[med-svn] [libbpp-raa] 02/06: New upstream version 2.3.1
Andreas Tille
tille at debian.org
Wed Jun 14 09:56:04 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository libbpp-raa.
commit 56807c250101d3c53e0737460898c1ea3ef52c3c
Author: Andreas Tille <tille at debian.org>
Date: Wed Jun 14 11:44:10 2017 +0200
New upstream version 2.3.1
---
CMakeLists.txt | 194 +-
ChangeLog | 4 +
Doxyfile | 2662 +++++++++++--------
INSTALL.txt | 19 +-
bpp-raa.spec | 132 +-
debian/changelog | 42 -
debian/compat | 1 -
debian/control | 29 -
debian/copyright | 66 -
debian/libbpp-raa-dev.install | 3 -
debian/libbpp-raa1.install | 1 -
debian/postinst | 57 -
debian/postrm | 59 -
debian/prerm | 41 -
debian/rules | 121 -
debian/source/format | 1 -
header.html | 27 +
package.cmake.in | 26 +
src/Bpp/Raa.all | 6 -
src/Bpp/Raa/RAA.cpp | 958 ++++---
src/Bpp/Raa/RAA.h | 861 +++---
src/Bpp/Raa/RAA_acnuc.c | 5766 ++++++++++++++++++++++------------------
src/Bpp/Raa/RAA_acnuc.h | 421 +--
src/Bpp/Raa/RaaList.cpp | 103 +-
src/Bpp/Raa/RaaList.h | 270 +-
src/Bpp/Raa/RaaSeqAttributes.h | 121 +-
src/Bpp/Raa/RaaSpeciesTree.cpp | 131 +-
src/Bpp/Raa/RaaSpeciesTree.h | 237 +-
src/Bpp/Raa/md5.c | 409 +--
src/Bpp/Raa/misc_acnuc.c | 62 +-
src/Bpp/Raa/parser.c | 166 +-
src/Bpp/Raa/parser.h | 19 +-
src/Bpp/Raa/zsockr.c | 212 +-
src/CMakeLists.txt | 93 +-
34 files changed, 7101 insertions(+), 6219 deletions(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index ad80d2b..da7a9d8 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,14 +1,22 @@
# CMake script for Bio++ Remote Acnuc Access
-# Author: Sylvain Gaillard and Julien Dutheil
+# Authors:
+# Sylvain Gaillard
+# Julien Dutheil
+# Francois Gindraud (2017)
# Created: 11/09/2009
-# Global parameters
-cmake_minimum_required(VERSION 2.6)
-project(bpp-raa C CXX)
-if(NOT DEFINED CMAKE_BUILD_TYPE)
- set(CMAKE_BUILD_TYPE "Release")
-endif(NOT DEFINED CMAKE_BUILD_TYPE)
-set(CMAKE_CXX_FLAGS "-Wall")
+cmake_minimum_required (VERSION 2.8.11)
+project (bpp-raa C CXX)
+
+# Compile options
+set (CMAKE_CXX_FLAGS "-std=c++11 -Wall")
+set (CMAKE_C_FLAGS "-Wall")
+
+IF(NOT CMAKE_BUILD_TYPE)
+ SET(CMAKE_BUILD_TYPE Release CACHE STRING
+ "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel."
+ FORCE)
+ENDIF(NOT CMAKE_BUILD_TYPE)
IF(NOT NO_DEP_CHECK)
SET(NO_DEP_CHECK FALSE CACHE BOOL
@@ -28,59 +36,58 @@ ELSE(NO_DEP_CHECK)
# library implements.
# In other words, the library implements all the interface numbers in the
# range from number current - age to current.
-set(BPPRAA_VERSION_CURRENT "2")
-set(BPPRAA_VERSION_REVISION "1")
-set(BPPRAA_VERSION_AGE "1")
+SET(${PROJECT_NAME}_VERSION_CURRENT "3")
+SET(${PROJECT_NAME}_VERSION_REVISION "0")
+SET(${PROJECT_NAME}_VERSION_AGE "0")
# Effective version number computation
-math(EXPR BPPRAA_VERSION_MAJOR "${BPPRAA_VERSION_CURRENT} -
-${BPPRAA_VERSION_AGE}")
-set(BPPRAA_VERSION_MINOR ${BPPRAA_VERSION_AGE})
-set(BPPRAA_VERSION_PATCH ${BPPRAA_VERSION_REVISION})
-set(BPPRAA_VERSION "${BPPRAA_VERSION_MAJOR}.${BPPRAA_VERSION_MINOR}.${BPPRAA_VERSION_PATCH}")
-
-# Set the CMAKE_PREFIX_PATH for the find_library fonction when using non
-# standard install location
-IF(CMAKE_INSTALL_PREFIX)
- SET(CMAKE_PREFIX_PATH "${CMAKE_INSTALL_PREFIX}" ${CMAKE_PREFIX_PATH})
-ENDIF(CMAKE_INSTALL_PREFIX)
-
-#here is a useful function:
-MACRO(IMPROVED_FIND_LIBRARY OUTPUT_LIBS lib_name include_to_find)
- #start:
- FIND_PATH(${lib_name}_INCLUDE_DIR ${include_to_find})
- SET(${lib_name}_NAMES ${lib_name} ${lib_name}lib ${lib_name}dll)
- FIND_LIBRARY(${lib_name}_LIBRARY NAMES ${${lib_name}_NAMES} PATH_SUFFIXES lib${LIB_SUFFIX})
-
- IF(${lib_name}_LIBRARY)
- MESSAGE("-- Library ${lib_name} found here:")
- MESSAGE(" includes : ${${lib_name}_INCLUDE_DIR}")
- MESSAGE(" libraries: ${${lib_name}_LIBRARY}")
- ELSE(${lib_name}_LIBRARY)
- MESSAGE(FATAL_ERROR "${lib_name} required but not found.")
- ENDIF(${lib_name}_LIBRARY)
-
- #add the dependency:
- INCLUDE_DIRECTORIES(${${lib_name}_INCLUDE_DIR})
- SET(${OUTPUT_LIBS} ${${OUTPUT_LIBS}} ${${lib_name}_LIBRARY})
-ENDMACRO(IMPROVED_FIND_LIBRARY)
-
-#Find the Bio++ libraries:
-IMPROVED_FIND_LIBRARY(LIBS bpp-seq Bpp/Seq/Alphabet/Alphabet.h)
-#Not explicitely needed:
-#IMPROVED_FIND_LIBRARY(LIBS bpp-core Bpp/Clonable.h)
-
-# Find the zlib installation
+MATH(EXPR ${PROJECT_NAME}_VERSION_MAJOR "${${PROJECT_NAME}_VERSION_CURRENT} - ${${PROJECT_NAME}_VERSION_AGE}")
+SET(${PROJECT_NAME}_VERSION_MINOR ${${PROJECT_NAME}_VERSION_AGE})
+SET(${PROJECT_NAME}_VERSION_PATCH ${${PROJECT_NAME}_VERSION_REVISION})
+SET(${PROJECT_NAME}_VERSION "${${PROJECT_NAME}_VERSION_MAJOR}.${${PROJECT_NAME}_VERSION_MINOR}.${${PROJECT_NAME}_VERSION_PATCH}")
+
+set (PROJECT_VERSION ${${PROJECT_NAME}_VERSION})
+
+# Find dependencies (add install directory to search)
+if (CMAKE_INSTALL_PREFIX)
+ set (CMAKE_PREFIX_PATH "${CMAKE_INSTALL_PREFIX}" ${CMAKE_PREFIX_PATH})
+endif (CMAKE_INSTALL_PREFIX)
+
+include (GNUInstallDirs)
+find_package (bpp-seq 11.0.0 REQUIRED)
+
+# Find the zlib installation (define zlib imported target)
find_package(ZLIB REQUIRED)
-include_directories(${ZLIB_INCLUDE_DIR})
-set(LIBS ${LIBS} ${ZLIB_LIBRARIES})
+add_library (zlib IMPORTED UNKNOWN)
+set_target_properties (zlib PROPERTIES
+ IMPORTED_LOCATION ${ZLIB_LIBRARIES}
+ INTERFACE_INCLUDE_DIRECTORIES ${ZLIB_INCLUDE_DIR}
+ )
+
+# CMake package
+set (cmake-package-location ${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME})
+include (CMakePackageConfigHelpers)
+configure_package_config_file (
+ package.cmake.in
+ ${CMAKE_CURRENT_BINARY_DIR}/package.cmake
+ INSTALL_DESTINATION ${cmake-package-location}
+ )
+write_basic_package_version_file (
+ ${CMAKE_CURRENT_BINARY_DIR}/package-version.cmake
+ VERSION ${PROJECT_VERSION}
+ COMPATIBILITY SameMajorVersion
+ )
+install (FILES ${CMAKE_CURRENT_BINARY_DIR}/package.cmake DESTINATION ${cmake-package-location}
+ RENAME ${PROJECT_NAME}-config.cmake)
+install (FILES ${CMAKE_CURRENT_BINARY_DIR}/package-version.cmake DESTINATION ${cmake-package-location}
+ RENAME ${PROJECT_NAME}-config-version.cmake)
-# Subdirectories
-add_subdirectory(src)
+# Define the libraries
+add_subdirectory (src)
# Doxygen
-find_package(Doxygen)
-if (DOXYGEN_FOUND)
+FIND_PACKAGE(Doxygen)
+IF (DOXYGEN_FOUND)
ADD_CUSTOM_TARGET (apidoc cp Doxyfile ${CMAKE_BINARY_DIR}/Doxyfile-build
COMMAND echo "OUTPUT_DIRECTORY=${CMAKE_BINARY_DIR}" >> ${CMAKE_BINARY_DIR}/Doxyfile-build
COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_BINARY_DIR}/Doxyfile-build
@@ -90,55 +97,29 @@ if (DOXYGEN_FOUND)
COMMAND echo "HTML_HEADER=header.html" >> ${CMAKE_BINARY_DIR}/Doxyfile-stable
COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_BINARY_DIR}/Doxyfile-stable
WORKING_DIRECTORY ${CMAKE_SOURCE_DIR})
-endif (DOXYGEN_FOUND)
+ENDIF (DOXYGEN_FOUND)
ENDIF(NO_DEP_CHECK)
# Packager
-set(CPACK_PACKAGE_NAME "libbpp-raa")
-set(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-set(CPACK_PACKAGE_VERSION "2.2.0")
-set(CPACK_PACKAGE_VERSION_MAJOR "2")
-set(CPACK_PACKAGE_VERSION_MINOR "2")
-set(CPACK_PACKAGE_VERSION_PATCH "0")
-set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Remote Acnuc Access library")
-set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
-set(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
-set(CPACK_RESOURCE_FILE_INSTALL "${CMAKE_SOURCE_DIR}/INSTALL.txt")
-set(CPACK_SOURCE_GENERATOR "TGZ")
-SET(CPACK_SOURCE_IGNORE_FILES
- "CMakeFiles"
- "Makefile"
- "_CPack_Packages"
- "CMakeCache.txt"
- ".*\\\\.cmake"
- ".*\\\\.git"
- ".*\\\\.gz"
- ".*\\\\.deb"
- ".*\\\\.rpm"
- ".*\\\\.dmg"
- ".*\\\\.sh"
- ".*\\\\..*\\\\.swp"
- "src/\\\\..*"
- "src/libbpp*"
- "debian/tmp"
- "debian/libbpp.*/"
- "debian/libbpp.*\\\\.so.*"
- "debian/libbpp.*\\\\.a"
- "debian/libbpp.*\\\\.substvars"
- "debian/libbpp.*\\\\.debhelper"
- "debian/debhelper\\\\.log"
- "html"
- "Raa.tag"
- "Testing"
- "build-stamp"
- "install_manifest.txt"
- "DartConfiguration.tcl"
- ${CPACK_SOURCE_IGNORE_FILES}
-)
-IF (MACOS)
- SET(CPACK_GENERATOR "Bundle")
-ENDIF()
+SET(CPACK_PACKAGE_NAME "libbpp-raa")
+SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
