdir.mk
--include src/subdir.mk
--include objects.mk
-
-ifneq ($(MAKECMDGOALS),clean)
-ifneq ($(strip $(C_DEPS)),)
--include $(C_DEPS)
-endif
-endif
-
--include ../makefile.defs
-
-# Add inputs and outputs from these tool invocations to the build variables 
-
-# All Target
-all: ecoPCR
-
-# Tool invocations
-ecoPCR: $(OBJS) $(USER_OBJS)
-	@echo 'Building target: $@'
-	@echo 'Invoking: MacOS X C Linker'
-	gcc  -o "ecoPCR" $(OBJS) $(USER_OBJS) $(LIBS)
-	@echo 'Finished building target: $@'
-	@echo ' '
-
-# Other Targets
-clean:
-	-$(RM) $(OBJS)$(EXECUTABLES)$(C_DEPS) ecoPCR
-	-@echo ' '
-
-.PHONY: all clean dependents
-.SECONDARY:
-
--include ../makefile.targets

Release/objects.mk

@@ -1,7 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-LIBS := -lz
-
-USER_OBJS :=

Release/sources.mk

@@ -1,19 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-C_SRCS := 
-O_SRCS := 
-ASM_SRCS := 
-S_SRCS := 
-OBJ_SRCS := 
-OBJS := 
-EXECUTABLES := 
-C_DEPS := 
-
-# Every subdirectory with source files must be described here
-SUBDIRS := \
-src/libecoPCR \
-src/libapat \
-src \
-

Release/src/libapat/subdir.mk

@@ -1,30 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-# Add inputs and outputs from these tool invocations to the build variables 
-C_SRCS += \
-../src/libapat/apat_parse.c \
-../src/libapat/apat_search.c \
-../src/libapat/libstki.c 
-
-OBJS += \
-./src/libapat/apat_parse.o \
-./src/libapat/apat_search.o \
-./src/libapat/libstki.o 
-
-C_DEPS += \
-./src/libapat/apat_parse.d \
-./src/libapat/apat_search.d \
-./src/libapat/libstki.d 
-
-
-# Each subdirectory must supply rules for building sources it contributes
-src/libapat/%.o: ../src/libapat/%.c
-	@echo 'Building file: $<'
-	@echo 'Invoking: GCC C Compiler'
-	gcc -DMAC_OS_X -O3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o"$@" "$<"
-	@echo 'Finished building: $<'
-	@echo ' '
-
-

Release/src/libecoPCR/subdir.mk

@@ -1,45 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-# Add inputs and outputs from these tool invocations to the build variables 
-C_SRCS += \
-../src/libecoPCR/ecoError.c \
-../src/libecoPCR/ecoIOUtils.c \
-../src/libecoPCR/ecoMalloc.c \
-../src/libecoPCR/ecoapat.c \
-../src/libecoPCR/ecodna.c \
-../src/libecoPCR/ecorank.c \
-../src/libecoPCR/ecoseq.c \
-../src/libecoPCR/ecotax.c 
-
-OBJS += \
-./src/libecoPCR/ecoError.o \
-./src/libecoPCR/ecoIOUtils.o \
-./src/libecoPCR/ecoMalloc.o \
-./src/libecoPCR/ecoapat.o \
-./src/libecoPCR/ecodna.o \
-./src/libecoPCR/ecorank.o \
-./src/libecoPCR/ecoseq.o \
-./src/libecoPCR/ecotax.o 
-
-C_DEPS += \
-./src/libecoPCR/ecoError.d \
-./src/libecoPCR/ecoIOUtils.d \
-./src/libecoPCR/ecoMalloc.d \
-./src/libecoPCR/ecoapat.d \
-./src/libecoPCR/ecodna.d \
-./src/libecoPCR/ecorank.d \
-./src/libecoPCR/ecoseq.d \
-./src/libecoPCR/ecotax.d 
-
-
-# Each subdirectory must supply rules for building sources it contributes
-src/libecoPCR/%.o: ../src/libecoPCR/%.c
-	@echo 'Building file: $<'
-	@echo 'Invoking: GCC C Compiler'
-	gcc -DMAC_OS_X -O3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o"$@" "$<"
-	@echo 'Finished building: $<'
-	@echo ' '
-
-

Release/src/subdir.mk

@@ -1,24 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-# Add inputs and outputs from these tool invocations to the build variables 
-C_SRCS += \
-../src/ecopcr.c 
-
-OBJS += \
-./src/ecopcr.o 
-
-C_DEPS += \
-./src/ecopcr.d 
-
-
-# Each subdirectory must supply rules for building sources it contributes
-src/%.o: ../src/%.c
-	@echo 'Building file: $<'
-	@echo 'Invoking: GCC C Compiler'
-	gcc -DMAC_OS_X -O3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o"$@" "$<"
-	@echo 'Finished building: $<'
-	@echo ' '
-
-

VERSION

@@ -0,0 +1 @@
+0.5.0

src/Makefile

@@ -0,0 +1,103 @@
+EXEC=ecoPCR ecofind ecogrep
+
+PCR_SRC= ecopcr.c
+PCR_OBJ= $(patsubst %.c,%.o,$(PCR_SRC))
+
+FIND_SRC= ecofind.c
+FIND_OBJ= $(patsubst %.c,%.o,$(FIND_SRC))
+
+GREP_SRC= ecogrep.c
+GREP_OBJ= $(patsubst %.c,%.o,$(GREP_SRC))
+
+IUT_SRC= ecoisundertaxon.c
+IUT_OBJ= $(patsubst %.c,%.o,$(IUT_SRC))
+
+SRCS= $(PCR_SRC) $(FIND_SRC) $(IUT_SRC)
+
+LIB= -lecoPCR -lthermo -lapat -lz -lm
+
+LIBFILE= libapat/libapat.a \
+         libecoPCR/libecoPCR.a \
+         libthermo/libthermo.a
+
+
+include global.mk
+
+all: $(EXEC)
+
+
+########
+#
+# ecoPCR compilation
+#
+########
+
+# executable compilation and link
+
+ecoPCR: $(PCR_OBJ) $(LIBFILE) 
+	$(CC) $(LDFLAGS) -o $@ $< $(LIBPATH) $(LIB)
+	
+########
+#
+# ecofind compilation
+#
+########
+	
+# executable compilation and link
+
+ecofind: $(FIND_OBJ) $(LIBFILE)
+	$(CC) $(LDFLAGS) -o $@ $< $(LIBPATH) $(LIB)
+	
+########
+#
+# ecogrep compilation
+#
+########
+	
+# executable compilation and link
+
+ecogrep: $(GREP_OBJ) $(LIBFILE)
+	$(CC) $(LDFLAGS) -o $@ $< $(LIBPATH) $(LIB)
+	
+########
+#
+# IsUnderTaxon compilation
+#
+########
+	
+# executable compilation and link
+
+ecoisundertaxon: $(IUT_OBJ) $(LIBFILE)
+	$(CC) $(LDFLAGS) -o $@ $< $(LIBPATH) $(LIB)
+
+########
+#
+# library compilation
+#
+########
+
+libapat/libapat.a:
+	$(MAKE) -C libapat
+	
+libecoPCR/libecoPCR.a:
+	$(MAKE) -C libecoPCR
+	
+libthermo/libthermo.a:
+	$(MAKE) -C libthermo
+	
+	
+########
+#
+# project management
+#
+########
+
+clean:
+	rm -f *.o	
+	rm -f $(EXEC)
+	$(MAKE) -C libapat clean
+	$(MAKE) -C libecoPCR clean
+	$(MAKE) -C libthermo clean
+		
+
+		

src/ecofind.c

@@ -0,0 +1,373 @@
+#include "libecoPCR/ecoPCR.h"
+#include <regex.h>
+#include <string.h>
+#include <stdlib.h>
+#include <getopt.h>
+#include <stdio.h>
+#define VERSION "0.1"
+
+/**
+ * display the result
+ **/
+
+void displayPath(ecotx_t *taxon, ecotaxonomy_t *taxonomy){
+
+	if (taxon != taxon->parent){
+		displayPath(taxon->parent,taxonomy);
+		printf(";");
+	}
+	if (rank_index("no rank",taxonomy->ranks) != taxon->rank)
+		printf("%s:", taxonomy->ranks->label[taxon->rank]);
+	printf("%s", taxon->name);
+}
+
+
+static void printresult(ecotx_t *taxon,econame_t* name,ecotaxonomy_t *taxonomy, int32_t pathDisplay)
+{
+	char* rankname;
+	char* classname;
+	char* matchedname=taxon->name;
+	
+	classname="scientific name";
+	if (name)
+	{
+		classname=name->classname;
+		matchedname=name->name;
+	}
+	
+	rankname= taxonomy->ranks->label[taxon->rank];	
+	
+	printf("%10d \t| %15s \t|\t %-50s \t|\t %15s \t|\t %s",
+			taxon->taxid,
+			rankname,
+			matchedname,
+			classname,
+			taxon->name);
+	if (pathDisplay) {
+	    printf("\t|\t");
+	    displayPath(taxon, taxonomy);
+	}
+    printf("\n");
+}
+
+/**
+ * display header before printing any result
+ **/
+static void printheader(int32_t pathDisplay)
+{
+	printf("# %12s \t| %15s \t|\t %-50s \t|\t %-15s \t|\t %s%s\n#\n",
+			"taxonomy id",
+			"taxonomy rank",
+			"name",
+			"class name",
+			"scientific name",
+			pathDisplay ? "\t|\t path":"");
+}
+
+
+/**
+ * display son's list for given taxon
+ **/
+static void get_son(ecotaxonomy_t *taxonomy, ecotx_t *taxon, int32_t *count, char *rankname, int32_t pathDisplay)
+{
+	int32_t		i;
+	ecotx_t 	*current_taxon;
+	
+	for (	i = 0, current_taxon = taxonomy->taxons->taxon;
+			i < taxonomy->taxons->count; 
+			i++, current_taxon++)
+	{	
+
+		if (taxon != current_taxon && taxon->taxid == current_taxon->parent->taxid)
+		{
+			if (rankname == NULL || !strcmp(rankname,taxonomy->ranks->label[current_taxon->rank]))
+			{
+				printresult(current_taxon, NULL, taxonomy, pathDisplay);
+				(*count)++;	
+			}
+			get_son(taxonomy,current_taxon,count,rankname, pathDisplay);
+		}
+	}
+}
+
+
+
+/**
+ * display list of rank filter option (-l option)
+ **/
+static void listfilteroptions(ecorankidx_t *ranks)
+{
+	int32_t		i;
+	
+	printf("#\n");
+	
+	for (	i=0;
+			i < ranks->count;
+			i++)
+	{
+		printf("#  %s \n",ranks->label[i]);
+	}
+	
+	printf("#\n");
+}
+
+
+/* ---------------------------------------- */
+/* get back on given taxid taxonomic parent	*/
+/* and display it							*/
+/* ---------------------------------------- */
+void gettaxidparents(int32_t taxid, ecotaxonomy_t *taxonomy, char *rankname, int32_t pathDisplay)
+{
+	ecotx_t *next_parent;
+	int32_t	c = 0;
+	
+	next_parent = eco_findtaxonbytaxid(taxonomy, taxid);		
+	
+	printheader(pathDisplay);
+	
+	printresult(next_parent, NULL,taxonomy, pathDisplay);
+		
+	while ( strcmp(next_parent->name, "root") )
+	{
+		next_parent = next_parent->parent;
+		if (rankname == NULL || !strcmp(rankname,taxonomy->ranks->label[next_parent->rank]))
+		{
+			printresult(next_parent, NULL,taxonomy, pathDisplay);
+			c++;
+		}
+	}
+	
+	printf("#  %d parent(s) found\n#\n",c);
+}
+
+
+/**
+ * printout usage and exit                     
+ **/
+#define PP fprintf(stderr, 
+
+static void ExitUsage(stat)
+        int stat;
+{
+        PP      "usage: ecofind [-d database] [-h] [-l] [-P] [-r taxonomic rank] [-p taxid] [-s taxid] <taxon name pattern> ... \n");
+        PP      "type \"ecofind -h\" for help\n");
+        if (stat)
+            exit(stat);
+}
+
+#undef  PP
+
+/**
+ * printout help
+ **/
+#define PP fprintf(stdout, 
+
+static void PrintHelp()
+{
+        PP      "------------------------------------------\n");
+        PP      " ecofind Version %s\n", VERSION);
+        PP      "------------------------------------------\n");
+        PP      "synopsis : searching for taxonomic and rank and\n");
+        PP		"           taxonomy id for given regular  expression patterns\n\n");
+        PP      "usage: ecofind [options] <patterns>\n");
+        PP      "------------------------------------------\n");
+        PP      "options:\n");
+        PP      "-a : [A]ll enable the search on all alternative names and not only scientific names.\n\n");        
+        PP      "-d : [D]atabase containing the taxonomy.\n");
+        PP		"     To match the expected format, the database\n");
+        PP		"     has to be formated first by the ecoPCRFormat.py\n");
+        PP		"     program located in the tools directory.\n");
+        PP		"     Write the database radical without any extension.\n\n");
+        PP      "-h : [H]elp - print <this> help\n\n");
+        PP      "-l : [L]ist all taxonomic rank available for -r option\n\n");
+        PP      "-P : [P]ath : add a column containing the full path for each displayed taxon\n\n");
+        PP      "-p : [P]arents : specifiying this option displays all parental tree's information for the given taxid.\n\n");
+        PP      "-r : [R]estrict to given taxonomic rank\n\n");      
+        PP      "-s : [S]ons: specifiying this option displays all subtree's information for the given taxid.\n\n");
+        PP      "-P : Display taxonomic [P]ath as suplementary column in output\n\n");
+        PP      "arguments:\n");        
+        PP      "<taxon> name pattern bearing regular expressions\n\n");
+        PP      "------------------------------------------\n");
+        PP		" http://www.grenoble.prabi.fr/trac/ecoPCR/\n");
+        PP      "------------------------------------------\n\n");
+}
+
+/* ----------------------------------------------- */
+
+#define PATTERN_NUMBER 	10
+#define PATTERN_LENGHT 	40
+#define	RESULT_LENGTH	100
+
+int main(int argc, char **argv) 
+{
+	int32_t     	carg		= 0;
+	int32_t			nummatch 	= 0;
+	int32_t 		k,j 		= 0;
+	int32_t     	errflag 	= 0;
+	int32_t			tax_count	= 0;
+	int32_t         alternative = 0;
+	char			*prefix		= NULL;
+	ecotaxonomy_t 	*taxonomy;	
+	econame_t		*name;
+	int32_t         name_count;
+	
+	int				re_error;
+	int				re_match;
+	regex_t			re_preg;
+	
+	int32_t 		uptree 		= 0;
+	int32_t 		subtree 	= 0;
+	char			*rankname	= NULL;
+	int32_t			rankfilter 	= 1;
+	int32_t			list 		= 0;
+	int32_t			path 		= 0;
+	
+	ecotx_t 		*subtree_parent;
+	int32_t			count_son = 0;
+
+
+	while ((carg = getopt(argc, argv, "had:p:s:r:lP")) != -1) {
+	    switch (carg) {                        
+	       case 's':               	/* path to the database     */
+	          sscanf(optarg,"%d",&subtree);
+	          break;
+
+	       case 'r':               	/* rank filter     */
+	          rankname = ECOMALLOC(strlen(optarg)+1,"allocation rankname");
+	          strcpy(rankname,optarg);
+	          rankfilter = 0;
+	          break;
+
+	       case 'd':               	/* path to the database     */
+	          prefix = ECOMALLOC(strlen(optarg)+1,"allocation prefix");
+	          strcpy(prefix,optarg);
+	          break;
+	          
+	       case 'l':               	/* list rank filter options */
+	          list = 1;
+	          break;
+
+	       case 'P':               	/* Path output option */
+	          path=1;
+	          break;
+	
+	       case 'a':               	/* allow alternative names  */
+	          alternative = 1;
+	          break;
+	
+	       case 'h':               	/* display help	           	*/      
+	          PrintHelp();
+	          exit(0);
+	          break;
+	          
+	       case 'p':               	/* taxid		           	*/      
+	          sscanf(optarg,"%d",&uptree);
+	          break;	          
+	           
+	       case '?':               	/* bad option   	        */
+	          errflag++;
+	     }
+	}
+	
+	if ((argc - optind) < 1)
+        errflag++;
+	
+	if (prefix == NULL)
+	{
+		prefix = getenv("ECOPCRDB");
+		if (prefix == NULL)
+			errflag++;
+	}
+		
+	if (errflag && !uptree && !rankname && !subtree && !list)
+		ExitUsage(errflag);
+		
+	/**
+	 * load taxonomy using libecoPCR functions
+	 **/
+	printf("# \n#  opening %s database\n",prefix);
+	
+	taxonomy = read_taxonomy(prefix,1);
+	tax_count = taxonomy->taxons->count;
+	name_count = taxonomy->names->count;
+		
+	
+	/* ----------------------------------------	*/
+	/* list -r option possibility		    	*/
+	/* ----------------------------------------	*/		
+	if (list)
+	{
+		listfilteroptions(taxonomy->ranks);
+		return 0;
+	}
+		
+	/* ----------------------------------------	*/
+	/* display taxid parent if -t option    	*/
+	/* specified in command line				*/
+	/* ----------------------------------------	*/	
+	if (uptree)
+	{
+		gettaxidparents(uptree,taxonomy,rankname, path);
+		return 0;	
+	}
+	
+	/* ----------------------------------------	*/
+	/* display taxid sons if -s option    		*/
+	/* specified in command line				*/
+	/* ----------------------------------------	*/		
+	if (subtree)
+	{
+		printheader(path);
+		subtree_parent = eco_findtaxonbytaxid(taxonomy,subtree);
+		printresult(subtree_parent, NULL,taxonomy, path);
+		get_son(taxonomy, subtree_parent,&count_son,rankname, path);
+		printf("#  %d son(s) found\n#\n",count_son);
+		return 0;
+	}
+	
+	printf("#  %d taxons\n", tax_count);
+		
+	/**
+	 * parse taxonomy
+	 **/
+	for (k=optind;k<argc;k++)
+	{
+		printf("#\n#  searching for '%s' pattern\n",argv[k]); 
+		
+		re_error = regcomp (&re_preg, argv[k], REG_NOSUB | REG_EXTENDED | REG_ICASE);
+		if (re_error)
+		{
+			fprintf(stderr,"#  misformed pattern '%s'\n",argv[k]);
+			exit(1);
+		}
+		
+		nummatch=0;
+		
+	    printheader(path);
+		
+		for (j=0,name=taxonomy->names->names;
+		     j < name_count;
+		     name++,j++)
+		{  			
+   			
+   			if(rankname)
+   				rankfilter = !(strcmp(rankname,taxonomy->ranks->label[name->taxon->rank]));
+
+   			re_match = regexec (&re_preg, name->name, 0, NULL, 0);
+   			
+   			if (!re_match && (alternative || name->is_scientificname) && rankfilter)
+   			{
+   				printresult(name->taxon,name,taxonomy, path);
+   				nummatch++;
+   			}
+   			
+		} 		
+			
+		printf("#  %d records found \n",nummatch);
+	   	regfree(&re_preg);
+	}		
+			
+	return 0;
+}
+
+