+SET(CPACK_PACKAGE_VERSION "2.3.1")
+SET(CPACK_PACKAGE_VERSION_MAJOR "2")
+SET(CPACK_PACKAGE_VERSION_MINOR "3")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
+SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Remote Acnuc Access library")
+SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
+SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
+SET(CPACK_RESOURCE_FILE_INSTALL "${CMAKE_SOURCE_DIR}/INSTALL.txt")
+SET(CPACK_SOURCE_GENERATOR "TGZ")
+# /!\ This assumes that an external build is used
+SET(CPACK_SOURCE_IGNORE_FILES
+ "/build/"
+ "/\\\\.git/"
+ "/\\\\.gitignore"
+ ${CPACK_SOURCE_IGNORE_FILES}
+ )
SET(CPACK_SOURCE_PACKAGE_FILE_NAME "${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}")
SET(CPACK_DEBSOURCE_PACKAGE_FILE_NAME "lib${CMAKE_PROJECT_NAME}_${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}.orig")
@@ -146,22 +127,9 @@ INCLUDE(CPack)
#This adds the 'dist' target
ADD_CUSTOM_TARGET(dist COMMAND ${CMAKE_MAKE_PROGRAM} package_source)
-# 'clean' is not (yet) a first class target. However, we need to clean the directories before building the sources:
-IF("${CMAKE_GENERATOR}" MATCHES "Make")
- ADD_CUSTOM_TARGET(make_clean
- COMMAND ${CMAKE_MAKE_PROGRAM} clean
- WORKING_DIRECTORY ${CMAKE_CURRENT_DIR}
- )
- ADD_DEPENDENCIES(dist make_clean)
-ENDIF()
IF(NOT NO_DEP_CHECK)
IF (UNIX)
-#This creates deb packages:
-ADD_CUSTOM_TARGET(origdist COMMAND cp ${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz ../${CPACK_DEBSOURCE_PACKAGE_FILE_NAME}.tar.gz)
-ADD_DEPENDENCIES(origdist dist)
-ADD_CUSTOM_TARGET(deb dpkg-buildpackage -uc -us -i${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz)
-ADD_DEPENDENCIES(deb origdist)
#This creates rpm packages:
ADD_CUSTOM_TARGET(rpm rpmbuild -ta ${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz)
diff --git a/ChangeLog b/ChangeLog
index ce44d20..fb18ab7 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,7 @@
+10/05/17 -*- version 2.3.0 -*-
+
+28/09/14 -*- Version 2.2.0 -*-
+
07/03/13 -*- version 2.1.0 -*-
09/02/12 -*- version 2.0.3 -*-
diff --git a/Doxyfile b/Doxyfile
index 42a5ff6..3d69b7d 100644
--- a/Doxyfile
+++ b/Doxyfile
@@ -1,358 +1,406 @@
-# Doxyfile 1.8.3.1-20130209
+# Doxyfile 1.8.11
# This file describes the settings to be used by the documentation system
-# doxygen (www.doxygen.org) for a project
+# doxygen (www.doxygen.org) for a project.
#
-# All text after a hash (#) is considered a comment and will be ignored
+# All text after a double hash (##) is considered a comment and is placed in
+# front of the TAG it is preceding.
+#
+# All text after a single hash (#) is considered a comment and will be ignored.
# The format is:
-# TAG = value [value, ...]
-# For lists items can also be appended using:
-# TAG += value [value, ...]
-# Values that contain spaces should be placed between quotes (" ")
+# TAG = value [value, ...]
+# For lists, items can also be appended using:
+# TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (\" \").
#---------------------------------------------------------------------------
# Project related configuration options
#---------------------------------------------------------------------------
-# This tag specifies the encoding used for all characters in the config file
-# that follow. The default is UTF-8 which is also the encoding used for all
-# text before the first occurrence of this tag. Doxygen uses libiconv (or the
-# iconv built into libc) for the transcoding. See
-# http://www.gnu.org/software/libiconv for the list of possible encodings.
+# This tag specifies the encoding used for all characters in the config file
+# that follow. The default is UTF-8 which is also the encoding used for all text
+# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv
+# built into libc) for the transcoding. See http://www.gnu.org/software/libiconv
+# for the list of possible encodings.
+# The default value is: UTF-8.
DOXYFILE_ENCODING = UTF-8
-# The PROJECT_NAME tag is a single word (or sequence of words) that should
-# identify the project. Note that if you do not use Doxywizard you need
-# to put quotes around the project name if it contains spaces.
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
+# double-quotes, unless you are using Doxywizard) that should identify the
+# project for which the documentation is generated. This name is used in the
+# title of most generated pages and in a few other places.
+# The default value is: My Project.
PROJECT_NAME = bpp-raa
-# The PROJECT_NUMBER tag can be used to enter a project or revision number.
-# This could be handy for archiving the generated documentation or
-# if some version control system is used.
+# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
+# could be handy for archiving the generated documentation or if some version
+# control system is used.
-PROJECT_NUMBER = 2.2.0
+PROJECT_NUMBER = 2.3.0
-# Using the PROJECT_BRIEF tag one can provide an optional one line description
-# for a project that appears at the top of each page and should give viewer
-# a quick idea about the purpose of the project. Keep the description short.
+# Using the PROJECT_BRIEF tag one can provide an optional one line description
+# for a project that appears at the top of each page and should give viewer a
+# quick idea about the purpose of the project. Keep the description short.
PROJECT_BRIEF =
-# With the PROJECT_LOGO tag one can specify an logo or icon that is
-# included in the documentation. The maximum height of the logo should not
-# exceed 55 pixels and the maximum width should not exceed 200 pixels.
-# Doxygen will copy the logo to the output directory.
+# With the PROJECT_LOGO tag one can specify a logo or an icon that is included
+# in the documentation. The maximum height of the logo should not exceed 55
+# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
+# the logo to the output directory.
PROJECT_LOGO =
-# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
-# base path where the generated documentation will be put.
-# If a relative path is entered, it will be relative to the location
-# where doxygen was started. If left blank the current directory will be used.
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
+# into which the generated documentation will be written. If a relative path is
+# entered, it will be relative to the location where doxygen was started. If
+# left blank the current directory will be used.
OUTPUT_DIRECTORY =
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-# Enabling this option can be useful when feeding doxygen a huge amount of
-# source files, where putting all generated files in the same directory would
-# otherwise cause performance problems for the file system.
+# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
+# directories (in 2 levels) under the output directory of each output format and
+# will distribute the generated files over these directories. Enabling this
+# option can be useful when feeding doxygen a huge amount of source files, where
+# putting all generated files in the same directory would otherwise causes
+# performance problems for the file system.
+# The default value is: NO.
CREATE_SUBDIRS = NO
-# The OUTPUT_LANGUAGE tag is used to specify the language in which all
-# documentation generated by doxygen is written. Doxygen will use this
-# information to generate all constant output in the proper language.
-# The default language is English, other supported languages are:
-# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
-# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German,
-# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English
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-# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak,
-# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
+# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
+# characters to appear in the names of generated files. If set to NO, non-ASCII
+# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode
+# U+3044.
+# The default value is: NO.
+
+ALLOW_UNICODE_NAMES = NO
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all
+# documentation generated by doxygen is written. Doxygen will use this
+# information to generate all constant output in the proper language.
+# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese,
+# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States),
+# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian,
+# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages),
+# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian,
+# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian,
+# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish,
+# Ukrainian and Vietnamese.
+# The default value is: English.
OUTPUT_LANGUAGE = English
-# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
-# include brief member descriptions after the members that are listed in
-# the file and class documentation (similar to JavaDoc).
-# Set to NO to disable this.
+# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member
+# descriptions after the members that are listed in the file and class
+# documentation (similar to Javadoc). Set to NO to disable this.
+# The default value is: YES.
BRIEF_MEMBER_DESC = YES
-# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
-# the brief description of a member or function before the detailed description.
-# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
+# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief
+# description of a member or function before the detailed description
+#
+# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
# brief descriptions will be completely suppressed.
+# The default value is: YES.
REPEAT_BRIEF = YES
-# This tag implements a quasi-intelligent brief description abbreviator
-# that is used to form the text in various listings. Each string
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-# "The $name file" "is" "provides" "specifies" "contains"
-# "represents" "a" "an" "the"
+# This tag implements a quasi-intelligent brief description abbreviator that is
+# used to form the text in various listings. Each string in this list, if found
+# as the leading text of the brief description, will be stripped from the text
+# and the result, after processing the whole list, is used as the annotated
+# text. Otherwise, the brief description is used as-is. If left blank, the
+# following values are used ($name is automatically replaced with the name of
+# the entity):The $name class, The $name widget, The $name file, is, provides,
+# specifies, contains, represents, a, an and the.
ABBREVIATE_BRIEF =
-# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
-# Doxygen will generate a detailed section even if there is only a brief
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
+# doxygen will generate a detailed section even if there is only a brief
# description.
+# The default value is: NO.
ALWAYS_DETAILED_SEC = NO
-# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
-# inherited members of a class in the documentation of that class as if those
-# members were ordinary class members. Constructors, destructors and assignment
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
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# operators of the base classes will not be shown.
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FULL_PATH_NAMES = YES
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-# started.
+# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
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+# If left blank the directory from which doxygen is run is used as the path to
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+#
+# Note that you can specify absolute paths here, but also relative paths, which
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+# This tag requires that the tag FULL_PATH_NAMES is set to YES.
STRIP_FROM_PATH = ./src/
-# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
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-# If left blank only the name of the header file containing the class
-# definition is used. Otherwise one should specify the include paths that
-# are normally passed to the compiler using the -I flag.
+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
+# path mentioned in the documentation of a class, which tells the reader which
+# header file to include in order to use a class. If left blank only the name of
+# the header file containing the class definition is used. Otherwise one should
+# specify the list of include paths that are normally passed to the compiler
+# using the -I flag.
STRIP_FROM_INC_PATH = ./src/
-# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
-# (but less readable) file names. This can be useful if your file system
-# doesn't support long names like on DOS, Mac, or CD-ROM.
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
+# less readable) file names. This can be useful is your file systems doesn't
+# support long names like on DOS, Mac, or CD-ROM.
+# The default value is: NO.
SHORT_NAMES = NO
-# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
-# will interpret the first line (until the first dot) of a JavaDoc-style
-# comment as the brief description. If set to NO, the JavaDoc
-# comments will behave just like regular Qt-style comments
-# (thus requiring an explicit @brief command for a brief description.)
+# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the
+# first line (until the first dot) of a Javadoc-style comment as the brief
+# description. If set to NO, the Javadoc-style will behave just like regular Qt-
+# style comments (thus requiring an explicit @brief command for a brief
+# description.)
+# The default value is: NO.
JAVADOC_AUTOBRIEF = NO
-# If the QT_AUTOBRIEF tag is set to YES then Doxygen will
-# interpret the first line (until the first dot) of a Qt-style
-# comment as the brief description. If set to NO, the comments
-# will behave just like regular Qt-style comments (thus requiring
-# an explicit \brief command for a brief description.)
+# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
+# line (until the first dot) of a Qt-style comment as the brief description. If
+# set to NO, the Qt-style will behave just like regular Qt-style comments (thus
+# requiring an explicit \brief command for a brief description.)
+# The default value is: NO.
QT_AUTOBRIEF = NO
-# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
-# treat a multi-line C++ special comment block (i.e. a block of //! or ///
-# comments) as a brief description. This used to be the default behaviour.
-# The new default is to treat a multi-line C++ comment block as a detailed
-# description. Set this tag to YES if you prefer the old behaviour instead.
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a
+# multi-line C++ special comment block (i.e. a block of //! or /// comments) as
+# a brief description. This used to be the default behavior. The new default is
+# to treat a multi-line C++ comment block as a detailed description. Set this
+# tag to YES if you prefer the old behavior instead.
+#
+# Note that setting this tag to YES also means that rational rose comments are
+# not recognized any more.
+# The default value is: NO.
MULTILINE_CPP_IS_BRIEF = NO
-# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
-# member inherits the documentation from any documented member that it
-# re-implements.
+# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
+# documentation from any documented member that it re-implements.
+# The default value is: YES.
INHERIT_DOCS = YES
-# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce
-# a new page for each member. If set to NO, the documentation of a member will
-# be part of the file/class/namespace that contains it.
+# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new
+# page for each member. If set to NO, the documentation of a member will be part
+# of the file/class/namespace that contains it.
+# The default value is: NO.
SEPARATE_MEMBER_PAGES = NO
-# The TAB_SIZE tag can be used to set the number of spaces in a tab.
-# Doxygen uses this value to replace tabs by spaces in code fragments.
+# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen
+# uses this value to replace tabs by spaces in code fragments.
+# Minimum value: 1, maximum value: 16, default value: 4.
TAB_SIZE = 2
-# This tag can be used to specify a number of aliases that acts
-# as commands in the documentation. An alias has the form "name=value".
-# For example adding "sideeffect=\par Side Effects:\n" will allow you to
-# put the command \sideeffect (or @sideeffect) in the documentation, which
-# will result in a user-defined paragraph with heading "Side Effects:".
-# You can put \n's in the value part of an alias to insert newlines.
+# This tag can be used to specify a number of aliases that act as commands in
+# the documentation. An alias has the form:
+# name=value
+# For example adding
+# "sideeffect=@par Side Effects:\n"
+# will allow you to put the command \sideeffect (or @sideeffect) in the
+# documentation, which will result in a user-defined paragraph with heading
+# "Side Effects:". You can put \n's in the value part of an alias to insert
+# newlines.
ALIASES =
-# This tag can be used to specify a number of word-keyword mappings (TCL only).
-# A mapping has the form "name=value". For example adding
-# "class=itcl::class" will allow you to use the command class in the
-# itcl::class meaning.
+# This tag can be used to specify a number of word-keyword mappings (TCL only).
+# A mapping has the form "name=value". For example adding "class=itcl::class"
+# will allow you to use the command class in the itcl::class meaning.
TCL_SUBST =
-# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
-# sources only. Doxygen will then generate output that is more tailored for C.
-# For instance, some of the names that are used will be different. The list
-# of all members will be omitted, etc.
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
+# only. Doxygen will then generate output that is more tailored for C. For
+# instance, some of the names that are used will be different. The list of all
+# members will be omitted, etc.
+# The default value is: NO.
OPTIMIZE_OUTPUT_FOR_C = NO
-# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
-# sources only. Doxygen will then generate output that is more tailored for
-# Java. For instance, namespaces will be presented as packages, qualified
-# scopes will look different, etc.
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
+# Python sources only. Doxygen will then generate output that is more tailored
+# for that language. For instance, namespaces will be presented as packages,
+# qualified scopes will look different, etc.
+# The default value is: NO.
OPTIMIZE_OUTPUT_JAVA = NO
-# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
-# sources only. Doxygen will then generate output that is more tailored for
-# Fortran.
+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
+# sources. Doxygen will then generate output that is tailored for Fortran.
+# The default value is: NO.
OPTIMIZE_FOR_FORTRAN = NO
-# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
-# sources. Doxygen will then generate output that is tailored for
-# VHDL.
+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
+# sources. Doxygen will then generate output that is tailored for VHDL.
+# The default value is: NO.
OPTIMIZE_OUTPUT_VHDL = NO
-# Doxygen selects the parser to use depending on the extension of the files it
-# parses. With this tag you can assign which parser to use for a given
-# extension. Doxygen has a built-in mapping, but you can override or extend it
-# using this tag. The format is ext=language, where ext is a file extension,
-# and language is one of the parsers supported by doxygen: IDL, Java,
-# Javascript, CSharp, C, C++, D, PHP, Objective-C, Python, Fortran, VHDL, C,
-# C++. For instance to make doxygen treat .inc files as Fortran files (default
-# is PHP), and .f files as C (default is Fortran), use: inc=Fortran f=C. Note
-# that for custom extensions you also need to set FILE_PATTERNS otherwise the
-# files are not read by doxygen.
+# Doxygen selects the parser to use depending on the extension of the files it
+# parses. With this tag you can assign which parser to use for a given
+# extension. Doxygen has a built-in mapping, but you can override or extend it
+# using this tag. The format is ext=language, where ext is a file extension, and
+# language is one of the parsers supported by doxygen: IDL, Java, Javascript,
+# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran:
+# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran:
+# Fortran. In the later case the parser tries to guess whether the code is fixed
+# or free formatted code, this is the default for Fortran type files), VHDL. For
+# instance to make doxygen treat .inc files as Fortran files (default is PHP),
+# and .f files as C (default is Fortran), use: inc=Fortran f=C.