src/ecogrep.c

@@ -0,0 +1,403 @@
+#include "libecoPCR/ecoPCR.h"
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include <getopt.h>
+#include <stdlib.h>
+#include <sys/stat.h>
+
+
+#define VERSION "0.1"
+
+void getLineContent(char *stream, ecoseq_t *seq, ecoseq_t *oligoseq_1, ecoseq_t *oligoseq_2){
+	
+	int		i;
+	char	*buffer;
+
+ 	for(	i=0, buffer = strtok(stream,"|");
+			buffer != NULL;
+			i++, buffer = strtok(NULL,"|"))
+	{
+			switch (i) {
+				case 0:
+					seq->AC = strdup(buffer);
+					break;
+				case 2:
+					sscanf(buffer,"%d",&seq->taxid);
+					break;
+				case 13:
+					oligoseq_1->SQ = strdup(buffer);
+					oligoseq_1->SQ_length = strlen(buffer);
+					break;
+				case 16:
+					oligoseq_2->SQ = strdup(buffer);
+					oligoseq_2->SQ_length = strlen(buffer);
+					break;
+				case 20:
+					seq->SQ = strdup(buffer);
+					seq->SQ_length = strlen(buffer);
+					break;
+				default:
+					break;
+			}
+	}
+}
+
+
+void freememory(char **tab, int32_t num){
+	int32_t i;
+	for (i=0;i<num-1;i++){
+		ECOFREE(tab[i],"Error in freememory function");	
+	}
+}
+
+/**
+ * Check if pattern match a string using mamberall libapat function
+ * @param	line		array containing sequence information
+ * @param	pattern		array containing patterns to test on the sequence
+ * @param	numpattern	number of pattern in pattern array
+ * @param	error_max	error rate allowed by the user
+ * 
+ * @return	int			1 if a pattern match, else 0
+ **/
+int	ispatternmatching(ecoseq_t *seq, PatternPtr pattern){
+	if (pattern != NULL)
+	{
+		SeqPtr 	apatseq	= NULL;
+		apatseq=ecoseq2apatseq(seq,apatseq,0);
+		return ManberAll(apatseq,pattern,0,0,apatseq->seqlen) > 0;
+	}
+	else return 0;
+}
+
+/* ----------------------------------------------- */
+/* printout help                                   */                                           
+/* ----------------------------------------------- */
+#define PP fprintf(stdout, 
+
+static void PrintHelp()
+{
+        PP      "\n------------------------------------------\n");
+        PP      " ecogrep Version %s\n", VERSION);
+        PP      "------------------------------------------\n");
+        PP      " synopsis : filtering ecoPCR result based on\n");
+        PP      " taxonomic id filter and regular expression pattern\n");
+        PP      " usage: ecogrep [options] filename\n");
+        PP      "------------------------------------------\n");
+        PP      " options:\n");
+        PP      " -1    : [FIRST] : compare the given pattern with direct strand oligonucleotide\n\n");
+        PP      " -2    : [SECOND] : compare the given pattern with reverse strand oligonucleotide\n\n");
+        PP      " -d    : [D]atabase containing taxonomic information\n\n");
+        PP      " -e    : [E]rrors : max error allowed in pattern match (option-1, -2 and -p) (0 by default)\n\n"); 
+        PP      " -p    : [P]attern : oligonucleotide pattern\n\n"); 
+        PP      " -h    : [H]elp : print <this> help\n\n");
+        PP      " -i    : [I]gnore subtree under given taxonomic id\n\n");
+        PP      " -r    : [R]estrict search to subtree under given taxomic id\n\n");
+        PP      " -v    : in[V]ert the sense of matching, to select non-matching lines.\n\n");
+        PP      " argument:\n");
+        PP      " ecoPCR ouput file name\n");
+        PP      "------------------------------------------\n\n");
+        PP		" http://www.grenoble.prabi.fr/trac/ecoPCR/\n");
+        PP      "------------------------------------------\n\n");
+}
+
+#undef PP
+
+/* ----------------------------------------------- */
+/* printout usage and exit                         */
+/* ----------------------------------------------- */
+
+#define PP fprintf(stderr, 
+
+static void ExitUsage(stat)
+        int stat;
+{
+        PP      "usage: ecogrep [-d database] [-p pattern] [-i taxid] [-r taxid] [-v] [-h] <file name>\n");
+        PP      "type \"ecogrep -h\" for help\n");
+
+        if (stat)
+            exit(stat);
+}
+
+#undef  PP
+
+/* ----------------------------------------------- */
+/* MAIN						                       */
+/* ----------------------------------------------- */
+
+#define LINE_BUFF_SIZE 10000
+
+int main(int argc, char **argv){
+	int32_t     	carg 			= 0;
+	int32_t			r				= 0;			// number of restricted taxid
+	int32_t			i				= 0;			// number of ignored taxid
+	int32_t			v				= 0;			// stores if -v mode is active
+	int32_t			k				= 0;			// file counter
+	int32_t			errflag			= 0;			
+	int32_t       	error_max		= 0;			// stores the error rate allowed by the user
+	int32_t			matchingresult 	= 0;			// stores number of matching result
+	
+	ecotaxonomy_t	*taxonomy;						// stores the taxonomy
+	
+	ecoseq_t		*seq				= NULL;		// stores sequence info
+	ecoseq_t		*oligoseq_1			= NULL;		// stores the oligo_1 info
+	ecoseq_t		*oligoseq_2			= NULL;		// stores the oligo_2 info
+	
+	char			*database			= NULL;		// stores the database path (for taxonomy)
+	
+	char			*p					= NULL;		// pattern for sequence 
+	PatternPtr		pattern				= NULL;		// stores the build pattern for sequence 
+	char			*o1					= NULL;		// pattern for direct strand oligo
+	PatternPtr		oligo_1				= NULL;		// stores the build pattern	for direct strand oligo
+	char			*o2					= NULL;		// pattern for reverse strand oligo
+	PatternPtr		oligo_2				= NULL;		// stores the build pattern for reverse strand oligo
+		
+	int32_t		  	*restricted_taxid 	= NULL;		// stores the restricted taxid
+	int32_t       	*ignored_taxid		= NULL;		// stores the ignored taxid
+
+	FILE			*file				= NULL;		// stores the data stream, stdin by default
+	char			*stream				= ECOMALLOC(sizeof(char *)*LINE_BUFF_SIZE,"error stream buffer allocation"); 
+	char			*orig				= ECOMALLOC(sizeof(char *)*LINE_BUFF_SIZE,"error orig buffer allocation"); 
+
+	int 			is_ignored 			= 0;		
+	int				is_included			= 0;
+	int				is_matching			= 0;
+	int 			match_o1			= 0;
+	int 			match_o2			= 0;
+	int				good				= 0;
+	
+	seq = new_ecoseq();
+	oligoseq_1 = new_ecoseq();
+	oligoseq_2 = new_ecoseq();
+	
+	/**
+	 * Parse commande line options
+	 **/
+	while ((carg = getopt(argc, argv, "1:2:p:d:i:r:e:vh")) != -1) {
+
+	    switch (carg) {                              
+	        case '1':
+	           o1 = ECOMALLOC(strlen(optarg)+1,
+	           						"Error on o1 allocation");
+	           strcpy(o1,optarg);
+	           break;
+
+	        case '2':
+	           o2 = ECOMALLOC(strlen(optarg)+1,
+	           						"Error on o2 allocation");
+	           strcpy(o2,optarg);
+	           break;
+	           	        
+	        case 'd':
+	           database = ECOMALLOC(strlen(optarg)+1,
+	           						"Error on datafile allocation");
+	           strcpy(database,optarg);
+	           break;
+	
+	        case 'i':   
+	           ignored_taxid = ECOREALLOC(	ignored_taxid,
+	           								sizeof(int32_t)*(i+1),
+	           								"Error on ignored_taxid reallocation");
+	           sscanf(optarg,"%d",&ignored_taxid[i]);
+	           i++;
+	           break;
+	        
+	        case 'r': 
+	           restricted_taxid = ECOREALLOC(	restricted_taxid, 
+	           									sizeof(int32_t)*(r+1),
+	           									"Error on restricted_taxid reallocation");  
+	           sscanf(optarg,"%d",&restricted_taxid[r]);
+	           r++;
+	           break;
+	           	           
+	        case 'v':     
+	           v = 1;
+	           break;
+	           
+	        case 'h':     
+	           PrintHelp();
+           	   exit(0);
+	           break;
+	           
+	        case 'e':	
+	           sscanf(optarg,"%d",&error_max);
+    	       break;
+
+	        case 'p':	
+	           p = ECOMALLOC(strlen(optarg)+1,
+	           						"Error on pattern allocation");		   
+	           strcpy(p,optarg);
+	           break;
+	           
+	        case '?':
+            	errflag++;
+	     }
+	}
+
+	/**
+	 * Check sequence pattern length and build it in PatternPtr format
+	 **/
+	if(p)
+	{
+		if (strlen(p) > 32){
+			printf("# Sorry, ecogrep doesn't handle pattern longer than 32 characters.\
+					\n# Please check it out : %s\n",p);
+			exit(EXIT_FAILURE);
+		}
+		else if ( (pattern = buildPattern(p,error_max)) == NULL)
+			exit(EXIT_FAILURE);
+	}
+	
+			
+			
+	/**
+	 * Check o1 pattern length and build it in PatternPtr format
+	 **/
+	if(o1)
+	{
+		if (strlen(o1) > 32){
+			printf("# Sorry, ecogrep doesn't handle pattern longer than 32 characters.\
+					\n# Please check it out : %s\n",o1);
+			exit(EXIT_FAILURE);
+		}
+		else if ( (oligo_1 = buildPattern(o1,error_max)) == NULL)
+			exit(EXIT_FAILURE);
+	}
+
+	/**
+	 * Check o2 pattern length and build it in PatternPtr format
+	 **/
+	if(o2)
+	{
+		if (strlen(o2) > 32){
+			printf("# Sorry, ecogrep doesn't handle pattern longer than 32 characters.\
+					\n# Please check it out : %s\n",o2);
+			exit(EXIT_FAILURE);
+		}
+		else if ( (oligo_2 = buildPattern(o2,error_max)) == NULL)
+			exit(EXIT_FAILURE);
+	}
+
+	/**
+	 * try to get the database name from environment variable
+	 * if no database name specified in the -d option
+	 **/
+	if (database == NULL)
+	{
+		database = getenv("ECOPCRDB");
+		if (database == NULL)
+			errflag++;
+	}
+	
+	/**
+	 * check at leat one processing is asked
+	 * either patterns or taxid filters
+	 **/			
+	if ( !p && !o1 && !o2 && restricted_taxid == NULL && ignored_taxid == NULL )
+	{
+		errflag++;
+	}		
+	if (errflag)
+    	ExitUsage(errflag);
+
+	/**
+	 * Get the taxonomy back
+	 **/
+	taxonomy = read_taxonomy(database,0);
+	 
+	/**
+	 * Parse the stream
+	 **/
+	for (k=0 ; argc >= optind ; optind++, k++){
+
+		matchingresult = 0;
+
+		if ( (file = fopen(argv[optind], "r")) == NULL)
+		{
+			if (isatty(fileno(stdin)) == 0)
+			{
+		 		file = stdin;
+		 		printf("# Processing standard input...\n");
+			}
+	 		else
+	 			break;	
+		}
+		else
+			printf("# Processing %s...\n",argv[optind]);
+		
+		while( fgets(stream, LINE_BUFF_SIZE, file) != NULL ){
+		 		
+		 	if (stream[0]!= '#')
+		 	{
+		 		
+		 		stream[LINE_BUFF_SIZE-1]=0;
+		 		
+		 		strcpy(orig,stream);
+		 		
+				getLineContent(stream,seq,oligoseq_1,oligoseq_2);	
+
+				/* -----------------------------------------------*/
+				/* is ignored if at least one option -i 		  */
+				/*  AND											  */
+				/* if current sequence is son of taxid 		 	  */
+				/* -----------------------------------------------*/ 	
+			    is_ignored = ( (i > 0) && (eco_is_taxid_included(	taxonomy, 
+			                            							ignored_taxid, 
+			                            							i, 
+			                            							seq->taxid))
+			                 );				
+
+				/* -----------------------------------------------*/
+				/* is included if no -r option					  */
+				/*  OR											  */
+				/*  if current sequence is son of taxid			  */
+				/* -----------------------------------------------*/ 				
+				is_included = ( (r == 0) || (eco_is_taxid_included(	taxonomy, 
+			                            									restricted_taxid, 
+			                            	 								r, 
+			                            									seq->taxid))
+			                  );
+
+				/* ----------------------------------------------------------- */
+				/* match if no pattern or if pattern match current sequence    */
+				/* ----------------------------------------------------------- */ 
+			    is_matching = ( !p || (ispatternmatching(seq,pattern)));
+			    
+			    /* ---------------------------------------------------------------------------- */
+				/* match if no direct oligo pattern or if pattern match current direct oligo    */
+				/* ---------------------------------------------------------------------------- */ 
+			    match_o1 = (!o1 || (ispatternmatching(oligoseq_1,oligo_1)));
+			    
+			    /* ------------------------------------------------------------------------------- */
+				/* match if no revesrse oligo pattern or if pattern match current reverse oligo    */
+				/* ------------------------------------------------------------------------------- */ 
+			    match_o2 = (!o2 || (ispatternmatching(oligoseq_2,oligo_2)));
+			        				
+			    good = (is_included  && 	is_matching && 	!is_ignored && match_o1 && match_o2);
+			    
+			    if (v)
+			       good=!good;
+			       			
+				if 	( good )
+				{
+					printf("%s",orig);
+	     			matchingresult++;
+				}
+		 	}
+		}
+		if ( file != stdin )
+    		fclose(file);
+    		
+    	printf("# %d matching result(s)\n#\n",matchingresult);
+	}
+	 	
+	/**
+	 * clean and free before leaving
+	 **/
+	ECOFREE(orig,"Error in free orig");
+	ECOFREE(stream,"Error in free stream");
+	ECOFREE(ignored_taxid,"Error in free stream");
+	ECOFREE(restricted_taxid,"Error in free stream");
+	
+	return 0;
+}

src/ecoisundertaxon.c

@@ -0,0 +1,123 @@
+#include "libecoPCR/ecoPCR.h"
+#include <getopt.h>
+#include <stdlib.h>
+
+#define VERSION "0.1"
+
+/* ----------------------------------------------- */
+/* printout verbose mode                           */                                           
+/* ----------------------------------------------- */
+static void printTaxon(ecotx_t *taxon){
+	printf("# taxid : %d | rank : %d | name : %s \n\n",taxon->taxid, taxon->rank, taxon->name);
+}
+
+/* ----------------------------------------------- */
+/* printout help                                   */                                           
+/* ----------------------------------------------- */
+#define PP fprintf(stdout, 
+
+static void PrintHelp()
+{
+        PP      "\n------------------------------------------\n");
+        PP      " ecoisundertaxon Version %s\n", VERSION);
+        PP      "------------------------------------------\n");
+        PP      " synopsis : searching relationship in taxonomy\n");
+        PP      " usage: ecoisundertaxon [options] database\n");
+        PP      "------------------------------------------\n");
+        PP      " options:\n");
+        PP      " -1    : [FIRST] taxomic id of the hypothetical son\n\n");
+        PP      " -2    : [SECOND] taxonomic id of the hypothetical parent\n\n");
+        PP      " -h    : [H]elp - print <this> help\n\n");
+        PP      " -v    : [V]erbose mode. Display taxonomic information for both\n");
+        PP      "       : taxonomic id.\n\n");
+        PP      "------------------------------------------\n");
+        PP      " database : to match the expected format, the database\n");
+        PP      " has to be formated first by the ecoPCRFormat.py program located.\n");
+        PP      " in the tools directory. Type the radical only, leaving out the extension\n");
+        PP      "------------------------------------------\n\n");
+        PP		" https://www.grenoble.prabi.fr/trac/ecoPCR/wiki");
+        PP      "------------------------------------------\n\n");        
+}
+
+#undef PP
+
+/* ----------------------------------------------- */
+/* printout usage and exit                         */
+/* ----------------------------------------------- */
+
+#define PP fprintf(stderr, 
+
+static void ExitUsage(stat)
+        int stat;
+{
+        PP      "usage: ecoisundertaxon [-1 taxid] [-2 taxid] [-v] [-h] datafile\n");
+        PP      "type \"ecoisundertaxon -h\" for help\n");
+
+        if (stat)
+            exit(stat);
+}
+
+#undef  PP
+
+/* ----------------------------------------------- */
+/* MAIN						                       */
+/* ----------------------------------------------- */
+
+int main(int argc, char **argv){
+	int32_t     	carg 		= 0;
+	int32_t			taxid_1		= 0;
+	int32_t			taxid_2		= 0;
+	int32_t			verbose		= 0;
+	int32_t			errflag		= 0;
+	ecotaxonomy_t 	*taxonomy	= NULL;
+	ecotx_t			*son		= NULL;
+	ecotx_t			*parent		= NULL;
+		
+	
+	while ((carg = getopt(argc, argv, "1:2:vh")) != -1) {
+	    switch (carg) {                              
+	        case '1':
+	           sscanf(optarg,"%d",&taxid_1);
+	           break;
+	
+	        case '2':     
+	           sscanf(optarg,"%d",&taxid_2);
+	           break;
+	           
+	        case 'v':     
+	           verbose = 1;
+	           break;
+	           
+	        case 'h':     
+	           PrintHelp();
+           	   exit(0);
+	           break;
+	           
+	        case '?':
+            	errflag++;
+	     }
+	}
+	
+	if ((argc -= optind) != 1)
+    	errflag++;
+    	
+    if (errflag)
+    	ExitUsage(errflag);
+  		
+	taxonomy = read_taxonomy(argv[optind],0);
+	
+	son = eco_findtaxonbytaxid(taxonomy, taxid_1);
+	
+	if (verbose){
+		parent = eco_findtaxonbytaxid(taxonomy, taxid_2);
+		printTaxon(son);
+		printTaxon(parent);
+	}
+	
+	if (eco_isundertaxon(son, taxid_2))
+		printf("# taxid_1 (%d) is son of taxid_2 (%d)\n",taxid_1, taxid_2);
+	else
+		printf("# taxid_1 (%d) is NOT son of taxid_2 (%d)\n",taxid_1, taxid_2);
+	
+	return 0;
+}

src/ecopcr.c

@@ -1,111 +1,87 @@
 #include "libecoPCR/ecoPCR.h"
+#include "libthermo/nnparams.h"
 #include <stdio.h>
 #include <string.h>
 #include <stdlib.h>
 #include <getopt.h>
 
 
-#define VERSION "0.1"
+#define VERSION "0.2"
+
 
 /* ----------------------------------------------- */
-/* printout help                                   */                                           /* ----------------------------------------------- */
-
+/* printout help                                   */                                           
+/* ----------------------------------------------- */
 #define PP fprintf(stdout, 
 
 static void PrintHelp()
 {
         PP      "------------------------------------------\n");
-        PP      " Apat Version %s\n", VERSION);
+        PP      " ecoPCR Version %s\n", VERSION);
         PP      "------------------------------------------\n");
-        PP      "synopsis : pattern(s) searching program\n");
-        PP      "usage: apat [options] patfile datafile\n");
+        PP      "synopsis : searching for sequence and taxonomy hybriding with given primers\n");
+        PP      "usage: ecoPCR [options] <nucleotidic patterns>\n");
         PP      "------------------------------------------\n");
         PP      "options:\n");
-        PP      "-a code         : [A]lphabet encoding for pattern\n");
-        PP      "                  code is one of : \n");
-        PP      "                  dna:   use IUPAC equivalences for dna/rna\n");
-        PP      "                  prot:  use IUPAC equivalences for proteins\n");
-        PP      "                  alpha: no equivalences, just treat plain symbols\n");
-        PP      "                  note: the equivalences are used in pattern only\n");
-        PP      "                  *not* in sequence(s) (see note (4) below)\n");
-        PP      "                  dft: alpha\n");
-        PP      "-c              : [C]ooccurences\n");
-        PP      "                  print patterns cooccurence matrix \n");     
-        PP      "                  dft: off\n");
-        PP      "-h              : [H]elp - print <this> help\n");
-        PP      "-m              : [M]ultiple occurences\n");
-        PP      "                  see -q option \n");
-        PP      "                  dft: off\n");
-        PP      "-o file         : [O]utput sequences\n");
-        PP      "                  additionaly output sequence(s) that match into\n");     
-        PP      "                  'file' in fasta format\n"); 
-        PP      "                  dft: off\n");
-        PP      "-p              : no [Print] - don't printout hits\n");
-        PP      "                  when just counts are needed\n");
-        PP      "                  dft: off\n");
-        PP      "-q nn           : [Quorum]\n");
-        PP      "                  printout result if at least nn\n");
-        PP      "                  different patterns are found on the sequence\n");
-        PP      "                  (with -m : at least nn different <hits>)\n");
-        PP      "                  dft: # of patterns read\n");
-        PP      "-s              : no [Sort] - don't sort hits before printing\n");
-        PP      "                  usually hits are printed by increasing position\n");
-        PP      "                  this option will list them by pattern\n");
-        PP      "                  dft: off\n");
-        PP      "-t              : [T]est sequence\n");
-        PP      "                  additionnaly check if sequences are uppercase\n");
-        PP      "                  this is mostly used for testing\n");
-        PP      "                  dft: off\n");
-        PP      "-u              : [U]pper\n");
-        PP      "                  force lower->upper sequence conversion\n");
-        PP      "                  without this option lowercase symbols in sequence\n");
-        PP      "                  will not be considered to as matches\n");
-        PP      "                  dft: off\n");
-        PP      "-v              : [V]erbose\n");
-        PP      "                  just display a kind of progress clock on stderr\n");
-        PP      "                  (this is only useful if you redirect stdout)\n");
-        PP      "\n");
-        PP      "patfile  : pattern file  (see below)\n");
-        PP      "datafile : database file (see below)\n");
-        PP      "------------------------------------------\n");
-        PP      "pattern file format :\n");
-        PP      "  one pattern/line\n");
-        PP      "  format : <pattern> <space> #errors\n");
-        PP      "           <pattern> := pattern<symbol>\n");
-        PP      "                 or     !pattern<symbol>\n");
-        PP      "                 or      pattern<symbol>#\n");
-        PP      "                 or     !pattern<symbol>#\n");
-        PP      "           <symbol>  := <letter>\n");
-        PP      "                 or     [<letter>....<letter>]\n");
-        PP      "           <letter>  := uppercase letter (A-Z)\n");
-        PP      "           <number>  := a positive number indicates max number of mismatches\n");
-        PP      "                        a negative number indicates max number of mismatches or indels\n");
-        PP      "  # means that no error is allowed at this position\n");
-        PP      "  ! complement the <symbol>\n");
-        PP      " [...] means that all symbols within [] are allowed\n");
-        PP      " in addition IUPAC equivalences may be used as symbols\n");
-        PP      " with the -a option\n");
-        PP      "\n");
-        PP      "example: G[DE]S#[GIV]!HP![DE]#  1\n");
+        PP      "-a    : Salt concentration in M for Tm computation (default 0.05 M)\n\n");
+        PP      "-c    : Consider that the database sequences are [c]ircular\n\n");
+        PP      "-d    : [D]atabase : to match the expected format, the database\n");
+        PP      "        has to be formated first by the ecoPCRFormat.py program located.\n");
+        PP      "        in the tools directory.\n");
+        PP      "        ecoPCRFormat.py creates three file types :\n");
+        PP      "            .sdx : contains the sequences\n");
+        PP      "            .tdx : contains information concerning the taxonomy\n");
+        PP      "            .rdx : contains the taxonomy rank\n\n");
+        PP      "        ecoPCR needs all the file type. As a result, you have to write the\n");
+        PP      "        database radical without any extension. For example /ecoPCRDB/gbmam\n\n");
+        PP      "-D    : Keeps the specified number of nucleotides on each side of the in silico \n");
+        PP      "        amplified sequences (including the amplified DNA fragment plus the two target \n");
+        PP      "        sequences of the primers).\n\n");
+        PP      "-e    : [E]rror : max errors allowed by oligonucleotide (0 by default)\n\n");
+        PP      "-h    : [H]elp - print <this> help\n\n");
+        PP      "-i    : [I]gnore the given taxonomy id.\n");
+        PP      "        Taxonomy id are available using the ecofind program.\n");
+        PP      "        see its help typing ecofind -h for more information.\n\n");        
+        PP      "-k    : [K]ingdom mode : set the kingdom mode\n");
+        PP      "        super kingdom mode by default.\n\n");
+        PP      "-l    : minimum [L]ength : define the minimum amplication length. \n\n");
+        PP      "-L    : maximum [L]ength : define the maximum amplicationlength. \n\n");
+        PP      "-m    : Salt correction method for Tm computation (SANTALUCIA : 1\n");
+		PP      "        or OWCZARZY:2, default=1)\n\n");
+        PP      "-r    : [R]estricts the search to the given taxonomic id.\n");
+        PP      "        Taxonomy id are available using the ecofind program.\n");
+        PP      "        see its help typing ecofind -h for more information.\n\n");
         PP      "\n");
         PP      "------------------------------------------\n");
-        PP      "datafile contains one or more sequences in\n");
-        PP      "Fasta format, with *uppercase* symbols \n");
-        PP      "\n");
+        PP      "first argument : oligonucleotide for direct strand\n\n");
+        PP      "second argument : oligonucleotide for reverse strand\n\n");
         PP      "------------------------------------------\n");
-        PP      "note (1): the maximum number of patterns is %d\n", MAX_PATTERN);
-        PP      "\n");
-        PP      "note (2): the maximum length for one pattern is %d\n", MAX_PAT_LEN);
-        PP      "\n");
-        PP      "note (3): indels are still experimental and are :\n");
-        PP      "     not handled gracefully with the # syntax\n");
-        PP      "     and hits are not printed very nicely\n");
-        PP      "\n");
-        PP      "note (4): the IUPAC equivalences (-a option) are used\n");
-        PP      "     in pattern only *not* in sequence(s).\n");
-        PP      "     for instance GATN (with option -a dna) is equivalent to GAT[ACGT]\n");
-        PP      "     and will match GATA/GATC/GATG/GATC but will not match GATN\n");
-        PP      "     (nor NNNN) in sequence.\n");
+        PP      "Table result description : \n");
+        PP      "column 1 : accession number\n");
+        PP      "column 2 : sequence length\n");
+        PP      "column 3 : taxonomic id\n");
+        PP      "column 4 : rank\n");
+        PP      "column 5 : species taxonomic id\n");
+        PP      "column 6 : scientific name\n");
+        PP      "column 7 : genus taxonomic id\n");
+        PP      "column 8 : genus name\n");
+        PP      "column 9 : family taxonomic id\n");
+        PP      "column 10 : family name\n");
+        PP      "column 11 : super kingdom taxonomic id\n");
+        PP      "column 12 : super kingdom name\n");
+        PP      "column 13 : strand (direct or reverse)\n");
+        PP      "column 14 : first oligonucleotide\n");
+        PP      "column 15 : number of errors for the first strand\n");
+        PP      "column 16 : Tm for hybridization of primer 1 at this site\n");
+        PP      "column 17 : second oligonucleotide\n");
+        PP      "column 18 : number of errors for the second strand\n");
+        PP      "column 19 : Tm for hybridization of primer 1 at this site\n");
+        PP      "column 20 : amplification length\n");
+        PP      "column 21 : sequence\n");
+        PP      "column 22 : definition\n");
+        PP      "------------------------------------------\n");
+        PP		" http://www.grenoble.prabi.fr/trac/ecoPCR/\n");
+        PP      "------------------------------------------\n\n");        
         PP      "\n");
 