+#
+# Note: For files without extension you can use no_extension as a placeholder.
+#
+# Note that for custom extensions you also need to set FILE_PATTERNS otherwise
+# the files are not read by doxygen.
EXTENSION_MAPPING =
-# If MARKDOWN_SUPPORT is enabled (the default) then doxygen pre-processes all
-# comments according to the Markdown format, which allows for more readable
-# documentation. See http://daringfireball.net/projects/markdown/ for details.
-# The output of markdown processing is further processed by doxygen, so you
-# can mix doxygen, HTML, and XML commands with Markdown formatting.
-# Disable only in case of backward compatibilities issues.
+# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
+# according to the Markdown format, which allows for more readable
+# documentation. See http://daringfireball.net/projects/markdown/ for details.
+# The output of markdown processing is further processed by doxygen, so you can
+# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in
+# case of backward compatibilities issues.
+# The default value is: YES.
MARKDOWN_SUPPORT = YES
-# When enabled doxygen tries to link words that correspond to documented classes,
-# or namespaces to their corresponding documentation. Such a link can be
-# prevented in individual cases by by putting a % sign in front of the word or
+# When enabled doxygen tries to link words that correspond to documented
+# classes, or namespaces to their corresponding documentation. Such a link can
+# be prevented in individual cases by putting a % sign in front of the word or
# globally by setting AUTOLINK_SUPPORT to NO.
+# The default value is: YES.
AUTOLINK_SUPPORT = YES
-# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
-# to include (a tag file for) the STL sources as input, then you should
-# set this tag to YES in order to let doxygen match functions declarations and
-# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
-# func(std::string) {}). This also makes the inheritance and collaboration
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
+# to include (a tag file for) the STL sources as input, then you should set this
+# tag to YES in order to let doxygen match functions declarations and
+# definitions whose arguments contain STL classes (e.g. func(std::string);
+# versus func(std::string) {}). This also make the inheritance and collaboration
# diagrams that involve STL classes more complete and accurate.
+# The default value is: NO.
BUILTIN_STL_SUPPORT = YES
-# If you use Microsoft's C++/CLI language, you should set this option to YES to
+# If you use Microsoft's C++/CLI language, you should set this option to YES to
# enable parsing support.
+# The default value is: NO.
CPP_CLI_SUPPORT = NO
-# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only.
-# Doxygen will parse them like normal C++ but will assume all classes use public
-# instead of private inheritance when no explicit protection keyword is present.
+# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
+# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen
+# will parse them like normal C++ but will assume all classes use public instead
+# of private inheritance when no explicit protection keyword is present.
+# The default value is: NO.
SIP_SUPPORT = NO
-# For Microsoft's IDL there are propget and propput attributes to indicate
-# getter and setter methods for a property. Setting this option to YES (the
-# default) will make doxygen replace the get and set methods by a property in
-# the documentation. This will only work if the methods are indeed getting or
-# setting a simple type. If this is not the case, or you want to show the
-# methods anyway, you should set this option to NO.
+# For Microsoft's IDL there are propget and propput attributes to indicate
+# getter and setter methods for a property. Setting this option to YES will make
+# doxygen to replace the get and set methods by a property in the documentation.
+# This will only work if the methods are indeed getting or setting a simple
+# type. If this is not the case, or you want to show the methods anyway, you
+# should set this option to NO.
+# The default value is: YES.
IDL_PROPERTY_SUPPORT = YES
-# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
-# tag is set to YES, then doxygen will reuse the documentation of the first
-# member in the group (if any) for the other members of the group. By default
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
+# tag is set to YES then doxygen will reuse the documentation of the first
+# member in the group (if any) for the other members of the group. By default
# all members of a group must be documented explicitly.
+# The default value is: NO.
DISTRIBUTE_GROUP_DOC = NO
-# Set the SUBGROUPING tag to YES (the default) to allow class member groups of
-# the same type (for instance a group of public functions) to be put as a
-# subgroup of that type (e.g. under the Public Functions section). Set it to
-# NO to prevent subgrouping. Alternatively, this can be done per class using
-# the \nosubgrouping command.
+# If one adds a struct or class to a group and this option is enabled, then also
+# any nested class or struct is added to the same group. By default this option
+# is disabled and one has to add nested compounds explicitly via \ingroup.
+# The default value is: NO.
+
+GROUP_NESTED_COMPOUNDS = NO
+
+# Set the SUBGROUPING tag to YES to allow class member groups of the same type
+# (for instance a group of public functions) to be put as a subgroup of that
+# type (e.g. under the Public Functions section). Set it to NO to prevent
+# subgrouping. Alternatively, this can be done per class using the
+# \nosubgrouping command.
+# The default value is: YES.
SUBGROUPING = YES
-# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and
-# unions are shown inside the group in which they are included (e.g. using
-# @ingroup) instead of on a separate page (for HTML and Man pages) or
-# section (for LaTeX and RTF).
+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
+# are shown inside the group in which they are included (e.g. using \ingroup)
+# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
+# and RTF).
+#
+# Note that this feature does not work in combination with
+# SEPARATE_MEMBER_PAGES.
+# The default value is: NO.
INLINE_GROUPED_CLASSES = NO
-# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and
-# unions with only public data fields or simple typedef fields will be shown
-# inline in the documentation of the scope in which they are defined (i.e. file,
-# namespace, or group documentation), provided this scope is documented. If set
-# to NO (the default), structs, classes, and unions are shown on a separate
-# page (for HTML and Man pages) or section (for LaTeX and RTF).
+# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
+# with only public data fields or simple typedef fields will be shown inline in
+# the documentation of the scope in which they are defined (i.e. file,
+# namespace, or group documentation), provided this scope is documented. If set
+# to NO, structs, classes, and unions are shown on a separate page (for HTML and
+# Man pages) or section (for LaTeX and RTF).
+# The default value is: NO.
INLINE_SIMPLE_STRUCTS = NO
-# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
-# is documented as struct, union, or enum with the name of the typedef. So
-# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
-# with name TypeT. When disabled the typedef will appear as a member of a file,
-# namespace, or class. And the struct will be named TypeS. This can typically
-# be useful for C code in case the coding convention dictates that all compound
+# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
+# enum is documented as struct, union, or enum with the name of the typedef. So
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+# with name TypeT. When disabled the typedef will appear as a member of a file,
+# namespace, or class. And the struct will be named TypeS. This can typically be
+# useful for C code in case the coding convention dictates that all compound
# types are typedef'ed and only the typedef is referenced, never the tag name.
+# The default value is: NO.
TYPEDEF_HIDES_STRUCT = NO
-# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to
-# determine which symbols to keep in memory and which to flush to disk.
-# When the cache is full, less often used symbols will be written to disk.
-# For small to medium size projects (<1000 input files) the default value is
-# probably good enough. For larger projects a too small cache size can cause
-# doxygen to be busy swapping symbols to and from disk most of the time
-# causing a significant performance penalty.
-# If the system has enough physical memory increasing the cache will improve the
-# performance by keeping more symbols in memory. Note that the value works on
-# a logarithmic scale so increasing the size by one will roughly double the
-# memory usage. The cache size is given by this formula:
-# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
-# corresponding to a cache size of 2^16 = 65536 symbols.
-
-SYMBOL_CACHE_SIZE = 0
-
-# Similar to the SYMBOL_CACHE_SIZE the size of the symbol lookup cache can be
-# set using LOOKUP_CACHE_SIZE. This cache is used to resolve symbols given
-# their name and scope. Since this can be an expensive process and often the
-# same symbol appear multiple times in the code, doxygen keeps a cache of
-# pre-resolved symbols. If the cache is too small doxygen will become slower.
-# If the cache is too large, memory is wasted. The cache size is given by this
-# formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range is 0..9, the default is 0,
-# corresponding to a cache size of 2^16 = 65536 symbols.
+# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
+# cache is used to resolve symbols given their name and scope. Since this can be
+# an expensive process and often the same symbol appears multiple times in the
+# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
+# doxygen will become slower. If the cache is too large, memory is wasted. The
+# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
+# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
+# symbols. At the end of a run doxygen will report the cache usage and suggest
+# the optimal cache size from a speed point of view.
+# Minimum value: 0, maximum value: 9, default value: 0.
LOOKUP_CACHE_SIZE = 0
@@ -360,1196 +408,1577 @@ LOOKUP_CACHE_SIZE = 0
# Build related configuration options
#---------------------------------------------------------------------------
-# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
-# documentation are documented, even if no documentation was available.
-# Private class members and static file members will be hidden unless
-# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
+# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in
+# documentation are documented, even if no documentation was available. Private
+# class members and static file members will be hidden unless the
+# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
+# Note: This will also disable the warnings about undocumented members that are
+# normally produced when WARNINGS is set to YES.
+# The default value is: NO.
EXTRACT_ALL = YES
-# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
-# will be included in the documentation.
+# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
+# be included in the documentation.
+# The default value is: NO.
EXTRACT_PRIVATE = NO
-# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal
+# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
# scope will be included in the documentation.
+# The default value is: NO.
EXTRACT_PACKAGE = NO
-# If the EXTRACT_STATIC tag is set to YES all static members of a file
-# will be included in the documentation.
+# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
+# included in the documentation.
+# The default value is: NO.
EXTRACT_STATIC = YES
-# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
-# defined locally in source files will be included in the documentation.
-# If set to NO only classes defined in header files are included.