 }
@@ -121,10 +97,8 @@ static void PrintHelp()
 static void ExitUsage(stat)
         int stat;
 {
-        PP      "usage: apat [-a dna|prot] [-c] [-h] [-m] [-o file] [-p]\n");
-        PP      "             [-q nn] [-t] [-u] [-v]\n");
-        PP      "       patfile datafile\n");
-        PP      "type \"apat -h\" for help\n");
+        PP      "usage: ecoPCR [-d database] [-l value] [-L value] [-e value] [-r taxid] [-i taxid] [-k] oligo1 oligo2\n");
+        PP      "type \"ecoPCR -h\" for help\n");
 
         if (stat)
             exit(stat);
@@ -133,12 +107,15 @@ static void ExitUsage(stat)
 #undef  PP
 
 void printRepeat(ecoseq_t *seq,
+				 char* primer1, char* primer2,
+				 PNNParams tparm,
                  PatternPtr o1, PatternPtr o2,
                  char strand, 
                  char kingdom,
                  int32_t pos1, int32_t pos2,
                  int32_t err1, int32_t err2,
-                 ecotaxonomy_t *taxonomy)
+                 ecotaxonomy_t *taxonomy,
+                 int32_t delta)
 {
 	char     *AC;
 	int32_t  seqlength;
@@ -161,12 +138,18 @@ void printRepeat(ecoseq_t *seq,
 	
 	int32_t  error1;
 	int32_t  error2;
+	int32_t  ldelta,rdelta;
 	
 	char     *amplifia = NULL;
 	int32_t  amplength;
+	double   tm1,tm2;
+	double   tm=0;
 	
+	int32_t i;
+
 	AC = seq->AC;
 	seqlength = seq->SQ_length;
+
 	
 	main_taxon    = &taxonomy->taxons->taxon[seq->taxid];
 	taxid         = main_taxon->taxid;
@@ -221,44 +204,81 @@ void printRepeat(ecoseq_t *seq,
 			superkingdom_name  = "###";
 		}
 	
-	amplength = pos2-pos1;     
-	
-	amplifia = getSubSequence(seq->SQ,pos1,pos2);
-	
+
+
+	ldelta=(pos1 <= delta)?pos1:delta;
+
+
+
+	/*rdelta=((pos2+delta)>=seqlength)?seqlength-pos2-1:delta;        */
+	rdelta=((pos2+delta)>=seqlength)?seqlength-pos2:delta;
+
+	amplifia = getSubSequence(seq->SQ,pos1-ldelta,pos2+rdelta);
+	amplength= strlen(amplifia)-rdelta-ldelta;
 	
 	if (strand=='R')
 	{
-		ecoComplementSequence(amplifia);
-		strncpy(oligo1,amplifia,o2->patlen);
+
+	    ecoComplementSequence(amplifia);
+
+		strncpy(oligo1,amplifia + rdelta ,o2->patlen);
+
 		oligo1[o2->patlen]=0;
 		error1=err2;
-		
-		strncpy(oligo2,amplifia + amplength - o1->patlen,o1->patlen);
+
+		strncpy(oligo2, amplifia + rdelta + amplength - o1->patlen,o1->patlen);
 		oligo2[o1->patlen]=0;
 		error2=err1;
 		
-		amplifia+=o2->patlen;
+		if (delta==0)
+			amplifia+=o2->patlen;
+		else
+		{
+			delta=ldelta;
+			ldelta=rdelta+o2->patlen;
+			rdelta=delta+o1->patlen;
+		}
 	}
-	else
+	else /* strand == 'D' */
 	{
-		strncpy(oligo1,amplifia,o1->patlen);
+		strncpy(oligo1,amplifia+ldelta,o1->patlen);
 		oligo1[o1->patlen]=0;
 		error1=err1;
 		
-		strncpy(oligo2,amplifia + amplength - o2->patlen,o2->patlen);
+		strncpy(oligo2,amplifia + ldelta + amplength - o2->patlen,o2->patlen);
 		oligo2[o2->patlen]=0;
 		error2=err2;
 		
-		amplifia+=o1->patlen;
+		if (delta==0)
+			amplifia+=o1->patlen;
+		else
+		{
+			ldelta+=o1->patlen;
+			rdelta+=o2->patlen;
+		}
 		
 	}
 	
-
 	
 	ecoComplementSequence(oligo2);
-	amplifia[amplength - o2->patlen - o1->patlen]=0;
+	if(delta==0)
+		amplifia[amplength - o2->patlen - o1->patlen]=0;
+	else
+	{
+		delta=ldelta+rdelta+amplength-o1->patlen-o2->patlen;
+		for (i=0;i<ldelta;i++)
+			amplifia[i]|=32;
+		for (i=1;i<=rdelta;i++)
+			amplifia[delta-i]|=32;
+
+		amplifia[delta]=0;
+
+	}
 	
-	printf("%-15s | %9d | %8d | %-20s | %8d | %-30s | %8d | %-30s | %8d | %-30s | %8d | %-30s | %c | %-32s | %2d | %-32s | %2d | %5d | %s | %s\n",
+	tm1=nparam_CalcTwoTM(tparm,oligo1,primer1,o1->patlen) - 273.15;
+	tm2=nparam_CalcTwoTM(tparm,oligo2,primer2,o2->patlen) - 273.15;
+	tm = (tm1 < tm2) ? tm1:tm2;
+	printf("%-15s | %9d | %8d | %-20s | %8d | %-30s | %8d | %-30s | %8d | %-30s | %8d | %-30s | %c | %-32s | %2d | %5.2f | %-32s | %2d | %5.2f | %5d | %s | %s\n",
 			AC,
 			seqlength,
 			taxid,
@@ -274,12 +294,15 @@ void printRepeat(ecoseq_t *seq,
 			strand,
 			oligo1,
 			error1,
+			tm1,
 			oligo2,
 			error2,
-			amplength,
+			tm2,
+			amplength - o1->patlen - o2->patlen,
 			amplifia,
 			seq->DE
 		  );
+
 }
 
 int main(int argc, char **argv) 
@@ -300,13 +323,14 @@ int main(int argc, char **argv)
 	PatternPtr    o1c;
 	PatternPtr 	  o2c;
 	
+	int32_t       delta=0;
 	int32_t       lmin=0;
 	int32_t       lmax=0;
 	int32_t       error_max=0;
 	int32_t       errflag=0;
 	char          kingdom_mode=0;
 	
-	char          *prefix;
+	char          *prefix = NULL;
 	
 	int32_t       checkedSequence = 0;
 	int32_t       positiveSequence= 0;
@@ -330,43 +354,49 @@ int main(int argc, char **argv)
 	int32_t       erri;
 	int32_t		  errj;
 	
+	int32_t		  *restricted_taxid = NULL;
+	int32_t       *ignored_taxid	= NULL;
+	int32_t		  r=0;
+	int32_t		  g=0;	
+	int32_t		  circular=0;
 	
-    while ((carg = getopt(argc, argv, "h1:2:l:L:e:k")) != -1) {
+	int32_t		  saltmethod=SALT_METHOD_SANTALUCIA;
+	double		  salt=0.05;
+	CNNParams     tparm;
 
+    while ((carg = getopt(argc, argv, "hcd:l:L:e:i:r:km:a:tD:")) != -1) {
+    	
      switch (carg) {
                                 /* -------------------- */
-        case '1':               /* prenier oligo        */
+        case 'd':               /* database name        */
                                 /* -------------------- */
-           oligo1 = ECOMALLOC(strlen(optarg)+1,
-                              "Error on oligo 1 allocation");
-           strcpy(oligo1,optarg);
-           break;
-
-                                /* -------------------- */
-        case '2':               /* coocurence option    */
-                                /* -------------------- */
-           oligo2 = ECOMALLOC(strlen(optarg)+1,
-                              "Error on oligo 1 allocation");
-           strcpy(oligo2,optarg);
+           prefix = ECOMALLOC(strlen(optarg)+1,
+                              "Error on prefix allocation");
+           strcpy(prefix,optarg);
            break;
 
                                 /* -------------------- */
         case 'h':               /* help                 */
                                 /* -------------------- */
-            
            PrintHelp();
            exit(0);
            break;
 
-                                /* -------------------- */
-        case 'l':               /* lmin amplification   */
-                                /* -------------------- */
+           	   	   	   	   	    /* ------------------------- */
+        case 'D':               /* min amplification lenght  */
+        						/* ------------------------- */
+        	sscanf(optarg,"%d",&delta);
+        	break;
+
+                                /* ------------------------- */
+        case 'l':               /* min amplification lenght  */
+                                /* ------------------------- */
            sscanf(optarg,"%d",&lmin);
            break;
 
-                                /* -------------------- */
-        case 'L':               /* lmax amplification   */
-                                /* -------------------- */
+                                /* -------------------------- */
+        case 'L':               /* max amplification lenght   */
+                                /* -------------------------- */
           sscanf(optarg,"%d",&lmax);
           break;
 
@@ -374,46 +404,121 @@ int main(int argc, char **argv)
         case 'e':               /* error max            */
                                 /* -------------------- */
           sscanf(optarg,"%d",&error_max);
+          break;
+          		
+          						/* -------------------- */
+        case 'k':               /* set the kingdom mode */
+          kingdom_mode = 1;		/* -------------------- */
+          break;
+         
+         						/* ------------------------------------------ */
+        case 'r':               /* stores the restricting search taxonomic id */
+        						/* ------------------------------------------ */
+          restricted_taxid = ECOREALLOC(restricted_taxid,sizeof(int32_t)*(r+1),
+          									"Error on restricted_taxid reallocation");
+          sscanf(optarg,"%d",&restricted_taxid[r]);
+          r++;		
           break;
           
-        case 'k':               /* error max            */
-                                /* -------------------- */
-          kingdom_mode = 1;
+         						/* --------------------------------- */
+        case 'i':               /* stores the taxonomic id to ignore */
+        						/* --------------------------------- */
+		  ignored_taxid = ECOREALLOC(ignored_taxid,sizeof(int32_t)*(g+1),
+          									"Error on excluded_taxid reallocation");
+          sscanf(optarg,"%d",&ignored_taxid[g]);
+          g++;
           break;
           
                                 /* -------------------- */
-        case '?':               /* bad option           */
+        case 'c':               /* stores the taxonomic id to ignore */
+        						/* --------------------------------- */
+		  circular = 1;
+          break;
+          
+
+					/* --------------------------------- */
+		case 'm':               /* set salt method                   */
+					/* --------------------------------- */
+		sscanf(optarg,"%d",&(saltmethod));
+		break;
+
+					/* --------------------------------- */
+		case 'a':               /* set salt 	         */
+					/* --------------------------------- */
+		sscanf(optarg,"%lf",&(salt));
+		break;
+
+		case '?':               /* bad option           */
                                 /* -------------------- */
             errflag++;
    		}
 
 	}
 	
-	if ((argc -= optind) != 1)
-            errflag++;
-            
+	/**
+	 * check the path to the database is given as last argument
+	 */
+	if ((argc -= optind) == 2)
+	{
+		
+		oligo1 = ECOMALLOC(strlen(argv[optind])+1,
+                              "Error on oligo1 allocation");
+		strcpy(oligo1,argv[optind]);
+		optind++;
+		oligo2 = ECOMALLOC(strlen(argv[optind])+1,
+                              "Error on oligo1 allocation");
+		strcpy(oligo2,argv[optind]);
+		
+		if (circular)
+		{
+			circular = strlen(oligo1);
+			if (strlen(oligo2)>(size_t)circular)
+				circular = strlen(oligo2);
+		}
+	}
+	else
+		errflag++;
+	
+	if (prefix == NULL)
+	{
+		prefix = getenv("ECOPCRDB");
+		if (prefix == NULL)
+			errflag++;
+	}
+	
+	nparam_InitParams(&tparm,DEF_CONC_PRIMERS,
+				 	  DEF_CONC_PRIMERS,
+					  salt,
+					  saltmethod);
+	                  
     if (!oligo1 || !oligo2)
     		errflag++;
 	
 	if (errflag)
 		ExitUsage(errflag);
 		
-	prefix = argv[optind];
-	
 	o1 = buildPattern(oligo1,error_max);
 	o2 = buildPattern(oligo2,error_max);
 	
 	o1c = complementPattern(o1);
 	o2c = complementPattern(o2);
 	
-	
-	
+	printf("#@ecopcr-v2\n");
 	printf("#\n");
 	printf("# ecoPCR version %s\n",VERSION);
 	printf("# direct  strand oligo1 : %-32s ; oligo2c : %32s\n", o1->cpat,o2c->cpat);
 	printf("# reverse strand oligo2 : %-32s ; oligo1c : %32s\n", o2->cpat,o1c->cpat);
 	printf("# max error count by oligonucleotide : %d\n",error_max);
 	
+	double tm,tm1,tm2;
+
+	tm1=nparam_CalcSelfTM(&tparm,o1->cpat,o1->patlen) - 273.15;
+	tm2=nparam_CalcSelfTM(&tparm,o2->cpat,o2->patlen) - 273.15;
+	tm = (tm1 < tm2) ? tm1:tm2;
+
+	printf("# optimal Tm for primers 1 : %5.2f\n",tm1);
+	printf("# optimal Tm for primers 2 : %5.2f\n",tm2);
+
 	printf("# database : %s\n",prefix);
 	if (lmin && lmax)
 		printf("# amplifiat length between [%d,%d] bp\n",lmin,lmax);
@@ -425,104 +530,166 @@ int main(int argc, char **argv)
 		printf("# output in kingdom mode\n");
 	else
 		printf("# output in superkingdom mode\n");
+	if (circular)
+		printf("# DB sequences are considered as circular\n");
+	else
+		printf("# DB sequences are considered as linear\n");
 	printf("#\n");
 
-	taxonomy = read_taxonomy(prefix);
-	
+	taxonomy = read_taxonomy(prefix,0);
+
 	seq = ecoseq_iterator(prefix);
-	
-	
+		
 	checkedSequence = 0;
 	positiveSequence= 0;
 	amplifiatCount  = 0;
 	
 	while(seq)
-	{
+	{	
 		checkedSequence++;
-
-		scname = taxonomy->taxons->taxon[seq->taxid].name;
-		strncpy(head,seq->SQ,10);
-		head[10]=0;
-		strncpy(tail,seq->SQ+seq->SQ_length-10,10);
-		tail[10]=0;
-
+		/**
+		* check if current sequence should be included
+		**/
+		if ( (r == 0) || 
+		     (eco_is_taxid_included(taxonomy, 
+		                            restricted_taxid, 
+		                            r, 
+		                            taxonomy->taxons->taxon[seq->taxid].taxid)
+		     ) 
+		   )
+		     if ((g == 0) || 
+		         !(eco_is_taxid_included(taxonomy, 
+		                                 ignored_taxid, 
+		                                 g, 
+		                                 taxonomy->taxons->taxon[seq->taxid].taxid)
+		          )
+		        )
+		     {
 		
-		apatseq=ecoseq2apatseq(seq,apatseq);
+				scname = taxonomy->taxons->taxon[seq->taxid].name;
+				strncpy(head,seq->SQ,10);
+				head[10]=0;
+				strncpy(tail,seq->SQ+seq->SQ_length-10,10);
+				tail[10]=0;
 		
-		o1Hits = ManberAll(apatseq,o1,0,0,apatseq->seqlen);
-		o2cHits= 0;
-		
-		
-		if (o1Hits)
-		{
-			stktmp = apatseq->hitpos[0];
-			begin = stktmp->val[0] + o1->patlen;
-			
-			if (lmax)
-				length= stktmp->val[stktmp->top-1] + o1->patlen - begin + lmax + o2->patlen;
-			else
-				length= apatseq->seqlen - begin;
+				apatseq=ecoseq2apatseq(seq,apatseq,circular);
 				
-			o2cHits = ManberAll(apatseq,o2c,1,begin,length);
-
-			if (o2cHits)
-				for (i=0; i < o1Hits;i++)
-				{
-					posi = apatseq->hitpos[0]->val[i];
-					erri = apatseq->hiterr[0]->val[i];
-					for (j=0; j < o2cHits; j++)
-					{
-						posj  =apatseq->hitpos[1]->val[j] + o2c->patlen;
-						errj  =apatseq->hiterr[1]->val[j];
-						length=posj - posi + 1  - o1->patlen - o2->patlen;
-						
-						if ((!lmin || (length >= lmin)) &&
-						    (!lmax || (length <= lmax)))
-						    printRepeat(seq,o1,o2c,'D',kingdom_mode,posi,posj,erri,errj,taxonomy);
-							//printf("%s\tD\t%s...%s (%d)\t%d\t%d\t%d\t%d\t%s\n",seq->AC,head,tail,seq->SQ_length,o1Hits,o2cHits,posi,posj,scname);
-					}
-				}
-		}
-			
-		o2Hits = ManberAll(apatseq,o2,2,0,apatseq->seqlen);
-		o1cHits= 0;
-		if (o2Hits)
-		{
-			stktmp = apatseq->hitpos[2];
-			begin = stktmp->val[0] + o2->patlen;
-			
-			if (lmax)
-				length= stktmp->val[stktmp->top-1] + o2->patlen - begin + lmax + o1->patlen;
-			else
-				length= apatseq->seqlen - begin;
+				o1Hits = ManberAll(apatseq,o1,0,0,apatseq->seqlen+apatseq->circular);
+				o2cHits= 0;
 				
-			o1cHits = ManberAll(apatseq,o1c,3,begin,length);
-			
-			if (o1cHits)
-				for (i=0; i < o2Hits;i++)
+				if (o1Hits)
 				{
-					posi = apatseq->hitpos[2]->val[i];
-					erri = apatseq->hiterr[2]->val[i];
-					for (j=0; j < o1cHits; j++)
+					stktmp = apatseq->hitpos[0];
+					begin = stktmp->val[0] + o1->patlen;
+					
+					if (lmax)
+						length= stktmp->val[stktmp->top-1] + o1->patlen - begin + lmax + o2->patlen;
+					else
+						length= apatseq->seqlen - begin;
+					
+					if (circular)
 					{
-						posj=apatseq->hitpos[3]->val[j] + o1c->patlen;
-						errj=apatseq->hiterr[3]->val[j];
-						length=posj - posi + 1 - o1->patlen - o2->patlen;
-						
-						if ((!lmin || (length >= lmin)) &&
-						    (!lmax || (length <= lmax)))
-						    printRepeat(seq,o2,o1c,'R',kingdom_mode,posi,posj,erri,errj,taxonomy);
-							//printf("%s\tR\t%s...%s (%d)\t%d\t%d\t%d\t%d\t%s\n",seq->AC,head,tail,seq->SQ_length,o2Hits,o1cHits,posi,posj,scname);
-					}
+						begin = 0;
+						length=apatseq->seqlen+circular;
+					}	
+					o2cHits = ManberAll(apatseq,o2c,1,begin,length);
+		
+					if (o2cHits)
+						for (i=0; i < o1Hits;i++)
+						{
+							posi = apatseq->hitpos[0]->val[i];
+														
+							if (posi < apatseq->seqlen)
+							{
+								erri = apatseq->hiterr[0]->val[i];
+								for (j=0; j < o2cHits; j++)
+								{
+									posj  =apatseq->hitpos[1]->val[j];
+									
+									if (posj < apatseq->seqlen)
+									{
+										posj+=o2c->patlen;
+										// printf("coucou %d %d %d\n",posi,posj,apatseq->seqlen);
+										errj  =apatseq->hiterr[1]->val[j];
+										length = 0;
+										if (posj > posi)
+											length=posj - posi  - o1->patlen - o2->patlen; 
+										if (posj < posi)
+											length= posj + apatseq->seqlen - posi - o1->patlen - o2->patlen;
+										if (length &&
+											(!lmin || (length >= lmin)) &&
+										    (!lmax || (length <= lmax)))
+										    printRepeat(seq,oligo1,oligo2,&tparm,o1,o2c,'D',kingdom_mode,posi,posj,erri,errj,taxonomy,delta);
+											//printf("%s\tD\t%s...%s (%d)\t%d\t%d\t%d\t%d\t%s\n",seq->AC,head,tail,seq->SQ_length,o1Hits,o2cHits,posi,posj,scname);
+	
+									}
+								}
+							}
+						}
 				}
-		}	
-		
-		
+					
+				o2Hits = ManberAll(apatseq,o2,2,0,apatseq->seqlen);
+				o1cHits= 0;
+				if (o2Hits)
+				{
+					stktmp = apatseq->hitpos[2];
+					begin = stktmp->val[0] + o2->patlen;
+					
+					if (lmax)
+						length= stktmp->val[stktmp->top-1] + o2->patlen - begin + lmax + o1->patlen;
+					else
+						length= apatseq->seqlen - begin;
+						
+					if (circular)
+					{
+						begin = 0;
+						length=apatseq->seqlen+circular;
+					}	
+
+					o1cHits = ManberAll(apatseq,o1c,3,begin,length);
+					
+					if (o1cHits)
+						for (i=0; i < o2Hits;i++)
+						{
+							posi = apatseq->hitpos[2]->val[i];
+
+							if (posi < apatseq->seqlen)
+							{
+								erri = apatseq->hiterr[2]->val[i];
+								for (j=0; j < o1cHits; j++)
+								{
+									posj=apatseq->hitpos[3]->val[j];
+									if (posj < apatseq->seqlen)
+									{
+										posj+=o1c->patlen;
+										errj=apatseq->hiterr[3]->val[j];
+
+										length = 0;
+										if (posj > posi)
+											length=posj - posi + 1  - o2->patlen - o1->patlen; /* - o1->patlen : suppress by <EC> */
+										if (posj < posi)
+											length= posj + apatseq->seqlen - posi - o1->patlen - o2->patlen;
+
+										if (length &&
+											(!lmin || (length >= lmin)) &&
+										    (!lmax || (length <= lmax)))
+										    printRepeat(seq,oligo1,oligo2,&tparm,o2,o1c,'R',kingdom_mode,posi,posj,erri,errj,taxonomy,delta);
+											//printf("%s\tR\t%s...%s (%d)\t%d\t%d\t%d\t%d\t%s\n",seq->AC,head,tail,seq->SQ_length,o2Hits,o1cHits,posi,posj,scname);								
+									}
+								}
+							}
+						}
+				}	
+				
+		} /* End of taxonomic selection */
 		
 		delete_ecoseq(seq);
 		
 		seq = ecoseq_iterator(NULL);
 	}
+	
+	ECOFREE(restricted_taxid, "Error: could not free restricted_taxid\n");
+	ECOFREE(ignored_taxid, "Error: could not free excluded_taxid\n");
 		
 	return 0;
 }

src/global.mk

@@ -0,0 +1,18 @@
+MACHINE=MAC_OS_X
+LIBPATH= -Llibapat -LlibecoPCR -Llibthermo
+MAKEDEPEND = gcc -D$(MACHINE) -M $(CPPFLAGS) -o $*.d $<
+
+CC=gcc
+CFLAGS= -W -Wall -O2 -g
+
+default: all
+
+%.o: %.c
+	$(CC) -D$(MACHINE) $(CFLAGS) -c -o $@ $<
+
+%.P : %.c
+	$(MAKEDEPEND)
+	@sed 's/\($*\)\.o[ :]*/\1.o $@ : /g' < $*.d > $@; \
+	rm -f $*.d; [ -s $@ ] || rm -f $@
+
+include $(SRCS:.c=.P)

src/libapat/Makefile

@@ -0,0 +1,24 @@
+
+SOURCES = apat_parse.c \
+         apat_search.c \
+         libstki.c
+         
+SRCS=$(SOURCES)
+
+         
+OBJECTS= $(patsubst %.c,%.o,$(SOURCES))
+
+LIBFILE= libapat.a
+RANLIB=ranlib
+
+
+include ../global.mk
+
+all: $(LIBFILE)
+
+clean:
+	rm -rf $(OBJECTS) $(LIBFILE)
+
+$(LIBFILE): $(OBJECTS)
+	ar -cr $@ $?
+	$(RANLIB) $@

src/libapat/apat.h

@@ -103,6 +103,7 @@ typedef struct {                        /* sequence             */
     Int32     seqlen;                   /* sequence length      */
     Int32     seqsiz;                   /* sequence buffer size */
     Int32     datsiz;                   /* data buffer size     */
+    Int32     circular;
     UInt8     *data;                    /* data buffer          */
     char      *cseq;                    /* sequence buffer      */
     StackiPtr hitpos[MAX_PATTERN];      /* stack of hit pos.    */

src/libapat/apat_search.c

@@ -80,14 +80,14 @@ int CreateS(Pattern *ppat, Int32 lalpha)
 /* -------------------------------------------- */
 Int32 ManberNoErr(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
 {
-        Int32     pos;
+        UInt32     pos;
         UInt32    smask, r;
         UInt8     *data;
         StackiPtr *stkpos, *stkerr;
         UInt32    end;
         
         end = begin + length;
-        end = (end <= pseq->seqlen) ? end:pseq->seqlen;
+        end = (end <= (size_t)(pseq->seqlen+pseq->circular)) ? end:(size_t)(pseq->seqlen+pseq->circular);
         
 
                                         /* create local masks   */
@@ -127,7 +127,7 @@ Int32 ManberNoErr(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
 Int32 ManberSub(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
 {
         int       e, emax, found;
-        Int32     pos;
+        UInt32     pos;
         UInt32    smask, cmask, sindx;
         UInt32    *pr, r[2 * MAX_PAT_ERR + 2];
         UInt8     *data;
@@ -135,7 +135,7 @@ Int32 ManberSub(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
         UInt32    end;
         
         end = begin + length;
-        end = (end <= pseq->seqlen) ? end:pseq->seqlen;
+        end = (end <= (size_t)(pseq->seqlen+pseq->circular)) ? end:(size_t)(pseq->seqlen+pseq->circular);
 
                                         /* create local masks   */
         emax = ppat->maxerr;
@@ -193,7 +193,7 @@ Int32 ManberSub(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
 Int32 ManberIndel(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
 {
         int       e, emax, found;
-        Int32     pos;
+        UInt32     pos;
         UInt32    smask, cmask, sindx;
         UInt32    *pr, r[2 * MAX_PAT_ERR + 2];
         UInt8     *data;
@@ -201,7 +201,7 @@ Int32 ManberIndel(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
         UInt32    end;
         
         end = begin + length;
-        end = (end <= pseq->seqlen) ? end:pseq->seqlen;
+        end = (end <= (size_t)(pseq->seqlen+pseq->circular)) ? end:(size_t)(pseq->seqlen+pseq->circular);
 
                                         /* create local masks   */
         emax = ppat->maxerr;

src/libecoPCR/Makefile

@@ -0,0 +1,31 @@
+
+SOURCES = ecoapat.c \
+         ecodna.c \
+         ecoError.c \
+         ecoIOUtils.c \
+         ecoMalloc.c \
+         ecorank.c \
+         ecoseq.c \
+         ecotax.c \
+         ecofilter.c \
+         econame.c     
+
+SRCS=$(SOURCES)
+         
+OBJECTS= $(patsubst %.c,%.o,$(SOURCES))
+
+LIBFILE= libecoPCR.a
+RANLIB= ranlib
+
+
+include ../global.mk
+
+
+all: $(LIBFILE)
+
+clean:
+	rm -rf $(OBJECTS) $(LIBFILE)
+
+$(LIBFILE): $(OBJECTS)
+	ar -cr $@ $?
+	$(RANLIB) $@

src/libecoPCR/ecoError.c

@@ -2,7 +2,15 @@
 #include <stdio.h>
 #include <stdlib.h>
 
-
+/*
+ * print the message given as argument and exit the program
+ * @param error		error number	
+ * @param message 	the text explaining what's going on
+ * @param filename	the file source where the program failed
+ * @param linenumber	the line where it has failed
+ * filename and linenumber are written at pre-processing 
+ * time by a macro
+ */
 void ecoError(int32_t error,
               const char* message,
               const char * filename,

src/libecoPCR/ecoIOUtils.c

@@ -16,20 +16,19 @@ int32_t is_big_endian()
 
 
 
-
-
-
 int32_t swap_int32_t(int32_t i)
 {
 	return SWAPINT32(i);
 }
 
 
-
-
-
-
-
+/**
+ * Read part of the file
+ * @param	*f	the database
+ * @param	recordSize the size to be read
+ * 
+ * @return	buffer
+ */
 void *read_ecorecord(FILE *f,int32_t *recordSize)
 {
 	static void *buffer    =NULL;
@@ -79,10 +78,14 @@ void *read_ecorecord(FILE *f,int32_t *recordSize)
 
 
 
-
-
-
-
+/**
+ * Open the database and check it's readable
+ * @param 	filename 		name of the database (.sdx, .rdx, .tbx)
+ * @param 	sequencecount	buffer - pointer to variable storing the number of occurence    
+ * @param 	abort_on_open_error		 	boolean to define the behaviour in case of error 
+ * 										while opening the database
+ * @return 	FILE type
+ **/
 FILE *open_ecorecorddb(const char *filename,
                        int32_t    *sequencecount,
                        int32_t    abort_on_open_error)

src/libecoPCR/ecoPCR.h

@@ -56,11 +56,11 @@ typedef struct {
 	
 } ecotxformat_t;
 
-typedef struct {
-	int32_t  taxid;
-	int32_t  rank;
-	int32_t  parent;
-	char     *name;
+typedef struct ecotxnode {
+	int32_t           taxid;
+	int32_t           rank;
+	struct ecotxnode  *parent;
+	char              *name;
 } ecotx_t;
 
 typedef struct {
@@ -80,12 +80,42 @@ typedef struct {
 	char*   label[1];
 } ecorankidx_t;
 
+/*
+ * 
+ * Taxonomy name types
+ * 
+ */
+
 typedef struct {
+ 	int32_t is_scientificname;
+	int32_t  namelength;
+	int32_t  classlength;
+	int32_t  taxid;
+	char     names[1];	
+} econameformat_t;
+ 
+ 
+ typedef struct {
+ 	char 	*name;
+ 	char 	*classname;
+ 	int32_t is_scientificname;
+ 	struct ecotxnode  *taxon;
+} econame_t;
+
+ 
+typedef struct {
+	int32_t count;
+	econame_t   names[1];
+} econameidx_t;
+
+
+ typedef struct {
 	ecorankidx_t *ranks;
+	econameidx_t *names;
 	ecotxidx_t   *taxons;
 } ecotaxonomy_t;
 
-
+ 
 /*****************************************************
  * 
  *  Function declarations
@@ -175,6 +205,9 @@ ecoseq_t         *readnext_ecoseq(FILE *);
 
 ecorankidx_t     *read_rankidx(const char *filename);
 
+econameidx_t     *read_nameidx(const char *filename,ecotaxonomy_t *taxonomy);
+
+
 
 	/**
 	 * Read taxonomy data as formated by the ecoPCRFormat.py script.
@@ -187,10 +220,13 @@ ecorankidx_t     *read_rankidx(const char *filename);
 	 * @return pointer to a taxonomy index structure
 	 */
  
-ecotxidx_t       *read_taxonomyidx(const char *filename);
+ecotxidx_t       *read_taxonomyidx(const char *filename,const char *filename2);
 
-ecotaxonomy_t    *read_taxonomy(const char *prefix);
+ecotaxonomy_t    *read_taxonomy(const char *prefix,int32_t readAlternativeName);
 
+ecotx_t *eco_findtaxonbytaxid(ecotaxonomy_t *taxonomy, int32_t taxid);
+
+int eco_isundertaxon(ecotx_t *taxon, int other_taxid);
 
 ecoseq_t *ecoseq_iterator(const char *prefix);
 
@@ -215,7 +251,7 @@ int32_t  delete_apatseq(SeqPtr pseq);
 PatternPtr buildPattern(const char *pat, int32_t error_max);
 PatternPtr complementPattern(PatternPtr pat);
 
-SeqPtr ecoseq2apatseq(ecoseq_t *in,SeqPtr out);
+SeqPtr ecoseq2apatseq(ecoseq_t *in,SeqPtr out,int32_t circular);
 
 char *ecoComplementPattern(char *nucAcSeq);
 char *ecoComplementSequence(char *nucAcSeq);
@@ -227,4 +263,7 @@ ecotx_t *eco_getfamily(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
 ecotx_t *eco_getkingdom(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
 ecotx_t *eco_getsuperkingdom(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
 
+int eco_is_taxid_ignored(int32_t *ignored_taxid, int32_t tab_len, int32_t taxid);
+int eco_is_taxid_included(ecotaxonomy_t *taxonomy, int32_t *included_taxid, int32_t tab_len, int32_t taxid);
+
 #endif /*ECOPCR_H_*/

src/libecoPCR/ecoapat.c

@@ -50,10 +50,13 @@ void EncodeSequence(SeqPtr seq)
 
         while (*cseq) {
 
-            *data++ = (IS_UPPER(*cseq) ? *cseq - 'A' : 0x0);
-
+            *data = (IS_UPPER(*cseq) ? *cseq - 'A' : 0x0);
+            data++;
             cseq++;
         }
+        
+        for (i=0,cseq=seq->cseq;i < seq->circular; i++,cseq++,data++)
+            *data = (IS_UPPER(*cseq) ? *cseq - 'A' : 0x0);
 
         for (i = 0 ; i < MAX_PATTERN ; i++)
             seq->hitpos[i]->top = seq->hiterr[i]->top = 0;
@@ -63,7 +66,7 @@ void EncodeSequence(SeqPtr seq)
 #undef IS_UPPER
 
 
-SeqPtr ecoseq2apatseq(ecoseq_t *in,SeqPtr out)
+SeqPtr ecoseq2apatseq(ecoseq_t *in,SeqPtr out,int32_t circular)
 {
         int    i;
 
@@ -83,20 +86,22 @@ SeqPtr ecoseq2apatseq(ecoseq_t *in,SeqPtr out)
 	        }
 		}
 
+		
 		out->name    = in->AC;
 		out->seqsiz = out->seqlen = in->SQ_length;
-
+		out->circular = circular;
+		
 		if (!out->data)
 		{
-			out->data = ECOMALLOC(out->seqlen *sizeof(UInt8),
+			out->data = ECOMALLOC((out->seqlen+circular) *sizeof(UInt8),
 		    	     			  "Error in Allocation of a new Seq data member");    
-		   	out->datsiz=  out->seqlen;
+		   	out->datsiz=  out->seqlen+circular;
 		}
-		else if (out->seqlen >= out->datsiz)
+		else if ((out->seqlen +circular) >= out->datsiz)
 		{
-			out->data = ECOREALLOC(out->data,out->seqlen,
+			out->data = ECOREALLOC(out->data,(out->seqlen+circular),
 			                      "Error during Seq data buffer realloc");
-		   	out->datsiz=  out->seqlen;			                      
+		   	out->datsiz=  out->seqlen+circular;			                      
 		}
 
 		out->cseq = in->SQ;
@@ -191,4 +196,4 @@ PatternPtr complementPattern(PatternPtr pat)
 	
 	return pattern;
 		
-}
+}

src/libecoPCR/ecodna.c

@@ -104,27 +104,52 @@ char *ecoComplementSequence(char *nucAcSeq)
 
 
 char *getSubSequence(char* nucAcSeq,int32_t begin,int32_t end)
+/*
+   extract subsequence from nucAcSeq [begin,end[
+*/
 {
 	static char *buffer  = NULL;
 	static int32_t buffSize= 0;
 	int32_t length;
 	
-	length = end - begin;
-	
-	if (length >= buffSize)
+	if (begin < end)
 	{
-		buffSize = length+1;
-		if (buffer)
-			buffer=ECOREALLOC(buffer,buffSize,
-					   	      "Error in reallocating sub sequence buffer");
-		else
-			buffer=ECOMALLOC(buffSize,
-			          		 "Error in allocating sub sequence buffer");
-			
+		length = end - begin;
+		
+		if (length >= buffSize)
+		{
+			buffSize = length+1;
+			if (buffer)
+				buffer=ECOREALLOC(buffer,buffSize,
+						   	      "Error in reallocating sub sequence buffer");
+			else
+				buffer=ECOMALLOC(buffSize,
+				          		 "Error in allocating sub sequence buffer");
+				
+		}
+		
+		strncpy(buffer,nucAcSeq + begin,length);
+		buffer[length]=0;
+	}
+	else
+	{
+		length = end + strlen(nucAcSeq) - begin;
+		
+		if (length >= buffSize)
+		{
+			buffSize = length+1;
+			if (buffer)
+				buffer=ECOREALLOC(buffer,buffSize,
+						   	      "Error in reallocating sub sequence buffer");
+			else
+				buffer=ECOMALLOC(buffSize,
+				          		 "Error in allocating sub sequence buffer");
+				
+		}
+		strncpy(buffer,nucAcSeq+begin,length - end);
+		strncpy(buffer+(length-end),nucAcSeq ,end);
+		buffer[length]=0;
 	}
-	
-	strncpy(buffer,nucAcSeq + begin,length);
-	buffer[length]=0;
 	
 	return buffer;
 }

src/libecoPCR/ecofilter.c

@@ -0,0 +1,20 @@
+#include "ecoPCR.h"
+
+int eco_is_taxid_included(	ecotaxonomy_t *taxonomy, 
+							int32_t *restricted_taxid, 
+							int32_t tab_len, 
+							int32_t taxid)
+{
+	int i;
+	ecotx_t *taxon;
+	
+	taxon = eco_findtaxonbytaxid(taxonomy, taxid);
+	
+	if (taxon)
+		for (i=0; i < tab_len; i++)
+			if ( (taxon->taxid == restricted_taxid[i]) ||
+				 (eco_isundertaxon(taxon, restricted_taxid[i])) )
+				return 1;
+	
+	return 0;
+}

src/libecoPCR/econame.c

@@ -0,0 +1,61 @@
+#include "ecoPCR.h"
+#include <string.h>
+#include <stdlib.h>
+
+static econame_t *readnext_econame(FILE *f,econame_t *name,ecotaxonomy_t *taxonomy);
+
+econameidx_t *read_nameidx(const char *filename,ecotaxonomy_t *taxonomy)
+{
+
+	int32_t      		count;
+	FILE         		*f;
+	econameidx_t		*indexname;
+	int32_t      		i;
+	
+	f = open_ecorecorddb(filename,&count,1);
+	
+	indexname = (econameidx_t*) ECOMALLOC(sizeof(econameidx_t) + sizeof(econame_t) * (count-1),"Allocate names");
+	
+	indexname->count=count;
+	                                    
+	for (i=0; i < count; i++){
+		readnext_econame(f,(indexname->names)+i,taxonomy);
+	}
+
+	return indexname;
+}
+
+econame_t *readnext_econame(FILE *f,econame_t *name,ecotaxonomy_t *taxonomy)
+{
+	
+	econameformat_t *raw;
+	int32_t  rs;
+	
+	raw = read_ecorecord(f,&rs);
+	
+	if (!raw)
+		return NULL;
+
+	if (is_big_endian())
+	{
+		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_scientificname=raw->is_scientificname;
+	
+	name->name   	= ECOMALLOC((raw->namelength+1) * sizeof(char),"Allocate name");
+	strncpy(name->name,raw->names,raw->namelength);
+	name->name[raw->namelength]=0;
+	
+	name->classname = ECOMALLOC((raw->classlength+1) * sizeof(char),"Allocate classname");
+	strncpy(name->classname,(raw->names+raw->namelength),raw->classlength);
+	name->classname[raw->classlength]=0;
+	
+	name->taxon = taxonomy->taxons->taxon + raw->taxid;
+
+	return name;
+}
+

src/libecoPCR/ecoseq.c

@@ -4,6 +4,7 @@
 #include <zlib.h>
 #include <string.h>
 #include <stdio.h>
+#include <ctype.h>
 
 static FILE *open_seqfile(const char *prefix,int32_t index);
 
@@ -11,32 +12,32 @@ static FILE *open_seqfile(const char *prefix,int32_t index);
 ecoseq_t *new_ecoseq()
 {
 	void *tmp;
-	
+
 	tmp = ECOMALLOC(sizeof(ecoseq_t),"Allocate new ecoseq structure");
-	
+
 	return tmp;
 }
 
 int32_t delete_ecoseq(ecoseq_t * seq)
 {
-	
+
 	if (seq)
 	{
 		if (seq->AC)
 			ECOFREE(seq->AC,"Free sequence AC");
-			
+
 		if (seq->DE)
 			ECOFREE(seq->DE,"Free sequence DE");
-			
+
 		if (seq->SQ)
 			ECOFREE(seq->SQ,"Free sequence SQ");
-			
+
 		ECOFREE(seq,"Free sequence structure");
-		
+
 		return 0;
-			
+
 	}
-	
+
 	return 1;
 }
 
@@ -49,9 +50,9 @@ ecoseq_t *new_ecoseq_with_data( char *AC,
 	ecoseq_t *tmp;
 	int32_t lstr;
 	tmp = new_ecoseq();
-	
+
 	tmp->taxid=taxid_idx;
-	
+
 	if (AC)
 		{
 			lstr =strlen(AC);
@@ -79,7 +80,9 @@ ecoseq_t *new_ecoseq_with_data( char *AC,
 
 }
 
-
+/**
+ * ?? used ??
+ **/
 FILE *open_ecoseqdb(const char *filename,
                     int32_t    *sequencecount)
 {
@@ -95,12 +98,14 @@ ecoseq_t *readnext_ecoseq(FILE *f)
 	int32_t  comp_status;
 	unsigned long int seqlength;
 	int32_t  rs;
-	
+	char *c;
+	int32_t i;
+
 	raw = read_ecorecord(f,&rs);
-	
+
 	if (!raw)
 		return NULL;
-		
+
 	if (is_big_endian())
 	{
 		raw->CSQ_length = swap_int32_t(raw->CSQ_length);
@@ -108,38 +113,49 @@ ecoseq_t *readnext_ecoseq(FILE *f)
 		raw->SQ_length  = swap_int32_t(raw->SQ_length);
 		raw->taxid      = swap_int32_t(raw->taxid);
 	}
-	
+
 	seq = new_ecoseq();
-	
+
 	seq->taxid = raw->taxid;
-	
+
     seq->AC    = ECOMALLOC(strlen(raw->AC) +1,
                            "Allocate Sequence Accesion number");
     strncpy(seq->AC,raw->AC,strlen(raw->AC));
 
-                           
+
     seq->DE    = ECOMALLOC(raw->DE_length+1,
                            "Allocate Sequence definition");
     strncpy(seq->DE,raw->data,raw->DE_length);
-    
+
 	seqlength = seq->SQ_length = raw->SQ_length;
-    
+
     compressed = raw->data + raw->DE_length;
 
     seq->SQ = ECOMALLOC(seqlength+1,
                         "Allocate sequence buffer");
-                        
+
     comp_status = uncompress((unsigned char*)seq->SQ,
                              &seqlength,
                              (unsigned char*)compressed,
                              raw->CSQ_length);
-    
+
     if (comp_status != Z_OK)
     	ECOERROR(ECO_IO_ERROR,"I cannot uncompress sequence data");
-    
+
+    for (c=seq->SQ,i=0;i<seqlength;c++,i++)
+    	*c=toupper(*c);
+
+
 	return seq;
 }
 
+/**
+ * Open the sequences database (.sdx file)
+ * @param	prefix	name of the database (radical without extension)
+ * @param	index 	integer
+ *
+ * @return	file object
+ */
 FILE *open_seqfile(const char *prefix,int32_t index)
 {
 	char           filename_buffer[1024];
@@ -152,22 +168,22 @@ FILE *open_seqfile(const char *prefix,int32_t index)
 	                           "%s_%03d.sdx",
 	                           prefix,
 	                           index);
-	                           
-			fprintf(stderr,"Coucou %s\n",filename_buffer);
-	                           
+
+		//	fprintf(stderr,"# Coucou %s\n",filename_buffer);
+
 
 	if (filename_length >= 1024)
 		ECOERROR(ECO_ASSERT_ERROR,"file name is too long");
 
 	filename_buffer[filename_length]=0;
-		
+
 	input=open_ecorecorddb(filename_buffer,&seqcount,0);
-	
+
 	if (input)
-		fprintf(stderr,"Reading file %s containing %d sequences...\n",
+		fprintf(stderr,"# Reading file %s containing %d sequences...\n",
 				filename_buffer,
 				seqcount);
-				
+
 	return input;
 }
 
@@ -177,38 +193,38 @@ ecoseq_t *ecoseq_iterator(const char *prefix)
 	static int32_t current_file_idx = 1;
 	static char    current_prefix[1024];
 	ecoseq_t       *seq;
-	
+
 	if (prefix)
 	{
 		current_file_idx = 1;
 
 		if (current_seq_file)
 			fclose(current_seq_file);
-			
+
 		strncpy(current_prefix,prefix,1023);
 		current_prefix[1024]=0;
-		
+
 		current_seq_file = open_seqfile(current_prefix,
 		 							    current_file_idx);
-		
+
 		if (!current_seq_file)
 			return NULL;
-			
+
 	}
-	
+
 	seq = readnext_ecoseq(current_seq_file);
-	
+
 	if (!seq && feof(current_seq_file))
 	{
 		current_file_idx++;
 		fclose(current_seq_file);
 		current_seq_file = open_seqfile(current_prefix,
 		 							    current_file_idx);
-		 							    
-		
+
+
 		if (current_seq_file)
 			seq = readnext_ecoseq(current_seq_file);
 	}
-	
+
 	return seq;
-}
+}

src/libecoPCR/ecotax.c

@@ -5,27 +5,50 @@
 
 static ecotx_t *readnext_ecotaxon(FILE *f,ecotx_t *taxon);
 
-
-ecotxidx_t     *read_taxonomyidx(const char *filename)
+ /** 
+ * Open the taxonomy database 
+ * @param	pointer to the database (.tdx file) 
+ * @return	a ecotxidx_t structure 
+ */
+ecotxidx_t     *read_taxonomyidx(const char *filename,const char *filename2)
 {
 	int32_t      count;
+	int32_t      count2;
 	FILE         *f;
+	FILE         *f2;
 	ecotxidx_t *index;
 	int32_t      i;
 	
-	f = open_ecorecorddb(filename,&count,1);
+	f  = open_ecorecorddb(filename,&count,1);
+	f2 = open_ecorecorddb(filename2,&count2,0);
+
+
 	
-	index = (ecotxidx_t*) ECOMALLOC(sizeof(ecotxidx_t) + sizeof(ecotx_t) * (count-1),
+	index = (ecotxidx_t*) ECOMALLOC(sizeof(ecotxidx_t) + sizeof(ecotx_t) * (count+count2-1),
 	                                  "Allocate taxonomy");
 	 
-	index->count=count;                                 
-	          
-	for (i=0; i < count; i++)
+	index->count=count+count2;
+
+	fprintf(stderr,"Reading %d taxa...\n",count);
+	for (i=0; i < count; i++){
 		readnext_ecotaxon(f,&(index->taxon[i]));
-			
+		index->taxon[i].parent=index->taxon + (int32_t)index->taxon[i].parent;
+	}					
+
+	if (count2>0)
+		fprintf(stderr,"Reading %d local taxa...\n",count2);
+	else
+		fprintf(stderr,"No local taxon\n");
+
+	for (i=0; i < count2; i++){
+		readnext_ecotaxon(f2,&(index->taxon[count+i]));
+		index->taxon[count+i].parent=index->taxon + (int32_t)index->taxon[count+i].parent;
+	}
+
 	return index;
 }
 
+
 int32_t delete_taxonomy(ecotxidx_t *index)
 {
 	int32_t i;
@@ -61,6 +84,15 @@ int32_t delete_taxon(ecotx_t *taxon)
 	return 1;
 }
 