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
+# locally in source files will be included in the documentation. If set to NO,
+# only classes defined in header files are included. Does not have any effect
+# for Java sources.
+# The default value is: YES.
EXTRACT_LOCAL_CLASSES = NO
-# This flag is only useful for Objective-C code. When set to YES local
-# methods, which are defined in the implementation section but not in
-# the interface are included in the documentation.
-# If set to NO (the default) only methods in the interface are included.
+# This flag is only useful for Objective-C code. If set to YES, local methods,
+# which are defined in the implementation section but not in the interface are
+# included in the documentation. If set to NO, only methods in the interface are
+# included.
+# The default value is: NO.
EXTRACT_LOCAL_METHODS = NO
-# If this flag is set to YES, the members of anonymous namespaces will be
-# extracted and appear in the documentation as a namespace called
-# 'anonymous_namespace{file}', where file will be replaced with the base
-# name of the file that contains the anonymous namespace. By default
-# anonymous namespaces are hidden.
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base name of
+# the file that contains the anonymous namespace. By default anonymous namespace
+# are hidden.
+# The default value is: NO.
EXTRACT_ANON_NSPACES = NO
-# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
-# undocumented members of documented classes, files or namespaces.
-# If set to NO (the default) these members will be included in the
-# various overviews, but no documentation section is generated.
-# This option has no effect if EXTRACT_ALL is enabled.
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
+# undocumented members inside documented classes or files. If set to NO these
+# members will be included in the various overviews, but no documentation
+# section is generated. This option has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
HIDE_UNDOC_MEMBERS = NO
-# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
-# undocumented classes that are normally visible in the class hierarchy.
-# If set to NO (the default) these classes will be included in the various
-# overviews. This option has no effect if EXTRACT_ALL is enabled.
+# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy. If set
+# to NO, these classes will be included in the various overviews. This option
+# has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
HIDE_UNDOC_CLASSES = NO
-# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
-# friend (class|struct|union) declarations.
-# If set to NO (the default) these declarations will be included in the
-# documentation.
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
+# (class|struct|union) declarations. If set to NO, these declarations will be
+# included in the documentation.
+# The default value is: NO.
HIDE_FRIEND_COMPOUNDS = NO
-# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
-# documentation blocks found inside the body of a function.
-# If set to NO (the default) these blocks will be appended to the
-# function's detailed documentation block.
+# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
+# documentation blocks found inside the body of a function. If set to NO, these
+# blocks will be appended to the function's detailed documentation block.
+# The default value is: NO.
HIDE_IN_BODY_DOCS = NO
-# The INTERNAL_DOCS tag determines if documentation
-# that is typed after a \internal command is included. If the tag is set
-# to NO (the default) then the documentation will be excluded.
-# Set it to YES to include the internal documentation.
+# The INTERNAL_DOCS tag determines if documentation that is typed after a
+# \internal command is included. If the tag is set to NO then the documentation
+# will be excluded. Set it to YES to include the internal documentation.
+# The default value is: NO.
INTERNAL_DOCS = NO
-# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
-# file names in lower-case letters. If set to YES upper-case letters are also
-# allowed. This is useful if you have classes or files whose names only differ
-# in case and if your file system supports case sensitive file names. Windows
+# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file
+# names in lower-case letters. If set to YES, upper-case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
# and Mac users are advised to set this option to NO.
+# The default value is: system dependent.
CASE_SENSE_NAMES = YES
-# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
-# will show members with their full class and namespace scopes in the
-# documentation. If set to YES the scope will be hidden.
+# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
+# their full class and namespace scopes in the documentation. If set to YES, the
+# scope will be hidden.
+# The default value is: NO.
HIDE_SCOPE_NAMES = NO
-# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
-# will put a list of the files that are included by a file in the documentation
-# of that file.
+# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
+# append additional text to a page's title, such as Class Reference. If set to
+# YES the compound reference will be hidden.
+# The default value is: NO.
+
+HIDE_COMPOUND_REFERENCE= NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
+# the files that are included by a file in the documentation of that file.
+# The default value is: YES.
SHOW_INCLUDE_FILES = YES
-# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen
-# will list include files with double quotes in the documentation
-# rather than with sharp brackets.
+# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
+# grouped member an include statement to the documentation, telling the reader
+# which file to include in order to use the member.
+# The default value is: NO.
+
+SHOW_GROUPED_MEMB_INC = NO
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
+# files with double quotes in the documentation rather than with sharp brackets.
+# The default value is: NO.
FORCE_LOCAL_INCLUDES = NO
-# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
-# is inserted in the documentation for inline members.
+# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
+# documentation for inline members.
+# The default value is: YES.
INLINE_INFO = YES
-# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
-# will sort the (detailed) documentation of file and class members
-# alphabetically by member name. If set to NO the members will appear in
-# declaration order.
+# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
+# (detailed) documentation of file and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order.
+# The default value is: YES.
SORT_MEMBER_DOCS = YES
-# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
-# brief documentation of file, namespace and class members alphabetically
-# by member name. If set to NO (the default) the members will appear in
-# declaration order.
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
+# descriptions of file, namespace and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order. Note that
+# this will also influence the order of the classes in the class list.
+# The default value is: NO.
SORT_BRIEF_DOCS = NO
-# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen
-# will sort the (brief and detailed) documentation of class members so that
-# constructors and destructors are listed first. If set to NO (the default)
-# the constructors will appear in the respective orders defined by
-# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS.
-# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO
-# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO.
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
+# (brief and detailed) documentation of class members so that constructors and
+# destructors are listed first. If set to NO the constructors will appear in the
+# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
+# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
+# member documentation.
+# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
+# detailed member documentation.
+# The default value is: NO.
SORT_MEMBERS_CTORS_1ST = NO
-# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the
-# hierarchy of group names into alphabetical order. If set to NO (the default)
-# the group names will appear in their defined order.
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
+# of group names into alphabetical order. If set to NO the group names will
+# appear in their defined order.
+# The default value is: NO.
SORT_GROUP_NAMES = NO
-# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
-# sorted by fully-qualified names, including namespaces. If set to
-# NO (the default), the class list will be sorted only by class name,
-# not including the namespace part.
-# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
-# Note: This option applies only to the class list, not to the
-# alphabetical list.
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
+# fully-qualified names, including namespaces. If set to NO, the class list will
+# be sorted only by class name, not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the alphabetical
+# list.
+# The default value is: NO.
SORT_BY_SCOPE_NAME = NO
-# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to
-# do proper type resolution of all parameters of a function it will reject a
-# match between the prototype and the implementation of a member function even
-# if there is only one candidate or it is obvious which candidate to choose
-# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen
-# will still accept a match between prototype and implementation in such cases.
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
+# type resolution of all parameters of a function it will reject a match between
+# the prototype and the implementation of a member function even if there is
+# only one candidate or it is obvious which candidate to choose by doing a
+# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
+# accept a match between prototype and implementation in such cases.
+# The default value is: NO.
STRICT_PROTO_MATCHING = NO
-# The GENERATE_TODOLIST tag can be used to enable (YES) or
-# disable (NO) the todo list. This list is created by putting \todo
-# commands in the documentation.
+# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo
+# list. This list is created by putting \todo commands in the documentation.
+# The default value is: YES.
GENERATE_TODOLIST = NO
-# The GENERATE_TESTLIST tag can be used to enable (YES) or
-# disable (NO) the test list. This list is created by putting \test
-# commands in the documentation.
+# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
+# list. This list is created by putting \test commands in the documentation.
+# The default value is: YES.
GENERATE_TESTLIST = NO
-# The GENERATE_BUGLIST tag can be used to enable (YES) or
-# disable (NO) the bug list. This list is created by putting \bug
-# commands in the documentation.
+# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug
+# list. This list is created by putting \bug commands in the documentation.
+# The default value is: YES.
GENERATE_BUGLIST = NO
-# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
-# disable (NO) the deprecated list. This list is created by putting
-# \deprecated commands in the documentation.
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO)
+# the deprecated list. This list is created by putting \deprecated commands in
+# the documentation.
+# The default value is: YES.
GENERATE_DEPRECATEDLIST= NO
-# The ENABLED_SECTIONS tag can be used to enable conditional
-# documentation sections, marked by \if section-label ... \endif
-# and \cond section-label ... \endcond blocks.
+# The ENABLED_SECTIONS tag can be used to enable conditional documentation
+# sections, marked by \if <section_label> ... \endif and \cond <section_label>
+# ... \endcond blocks.
ENABLED_SECTIONS =
-# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
-# the initial value of a variable or macro consists of for it to appear in
-# the documentation. If the initializer consists of more lines than specified
-# here it will be hidden. Use a value of 0 to hide initializers completely.
-# The appearance of the initializer of individual variables and macros in the
-# documentation can be controlled using \showinitializer or \hideinitializer
-# command in the documentation regardless of this setting.
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
+# initial value of a variable or macro / define can have for it to appear in the
+# documentation. If the initializer consists of more lines than specified here
+# it will be hidden. Use a value of 0 to hide initializers completely. The
+# appearance of the value of individual variables and macros / defines can be
+# controlled using \showinitializer or \hideinitializer command in the
+# documentation regardless of this setting.
+# Minimum value: 0, maximum value: 10000, default value: 30.
MAX_INITIALIZER_LINES = 30
-# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
-# at the bottom of the documentation of classes and structs. If set to YES the
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
+# the bottom of the documentation of classes and structs. If set to YES, the
# list will mention the files that were used to generate the documentation.
+# The default value is: YES.