+
+/**
+ * Read the database for a given taxon a save the data 
+ * into the taxon structure(if any found)
+ * @param	*f	pointer to FILE type returned by fopen
+ * @param	*taxon	pointer to the structure
+ * 
+ * @return	a ecotx_t structure if any taxon found else NULL 
+ */
 ecotx_t *readnext_ecotaxon(FILE *f,ecotx_t *taxon)
 {
 	
@@ -80,7 +112,7 @@ ecotx_t *readnext_ecotaxon(FILE *f,ecotx_t *taxon)
 		raw->taxid      = swap_int32_t(raw->taxid); 
 	}
 	
-	taxon->parent = raw->parent;
+	taxon->parent = (ecotx_t*)raw->parent;
 	taxon->taxid  = raw->taxid;
 	taxon->rank   = raw->rank;
 	
@@ -88,15 +120,16 @@ ecotx_t *readnext_ecotaxon(FILE *f,ecotx_t *taxon)
 	                          "Allocate taxon scientific name");
 	                          
 	strncpy(taxon->name,raw->name,raw->namelength);
-	
+		
 	return taxon;
 }
 
 
-ecotaxonomy_t    *read_taxonomy(const char *prefix)
+ecotaxonomy_t    *read_taxonomy(const char *prefix,int32_t readAlternativeName)
 {
 	ecotaxonomy_t *tax;
 	char          *filename;
+	char          *filename2;
 	int           buffsize;
 	
 	tax = ECOMALLOC(sizeof(ecotaxonomy_t),
@@ -106,19 +139,31 @@ ecotaxonomy_t    *read_taxonomy(const char *prefix)
 	
 	filename = ECOMALLOC(buffsize,
 	                     "Allocate filename");
+	filename2= ECOMALLOC(buffsize,
+	                     "Allocate filename");
 	
 	snprintf(filename,buffsize,"%s.rdx",prefix);
 	
 	tax->ranks = read_rankidx(filename);
 	
 	snprintf(filename,buffsize,"%s.tdx",prefix);
+	snprintf(filename2,buffsize,"%s.ldx",prefix);
 	
-	tax->taxons = read_taxonomyidx(filename);
+	tax->taxons = read_taxonomyidx(filename,filename2);
 	
+	if (readAlternativeName)
+	{
+  	   snprintf(filename,buffsize,"%s.ndx",prefix);
+	   tax->names=read_nameidx(filename,tax);
+	}
+	else
+	   tax->names=NULL;
 	return tax;
 	
 }
 
+
+
 int32_t delete_ecotaxonomy(ecotaxonomy_t *taxonomy)
 {
 	if (taxonomy)
@@ -138,20 +183,19 @@ int32_t delete_ecotaxonomy(ecotaxonomy_t *taxonomy)
 }
 
 ecotx_t *eco_findtaxonatrank(ecotx_t *taxon,
-                                int32_t rankidx,
-                                ecotaxonomy_t *taxonomy)
+                                int32_t rankidx)
 {
 	ecotx_t *current_taxon;
 	ecotx_t *next_taxon;
 	
 	current_taxon = taxon;
-	next_taxon    = &(taxonomy->taxons->taxon[current_taxon->parent]);
+	next_taxon    = current_taxon->parent;
 	
-	while ((current_taxon!=next_taxon) &&
+	while ((current_taxon!=next_taxon) &&  // I' am the root node
 		   (current_taxon->rank!=rankidx))
 		   {
 		   	current_taxon = next_taxon;
-		   	next_taxon    = &(taxonomy->taxons->taxon[current_taxon->parent]);
+		   	next_taxon    = current_taxon->parent;
 		   }
 		   
 	if (current_taxon->rank==rankidx)
@@ -160,6 +204,61 @@ ecotx_t *eco_findtaxonatrank(ecotx_t *taxon,
 		return NULL;
 }
 
+/**
+ * Get back information concerning a taxon from a taxonomic id
+ * @param 	*taxonomy 	the taxonomy database
+ * @param	taxid		the taxonomic id 
+ * 
+ * @result	a ecotx_t structure containing the taxonimic information  
+ **/
+ecotx_t *eco_findtaxonbytaxid(ecotaxonomy_t *taxonomy, 
+							  int32_t taxid)
+{
+	ecotx_t    *current_taxon;
+	int32_t     taxoncount;
+	int32_t     i;
+	
+	taxoncount=taxonomy->taxons->count;
+	
+	for (current_taxon=taxonomy->taxons->taxon,
+	     i=0;
+	     i < taxoncount;
+	     i++,
+	     current_taxon++){
+	     if (current_taxon->taxid==taxid){
+	     	return current_taxon;
+	     }
+	 }
+	
+	return (ecotx_t*)NULL;	
+}
+
+/**
+ * Find out if taxon is son of other taxon (identified by its taxid)
+ * @param	*taxon son 		taxon
+ * @param	parent_taxid 	taxonomic id of the other taxon
+ * 
+ * @return 	1 is the other taxid math a parent taxid, else 0
+ **/
+int eco_isundertaxon(ecotx_t *taxon, 
+						int 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 *eco_getspecies(ecotx_t *taxon,
 						ecotaxonomy_t *taxonomy)
 {
@@ -175,7 +274,7 @@ ecotx_t *eco_getspecies(ecotx_t *taxon,
 	if (!tax || rankindex < 0)
 		ECOERROR(ECO_ASSERT_ERROR,"No taxonomy defined");
 		
-	return eco_findtaxonatrank(taxon,rankindex,tax);
+	return eco_findtaxonatrank(taxon,rankindex);
 }
 
 ecotx_t *eco_getgenus(ecotx_t *taxon,
@@ -193,7 +292,7 @@ ecotx_t *eco_getgenus(ecotx_t *taxon,
 	if (!tax || rankindex < 0)
 		ECOERROR(ECO_ASSERT_ERROR,"No taxonomy defined");
 		
-	return eco_findtaxonatrank(taxon,rankindex,tax);
+	return eco_findtaxonatrank(taxon,rankindex);
 }
 
 
@@ -212,7 +311,7 @@ ecotx_t *eco_getfamily(ecotx_t *taxon,
 	if (!tax || rankindex < 0)
 		ECOERROR(ECO_ASSERT_ERROR,"No taxonomy defined");
 		
-	return eco_findtaxonatrank(taxon,rankindex,tax);
+	return eco_findtaxonatrank(taxon,rankindex);
 }
 
 ecotx_t *eco_getkingdom(ecotx_t *taxon,
@@ -230,7 +329,7 @@ ecotx_t *eco_getkingdom(ecotx_t *taxon,
 	if (!tax || rankindex < 0)
 		ECOERROR(ECO_ASSERT_ERROR,"No taxonomy defined");
 		
-	return eco_findtaxonatrank(taxon,rankindex,tax);
+	return eco_findtaxonatrank(taxon,rankindex);
 }
 
 ecotx_t *eco_getsuperkingdom(ecotx_t *taxon,
@@ -248,5 +347,5 @@ ecotx_t *eco_getsuperkingdom(ecotx_t *taxon,
 	if (!tax || rankindex < 0)
 		ECOERROR(ECO_ASSERT_ERROR,"No taxonomy defined");
 		
-	return eco_findtaxonatrank(taxon,rankindex,tax);
-}
+	return eco_findtaxonatrank(taxon,rankindex);
+}

src/libthermo/Makefile

@@ -0,0 +1,22 @@
+
+SOURCES = nnparams.c 
+
+SRCS=$(SOURCES)
+         
+OBJECTS= $(patsubst %.c,%.o,$(SOURCES))
+
+LIBFILE= libthermo.a
+RANLIB= ranlib
+
+
+include ../global.mk
+
+
+all: $(LIBFILE)
+
+clean:
+	rm -rf $(OBJECTS) $(LIBFILE)
+
+$(LIBFILE): $(OBJECTS)
+	ar -cr $@ $?
+	$(RANLIB) $@