SHOW_USED_FILES = YES
-# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
-# This will remove the Files entry from the Quick Index and from the
-# Folder Tree View (if specified). The default is YES.
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
+# will remove the Files entry from the Quick Index and from the Folder Tree View
+# (if specified).
+# The default value is: YES.
SHOW_FILES = YES
-# Set the SHOW_NAMESPACES tag to NO to disable the generation of the
-# Namespaces page. This will remove the Namespaces entry from the Quick Index
-# and from the Folder Tree View (if specified). The default is YES.
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
+# page. This will remove the Namespaces entry from the Quick Index and from the
+# Folder Tree View (if specified).
+# The default value is: YES.
SHOW_NAMESPACES = YES
-# The FILE_VERSION_FILTER tag can be used to specify a program or script that
-# doxygen should invoke to get the current version for each file (typically from
-# the version control system). Doxygen will invoke the program by executing (via
-# popen()) the command <command> <input-file>, where <command> is the value of
-# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
-# provided by doxygen. Whatever the program writes to standard output
-# is used as the file version. See the manual for examples.
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command command input-file, where command is the value of the
+# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
+# by doxygen. Whatever the program writes to standard output is used as the file
+# version. For an example see the documentation.
FILE_VERSION_FILTER =
-# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
-# by doxygen. The layout file controls the global structure of the generated
-# output files in an output format independent way. To create the layout file
-# that represents doxygen's defaults, run doxygen with the -l option.
-# You can optionally specify a file name after the option, if omitted
-# DoxygenLayout.xml will be used as the name of the layout file.
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. To create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option. You can
+# optionally specify a file name after the option, if omitted DoxygenLayout.xml
+# will be used as the name of the layout file.
+#
+# Note that if you run doxygen from a directory containing a file called
+# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
+# tag is left empty.
LAYOUT_FILE =
-# The CITE_BIB_FILES tag can be used to specify one or more bib files
-# containing the references data. This must be a list of .bib files. The
-# .bib extension is automatically appended if omitted. Using this command
-# requires the bibtex tool to be installed. See also
-# http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style
-# of the bibliography can be controlled using LATEX_BIB_STYLE. To use this
-# feature you need bibtex and perl available in the search path. Do not use
-# file names with spaces, bibtex cannot handle them.
+# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
+# the reference definitions. This must be a list of .bib files. The .bib
+# extension is automatically appended if omitted. This requires the bibtex tool
+# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info.
+# For LaTeX the style of the bibliography can be controlled using
+# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
+# search path. See also \cite for info how to create references.
CITE_BIB_FILES =
#---------------------------------------------------------------------------
-# configuration options related to warning and progress messages
+# Configuration options related to warning and progress messages
#---------------------------------------------------------------------------
-# The QUIET tag can be used to turn on/off the messages that are generated
-# by doxygen. Possible values are YES and NO. If left blank NO is used.
+# The QUIET tag can be used to turn on/off the messages that are generated to
+# standard output by doxygen. If QUIET is set to YES this implies that the
+# messages are off.
+# The default value is: NO.
QUIET = NO
-# The WARNINGS tag can be used to turn on/off the warning messages that are
-# generated by doxygen. Possible values are YES and NO. If left blank
-# NO is used.
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
+# this implies that the warnings are on.
+#
+# Tip: Turn warnings on while writing the documentation.
+# The default value is: YES.
WARNINGS = YES
-# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
-# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
-# automatically be disabled.
+# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
+# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
+# will automatically be disabled.
+# The default value is: YES.
WARN_IF_UNDOCUMENTED = YES
-# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
-# potential errors in the documentation, such as not documenting some
-# parameters in a documented function, or documenting parameters that
-# don't exist or using markup commands wrongly.
+# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some parameters
+# in a documented function, or documenting parameters that don't exist or using
+# markup commands wrongly.
+# The default value is: YES.
WARN_IF_DOC_ERROR = YES
-# The WARN_NO_PARAMDOC option can be enabled to get warnings for
-# functions that are documented, but have no documentation for their parameters
-# or return value. If set to NO (the default) doxygen will only warn about
-# wrong or incomplete parameter documentation, but not about the absence of
-# documentation.
+# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
+# are documented, but have no documentation for their parameters or return
+# value. If set to NO, doxygen will only warn about wrong or incomplete
+# parameter documentation, but not about the absence of documentation.
+# The default value is: NO.
WARN_NO_PARAMDOC = NO
-# The WARN_FORMAT tag determines the format of the warning messages that
-# doxygen can produce. The string should contain the $file, $line, and $text
-# tags, which will be replaced by the file and line number from which the
-# warning originated and the warning text. Optionally the format may contain
-# $version, which will be replaced by the version of the file (if it could
-# be obtained via FILE_VERSION_FILTER)
+# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
+# a warning is encountered.
+# The default value is: NO.
+
+WARN_AS_ERROR = NO
+
+# The WARN_FORMAT tag determines the format of the warning messages that doxygen
+# can produce. The string should contain the $file, $line, and $text tags, which
+# will be replaced by the file and line number from which the warning originated
+# and the warning text. Optionally the format may contain $version, which will
+# be replaced by the version of the file (if it could be obtained via
+# FILE_VERSION_FILTER)
+# The default value is: $file:$line: $text.
WARN_FORMAT = "$file:$line: $text"
-# The WARN_LOGFILE tag can be used to specify a file to which warning
-# and error messages should be written. If left blank the output is written
-# to stderr.
+# The WARN_LOGFILE tag can be used to specify a file to which warning and error
+# messages should be written. If left blank the output is written to standard
+# error (stderr).
WARN_LOGFILE =
#---------------------------------------------------------------------------
-# configuration options related to the input files
+# Configuration options related to the input files
#---------------------------------------------------------------------------
-# The INPUT tag can be used to specify the files and/or directories that contain
-# documented source files. You may enter file names like "myfile.cpp" or
-# directories like "/usr/src/myproject". Separate the files or directories
-# with spaces.
+# The INPUT tag is used to specify the files and/or directories that contain
+# documented source files. You may enter file names like myfile.cpp or
+# directories like /usr/src/myproject. Separate the files or directories with
+# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
+# Note: If this tag is empty the current directory is searched.
INPUT = src
-# This tag can be used to specify the character encoding of the source files
-# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
-# also the default input encoding. Doxygen uses libiconv (or the iconv built
-# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for
-# the list of possible encodings.
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
+# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
+# documentation (see: http://www.gnu.org/software/libiconv) for the list of
+# possible encodings.
+# The default value is: UTF-8.
INPUT_ENCODING = UTF-8
-# If the value of the INPUT tag contains directories, you can use the
-# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
-# and *.h) to filter out the source-files in the directories. If left
-# blank the following patterns are tested:
-# *.c *.cc *.cxx *.cpp *.c++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh
-# *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py
-# *.f90 *.f *.for *.vhd *.vhdl
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
+# *.h) to filter out the source-files in the directories.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# read by doxygen.
+#
+# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
+# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
+# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc,
+# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f, *.for, *.tcl,
+# *.vhd, *.vhdl, *.ucf, *.qsf, *.as and *.js.
FILE_PATTERNS = Raa*.h \
*.cpp \
RAA.h
-# The RECURSIVE tag can be used to turn specify whether or not subdirectories
-# should be searched for input files as well. Possible values are YES and NO.
-# If left blank NO is used.
+# The RECURSIVE tag can be used to specify whether or not subdirectories should
+# be searched for input files as well.
+# The default value is: NO.
RECURSIVE = YES
-# The EXCLUDE tag can be used to specify files and/or directories that should be
-# excluded from the INPUT source files. This way you can easily exclude a
-# subdirectory from a directory tree whose root is specified with the INPUT tag.
-# Note that relative paths are relative to the directory from which doxygen is
+# The EXCLUDE tag can be used to specify files and/or directories that should be
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+#
+# Note that relative paths are relative to the directory from which doxygen is
# run.
EXCLUDE =
-# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
-# directories that are symbolic links (a Unix file system feature) are excluded
+# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
+# directories that are symbolic links (a Unix file system feature) are excluded
# from the input.
+# The default value is: NO.
EXCLUDE_SYMLINKS = NO
-# If the value of the INPUT tag contains directories, you can use the
-# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
-# certain files from those directories. Note that the wildcards are matched
-# against the file with absolute path, so to exclude all test directories
-# for example use the pattern */test/*
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories.
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories for example use the pattern */test/*
EXCLUDE_PATTERNS =
-# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
-# (namespaces, classes, functions, etc.) that should be excluded from the
-# output. The symbol name can be a fully qualified name, a word, or if the
-# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
# AClass::ANamespace, ANamespace::*Test
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories use the pattern */test/*
EXCLUDE_SYMBOLS =
-# The EXAMPLE_PATH tag can be used to specify one or more files or
-# directories that contain example code fragments that are included (see
-# the \include command).
+# The EXAMPLE_PATH tag can be used to specify one or more files or directories
+# that contain example code fragments that are included (see the \include
+# command).
EXAMPLE_PATH =
-# If the value of the EXAMPLE_PATH tag contains directories, you can use the
-# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
-# and *.h) to filter out the source-files in the directories. If left
-# blank all files are included.
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
+# *.h) to filter out the source-files in the directories. If left blank all
+# files are included.
EXAMPLE_PATTERNS =
-# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
-# searched for input files to be used with the \include or \dontinclude
-# commands irrespective of the value of the RECURSIVE tag.
-# Possible values are YES and NO. If left blank NO is used.
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude commands
+# irrespective of the value of the RECURSIVE tag.
+# The default value is: NO.