src/libthermo/nnparams.c

@@ -0,0 +1,619 @@
+/*
+ *  nnparams.cpp
+ *  PHunterLib
+ *
+ *  Nearest Neighbor Model / Parameters
+ *
+ *  Created by Tiayyba Riaz on 7/2/09.
+ *
+ */
+
+#include <memory.h>
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
+#include"nnparams.h"
+
+static char bpencoder[] = {	1,							// A
+		                   	0,                          // b
+		                   	2,                          // C
+		                   	0,0,0,                      // d, e, f
+		                   	3,                          // G
+		                   	0,0,0,0,0,0,0,0,0,0,0,0,    // h,i,j,k,l,m,n,o,p,q,r,s
+		                   	4,0,                        // T,U
+		                   	0,0,0,0,0};                 // v,w,x,y,z
+
+
+double forbidden_entropy;
+
+
+double nparam_GetInitialEntropy(PNNParams nparm)
+{
+	return 	-5.9f+nparm->rlogc;
+}
+
+
+//Retrieve Enthalpy for given NN-Pair from parameter table
+double nparam_GetEnthalpy(PNNParams nparm, char x0, char x1, char y0, char y1)
+{
+	return ndH(x0,x1,y0,y1); //xx, yx are already numbers
+}
+
+
+//Retrieve Entropy for given NN-Pair from parameter table
+double nparam_GetEntropy(PNNParams nparm, char x0, char x1, char y0, char y1)
+{
+	//xx and yx are already numbers
+	char nx0=x0;//nparam_convertNum(x0);
+	char nx1=x1;//nparam_convertNum(x1);
+	char ny0=y0;//nparam_convertNum(y0);
+	char ny1=y1;//nparam_convertNum(y1);
+	double answer = ndS(nx0,nx1,ny0,ny1);
+	/*Salt correction Santalucia*/
+	if (nparm->saltMethod == SALT_METHOD_SANTALUCIA) {
+		if(nx0!=5 && 1<= nx1 && nx1<=4) {
+			answer += 0.5*nparm->kfac;
+		}
+		if(ny1!=5 && 1<= ny0 && ny0<=4) {
+			answer += 0.5*nparm->kfac;
+		}
+	}
+	/*Salt correction Owczarzy*/
+	if (nparm->saltMethod == SALT_METHOD_OWCZARZY) {
+		double logk = log(nparm->kplus);
+		answer += ndH(nx0,nx1,ny0,ny1)*((4.29 * nparm->gcContent-3.95)*0.00001*logk+ 0.0000094*logk*logk);
+	}
+	return answer;
+}
+
+/* PURPOSE:    Return melting temperature TM for given entropy and enthalpy
+*              Assuming a one-state transition and using the formula
+*                TM = dH / (dS + R ln(Ct/4))
+*              entropy = dS + R ln Ct/4 (must already be included!)
+*              enthaklpy = dH
+*              where
+*                dH = enthalpy
+*                dS = entropy
+*                R  = Boltzmann factor
+*                Ct = Strand Concentration
+*
+*  PARAMETERS:
+*	entrypy and enthalpy
+*
+*  RETURN VALUE:
+* 	temperature
+*/
+
+double nparam_CalcTM(double entropy,double enthalpy)
+{
+	double tm = 0;               // absolute zero - return if model fails!
+    if (enthalpy>=forbidden_enthalpy)   //||(entropy==-cfact))
+		return 0;
+	if (entropy<0)         // avoid division by zero and model errors!
+	{
+	  tm = enthalpy/entropy;// - kfac; //LKFEB
+		if (tm<0)
+			return 0;
+	}
+	return tm;
+}
+
+
+void nparam_InitParams(PNNParams nparm, double c1, double c2, double kp, int sm)
+{
+	nparm->Ct1 = c1;
+	nparm->Ct2 = c2;
+	nparm->kplus = kp;
+	int maxCT = 1;
+	if(nparm->Ct2 > nparm->Ct1)
+	{
+		maxCT = 2;
+	}
+	double ctFactor;
+ 	if(nparm->Ct1 == nparm->Ct2)
+	{
+		ctFactor = nparm->Ct1/2;
+	}
+	else if (maxCT == 1)
+	{
+		ctFactor = nparm->Ct1-nparm->Ct2/2;
+	}
+	else
+	{
+		ctFactor = nparm->Ct2-nparm->Ct1/2;
+	}
+	nparm->rlogc = R * log(ctFactor);
+	forbidden_entropy = nparm->rlogc;
+	nparm->kfac = 0.368 * log (nparm->kplus);
+	nparm->saltMethod = sm;
+	int x,y,a,b;  // variables used as counters...
+
+	// Set all parameters to zero!
+	memset(nparm->dH,0,sizeof(nparm->dH));
+	memset(nparm->dS,0,sizeof(nparm->dS));
+
+	// Set all X-/Y-, -X/Y- and X-/-Y so, that TM will be VERY small!
+	for (x=1;x<=4;x++)
+	{
+		for (y=1;y<=4;y++)
+		{
+			ndH(0,x,y,0)=forbidden_enthalpy;
+			ndS(0,x,y,0)=forbidden_entropy;
+			ndH(x,0,0,y)=forbidden_enthalpy;
+			ndS(x,0,0,y)=forbidden_entropy;
+			ndH(x,0,y,0)=forbidden_enthalpy;
+			ndS(x,0,y,0)=forbidden_entropy;
+			// forbid X-/Y$ and X$/Y- etc., i.e. terminal must not be paired with gap!
+			ndH(x,5,y,0)=forbidden_enthalpy;
+			ndS(x,5,y,0)=forbidden_entropy;
+			ndH(x,0,y,5)=forbidden_enthalpy;
+			ndS(x,0,y,5)=forbidden_entropy;
+			ndH(5,x,0,y)=forbidden_enthalpy;
+			ndS(5,x,0,y)=forbidden_entropy;
+			ndH(0,x,5,y)=forbidden_enthalpy;
+			ndS(0,x,5,y)=forbidden_entropy;
+			// forbid X$/-Y etc.
+			ndH(x,5,0,y)=forbidden_enthalpy;
+			ndS(x,5,0,y)=forbidden_entropy;
+			ndH(x,0,5,y)=forbidden_enthalpy;
+			ndS(x,0,5,y)=forbidden_entropy;
+			ndH(5,x,y,0)=forbidden_enthalpy;
+			ndS(5,x,y,0)=forbidden_entropy;
+			ndH(0,x,y,5)=forbidden_enthalpy;
+			ndS(0,x,y,5)=forbidden_entropy;
+
+		}
+		// also, forbid x-/-- and --/x-, i.e. no two inner gaps paired
+		ndH(x,0,0,0)=forbidden_enthalpy;
+		ndS(x,0,0,0)=forbidden_entropy;
+		ndH(0,0,x,0)=forbidden_enthalpy;
+		ndS(0,0,x,0)=forbidden_entropy;
+		// x-/-$
+		ndH(x,0,0,5)=forbidden_enthalpy;
+		ndS(x,0,0,5)=forbidden_entropy;
+		ndH(5,0,0,x)=forbidden_enthalpy;
+		ndS(5,0,0,x)=forbidden_entropy;
+		ndH(0,5,x,0)=forbidden_enthalpy;
+		ndS(x,0,0,5)=forbidden_entropy;
+		ndH(0,x,5,0)=forbidden_enthalpy;
+		ndS(0,x,5,0)=forbidden_entropy;
+	}
+	// forbid --/--
+	ndH(0,0,0,0)=forbidden_enthalpy;
+	ndS(0,0,0,0)=forbidden_entropy;
+
+	ndH(5,0,0,0)=forbidden_enthalpy;
+	ndS(5,0,0,0)=forbidden_entropy;
+	ndH(0,0,5,0)=forbidden_enthalpy;
+	ndS(0,0,5,0)=forbidden_entropy;
+	ndH(0,5,5,0)=forbidden_enthalpy;
+	ndS(0,5,5,0)=forbidden_entropy;
+
+	// Interior loops (double Mismatches)
+    #define iloop_entropy -0.97f
+    #define iloop_enthalpy 0.0f
+	for (x=1; x<=4; x++)
+		for (y=1; y<=4; y++)
+			for (a=1; a<=4; a++)
+				for (b=1; b<=4; b++)
+					// AT and CG pair, and as A=1, C=2, G=3, T=4 this means
+					// we have Watson-Crick pairs if (x+a==5) and (y+b)==5.
+					if (!((x+a==5)||(y+b==5)))
+					{
+						// No watson-crick-pair, i.e. double mismatch!
+						// set enthalpy/entropy to loop expansion!
+						ndH(x,y,a,b) = iloop_enthalpy;
+						ndS(x,y,a,b) = iloop_entropy;
+					}
+
+	// xy/-- and --/xy (Bulge Loops of size > 1)
+    #define bloop_entropy -1.3f
+    #define bloop_enthalpy 0.0f
+	for (x=1; x<=4; x++)
+		for (y=1; y<=4; y++)
+		{
+			ndH(x,y,0,0) = bloop_enthalpy;
+			ndS(x,y,0,0) = bloop_entropy;
+			ndH(0,0,x,y) = bloop_enthalpy;
+			ndS(0,0,x,y) = bloop_entropy;
+		}
+
+    // x-/ya abd xa/y- as well as -x/ay and ax/-y
+	// bulge opening and closing parameters with
+	// adjacent matches / mismatches
+	// obulge_mism and cbulge_mism chosen so high to avoid
+	//     AAAAAAAAA
+	//     T--G----T
+	// being better than
+	//     AAAAAAAAA
+	//     TG------T
+    #define obulge_match_H (-2.66f * 1000)
+    #define obulge_match_S -14.22f
+    #define cbulge_match_H (-2.66f * 1000)
+    #define cbulge_match_S -14.22f
+    #define obulge_mism_H (0.0f * 1000)
+    #define obulge_mism_S -6.45f
+    #define cbulge_mism_H 0.0f
+    #define cbulge_mism_S -6.45f
+	for (x=1; x<=4; x++)
+		for (y=1; y<=4; y++)
+			for (a=1; a<=4; a++)
+			{
+				if (x+y==5)  // other base pair matches!
+				{
+					ndH(x,0,y,a)=obulge_match_H;  // bulge opening
+					ndS(x,0,y,a)=obulge_match_S;
+					ndH(x,a,y,0)=obulge_match_H;
+					ndS(x,a,y,0)=obulge_match_S;
+					ndH(0,x,a,y)=cbulge_match_H;  // bulge closing
+					ndS(0,x,a,y)=cbulge_match_S;
+					ndH(a,x,0,y)=cbulge_match_H;
+					ndS(a,x,0,y)=cbulge_match_S;
+				}
+				else
+				{           // mismatch in other base pair!
+					ndH(x,0,y,a)=obulge_mism_H;   // bulge opening
+					ndS(x,0,y,a)=obulge_mism_S;
+					ndH(x,a,y,0)=obulge_mism_H;
+					ndS(x,a,y,0)=obulge_mism_S;
+					ndH(0,x,a,y)=cbulge_mism_H;   // bulge closing
+					ndS(0,x,a,y)=cbulge_mism_S;
+					ndH(a,x,0,y)=cbulge_mism_H;
+					ndS(a,x,0,y)=cbulge_mism_S;
+				}
+			}
+
+	// Watson-Crick pairs (note that only ten are unique, as obviously
+	// 5'-AG-3'/3'-TC-5'  =  5'-CT-3'/3'-GA-5' etc.
+	ndH(1,1,4,4)=-7.6f*1000;  ndS(1,1,4,4)=-21.3f;   // AA/TT 04
+	ndH(1,2,4,3)=-8.4f*1000;  ndS(1,2,4,3)=-22.4f;   // AC/TG adapted GT/CA
+	ndH(1,3,4,2)=-7.8f*1000;  ndS(1,3,4,2)=-21.0f;   // AG/TC adapted CT/GA
+	ndH(1,4,4,1)=-7.2f*1000;  ndS(1,4,4,1)=-20.4f;   // AT/TA 04
+	ndH(2,1,3,4)=-8.5f*1000;  ndS(2,1,3,4)=-22.7f;   // CA/GT 04
+	ndH(2,2,3,3)=-8.0f*1000;  ndS(2,2,3,3)=-19.9f;   // CC/GG adapted GG/CC
+	ndH(2,3,3,2)=-10.6f*1000; ndS(2,3,3,2)=-27.2f;   // CG/GC 04
+	ndH(2,4,3,1)=-7.8f*1000;  ndS(2,4,3,1)=-21.0f;   // CT/GA 04
+	ndH(3,1,2,4)=-8.2f*1000;  ndS(3,1,2,4)=-22.2f;   // GA/CT 04
+	ndH(3,2,2,3)=-9.8f*1000;  ndS(3,2,2,3)=-24.4f;   // GC/CG 04
+	ndH(3,3,2,2)=-8.0f*1000;  ndS(3,3,2,2)=-19.9f;   // GG/CC 04
+	ndH(3,4,2,1)=-8.4f*1000;  ndS(3,4,2,1)=-22.4f;   // GT/CA 04
+	ndH(4,1,1,4)=-7.2f*1000;  ndS(4,1,1,4)=-21.3f;   // TA/AT 04
+	ndH(4,2,1,3)=-8.2f*1000;  ndS(4,2,1,3)=-22.2f;   // TC/AG adapted GA/CT
+	ndH(4,3,1,2)=-8.5f*1000;  ndS(4,3,1,2)=-22.7f;   // TG/AC adapted CA/GT
+	ndH(4,4,1,1)=-7.6f*1000;  ndS(4,4,1,1)=-21.3f;   // TT/AA adapted AA/TT
+
+    // A-C Mismatches (Values for pH 7.0)
+	ndH(1,1,2,4)=7.6f*1000;   ndS(1,1,2,4)=20.2f;    // AA/CT
+	ndH(1,1,4,2)=2.3f*1000;   ndS(1,1,4,2)=4.6f;     // AA/TC
+	ndH(1,2,2,3)=-0.7f*1000;  ndS(1,2,2,3)=-3.8f;    // AC/CG
+	ndH(1,2,4,1)=5.3f*1000;   ndS(1,2,4,1)=14.6f;    // AC/TA
+	ndH(1,3,2,2)=0.6f*1000;   ndS(1,3,2,2)=-0.6f;    // AG/CC
+	ndH(1,4,2,1)=5.3f*1000;   ndS(1,4,2,1)=14.6f;    // AT/CA
+	ndH(2,1,1,4)=3.4f*1000;   ndS(2,1,1,4)=8.0f;     // CA/AT
+	ndH(2,1,3,2)=1.9f*1000;   ndS(2,1,3,2)=3.7f;     // CA/GC
+	ndH(2,2,1,3)=5.2f*1000;   ndS(2,2,1,3)=14.2f;    // CC/AG
+	ndH(2,2,3,1)=0.6f*1000;   ndS(2,2,3,1)=-0.6f;    // CC/GA
+	ndH(2,3,1,2)=1.9f*1000;   ndS(2,3,1,2)=3.7f;     // CG/AC
+	ndH(2,4,1,1)=2.3f*1000;   ndS(2,4,1,1)=4.6f;     // CT/AA
+	ndH(3,1,2,2)=5.2f*1000;   ndS(3,1,2,2)=14.2f;    // GA/CC
+	ndH(3,2,2,1)=-0.7f*1000;  ndS(3,2,2,1)=-3.8f;    // GC/CA
+	ndH(4,1,1,2)=3.4f*1000;   ndS(4,1,1,2)=8.0f;     // TA/AC
+	ndH(4,2,1,1)=7.6f*1000;   ndS(4,2,1,1)=20.2f;    // TC/AA
+
+	// C-T Mismatches
+	ndH(1,2,4,4)=0.7f*1000;   ndS(1,2,4,4)=0.2f;     // AC/TT
+	ndH(1,4,4,2)=-1.2f*1000;  ndS(1,4,4,2)=-6.2f;    // AT/TC
+	ndH(2,1,4,4)=1.0f*1000;   ndS(2,1,4,4)=0.7f;     // CA/TT
+	ndH(2,2,3,4)=-0.8f*1000;  ndS(2,2,3,4)=-4.5f;    // CC/GT
+	ndH(2,2,4,3)=5.2f*1000;   ndS(2,2,4,3)=13.5f;    // CC/TG
+	ndH(2,3,4,2)=-1.5f*1000;  ndS(2,3,4,2)=-6.1f;    // CG/TC
+	ndH(2,4,3,2)=-1.5f*1000;  ndS(2,4,3,2)=-6.1f;    // CT/GC
+	ndH(2,4,4,1)=-1.2f*1000;  ndS(2,4,4,1)=-6.2f;    // CT/TA
+	ndH(3,2,2,4)=2.3f*1000;   ndS(3,2,2,4)=5.4f;     // GC/CT
+	ndH(3,4,2,2)=5.2f*1000;   ndS(3,4,2,2)=13.5f;    // GT/CC
+	ndH(4,1,2,4)=1.2f*1000;   ndS(4,1,2,4)=0.7f;     // TA/CT
+	ndH(4,2,2,3)=2.3f*1000;   ndS(4,2,2,3)=5.4f;     // TC/CG
+	ndH(4,2,1,4)=1.2f*1000;   ndS(4,2,1,4)=0.7f;     // TC/AT
+	ndH(4,3,2,2)=-0.8f*1000;  ndS(4,3,2,2)=-4.5f;    // TG/CC
+	ndH(4,4,2,1)=0.7f*1000;   ndS(4,4,2,1)=0.2f;     // TT/CA
+	ndH(4,4,1,2)=1.0f*1000;   ndS(4,4,1,2)=0.7f;     // TT/AC
+
+	// G-A Mismatches
+	ndH(1,1,3,4)=3.0f*1000;   ndS(1,1,3,4)=7.4f;     // AA/GT
+	ndH(1,1,4,3)=-0.6f*1000;  ndS(1,1,4,3)=-2.3f;    // AA/TG
+	ndH(1,2,3,3)=0.5f*1000;   ndS(1,2,3,3)=3.2f;     // AC/GG
+	ndH(1,3,3,2)=-4.0f*1000;  ndS(1,3,3,2)=-13.2f;   // AG/GC
+	ndH(1,3,4,1)=-0.7f*1000;  ndS(1,3,4,1)=-2.3f;    // AG/TA
+	ndH(1,4,3,1)=-0.7f*1000;  ndS(1,4,3,1)=-2.3f;    // AT/GA
+	ndH(2,1,3,3)=-0.7f*1000;  ndS(2,1,3,3)=-2.3f;    // CA/GG
+	ndH(2,3,3,1)=-4.0f*1000;  ndS(2,3,3,1)=-13.2f;   // CG/GA
+	ndH(3,1,1,4)=0.7f*1000;   ndS(3,1,1,4)=0.7f;     // GA/AT
+	ndH(3,1,2,3)=-0.6f*1000;  ndS(3,1,2,3)=-1.0f;    // GA/CG
+	ndH(3,2,1,3)=-0.6f*1000;  ndS(3,2,1,3)=-1.0f;    // GC/AG
+	ndH(3,3,1,2)=-0.7f*1000;  ndS(3,3,1,2)=-2.3f;    // GG/AC
+	ndH(3,3,2,1)=0.5f*1000;   ndS(3,3,2,1)=3.2f;     // GG/CA
+	ndH(3,4,1,1)=-0.6f*1000;  ndS(3,4,1,1)=-2.3f;    // GT/AA
+	ndH(4,1,1,3)=0.7f*1000;   ndS(4,1,1,3)=0.7f;     // TA/AG
+	ndH(4,3,1,1)=3.0f*1000;   ndS(4,3,1,1)=7.4f;     // TG/AA
+
+	// G-T Mismatches
+	ndH(1,3,4,4)=1.0f*1000;   ndS(1,3,4,4)=0.9f;     // AG/TT
+	ndH(1,4,4,3)=-2.5f*1000;  ndS(1,4,4,3)=-8.3f;    // AT/TG
+	ndH(2,3,3,4)=-4.1f*1000;  ndS(2,3,3,4)=-11.7f;   // CG/GT
+	ndH(2,4,3,3)=-2.8f*1000;  ndS(2,4,3,3)=-8.0f;    // CT/GG
+	ndH(3,1,4,4)=-1.3f*1000;  ndS(3,1,4,4)=-5.3f;    // GA/TT
+	ndH(3,2,4,3)=-4.4f*1000;  ndS(3,2,4,3)=-12.3f;   // GC/TG
+	ndH(3,3,2,4)=3.3f*1000;   ndS(3,3,2,4)=10.4f;    // GG/CT
+	ndH(3,3,4,2)=-2.8f*1000;  ndS(3,3,4,2)=-8.0f;    // GG/TC
+//	ndH(3,3,4,4)=5.8f*1000;   ndS(3,3,4,4)=16.3f;    // GG/TT
+	ndH(3,4,2,3)=-4.4f*1000;  ndS(3,4,2,3)=-12.3f;   // GT/CG
+	ndH(3,4,4,1)=-2.5f*1000;  ndS(3,4,4,1)=-8.3f;    // GT/TA
+//	ndH(3,4,4,3)=4.1f*1000;   ndS(3,4,4,3)=9.5f;     // GT/TG
+	ndH(4,1,3,4)=-0.1f*1000;  ndS(4,1,3,4)=-1.7f;    // TA/GT
+	ndH(4,2,3,3)=3.3f*1000;   ndS(4,2,3,3)=10.4f;    // TC/GG
+	ndH(4,3,1,4)=-0.1f*1000;  ndS(4,3,1,4)=-1.7f;    // TG/AT
+	ndH(4,3,3,2)=-4.1f*1000;  ndS(4,3,3,2)=-11.7f;   // TG/GC
+//	ndH(4,3,3,4)=-1.4f*1000;  ndS(4,3,3,4)=-6.2f;    // TG/GT
+	ndH(4,4,1,3)=-1.3f*1000;  ndS(4,4,1,3)=-5.3f;    // TT/AG
+	ndH(4,4,3,1)=1.0f*1000;   ndS(4,4,3,1)=0.9f;     // TT/GA
+//	ndH(4,4,3,3)=5.8f*1000;   ndS(4,4,3,3)=16.3f;    // TT/GG
+
+	// A-A Mismatches
+	ndH(1,1,1,4)=4.7f*1000;   ndS(1,1,1,4)=12.9f;    // AA/AT
+	ndH(1,1,4,1)=1.2f*1000;   ndS(1,1,4,1)=1.7f;     // AA/TA
+	ndH(1,2,1,3)=-2.9f*1000;  ndS(1,2,1,3)=-9.8f;    // AC/AG
+	ndH(1,3,1,2)=-0.9f*1000;  ndS(1,3,1,2)=-4.2f;    // AG/AC
+	ndH(1,4,1,1)=1.2f*1000;   ndS(1,4,1,1)=1.7f;     // AT/AA
+	ndH(2,1,3,1)=-0.9f*1000;  ndS(2,1,3,1)=-4.2f;    // CA/GA
+    ndH(3,1,2,1)=-2.9f*1000;  ndS(3,1,2,1)=-9.8f;    // GA/CA
+	ndH(4,1,1,1)=4.7f*1000;   ndS(4,1,1,1)=12.9f;    // TA/AA
+
+	// C-C Mismatches
+	ndH(1,2,4,2)=0.0f*1000;   ndS(1,2,4,2)=-4.4f;    // AC/TC
+	ndH(2,1,2,4)=6.1f*1000;   ndS(2,1,2,4)=16.4f;    // CA/CT
+	ndH(2,2,2,3)=3.6f*1000;   ndS(2,2,2,3)=8.9f;     // CC/CG
+	ndH(2,2,3,2)=-1.5f*1000;  ndS(2,2,3,2)=-7.2f;    // CC/GC
+	ndH(2,3,2,2)=-1.5f*1000;  ndS(2,3,2,2)=-7.2f;    // CG/CC
+	ndH(2,4,2,1)=0.0f*1000;   ndS(2,4,2,1)=-4.4f;    // CT/CA
+	ndH(3,2,2,2)=3.6f*1000;   ndS(3,2,2,2)=8.9f;     // GC/CC
+	ndH(4,2,1,2)=6.1f*1000;   ndS(4,2,1,2)=16.4f;    // TC/AC
+
+	// G-G Mismatches
+	ndH(1,3,4,3)=-3.1f*1000;  ndS(1,3,4,3)=-9.5f;    // AG/TG
+	ndH(2,3,3,3)=-4.9f*1000;  ndS(2,3,3,3)=-15.3f;   // CG/GG
+	ndH(3,1,3,4)=1.6f*1000;   ndS(3,1,3,4)=3.6f;     // GA/GT
+	ndH(3,2,3,3)=-6.0f*1000;  ndS(3,2,3,3)=-15.8f;   // GC/GG
+	ndH(3,3,2,3)=-6.0f*1000;  ndS(3,3,2,3)=-15.8f;   // GG/CG
+	ndH(3,3,3,2)=-4.9f*1000;  ndS(3,3,3,2)=-15.3f;   // GG/GC
+	ndH(3,4,3,1)=-3.1f*1000;  ndS(3,4,3,1)=-9.5f;    // GT/GA
+	ndH(4,3,1,3)=1.6f*1000;   ndS(4,3,1,3)=3.6f;     // TG/AG
+
+	// T-T Mismatches
+	ndH(1,4,4,4)=-2.7f*1000;  ndS(1,4,4,4)=-10.8f;   // AT/TT
+	ndH(2,4,3,4)=-5.0f*1000;  ndS(2,4,3,4)=-15.8f;   // CT/GT
+	ndH(3,4,2,4)=-2.2f*1000;  ndS(3,4,2,4)=-8.4f;    // GT/CT
+	ndH(4,1,4,4)=0.2f*1000;   ndS(4,1,4,4)=-1.5f;    // TA/TT
+	ndH(4,2,4,3)=-2.2f*1000;  ndS(4,2,4,3)=-8.4f;    // TC/TG
+	ndH(4,3,4,2)=-5.0f*1000;  ndS(4,3,4,2)=-15.8f;   // TG/TC
+	ndH(4,4,1,4)=0.2f*1000;   ndS(4,4,1,4)=-1.5f;    // TT/AT
+	ndH(4,4,4,1)=-2.7f*1000;  ndS(4,4,4,1)=-10.8f;   // TT/TA
+
+	// Dangling Ends
+	ndH(5,1,1,4)=-0.7f*1000;  ndS(5,1,1,4)=-0.8f;    // $A/AT
+	ndH(5,1,2,4)=4.4f*1000;   ndS(5,1,2,4)=14.9f;    // $A/CT
+	ndH(5,1,3,4)=-1.6f*1000;  ndS(5,1,3,4)=-3.6f;    // $A/GT
+	ndH(5,1,4,4)=2.9f*1000;   ndS(5,1,4,4)=10.4f;    // $A/TT
+	ndH(5,2,1,3)=-2.1f*1000;  ndS(5,2,1,3)=-3.9f;    // $C/AG
+	ndH(5,2,2,3)=-0.2f*1000;  ndS(5,2,2,3)=-0.1f;    // $C/CG
+	ndH(5,2,3,3)=-3.9f*1000;  ndS(5,2,3,3)=-11.2f;   // $C/GG
+	ndH(5,2,4,3)=-4.4f*1000;  ndS(5,2,4,3)=-13.1f;   // $C/TG
+	ndH(5,3,1,2)=-5.9f*1000;  ndS(5,3,1,2)=-16.5f;   // $G/AC
+	ndH(5,3,2,2)=-2.6f*1000;  ndS(5,3,2,2)=-7.4f;    // $G/CC
+	ndH(5,3,3,2)=-3.2f*1000;  ndS(5,3,3,2)=-10.4f;   // $G/GC
+	ndH(5,3,4,2)=-5.2f*1000;  ndS(5,3,4,2)=-15.0f;   // $G/TC
+	ndH(5,4,1,1)=-0.5f*1000;  ndS(5,4,1,1)=-1.1f;    // $T/AA
+	ndH(5,4,2,1)=4.7f*1000;   ndS(5,4,2,1)=14.2f;    // $T/CA
+	ndH(5,4,3,1)=-4.1f*1000;  ndS(5,4,3,1)=-13.1f;   // $T/GA
+	ndH(5,4,4,1)=-3.8f*1000;  ndS(5,4,4,1)=-12.6f;   // $T/TA
+	ndH(1,5,4,1)=-2.9f*1000;  ndS(1,5,4,1)=-7.6f;    // A$/TA
+	ndH(1,5,4,2)=-4.1f*1000;  ndS(1,5,4,2)=-13.0f;   // A$/TC
+	ndH(1,5,4,3)=-4.2f*1000;  ndS(1,5,4,3)=-15.0f;   // A$/TG
+	ndH(1,5,4,4)=-0.2f*1000;  ndS(1,5,4,4)=-0.5f;    // A$/TT
+	ndH(1,1,5,4)=0.2f*1000;   ndS(1,1,5,4)=2.3f;     // AA/$T
+	ndH(1,1,4,5)=-0.5f*1000;  ndS(1,1,4,5)=-1.1f;    // AA/T$
+	ndH(1,2,5,3)=-6.3f*1000;  ndS(1,2,5,3)=-17.1f;   // AC/$G
+	ndH(1,2,4,5)=4.7f*1000;   ndS(1,2,4,5)=14.2f;    // AC/T$
+	ndH(1,3,5,2)=-3.7f*1000;  ndS(1,3,5,2)=-10.0f;   // AG/$C
+	ndH(1,3,4,5)=-4.1f*1000;  ndS(1,3,4,5)=-13.1f;   // AG/T$
+	ndH(1,4,5,1)=-2.9f*1000;  ndS(1,4,5,1)=-7.6f;    // AT/$A
+	ndH(1,4,4,5)=-3.8f*1000;  ndS(1,4,4,5)=-12.6f;   // AT/T$
+	ndH(2,5,3,1)=-3.7f*1000;  ndS(2,5,3,1)=-10.0f;   // C$/GA
+	ndH(2,5,3,2)=-4.0f*1000;  ndS(2,5,3,2)=-11.9f;   // C$/GC
+	ndH(2,5,3,3)=-3.9f*1000;  ndS(2,5,3,3)=-10.9f;   // C$/GG
+	ndH(2,5,3,4)=-4.9f*1000;  ndS(2,5,3,4)=-13.8f;   // C$/GT
+	ndH(2,1,5,4)=0.6f*1000;   ndS(2,1,5,4)=3.3f;     // CA/$T
+	ndH(2,1,3,5)=-5.9f*1000;  ndS(2,1,3,5)=-16.5f;   // CA/G$
+	ndH(2,2,5,3)=-4.4f*1000;  ndS(2,2,5,3)=-12.6f;   // CC/$G
+	ndH(2,2,3,5)=-2.6f*1000;  ndS(2,2,3,5)=-7.4f;    // CC/G$
+	ndH(2,3,5,2)=-4.0f*1000;  ndS(2,3,5,2)=-11.9f;   // CG/$C
+	ndH(2,3,3,5)=-3.2f*1000;  ndS(2,3,3,5)=-10.4f;   // CG/G$
+	ndH(2,4,5,1)=-4.1f*1000;  ndS(2,4,5,1)=-13.0f;   // CT/$A
+	ndH(2,4,3,5)=-5.2f*1000;  ndS(2,4,3,5)=-15.0f;   // CT/G$
+	ndH(3,5,2,1)=-6.3f*1000;  ndS(3,5,2,1)=-17.1f;   // G$/CA
+	ndH(3,5,2,2)=-4.4f*1000;  ndS(3,5,2,2)=-12.6f;   // G$/CC
+	ndH(3,5,2,3)=-5.1f*1000;  ndS(3,5,2,3)=-14.0f;   // G$/CG
+	ndH(3,5,2,4)=-4.0f*1000;  ndS(3,5,2,4)=-10.9f;   // G$/CT
+	ndH(3,1,5,4)=-1.1f*1000;  ndS(3,1,5,4)=-1.6f;    // GA/$T
+	ndH(3,1,2,5)=-2.1f*1000;  ndS(3,1,2,5)=-3.9f;    // GA/C$
+	ndH(3,2,5,3)=-5.1f*1000;  ndS(3,2,5,3)=-14.0f;   // GC/$G
+	ndH(3,2,2,5)=-0.2f*1000;  ndS(3,2,2,5)=-0.1f;    // GC/C$
+	ndH(3,3,5,2)=-3.9f*1000;  ndS(3,3,5,2)=-10.9f;   // GG/$C
+	ndH(3,3,2,5)=-3.9f*1000;  ndS(3,3,2,5)=-11.2f;   // GG/C$
+	ndH(3,4,5,1)=-4.2f*1000;  ndS(3,4,5,1)=-15.0f;   // GT/$A
+	ndH(3,4,2,5)=-4.4f*1000;  ndS(3,4,2,5)=-13.1f;   // GT/C$
+	ndH(4,5,1,1)=0.2f*1000;   ndS(4,5,1,1)=2.3f;     // T$/AA
+	ndH(4,5,1,2)=0.6f*1000;   ndS(4,5,1,2)=3.3f;     // T$/AC
+	ndH(4,5,1,3)=-1.1f*1000;  ndS(4,5,1,3)=-1.6f;    // T$/AG
+	ndH(4,5,1,4)=-6.9f*1000;  ndS(4,5,1,4)=-20.0f;   // T$/AT
+	ndH(4,1,5,4)=-6.9f*1000;  ndS(4,1,5,4)=-20.0f;   // TA/$T
+	ndH(4,1,1,5)=-0.7f*1000;  ndS(4,1,1,5)=-0.7f;    // TA/A$
+	ndH(4,2,5,3)=-4.0f*1000;  ndS(4,2,5,3)=-10.9f;   // TC/$G
+	ndH(4,2,1,5)=4.4f*1000;   ndS(4,2,1,5)=14.9f;    // TC/A$
+	ndH(4,3,5,2)=-4.9f*1000;  ndS(4,3,5,2)=-13.8f;   // TG/$C
+	ndH(4,3,1,5)=-1.6f*1000;  ndS(4,3,1,5)=-3.6f;    // TG/A$
+	ndH(4,4,5,1)=-0.2f*1000;  ndS(4,4,5,1)=-0.5f;    // TT/$A
+	ndH(4,4,1,5)=2.9f*1000;   ndS(4,4,1,5)=10.4f;    // TT/A$
+
+	return;
+}
+
+int nparam_CountGCContent(char * seq ) {
+	int lseq = strlen(seq);
+	int k;
+	double count = 0;
+	for( k=0;k<lseq;k++) {
+		if (seq[k] == 'G' || seq[k] == 'C' ) {
+			count+=1;
+		}
+	}
+	return count;
+}
+
+void nparam_CleanSeq (char* inseq, char* outseq, int len)
+{
+	int seqlen = strlen (inseq);
+	int i, j;
+
+	if (len != 0)
+		seqlen = len;
+
+	outseq[0]='x';
+
+	for (i = 0, j = 0; i < seqlen && outseq[0]; i++,j++)
+	{
+		switch (inseq[i])
+		{
+		case 'a':
+		case '\0':
+		case 'A':
+			outseq[j] = 'A'; break;
+		case 'c':
+		case '\1':
+		case 'C':
+			outseq[j] = 'C'; break;
+		case 'g':
+		case '\2':
+		case 'G':
+			outseq[j] = 'G'; break;
+		case 't':
+		case '\3':
+		case 'T':
+			outseq[j] = 'T'; break;
+		default:
+			outseq[0]=0;
+		}
+	}
+	outseq[j] = '\0';
+}
+
+//Calculate TM for given sequence against its complement
+double nparam_CalcSelfTM(PNNParams nparm, char* seq, int len)
+{
+	const unsigned long long minus1 = 0xFFFFFFFFFFFFFFFFLLU;
+	const double NaN = *((double*)&minus1);
+	double thedH = 0;
+	//double thedS = nparam_GetInitialEntropy(nparm);
+	double thedS = -5.9f+nparm->rlogc;
+	double mtemp;
+	char c1;
+	char c2;
+	char c3;
+	char c4;
+	unsigned int i;
+	char nseq[50];
+	char *useq = seq;
+
+	nparam_CleanSeq (seq, nseq, len);
+	if (!nseq[0])
+	         return NaN;
+	useq = nseq;
+
+	for ( i=1;i<len;i++)
+	{
+		c1 = GETREVCODE(useq[i-1]); //nparam_getComplement(seq[i-1],1);
+		c2 = GETREVCODE(useq[i]); //nparam_getComplement(seq[i],1);
+		c3 = GETNUMCODE(useq[i-1]);
+		c4 = GETNUMCODE(useq[i]);
+
+
+		thedH += nparm->dH[c3][c4][c1][c2];//nparam_GetEnthalpy(nparm, c3,c4,c1,c2);
+		thedS += nparam_GetEntropy(nparm, c3,c4,c1,c2);
+	}
+	//printf("------------------\n");
+	mtemp = nparam_CalcTM(thedS,thedH);
+		//fprintf(stderr,"Enthalpy: %f, entropy: %f, seq: %s  rloc=%f\n", thedH, thedS, useq, nparm->rlogc);
+		//exit (0);
+	return mtemp;
+}
+
+double nparam_CalcTwoTM(PNNParams nparm, char* seq1, char* seq2, int len)
+{
+	const unsigned long long minus1 = 0xFFFFFFFFFFFFFFFFLLU;
+	const double NaN = *((double*)&minus1);
+	double thedH = 0;
+	//double thedS = nparam_GetInitialEntropy(nparm);
+	double thedS = -5.9f+nparm->rlogc;
+	double mtemp;
+	char c1;
+	char c2;
+	char c3;
+	char c4;
+	unsigned int i;
+	char nseq1[50];
+	char nseq2[50];
+	char *useq1;
+	char *useq2;
+
+	nparam_CleanSeq (seq1, nseq1, len);
+	if (!nseq1[0])
+	         return NaN;
+	useq1 = nseq1;
+
+	nparam_CleanSeq (seq2, nseq2, len);
+	if (!nseq2[0])
+	         return NaN;
+	useq2 = nseq2;
+
+	//fprintf (stderr,"Primer : %s\n",useq);
+	for ( i=1;i<len;i++)
+	{
+		c1 = GETREVCODE(useq2[i-1]); //nparam_getComplement(seq[i-1],1);
+		c2 = GETREVCODE(useq2[i]);   //nparam_getComplement(seq[i],1);
+		c3 = GETNUMCODE(useq1[i-1]);
+		c4 = GETNUMCODE(useq1[i]);
+
+		//fprintf (stderr,"Primer : %s %f %f %d %d, %d %d %f\n",useq,thedH,thedS,(int)c3,(int)c4,(int)c1,(int)c2,nparam_GetEnthalpy(nparm, c3,c4,c1,c2));
+
+		thedH += nparm->dH[c3][c4][c1][c2];//nparam_GetEnthalpy(nparm, c3,c4,c1,c2);
+		thedS += nparam_GetEntropy(nparm, c3,c4,c1,c2);
+	}
+	//fprintf(stderr,"------------------\n");
+	mtemp = nparam_CalcTM(thedS,thedH);
+	//if (mtemp == 0)
+	//{
+	//	fprintf(stderr,"Enthalpy: %f, entropy: %f, seq: %s\n", thedH, thedS, useq);
+		//exit (0);
+	//}
+	return mtemp;
+}
+
+double calculateMeltingTemperatureBasic (char * seq) {
+	int gccount;
+	double temp;
+	int seqlen;
+
+	seqlen = strlen (seq);
+	gccount = nparam_CountGCContent (seq);
+	temp = 64.9 + 41*(gccount - 16.4)/seqlen;
+	return temp;
+}

src/libthermo/nnparams.h

@@ -0,0 +1,63 @@
+/*
+ *  nnparams.h
+ *  PHunterLib
+ *
+ * Nearest Neighbor Model Parameters
+ *
+ *  Created by Tiayyba Riaz on 02/07/09.
+ *
+ */
+
+#ifndef NNPARAMS_H_
+#define NNPARAMS_H_
+
+#include <math.h>
+#include <string.h>
+//#include "../libecoprimer/ecoprimer.h"
+
+// following defines to simplify coding...
+#define ndH(a,b,c,d) nparm->dH[(int)a][(int)b][(int)c][(int)d]
+#define ndS(a,b,c,d) nparm->dS[(int)a][(int)b][(int)c][(int)d]
+#define forbidden_enthalpy 1000000000000000000.0f
+#define	R 1.987f
+#define	SALT_METHOD_SANTALUCIA 1
+#define	SALT_METHOD_OWCZARZY 2
+
+#define DEF_CONC_PRIMERS 0.0000008
+#define DEF_CONC_SEQUENCES 0
+#define DEF_SALT 0.05
+
+#define GETNUMCODE(a) bpencoder[a - 'A']
+#define GETREVCODE(a) 5-bpencoder[a - 'A']
+
+
+extern double forbidden_entropy;
+
+
+typedef struct CNNParams_st
+{
+	double Ct1;
+	double Ct2;
+	double rlogc;
+	double kplus;
+	double kfac;
+	int saltMethod;
+	double gcContent;
+	double new_TM;
+	double dH[6][6][6][6];  // A-C-G-T + gap + initiation (dangling end, $ sign)
+	double dS[6][6][6][6];
+}CNNParams, * PNNParams;
+
+void nparam_InitParams(PNNParams nparm, double c1, double c2, double kp, int sm);
+int nparam_CountGCContent(char * seq );
+double nparam_GetEntropy(PNNParams nparm, char x0, char x1, char y0, char y1);
+double nparam_GetEnthalpy(PNNParams nparm, char x0, char x1, char y0, char y1);
+double nparam_CalcTM(double entropy,double enthalpy);
+double nparam_CalcSelfTM(PNNParams nparm, char* seq, int len);
+double nparam_CalcTwoTM(PNNParams nparm, char* seq1, char* seq2, int len);
+
+double nparam_GetInitialEntropy(PNNParams nparm) ;
+double calculateMeltingTemperatureBasic (char * seq);
+//void getThermoProperties (ppair_t* pairs, size_t count, poptions_t options);
+
+#endif

tools/ecoPCRFilter.py

@@ -0,0 +1,303 @@
+#!/usr/bin/env python
+
+import struct
+import sys
+import os
+import gzip
+
+
+#####
+#
+# Generic file function
+#
+#####
+
+class Filter(object):
+    
+    
+    def __init__(self,path):
+        self._path = path
+        self._taxonFile =  "%s.tdx" % self._path
+        self._ranksFile =  "%s.rdx" % self._path
+        self._namesFile =  "%s.ndx" % self._path
+        self._taxonomy, self._index, self._ranks, self._name = self.__readNodeTable()
+
+
+    def __universalOpen(self,file):
+        if isinstance(file,str):
+            if file[-3:] == '.gz':
+                rep = gzip.open(file)
+            else:
+                rep = open(file)
+        else:
+            rep = file
+        return rep
+
+    def __universalTell(self,file):
+        if isinstance(file, gzip.GzipFile):
+            file=file.myfileobj
+        return file.tell()
+    
+    def __fileSize(self,file):
+        if isinstance(file, gzip.GzipFile):
+            file=file.myfileobj
+        pos = file.tell()
+        file.seek(0,2)
+        length = file.tell()
+        file.seek(pos,0)
+        return length
+    
+    def __progressBar(self,pos,max,reset=False,delta=[]):
+        if reset:
+            del delta[:]
+        if not delta:
+            delta.append(time.time())
+            delta.append(time.time())
+    
+        delta[1]=time.time()
+        elapsed = delta[1]-delta[0]
+        percent = float(pos)/max * 100
+        remain = time.strftime('%H:%M:%S',time.gmtime(elapsed / percent * (100-percent)))
+        bar = '#' * int(percent/2)
+        bar+= '|/-\\-'[pos % 5]
+        bar+= ' ' * (50 - int(percent/2))
+        sys.stderr.write('\r%5.1f %% |%s] remain : %s' %(percent,bar,remain))
+
+
+
+
+    #####
+    #
+    # Iterator functions
+    #
+    #####
+    
+    
+    
+    def __ecoRecordIterator(self,file):
+        file = self.__universalOpen(file)
+        (recordCount,) = struct.unpack('> I',file.read(4))
+    
+        for i in xrange(recordCount):
+            (recordSize,)=struct.unpack('>I',file.read(4))
+            record = file.read(recordSize)
+            yield record
+    
+               
+    def __ecoNameIterator(self):
+        for record in self.__ecoRecordIterator(self._namesFile):
+            lrecord = len(record)
+            lnames  = lrecord - 16
+            (isScientificName,namelength,classLength,indextaxid,names)=struct.unpack('> I I I I %ds' % lnames, record)
+            name=names[:namelength]
+            classname=names[namelength:]
+            yield (name,classname,indextaxid)
+    
+    
+    def __ecoTaxonomicIterator(self):
+        for record in self.__ecoRecordIterator(self._taxonFile):
+            lrecord = len(record)
+            lnames  = lrecord - 16
+            (taxid,rankid,parentidx,nameLength,name)=struct.unpack('> I I I I %ds' % lnames, record)
+            yield  (taxid,rankid,parentidx,name)
+    
+    
+    def __ecoSequenceIterator(self,file):
+        for record in self.__ecoRecordIterator(file):
+            lrecord = len(record)
+            lnames  = lrecord - (4*4+20)
+            (taxid,seqid,deflength,seqlength,cptseqlength,string)=struct.unpack('> I 20s I I I %ds' % lnames, record)
+            de = string[:deflength]
+            seq = gzip.zlib.decompress(string[deflength:])
+            yield  (taxid,seqid,deflength,seqlength,cptseqlength,de,seq)
+    
+            
+    def __ecoRankIterator(self):
+        for record in self.__ecoRecordIterator(self._ranksFile):
+            yield  record
+    
+    
+    #####
+    #
+    # Indexes
+    #
+    #####
+    
+    def __ecoNameIndex(self):
+        indexName = [x for x in self.__ecoNameIterator()]
+        return indexName
+
+    def __ecoRankIndex(self):
+        rank = [r for r in self.__ecoRankIterator()]
+        return rank
+
+    def __ecoTaxonomyIndex(self):
+        taxonomy = []
+        index = {}
+        i = 0;
+        for x in self.__ecoTaxonomicIterator():
+            taxonomy.append(x)
+            index[x[0]] = i 
+            i = i + 1
+        return taxonomy, index
+
+    def __readNodeTable(self):
+        taxonomy, index = self.__ecoTaxonomyIndex()
+        ranks = self.__ecoRankIndex()
+        name = self.__ecoNameIndex()
+        return taxonomy,index,ranks,name
+
+
+    def findTaxonByTaxid(self,taxid):
+        return self._taxonomy[self._index[taxid]]
+
+
+
+    #####
+    #
+    # PUBLIC METHODS
+    #
+    #####
+
+
+    def subTreeIterator(self, taxid):
+        "return subtree for given taxonomic id "
+        idx = self._index[taxid]
+        yield self._taxonomy[idx]
+        for t in self._taxonomy:
+            if t[2] == idx:
+                for subt in self.subTreeIterator(t[0]):
+                    yield subt
+    
+    
+    def parentalTreeIterator(self, taxid):
+        """
+           return parental tree for given taxonomic id starting from
+           first ancester to the root.
+        """
+        taxon=self.findTaxonByTaxid(taxid)
+        while taxon[2]!= 0: 
+            yield taxon
+            taxon = self._taxonomy[taxon[2]]
+        yield self._taxonomy[0]
+    
+    
+    def ecoPCRResultIterator(self, file):
+        "iteration on ecoPCR result file"
+        file = self.__universalOpen(file)
+        data = ColumnFile(file,
+                          sep='|',
+                          types=(str,int,int,
+                                 str,int,str,
+                                 int,str,int,
+                                 str,int,str,
+                                 str,str,int,
+                                 str,int,int,
+                                 str,str),skip='#')
+        
+        for ac, sq_len, taxid,\
+            rank, sp_taxid, species,\
+            ge_taxid, genus, fa_taxid,\
+            family, sk_taxid, s_kgdom,\
+            strand, oligo_1, error_1,\
+            oligo_2, error_2, amp_len,\
+            sq_des, definition in data:
+            
+            yield {'ac':ac, 'sq_len':sq_len, 'taxid':taxid,
+                   'rank':rank, 'sp_taxid':sp_taxid, 'species':species,
+                   'ge_taxid':ge_taxid, 'genus':genus, 'fa_taxid':fa_taxid,
+                   'family':family, 'sk_taxid':sk_taxid, 's_kgdom':s_kgdom,
+                   'strand':strand, 'oligo_1':oligo_1, 'error_1':error_1,
+                   'oligo_2':oligo_2, 'error_2':error_2, 'amp_len':amp_len,
+                   'sq_des':sq_des, 'definition':definition}
+    
+    def rankFilter(self,rankid,filter):
+        return self._ranks[rankid] == filter
+
+
+    def lastCommonTaxon(self,taxid_1, taxid_2): 
+        t1 = [x[0] for x in self.parentalTreeIterator(taxid_1)]
+        t2 = [x[0] for x in self.parentalTreeIterator(taxid_2)]
+        t1.reverse()
+        t2.reverse()
+        count = t1 < t2 and len(t1) or len(t2)
+        for i in range(count):
+            if t1[i] != t2[i]:
+               return t1[i-1]
+    
+    
+    
+
+class ColumnFile(object):
+    
+    def __init__(self,stream,sep=None,strip=True,types=None,skip=None):
+        if isinstance(stream,str):
+            self._stream = open(stream)
+        elif hasattr(stream,'next'):
+            self._stream = stream
+        else:
+            raise ValueError,'stream must be string or an iterator'
+        self._delimiter=sep
+        self._strip=strip
+        if types:
+            self._types=[x for x in types]
+            for i in xrange(len(self._types)):
+                if self._types[i] is bool:
+                    self._types[i]=ColumnFile.str2bool
+        else:
+            self._types=None
+        self._skip = skip
+            
+    def str2bool(x):
+        return bool(eval(x.strip()[0].upper(),{'T':True,'V':True,'F':False}))
+                    
+    str2bool = staticmethod(str2bool)
+            
+        
+    def __iter__(self):
+        return self
+    
+    def next(self):
+        ligne = self._stream.next()
+        while ligne[0] == self._skip:
+            ligne = self._stream.next()
+        data = ligne.split(self._delimiter)
+        if self._strip or self._types:
+            data = [x.strip() for x in data]
+        if self._types:
+            it = self.endLessIterator(self._types)
+            data = [x[1](x[0]) for x in ((y,it.next()) for y in data)]
+        return data
+    
+    def endLessIterator(self,endedlist):
+        for x in endedlist:
+            yield x
+        while(1):
+            yield endedlist[-1]
+
+
+class Table(list):
+    
+    def __init__(self, headers, types):
+        list.__init__(self)
+        self.headers = headers
+        self.types = types
+        self.lines = []
+        
+    def printTable(self):
+        for h in self.headers:
+            print "\t%s\t|" % h,
+        print "\n"
+        for l in self.lines:
+            for c in l:
+                print "\t%s\t|" % c
+            print "\n"
+            
+    def getColumn(self,n):
+        print "\t%s\n" % self.header[n]
+        for i in range(len(self.lines)):
+            print "\t%s\n" % i[n]
+        
+        
+        
+

tools/ecoPCRFormat.py

@@ -7,6 +7,12 @@ import sys
 import time
 import getopt
 
+try:
+    import psycopg2
+    _dbenable=True
+except ImportError:
+    _dbenable=False
+
 #####
 #
 #
@@ -68,8 +74,7 @@ def endLessIterator(endedlist):
         yield x
     while(1):
         yield endedlist[-1]
-    
-    
+   
 class ColumnFile(object):
     
     def __init__(self,stream,sep=None,strip=True,types=None):
@@ -135,7 +140,7 @@ def bsearchTaxon(taxonomy,taxid):
     else:
         return None
         
-        
+    
     
 def readNodeTable(file):
 
@@ -149,7 +154,6 @@ def readNodeTable(file):
                               bool,bool,bool,str))
     print >>sys.stderr,"Reading taxonomy dump file..."
     taxonomy=[[n[0],n[2],n[1]] for n in nodes]
-    
     print >>sys.stderr,"List all taxonomy rank..."    
     ranks =list(set(x[1] for x in taxonomy))
     ranks.sort()
@@ -171,15 +175,14 @@ def readNodeTable(file):
         
     return taxonomy,ranks,index
 
-def scientificNameIterator(file):
+def nameIterator(file):
     file = universalOpen(file)
     names = ColumnFile(file, 
                        sep='|', 
                        types=(int,str,
                               str,str))
     for taxid,name,unique,classname,white in names:
-        if classname == 'scientific name':
-            yield taxid,name
+        yield taxid,name,classname
         
 def mergedNodeIterator(file):
     file = universalOpen(file)
@@ -201,8 +204,12 @@ def readTaxonomyDump(taxdir):
     taxonomy,ranks,index = readNodeTable('%s/nodes.dmp' % taxdir)
     
     print >>sys.stderr,"Adding scientific name..."
-    for taxid,name in scientificNameIterator('%s/names.dmp' % taxdir):
-        taxonomy[index[taxid]].append(name)
+
+    alternativeName=[]
+    for taxid,name,classname in nameIterator('%s/names.dmp' % taxdir):
+        alternativeName.append((name,classname,index[taxid]))
+        if classname == 'scientific name':
+            taxonomy[index[taxid]].append(name)
         
     print >>sys.stderr,"Adding taxid alias..."
     for taxid,current in mergedNodeIterator('%s/merged.dmp' % taxdir):
@@ -212,9 +219,58 @@ def readTaxonomyDump(taxdir):
     for taxid in deletedNodeIterator('%s/delnodes.dmp' % taxdir):
         index[taxid]=None
     
-    return taxonomy,ranks,index
+    return taxonomy,ranks,alternativeName,index
 
+def readTaxonomyDB(dbname):
+    connection = psycopg2.connect(database=dbname)
+    
+    cursor = connection.cursor()
+    cursor.execute("select numid,rank,parent from ncbi_taxonomy.taxon")
+    taxonomy=[list(x) for x in cursor]
 
+    cursor.execute("select rank_class from ncbi_taxonomy.taxon_rank_class order by rank_class")
+    ranks=cursor.fetchall()
+    ranks = dict(map(None,(x[0] for x in ranks),xrange(len(ranks))))
+    
+    print >>sys.stderr,"Sorting taxons..."
+    taxonomy.sort(taxonCmp)
+
+    print >>sys.stderr,"Indexing taxonomy..."
+    index = {}
+    for t in taxonomy:
+        index[t[0]]=bsearchTaxon(taxonomy, t[0])
+    
+    print >>sys.stderr,"Indexing parent and rank..."
+    for t in taxonomy:
+        t[1]=ranks[t[1]]
+        try:
+            t[2]=index[t[2]]
+        except KeyError,e:
+            if t[2] is None and t[0]==1:
+                t[2]=index[t[0]]
+            else:
+                raise e
+        
+    cursor.execute("select taxid,name,category from ncbi_taxonomy.name")
+    
+    alternativeName=[]
+    for taxid,name,classname in cursor:
+        alternativeName.append((name,classname,index[taxid]))
+        if classname == 'scientific name':
+            taxonomy[index[taxid]].append(name)
+    
+    cursor.execute("select old_numid,current_numid from ncbi_taxonomy.taxon_id_alias")
+ 
+    print >>sys.stderr,"Adding taxid alias..."
+    for taxid,current in cursor:
+        if current is not None:
+            index[taxid]=index[current]
+        else:
+            index[taxid]=None
+            
+       
+    return taxonomy,ranks,alternativeName,index
+    
 #####
 #
 #
@@ -267,28 +323,55 @@ def genbankEntryParser(entry):
         Tx = None
     return {'id':Id,'taxid':Tx,'definition':De,'sequence':Sq}
 
-_fastaParseID = re.compile('(?<=^>)[^ ]+')
-_fastaParseDE = re.compile('(?<=^>).+',)   
-_fastaParseSQ = re.compile('^[^>].+',re.MULTILINE+re.DOTALL)
-_fastaParseTX = re.compile('(?<=[[Tt]axon:) *[0-9]+ *(?=])')
-  
-def fastaEntryParser(entry):
-    Id = _fastaParseID.findall(entry)[0]
-    De = _fastaParseDE.findall(entry)[0].split(None,1)[1:]
-    if not De:
-        De=''
-    else:
-        De=De[0]
-    Sq = cleanSeq(_fastaParseSQ.findall(entry)[0].upper())  
+######################
+
+_cleanDef = re.compile('[\nDE]')
+
+def cleanDef(definition):
+    return _cleanDef.sub('',definition)
+
+_emblParseID = re.compile('(?<=^ID {3})[^ ]+(?=;)',re.MULTILINE)   
+_emblParseDE = re.compile('(?<=^DE {3}).+?\. *$(?=[^ ])',re.MULTILINE+re.DOTALL)   
+_emblParseSQ = re.compile('(?<=^  ).+?(?=^//$)',re.MULTILINE+re.DOTALL)  
+_emblParseTX = re.compile('(?<= /db_xref="taxon:)[0-9]+(?=")')
+
+def emblEntryParser(entry):
+    Id = _emblParseID.findall(entry)[0]
+    De = ' '.join(cleanDef(_emblParseDE.findall(entry)[0]).split())
+    Sq = cleanSeq(_emblParseSQ.findall(entry)[0].upper())
     try:
-        Tx = int(_fastaParseTX.findall(entry)[0])
+        Tx = int(_emblParseTX.findall(entry)[0])
     except IndexError:
         Tx = None
-          
     return {'id':Id,'taxid':Tx,'definition':De,'sequence':Sq}
+
+
+######################
+
+_fastaSplit=re.compile(';\W*')
+
+def parseFasta(seq):
+    seq=seq.split('\n')
+    title = seq[0].strip()[1:].split(None,1)
+    id=title[0]
+    if len(title) == 2:
+        field = _fastaSplit.split(title[1])
+    else:
+        field=[]
+    info = dict(x.split('=',1) for x in field if '=' in x)
+    definition = ' '.join([x for x in field if '=' not in x])
+    seq=(''.join([x.strip() for x in seq[1:]])).upper()   
+    return id,seq,definition,info
+
+  
+def fastaEntryParser(entry):
+    id,seq,definition,info = parseFasta(entry)
+    Tx = info.get('taxid',None)   
+    if Tx is not None:
+        Tx=int(Tx)
+    return {'id':id,'taxid':Tx,'definition':definition,'sequence':seq}
     
 
-    
 def sequenceIteratorFactory(entryParser,entryIterator):
     def sequenceIterator(file):
         for entry in entryIterator(file):
@@ -381,6 +464,22 @@ def ecoRankPacker(rank):
     
     return packed
                 
+def ecoNamePacker(name):
+    
+    namelength = len(name[0])
+    classlength= len(name[1])
+    totalSize =  namelength + classlength + 4 + 4 + 4 + 4
+    
+    packed = struct.pack('> I I I I I %ds %ds' % (namelength,classlength),
+                         totalSize,
+                         int(name[1]=='scientific name'),
+                         namelength,
+                         classlength,
+                         name[2],
+                         name[0],
+                         name[1])
+    
+    return packed
     
 def ecoSeqWriter(file,input,taxindex,parser):
     output = open(file,'wb')
@@ -438,18 +537,40 @@ def ecoRankWriter(file,ranks):
         output.write(ecoRankPacker(rank))
 
     output.close()
+
+def nameCmp(n1,n2):
+    name1=n1[0].upper()
+    name2=n2[0].upper()
+    if name1 < name2:
+        return -1
+    elif name1 > name2:
+        return 1
+    return 0
+
+
+def ecoNameWriter(file,names):
+    output = open(file,'wb')
+    output.write(struct.pack('> I',len(names)))
+
+    names.sort(nameCmp)
+    
+    for name in names:
+        output.write(ecoNamePacker(name))
+
+    output.close()
     
 def ecoDBWriter(prefix,taxonomy,seqFileNames,parser):
     
     ecoRankWriter('%s.rdx' % prefix, taxonomy[1])
     ecoTaxWriter('%s.tdx' % prefix, taxonomy[0])
-    
+    ecoNameWriter('%s.ndx' % prefix, taxonomy[2])
+  
     filecount = 0
     for filename in seqFileNames:
         filecount+=1
         sk=ecoSeqWriter('%s_%03d.sdx' % (prefix,filecount), 
                      filename, 
-                     taxonomy[2], 
+                     taxonomy[3], 
                      parser)
         if sk:
             print >>sys.stderr,"Skipped entry :"
@@ -464,37 +585,67 @@ def ecoParseOptions(arguments):
            }
     
     o,filenames = getopt.getopt(arguments,
-                                'ht:n:gf',
+                                'ht:T:n:gfe',
                                 ['help',
                                  'taxonomy=',
+                                 'taxonomy_db=',
                                  'name=',
                                  'genbank',
-                                 'fasta'])
+                                 'fasta',
+                                 'embl'])
     
     for name,value in o:
         if name in ('-h','--help'):
-            pass
+            printHelp()
+            exit()
         elif name in ('-t','--taxonomy'):
+            opt['taxmod']='dump'
             opt['taxdir']=value
+        elif name in ('-T','--taxonomy_db'):
+            opt['taxmod']='db'
+            opt['taxdb']=value
         elif name in ('-n','--name'):
             opt['prefix']=value
         elif name in ('-g','--genbank'):
             opt['parser']=sequenceIteratorFactory(genbankEntryParser,
-                                                  entryIterator
-                                                  )
+                                                  entryIterator)
+
         elif name in ('-f','--fasta'):
             opt['parser']=sequenceIteratorFactory(fastaEntryParser,
                                                   fastaEntryIterator)
+            
+        elif name in ('-e','--embl'):
+            opt['parser']=sequenceIteratorFactory(emblEntryParser,
+                                                  entryIterator)
         else:
             raise ValueError,'Unknown option %s' % name
 
     return opt,filenames
 
+def printHelp():
+    print "-----------------------------------"
+    print " ecoPCRFormat.py"
+    print "-----------------------------------"
+    print "ecoPCRFormat.py [option] <argument>"
+    print "-----------------------------------"
+    print "-e    --embl        :[E]mbl format"
+    print "-f    --fasta       :[F]asta format"
+    print "-g    --genbank     :[G]enbank format"
+    print "-h    --help        :[H]elp - print this help"
+    print "-n    --name        :[N]ame of the new database created"
+    print "-t    --taxonomy    :[T]axonomy - path to the taxonomy database"
+    print "                    :bcp-like dump from GenBank taxonomy database."
+    print "-----------------------------------"
+
 if __name__ == '__main__':
     
     opt,filenames = ecoParseOptions(sys.argv[1:])
     
-    taxonomy = readTaxonomyDump(opt['taxdir'])
-    
+    if opt['taxmod']=='dump':
+        taxonomy = readTaxonomyDump(opt['taxdir'])
+    elif opt['taxmod']=='db':
+        taxonomy = readTaxonomyDB(opt['taxdb'])
+        
+   
     ecoDBWriter(opt['prefix'], taxonomy, filenames, opt['parser'])
     

tools/ecoSort.py

@@ -0,0 +1,811 @@
+#!/usr/bin/env python
+
+import struct
+import sys
+import os
+import gzip
+import re
+import string
+
+from reportlab.graphics.shapes import *
+from reportlab.graphics.charts.barcharts import VerticalBarChart
+from reportlab.graphics.charts.piecharts import Pie
+from reportlab.lib.styles import getSampleStyleSheet
+from reportlab.lib.units import cm
+from reportlab.lib import colors
+from reportlab.platypus import *
+
+
+#####
+#
+# Generic file function
+#
+#####
+
+class Filter(object):
+    """
+       This object provides different iterators and method :
+        * findTaxonByTaxid
+        * subTreeIterator
+        * parentalTreeIterator
+        * ecoPCRResultIterator
+        * rankFilter
+        * lastCommonTaxon
+        
+        see each method for more informations
+    """
+    
+    def __init__(self,path):
+        self._path = path
+        self._taxonFile =  "%s.tdx" % self._path
+        self._ranksFile =  "%s.rdx" % self._path
+        self._namesFile =  "%s.ndx" % self._path
+        self._taxonomy, self._index, self._ranks, self._name = self.__readNodeTable()
+
+
+    def __universalOpen(self,file):
+        if isinstance(file,str):
+            if file[-3:] == '.gz':
+                rep = gzip.open(file)
+            else:
+                rep = open(file)
+        else:
+            rep = file
+        return rep
+
+    def __universalTell(self,file):
+        if isinstance(file, gzip.GzipFile):
+            file=file.myfileobj
+        return file.tell()
+    
+    def __fileSize(self,file):
+        if isinstance(file, gzip.GzipFile):
+            file=file.myfileobj
+        pos = file.tell()
+        file.seek(0,2)
+        length = file.tell()
+        file.seek(pos,0)
+        return length
+    
+    def __progressBar(self,pos,max,reset=False,delta=[]):
+        if reset:
+            del delta[:]
+        if not delta:
+            delta.append(time.time())
+            delta.append(time.time())
+    
+        delta[1]=time.time()
+        elapsed = delta[1]-delta[0]
+        percent = float(pos)/max * 100
+        remain = time.strftime('%H:%M:%S',time.gmtime(elapsed / percent * (100-percent)))
+        bar = '#' * int(percent/2)
+        bar+= '|/-\\-'[pos % 5]
+        bar+= ' ' * (50 - int(percent/2))
+        sys.stderr.write('\r%5.1f %% |%s] remain : %s' %(percent,bar,remain))
+
+
+
+
+    #####
+    #
+    # Iterator functions
+    #
+    #####
+    
+    
+    
+    def __ecoRecordIterator(self,file):
+        file = self.__universalOpen(file)
+        (recordCount,) = struct.unpack('> I',file.read(4))
+    
+        for i in xrange(recordCount):
+            (recordSize,)=struct.unpack('>I',file.read(4))
+            record = file.read(recordSize)
+            yield record
+    
+               
+    def __ecoNameIterator(self):
+        for record in self.__ecoRecordIterator(self._namesFile):
+            lrecord = len(record)
+            lnames  = lrecord - 16
+            (isScientificName,namelength,classLength,indextaxid,names)=struct.unpack('> I I I I %ds' % lnames, record)
+            name=names[:namelength]
+            classname=names[namelength:]
+            yield (name,classname,indextaxid)
+    
+    
+    def __ecoTaxonomicIterator(self):
+        for record in self.__ecoRecordIterator(self._taxonFile):
+            lrecord = len(record)
+            lnames  = lrecord - 16
+            (taxid,rankid,parentidx,nameLength,name)=struct.unpack('> I I I I %ds' % lnames, record)
+            yield  (taxid,rankid,parentidx,name)
+    
+    
+    def __ecoSequenceIterator(self,file):
+        for record in self.__ecoRecordIterator(file):
+            lrecord = len(record)
+            lnames  = lrecord - (4*4+20)
+            (taxid,seqid,deflength,seqlength,cptseqlength,string)=struct.unpack('> I 20s I I I %ds' % lnames, record)
+            de = string[:deflength]
+            seq = gzip.zlib.decompress(string[deflength:])
+            yield  (taxid,seqid,deflength,seqlength,cptseqlength,de,seq)
+    
+            
+    def __ecoRankIterator(self):
+        for record in self.__ecoRecordIterator(self._ranksFile):
+            yield  record
+    
+    
+    #####
+    #
+    # Indexes
+    #
+    #####
+    
+    def __ecoNameIndex(self):
+        indexName = [x for x in self.__ecoNameIterator()]
+        return indexName
+
+    def __ecoRankIndex(self):
+        rank = [r for r in self.__ecoRankIterator()]
+        return rank
+
+    def __ecoTaxonomyIndex(self):
+        taxonomy = []
+        index = {}
+        i = 0;
+        for x in self.__ecoTaxonomicIterator():
+            taxonomy.append(x)
+            index[x[0]] = i 
+            i = i + 1
+        return taxonomy, index
+
+    def __readNodeTable(self):
+        taxonomy, index = self.__ecoTaxonomyIndex()
+        ranks = self.__ecoRankIndex()
+        name = self.__ecoNameIndex()
+        return taxonomy,index,ranks,name
+
+
+    #####
+    #
+    # PUBLIC METHODS
+    #
+    #####
+
+    def findTaxonByTaxid(self,taxid):
+        """
+            Returns a list containing [taxid,rankid,parent_index,nameLength,name]
+            It takes one argument : a taxonomic id
+        """
+        return self._taxonomy[self._index[taxid]]
+
+
+    def subTreeIterator(self, taxid):
+        """
+            Returns subtree for given taxid from first child
+            to last child. It takes one argument : a taxonomic id
+        """
+        idx = self._index[taxid]
+        yield self._taxonomy[idx]
+        for t in self._taxonomy:
+            if t[2] == idx:
+                for subt in self.subTreeIterator(t[0]):
+                    yield subt
+    
+    
+    def parentalTreeIterator(self, taxid):
+        """
+           return parental tree for given taxonomic id starting from
+           first ancester to the root.
+        """
+        taxon=self.findTaxonByTaxid(taxid)
+        while taxon[2]!= 0: 
+            yield taxon
+            taxon = self._taxonomy[taxon[2]]
+        yield self._taxonomy[0]    
+    
+    
+    def ecoPCRResultIterator(self, file):
+        """
+           iteration on ecoPCR result file"
+           It returns a dictionnary
+        """
+        file = self.__universalOpen(file)
+        data = ColumnFile(file,
+                          sep='|',
+                          types=(str,int,int,
+                                 str,int,str,
+                                 int,str,int,
+                                 str,int,str,
+                                 str,str,int,
+                                 str,int,int,
+                                 str,str),skip='#')
+     
+        
+        for ac, sq_len, taxid,\
+            rank, sp_taxid, species,\
+            ge_taxid, genus, fa_taxid,\
+            family, sk_taxid, s_kgdom,\
+            strand, oligo_1, error_1,\
+            oligo_2, error_2, amp_len,\
+            sq_des, definition in data:
+            
+            yield {'ac':ac, 'sq_len':sq_len, 'taxid':taxid,
+                   'rank':rank, 'sp_taxid':sp_taxid, 'species':species,
+                   'ge_taxid':ge_taxid, 'genus':genus, 'fa_taxid':fa_taxid,
+                   'family':family, 'sk_taxid':sk_taxid, 's_kgdom':s_kgdom,
+                   'strand':strand, 'oligo_1':oligo_1, 'error_1':error_1,
+                   'oligo_2':oligo_2, 'error_2':error_2, 'amp_len':amp_len,
+                   'sq_des':sq_des, 'definition':definition}
+    
+    def rankFilter(self,rankid,filter):
+        """
+            boolean telling whether rankid match filter
+            takes 2 arguments : 
+            1- rankid
+            2- filter (i.e genus)
+        """
+        return self._ranks[rankid] == filter
+
+
+    def lastCommonTaxon(self,taxid_1, taxid_2):
+        """
+            returns a last common parent for two given taxon.
+            It starts from the root and goes down the tree
+            until their parents diverge.
+            It takes 2 arguments :
+            1- taxid 1
+            2- taxid 2
+        """
+        t1 = [x[0] for x in self.parentalTreeIterator(taxid_1)]
+        t2 = [x[0] for x in self.parentalTreeIterator(taxid_2)]
+        t1.reverse()
+        t2.reverse()
+        count = t1 < t2 and len(t1) or len(t2)
+        for i in range(count):
+            if t1[i] != t2[i]:
+               return t1[i-1]
+        return t1[count-1]
+       
+    
+    
+    
+
+class ColumnFile(object):
+    """
+        cut an ecoPCR file into a list
+    """
+    def __init__(self,stream,sep=None,strip=True,types=None,skip=None):
+        if isinstance(stream,str):
+            self._stream = open(stream)
+        elif hasattr(stream,'next'):
+            self._stream = stream
+        else:
+            raise ValueError,'stream must be string or an iterator'
+        self._delimiter=sep
+        self._strip=strip
+        if types:
+            self._types=[x for x in types]
+            for i in xrange(len(self._types)):
+                if self._types[i] is bool:
+                    self._types[i]=ColumnFile.str2bool
+        else:
+            self._types=None
+        self._skip = skip
+        self._oligo = {}
+            
+    def str2bool(x):
+        return bool(eval(x.strip()[0].upper(),{'T':True,'V':True,'F':False}))
+                    
+    str2bool = staticmethod(str2bool)
+            
+        
+    def __iter__(self):
+        return self
+    
+    def next(self):
+        ligne = self._stream.next()
+        while ligne[0] == self._skip:
+            ligne = self._stream.next()
+        data = ligne.split(self._delimiter)
+        if self._strip or self._types:
+            data = [x.strip() for x in data]
+        if self._types:
+            it = self.endLessIterator(self._types)
+            data = [x[1](x[0]) for x in ((y,it.next()) for y in data)]
+        return data
+    
+    def endLessIterator(self,endedlist):
+        for x in endedlist:
+            yield x
+        while(1):
+            yield endedlist[-1]
+        
+    def getOligo(self,line):
+        if line[2:8] == 'direct':
+            r = re.compile('(?<=direct  strand oligo1 : )[A-Z]+(?= *)')
+            self._oligo['o1'] = r.findall(line)
+        if line[2:9] == 'reverse':
+            r = re.compile('(?<=reverse strand oligo2 : )[A-Z]+(?= *)')
+            self._oligo['o2'] = r.findall(line) 
+        return None
+            
+            
+
+
+###########
+#
+# DATA STRUCTURE
+#
+###########
+
+
+class ecoTable(list):
+    """
+        Data object inheriting from list
+    """
+    def __init__(self, headers, types):
+        list.__init__(self)
+        self.headers = headers
+        self.types = types
+
+
+    def __setitem__ (self,key,value):
+        """
+            method overloaded to check data types
+        """
+        for e in range(len(value)):
+            value[e] = self.types[e](value[e])
+        list.__setitem__(self,key,value)
+        
+    def __getitem__(self,index):
+        newtable = ecoTable(self.headers,self.types)
+        if isinstance(index,slice):
+            newtable.extend(list.__getitem__(self,index))
+        else:
+            newtable.append(list.__getitem__(self,index))
+        
+        return newtable
+    
+    def getColumns(self,columnList):
+        newhead = [self.headers[x] for x in columnList]
+        newtype = [self.types[x] for x in columnList]
+        newtable = ecoTable(newhead,newtype)
+        for line in self:
+            newtable.append([line[x] for x in columnList])
+        
+        return newtable
+
+
+###########
+#
+# PARSE FUNCTIONS
+#
+###########
+
+def _parseOligoResult(filter,file,strand):
+    seq = {}
+    
+    if strand == 'direct':
+        key = 'oligo_1'
+    elif strand == 'reverse':
+        key = 'oligo_2'
+        
+    for s in filter.ecoPCRResultIterator(file):
+        o = s[key]
+        taxid = s['taxid']
+        if not seq.has_key(o):
+            seq[o] = [1,taxid]
+        else:
+            seq[o][0] = seq[o][0] + 1
+            seq[o][1] = filter.lastCommonTaxon(seq[o][1],taxid)
+    return seq
+
+    
+def _parseTaxonomyResult(table):
+    tax = {}
+    for l in table:
+        taxid = l[2]
+        scName = l[3]
+        count = l[1]
+        if not tax.has_key(taxid):
+            tax[taxid] = [1,scName,count]
+        else:
+            tax[taxid][0] = tax[taxid][0] + 1
+            tax[taxid][2] = tax[taxid][2] + count
+    return tax
+
+
+def _sortTable(e1,e2):
+    e1 = e1[1]
+    e2 = e2[1]
+    if e1 < e2:
+        return 1
+    if e1 > e2:
+        return -1
+    return 0 
+
+
+def _countOligoMismatch(o1,o2):
+    """
+        define mismatch between two oligonucleotids
+        return number of mismatch
+    """ 
+    mmatch = 0
+    if len(o1) < len(o2):
+        mmatch = int(len(o2) - len(o1))
+    for i in range(len(o1)):
+        try:
+            if o1[i] != o2[i]:
+                mmatch = mmatch + 1
+        except:
+            mmatch = mmatch + 1    
+
+    return mmatch
+
+###########
+#
+# TOOLS FUNCTIONS
+#
+###########
+
+def customSort(table,x,y):
+    """
+        
+    """
+    x = x-1
+    y = y-1
+    h = (table.headers[x],table.headers[y])
+    t = (table.types[x],table.types[y])
+    cTable = ecoTable(h,t)
+    
+    tmp = {}
+    
+    for l in table:
+        if tmp.has_key(l[x]):
+            tmp[l[x]] = tmp[l[x]] + l[y]
+        else:
+            tmp[l[x]] = l[y]
+    
+    for k,v in tmp.items():
+        cTable.append([k,v])
+    
+    return cTable
+    
+
+def countColumnOccurrence(table,x):
+    x = x-1
+    h = (table.headers[x],"count")
+    t = (table.types[x],int)
+    cTable = Table(h,t)
+    
+    tmp = {}
+    
+    for l in table:
+        if tmp.has_key(l[x]):
+            tmp[l[x]] = tmp[l[x]] + 1
+        else:
+            tmp[l[x]] = 1
+    
+    for k,v in tmp.items():
+        cTable.append([k,v])
+    
+    return cTable
+
+
+def buildSpecificityTable(table):
+    header =  ("mismatch","taxon","count")
+    type = (int,str,int)
+    speTable = ecoTable(header,type)
+    
+    tmp = {}
+    for l in table:
+        if not tmp.has_key(l[5]):
+            tmp[l[5]] = {}
+        if not tmp[l[5]].has_key(l[3]):
+            tmp[l[5]][l[3]] = l[1]
+        else:
+            tmp[l[5]][l[3]] = tmp[l[5]][l[3]] + l[1]
+    
+    for mismatch in tmp.items():
+        for taxon,count in mismatch[1].items():
+            speTable.append([mismatch[0],taxon,count])     
+
+    return speTable
+   
+
+def buildOligoTable(table, file, filter, oligoRef, strand='direct'):
+    """
+        Fills and sorts a Table object with ecoPCR result file
+        
+        Takes 4 arguments
+        1- Table object
+        2- ecoPCR result file path
+        3- Filter Object
+        4- the oligo used in ecoPCR
+        5- the oligo type : direct or reverse
+        
+    """
+    seq = _parseOligoResult(filter, file, strand)
+    
+    i = 0
+    for oligo, info in seq.items():
+        table.append(0)
+        count, lctTaxid = info[0], info[1]
+        scName = filter.findTaxonByTaxid(info[1])[3]
+        rank = filter._ranks[filter.findTaxonByTaxid(info[1])[1]]
+        mismatch = _countOligoMismatch(oligoRef,oligo)
+        table[i]=[oligo,count,lctTaxid,scName,rank,mismatch]
+        i = i + 1
+        
+    table.sort(_sortTable)
+
+ 
+def buildTaxonomicTable(table):
+    """
+        Fill a Table object with a taxonomic synthesis
+    """
+    taxHeaders = ("scName","numOfOligo","numOfAmpl","taxid")
+    taxTypes = (str, int, int, int)
+    taxTable = ecoTable(taxHeaders, taxTypes)
+    
+    tax = _parseTaxonomyResult(table) 
+  
+    i = 0
+    for taxid, info in tax.items():
+        taxTable.append(0)
+        numOfOligo, scName, numOfAmpl = info[0], info[1], info[2]
+        taxTable[i]=[scName,numOfOligo,numOfAmpl,taxid]
+        i = i + 1 
+
+    taxTable.sort(_sortTable)
+
+    return taxTable
+
+def _parseSequenceResult(filter,file,id):
+    sequences = {}
+    idIndex = {}
+    
+    if id == 'family':
+        key = 'fa_taxid'
+    elif id == 'genus':
+        key = 'ge_taxid'
+    else:
+        key = 'taxid'
+    
+    for s in filter.ecoPCRResultIterator(file):
+        seq = s['sq_des']
+        id = s[key]
+        if not idIndex.has_key(id):
+            idIndex[id] = []
+        if not sequences.has_key(seq):
+            sequences[seq] = [id]
+        else:
+            sequences[seq].append(id)
+    return sequences, idIndex
+
+
+def _sameValuesInList(array):
+    for i in range(len(array)-1):
+        if array[i] != array[i+1]:
+            return False
+    return True
+
+
+def _sortSequences(file,filter):
+    
+    sequences, idIndex = _parseSequenceResult(filter,file,'species')
+    
+    for s,id in sequences.items():
+        if len(id) == 1 or _sameValuesInList(id):
+            idIndex[id[0]].append(1)
+        else:
+            for e in id:
+                idIndex[e].append(0)
+    
+   
+    for id,values in idIndex.items():
+        idIndex[id] = float(values.count(1)) / float(len(values)) * 100
+
+            
+    identified = {}
+    non_identified = {}
+    ambiguous = {}
+     
+    return sequences, idIndex
+
+def getIntraSpeciesDiversity(table,file,filter):
+    
+    intraDiv = {} 
+    
+    seq, idIndex = _sortSequences(file,filter)
+    
+    for id,percent in idIndex.items():
+        if percent == 100:
+            intraDiv[id] = [0,[]]
+            for seq,idList in sequences.items():
+                if id in idList:
+                    intraDiv[id][0] = intraDiv[id][0] + 1
+                    intraDiv[id][1].append(seq)
+                    
+    for id, values in intraDiv.items():
+        table.append(id,values[0],values[1])
+                    
+    
+
+###########
+#
+# OUTPUT FUNCTIONS
+#
+###########
+
+def printTable(table):
+    """
+        Displays the content a of Table object
+        Take 1 arguments
+        1- Table object
+    """
+
+    format = ("%20s | " * len(table.headers))[:-3]
+    print format % tuple([str(e) for e in table.headers ]) +"\n" + "-"*23*len(table.headers)
+    for l in table:
+        print format % tuple([str(e) for e in l ])
+    print "# %d results" % len(table)
+       
+        
+def saveAsCSV(table,path):
+    """
+        Creates a csv file from a Table object
+        Takes 2 arguments
+        1- Table object
+        2- path of the file-to-be    
+    """
+    file = open(path,'w')
+    file.write(','.join([str(e) for e in table.headers ]) + "\n")
+    for l in table:
+        file.write(','.join([str(e) for e in l ]) + "\n")
+    file.close()
+
+
+def grepTable(table,col,pattern):
+    """
+        Filters a Table object with regular expression
+        Takes 3 arguments :
+        1- Table object
+        2- number of column to match with
+        3- regular expression pattern
+        
+        Returns a Table object
+    """
+    col = col -1
+    p = re.compile(pattern, re.IGNORECASE)
+    out = ecoTable(table.headers,table.types)
+    for l in table:
+        if p.search(l[col]):
+            out.append(l)
+    return out
+
+
+###########
+#
+# GRAPH FUNCTIONS
+#
+###########
+
+class EcoGraph(object):
+    
+    def __init__(self):
+        self._styles = getSampleStyleSheet()
+        
+        self._element = []
+        self._element.append(self._box(Paragraph("EcoPCR report",  self._styles['Title'])))
+        self._element.append(Spacer(0, 0.5 * cm))
+    
+    def _box(self,flt, center=True):
+        box_style = [('BOX', (0, 0), (-1, -1), 0.5, colors.lightgrey)]
+        if center:
+            box_style += [('ALIGN', (0, 0), (-1, -1), 'CENTER')]
+        return Table([[flt]], style=box_style)
+
+    def _addChart(self,chart,title):
+        drawing = Drawing(300, 250)
+        drawing.add(chart)
+        self._element.append(self._box(Paragraph(title, self._styles['Normal'])))
+        self._element.append(self._box(drawing))
+        self._element.append(Spacer(0, 0.5 * cm))
+    
+    def _formatData(self,table):
+        data, label = [],[]
+        for i in range(len(table)):
+            label.append(table[i][0])
+            data.append(table[i][1])
+        return data, label
+     
+    def makePie(self, table, title):
+        data, label = self._formatData(table)
+        pie = Pie()
+        pie.x = 100
+        pie.y = 100
+        pie.data = data
+        pie.labels = label
+        self._addChart(pie, title)
+    
+    def makeHistogram(self, table, title):    
+        data, label = self._formatData(table)
+        data = [tuple(data)]
+        
+        histo = VerticalBarChart() 
+        histo.x = 10 
+        histo.y = 70 
+        histo.height = 150 
+        histo.width = 300
+        histo.bars.strokeWidth = 1
+        histo.barSpacing = 1
+        histo.barLabels.dy = 5
+        histo.barLabelFormat = '%d'
+        histo.barLabels.fontSize = 9 - (len(data[0])/10)
+        histo.data = data
+        
+        histo.categoryAxis.labels.boxAnchor = 'e'
+        histo.categoryAxis.labels.textAnchor = 'start'        
+        histo.categoryAxis.labels.dx = -40
+        histo.categoryAxis.labels.dy = -50
+        histo.categoryAxis.labels.angle = 45
+        histo.categoryAxis.labels.width = 10
+        histo.categoryAxis.labels.height = 4
+        histo.categoryAxis.categoryNames = label
+        histo.categoryAxis.strokeWidth = 1
+        histo.categoryAxis.labels.fontSize = 8
+                
+        histo.valueAxis.valueMin = min(data[0])*0.7 
+        histo.valueAxis.valueMax = max(data[0])
+        step = (max(data[0]) - min(data[0])) / 10
+        histo.valueAxis.valueStep = step > 1 and step or 1
+        
+        self._addChart(histo, title)
+        
+    def makeReport(self,path):
+        doc = SimpleDocTemplate(path)       
+        doc.build(self._element)
+
+    
+###################### 
+
+ 
+def init():
+    file = "/Users/bessiere/Documents/workspace/ecoPCR/src/toto.tmp"
+    oligo = {'o1':'ATGTTTAAAA','o2':'ATGGGGGTATTG'}
+     
+    filter = Filter("/ecoPCRDB/gbmam")
+    
+    headers = ("oligo", "Num", "LCT Taxid", "Sc Name", "Rank", "distance")
+    types = (str, int, int, str, str, int)
+    
+    o1Table = ecoTable(headers, types)
+    o2Table = ecoTable(headers, types)
+    
+    buildOligoTable(o1Table, file, filter, oligo['o1'], 'direct')
+    buildOligoTable(o2Table, file, filter, oligo['o2'], 'reverse')
+
+ 
+    taxTable = buildTaxonomicTable(o1Table)
+    speTable = buildSpecificityTable(o1Table)
+       
+    return o1Table, o2Table, taxTable
+
+
+
+def start():
+    file = "/Users/bessiere/Documents/workspace/ecoPCR/src/toto.tmp"
+    filter = Filter("/ecoPCRDB/gbmam")
+       
+    speHeaders = ("taxid","num of seq","list of seq")
+    speTypes = (int,int,list) 
+    speTable = ecoTable(speHeaders,speTypes)
+        
+    getIntraSpeciesDiversity(speTable, file, filter)
+
+
+