EXAMPLE_RECURSIVE = NO
-# The IMAGE_PATH tag can be used to specify one or more files or
-# directories that contain image that are included in the documentation (see
-# the \image command).
+# The IMAGE_PATH tag can be used to specify one or more files or directories
+# that contain images that are to be included in the documentation (see the
+# \image command).
IMAGE_PATH =
-# The INPUT_FILTER tag can be used to specify a program that doxygen should
-# invoke to filter for each input file. Doxygen will invoke the filter program
-# by executing (via popen()) the command <filter> <input-file>, where <filter>
-# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
-# input file. Doxygen will then use the output that the filter program writes
-# to standard output. If FILTER_PATTERNS is specified, this tag will be
-# ignored.
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command:
+#
+# <filter> <input-file>
+#
+# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
+# name of an input file. Doxygen will then use the output that the filter
+# program writes to standard output. If FILTER_PATTERNS is specified, this tag
+# will be ignored.
+#
+# Note that the filter must not add or remove lines; it is applied before the
+# code is scanned, but not when the output code is generated. If lines are added
+# or removed, the anchors will not be placed correctly.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
INPUT_FILTER =
-# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
-# basis. Doxygen will compare the file name with each pattern and apply the
-# filter if there is a match. The filters are a list of the form:
-# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
-# info on how filters are used. If FILTER_PATTERNS is empty or if
-# non of the patterns match the file name, INPUT_FILTER is applied.
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis. Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match. The filters are a list of the form: pattern=filter
+# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
+# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
+# patterns match the file name, INPUT_FILTER is applied.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
FILTER_PATTERNS =
-# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
-# INPUT_FILTER) will be used to filter the input files when producing source
-# files to browse (i.e. when SOURCE_BROWSER is set to YES).
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER) will also be used to filter the input files that are used for
+# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
+# The default value is: NO.
FILTER_SOURCE_FILES = NO
-# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
-# pattern. A pattern will override the setting for FILTER_PATTERN (if any)
-# and it is also possible to disable source filtering for a specific pattern
-# using *.ext= (so without naming a filter). This option only has effect when
-# FILTER_SOURCE_FILES is enabled.
+# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
+# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
+# it is also possible to disable source filtering for a specific pattern using
+# *.ext= (so without naming a filter).
+# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
FILTER_SOURCE_PATTERNS =
-# If the USE_MD_FILE_AS_MAINPAGE tag refers to the name of a markdown file that
-# is part of the input, its contents will be placed on the main page (index.html).
-# This can be useful if you have a project on for instance GitHub and want reuse
-# the introduction page also for the doxygen output.
+# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
+# is part of the input, its contents will be placed on the main page
+# (index.html). This can be useful if you have a project on for instance GitHub
+# and want to reuse the introduction page also for the doxygen output.
USE_MDFILE_AS_MAINPAGE =
#---------------------------------------------------------------------------
-# configuration options related to source browsing
+# Configuration options related to source browsing
#---------------------------------------------------------------------------
-# If the SOURCE_BROWSER tag is set to YES then a list of source files will
-# be generated. Documented entities will be cross-referenced with these sources.
-# Note: To get rid of all source code in the generated output, make sure also
-# VERBATIM_HEADERS is set to NO.
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
+# generated. Documented entities will be cross-referenced with these sources.
+#
+# Note: To get rid of all source code in the generated output, make sure that
+# also VERBATIM_HEADERS is set to NO.
+# The default value is: NO.
SOURCE_BROWSER = YES
-# Setting the INLINE_SOURCES tag to YES will include the body
-# of functions and classes directly in the documentation.
+# Setting the INLINE_SOURCES tag to YES will include the body of functions,
+# classes and enums directly into the documentation.
+# The default value is: NO.
INLINE_SOURCES = NO
-# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
-# doxygen to hide any special comment blocks from generated source code
-# fragments. Normal C, C++ and Fortran comments will always remain visible.
+# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
+# special comment blocks from generated source code fragments. Normal C, C++ and
+# Fortran comments will always remain visible.
+# The default value is: YES.
STRIP_CODE_COMMENTS = YES
-# If the REFERENCED_BY_RELATION tag is set to YES
-# then for each documented function all documented
-# functions referencing it will be listed.
+# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
+# function all documented functions referencing it will be listed.
+# The default value is: NO.
REFERENCED_BY_RELATION = YES
-# If the REFERENCES_RELATION tag is set to YES
-# then for each documented function all documented entities
-# called/used by that function will be listed.
+# If the REFERENCES_RELATION tag is set to YES then for each documented function
+# all documented entities called/used by that function will be listed.
+# The default value is: NO.
REFERENCES_RELATION = YES
-# If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
-# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
-# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
-# link to the source code. Otherwise they will link to the documentation.
+# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
+# to YES then the hyperlinks from functions in REFERENCES_RELATION and
+# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
+# link to the documentation.
+# The default value is: YES.
REFERENCES_LINK_SOURCE = YES
-# If the USE_HTAGS tag is set to YES then the references to source code
-# will point to the HTML generated by the htags(1) tool instead of doxygen
-# built-in source browser. The htags tool is part of GNU's global source
-# tagging system (see http://www.gnu.org/software/global/global.html). You
-# will need version 4.8.6 or higher.
+# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
+# source code will show a tooltip with additional information such as prototype,
+# brief description and links to the definition and documentation. Since this
+# will make the HTML file larger and loading of large files a bit slower, you
+# can opt to disable this feature.
+# The default value is: YES.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+SOURCE_TOOLTIPS = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code will
+# point to the HTML generated by the htags(1) tool instead of doxygen built-in
+# source browser. The htags tool is part of GNU's global source tagging system
+# (see http://www.gnu.org/software/global/global.html). You will need version
+# 4.8.6 or higher.
+#
+# To use it do the following:
+# - Install the latest version of global
+# - Enable SOURCE_BROWSER and USE_HTAGS in the config file
+# - Make sure the INPUT points to the root of the source tree
+# - Run doxygen as normal
+#
+# Doxygen will invoke htags (and that will in turn invoke gtags), so these
+# tools must be available from the command line (i.e. in the search path).
+#
+# The result: instead of the source browser generated by doxygen, the links to
+# source code will now point to the output of htags.
+# The default value is: NO.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
USE_HTAGS = NO
-# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
-# will generate a verbatim copy of the header file for each class for
-# which an include is specified. Set to NO to disable this.
+# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
+# verbatim copy of the header file for each class for which an include is
+# specified. Set to NO to disable this.
+# See also: Section \class.
+# The default value is: YES.
VERBATIM_HEADERS = YES
+# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the
+# clang parser (see: http://clang.llvm.org/) for more accurate parsing at the
+# cost of reduced performance. This can be particularly helpful with template
+# rich C++ code for which doxygen's built-in parser lacks the necessary type
+# information.
+# Note: The availability of this option depends on whether or not doxygen was
+# generated with the -Duse-libclang=ON option for CMake.
+# The default value is: NO.
+
+CLANG_ASSISTED_PARSING = NO
+
+# If clang assisted parsing is enabled you can provide the compiler with command
+# line options that you would normally use when invoking the compiler. Note that
+# the include paths will already be set by doxygen for the files and directories
+# specified with INPUT and INCLUDE_PATH.
+# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
+
+CLANG_OPTIONS =
+
#---------------------------------------------------------------------------
-# configuration options related to the alphabetical class index
+# Configuration options related to the alphabetical class index
#---------------------------------------------------------------------------
-# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
-# of all compounds will be generated. Enable this if the project
-# contains a lot of classes, structs, unions or interfaces.
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
+# compounds will be generated. Enable this if the project contains a lot of
+# classes, structs, unions or interfaces.
+# The default value is: YES.
ALPHABETICAL_INDEX = NO
-# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
-# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
-# in which this list will be split (can be a number in the range [1..20])
+# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
+# which the alphabetical index list will be split.
+# Minimum value: 1, maximum value: 20, default value: 5.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
COLS_IN_ALPHA_INDEX = 5
-# In case all classes in a project start with a common prefix, all
-# classes will be put under the same header in the alphabetical index.
-# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
-# should be ignored while generating the index headers.
+# In case all classes in a project start with a common prefix, all classes will
+# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
+# can be used to specify a prefix (or a list of prefixes) that should be ignored
+# while generating the index headers.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
IGNORE_PREFIX =
#---------------------------------------------------------------------------
-# configuration options related to the HTML output
+# Configuration options related to the HTML output
#---------------------------------------------------------------------------
-# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
-# generate HTML output.
+# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
+# The default value is: YES.
GENERATE_HTML = YES
-# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `html' will be used as the default path.
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_OUTPUT = html
-# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
-# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
-# doxygen will generate files with .html extension.
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
+# generated HTML page (for example: .htm, .php, .asp).
+# The default value is: .html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FILE_EXTENSION = .html
-# The HTML_HEADER tag can be used to specify a personal HTML header for
-# each generated HTML page. If it is left blank doxygen will generate a
-# standard header. Note that when using a custom header you are responsible
-# for the proper inclusion of any scripts and style sheets that doxygen
-# needs, which is dependent on the configuration options used.
-# It is advised to generate a default header using "doxygen -w html
-# header.html footer.html stylesheet.css YourConfigFile" and then modify
-# that header. Note that the header is subject to change so you typically
-# have to redo this when upgrading to a newer version of doxygen or when
-# changing the value of configuration settings such as GENERATE_TREEVIEW!
+# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
+# each generated HTML page. If the tag is left blank doxygen will generate a
+# standard header.
+#
+# To get valid HTML the header file that includes any scripts and style sheets
+# that doxygen needs, which is dependent on the configuration options used (e.g.
+# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
+# default header using
+# doxygen -w html new_header.html new_footer.html new_stylesheet.css
+# YourConfigFile
+# and then modify the file new_header.html. See also section "Doxygen usage"
+# for information on how to generate the default header that doxygen normally
+# uses.
+# Note: The header is subject to change so you typically have to regenerate the
+# default header when upgrading to a newer version of doxygen. For a description
+# of the possible markers and block names see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_HEADER =
-# The HTML_FOOTER tag can be used to specify a personal HTML footer for
-# each generated HTML page. If it is left blank doxygen will generate a
-# standard footer.
+# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
+# generated HTML page. If the tag is left blank doxygen will generate a standard
+# footer. See HTML_HEADER for more information on how to generate a default
+# footer and what special commands can be used inside the footer. See also
+# section "Doxygen usage" for information on how to generate the default footer
+# that doxygen normally uses.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FOOTER =
-# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
-# style sheet that is used by each HTML page. It can be used to
-# fine-tune the look of the HTML output. If left blank doxygen will
-# generate a default style sheet. Note that it is recommended to use
-# HTML_EXTRA_STYLESHEET instead of this one, as it is more robust and this
-# tag will in the future become obsolete.
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
+# sheet that is used by each HTML page. It can be used to fine-tune the look of
+# the HTML output. If left blank doxygen will generate a default style sheet.
+# See also section "Doxygen usage" for information on how to generate the style
+# sheet that doxygen normally uses.
+# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
+# it is more robust and this tag (HTML_STYLESHEET) will in the future become
+# obsolete.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_STYLESHEET =
-# The HTML_EXTRA_STYLESHEET tag can be used to specify an additional
-# user-defined cascading style sheet that is included after the standard
-# style sheets created by doxygen. Using this option one can overrule
-# certain style aspects. This is preferred over using HTML_STYLESHEET
-# since it does not replace the standard style sheet and is therefor more
-# robust against future updates. Doxygen will copy the style sheet file to
-# the output directory.
+# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# cascading style sheets that are included after the standard style sheets
+# created by doxygen. Using this option one can overrule certain style aspects.
+# This is preferred over using HTML_STYLESHEET since it does not replace the
+# standard style sheet and is therefore more robust against future updates.
+# Doxygen will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list). For an example see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_EXTRA_STYLESHEET =
-# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
-# other source files which should be copied to the HTML output directory. Note
-# that these files will be copied to the base HTML output directory. Use the
-# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
-# files. In the HTML_STYLESHEET file, use the file name only. Also note that
-# the files will be copied as-is; there are no commands or markers available.
+# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the HTML output directory. Note
+# that these files will be copied to the base HTML output directory. Use the
+# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
+# files will be copied as-is; there are no commands or markers available.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_EXTRA_FILES =
-# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output.
-# Doxygen will adjust the colors in the style sheet and background images
-# according to this color. Hue is specified as an angle on a colorwheel,
-# see http://en.wikipedia.org/wiki/Hue for more information.
-# For instance the value 0 represents red, 60 is yellow, 120 is green,
-# 180 is cyan, 240 is blue, 300 purple, and 360 is red again.
-# The allowed range is 0 to 359.
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
+# will adjust the colors in the style sheet and background images according to
+# this color. Hue is specified as an angle on a colorwheel, see
+# http://en.wikipedia.org/wiki/Hue for more information. For instance the value
+# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
+# purple, and 360 is red again.
+# Minimum value: 0, maximum value: 359, default value: 220.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_HUE = 220
-# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of
-# the colors in the HTML output. For a value of 0 the output will use
-# grayscales only. A value of 255 will produce the most vivid colors.
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
+# in the HTML output. For a value of 0 the output will use grayscales only. A
+# value of 255 will produce the most vivid colors.
+# Minimum value: 0, maximum value: 255, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_SAT = 100
-# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to
-# the luminance component of the colors in the HTML output. Values below
-# 100 gradually make the output lighter, whereas values above 100 make
-# the output darker. The value divided by 100 is the actual gamma applied,
-# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2,
-# and 100 does not change the gamma.
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
+# luminance component of the colors in the HTML output. Values below 100
+# gradually make the output lighter, whereas values above 100 make the output
+# darker. The value divided by 100 is the actual gamma applied, so 80 represents
+# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
+# change the gamma.
+# Minimum value: 40, maximum value: 240, default value: 80.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_GAMMA = 80
-# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
-# page will contain the date and time when the page was generated. Setting
-# this to NO can help when comparing the output of multiple runs.
+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
+# page will contain the date and time when the page was generated. Setting this
+# to YES can help to show when doxygen was last run and thus if the
+# documentation is up to date.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_TIMESTAMP = YES
-# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
-# documentation will contain sections that can be hidden and shown after the
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
# page has loaded.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_DYNAMIC_SECTIONS = YES
-# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
-# entries shown in the various tree structured indices initially; the user
-# can expand and collapse entries dynamically later on. Doxygen will expand
-# the tree to such a level that at most the specified number of entries are
-# visible (unless a fully collapsed tree already exceeds this amount).
-# So setting the number of entries 1 will produce a full collapsed tree by
-# default. 0 is a special value representing an infinite number of entries
-# and will result in a full expanded tree by default.
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
+# shown in the various tree structured indices initially; the user can expand
+# and collapse entries dynamically later on. Doxygen will expand the tree to
+# such a level that at most the specified number of entries are visible (unless
+# a fully collapsed tree already exceeds this amount). So setting the number of
+# entries 1 will produce a full collapsed tree by default. 0 is a special value
+# representing an infinite number of entries and will result in a full expanded
+# tree by default.
+# Minimum value: 0, maximum value: 9999, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_INDEX_NUM_ENTRIES = 100
-# If the GENERATE_DOCSET tag is set to YES, additional index files
-# will be generated that can be used as input for Apple's Xcode 3
-# integrated development environment, introduced with OSX 10.5 (Leopard).
-# To create a documentation set, doxygen will generate a Makefile in the
-# HTML output directory. Running make will produce the docset in that
-# directory and running "make install" will install the docset in
-# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
-# it at startup.
-# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
+# If the GENERATE_DOCSET tag is set to YES, additional index files will be
+# generated that can be used as input for Apple's Xcode 3 integrated development
+# environment (see: http://developer.apple.com/tools/xcode/), introduced with
+# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a
+# Makefile in the HTML output directory. Running make will produce the docset in
+# that directory and running make install will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
+# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
# for more information.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_DOCSET = YES
-# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
-# feed. A documentation feed provides an umbrella under which multiple
-# documentation sets from a single provider (such as a company or product suite)
-# can be grouped.
+# This tag determines the name of the docset feed. A documentation feed provides
+# an umbrella under which multiple documentation sets from a single provider
+# (such as a company or product suite) can be grouped.
+# The default value is: Doxygen generated docs.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_FEEDNAME = "Bio++ RAA"
-# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
-# should uniquely identify the documentation set bundle. This should be a
-# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
-# will append .docset to the name.
+# This tag specifies a string that should uniquely identify the documentation
+# set bundle. This should be a reverse domain-name style string, e.g.
+# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_BUNDLE_ID = bpp.RAA
-# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely
-# identify the documentation publisher. This should be a reverse domain-name
-# style string, e.g. com.mycompany.MyDocSet.documentation.
+# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
+# the documentation publisher. This should be a reverse domain-name style
+# string, e.g. com.mycompany.MyDocSet.documentation.
+# The default value is: org.doxygen.Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_PUBLISHER_ID = org.doxygen.Publisher
-# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher.
+# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
+# The default value is: Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_PUBLISHER_NAME = Publisher
-# If the GENERATE_HTMLHELP tag is set to YES, additional index files
-# will be generated that can be used as input for tools like the
-# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
-# of the generated HTML documentation.
+# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
+# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
+# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
+# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on
+# Windows.
+#
+# The HTML Help Workshop contains a compiler that can convert all HTML output
+# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
+# files are now used as the Windows 98 help format, and will replace the old
+# Windows help format (.hlp) on all Windows platforms in the future. Compressed
+# HTML files also contain an index, a table of contents, and you can search for
+# words in the documentation. The HTML workshop also contains a viewer for
+# compressed HTML files.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_HTMLHELP = NO
-# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
-# be used to specify the file name of the resulting .chm file. You
-# can add a path in front of the file if the result should not be
+# The CHM_FILE tag can be used to specify the file name of the resulting .chm
+# file. You can add a path in front of the file if the result should not be
# written to the html output directory.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
CHM_FILE =
-# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
-# be used to specify the location (absolute path including file name) of
-# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
-# the HTML help compiler on the generated index.hhp.
+# The HHC_LOCATION tag can be used to specify the location (absolute path
+# including file name) of the HTML help compiler (hhc.exe). If non-empty,
+# doxygen will try to run the HTML help compiler on the generated index.hhp.
+# The file has to be specified with full path.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
HHC_LOCATION =
-# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
-# controls if a separate .chi index file is generated (YES) or that
-# it should be included in the master .chm file (NO).
+# The GENERATE_CHI flag controls if a separate .chi index file is generated
+# (YES) or that it should be included in the master .chm file (NO).
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
GENERATE_CHI = NO
-# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
-# is used to encode HtmlHelp index (hhk), content (hhc) and project file
-# content.
+# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc)
+# and project file content.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
CHM_INDEX_ENCODING =
-# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
-# controls whether a binary table of contents is generated (YES) or a
-# normal table of contents (NO) in the .chm file.
+# The BINARY_TOC flag controls whether a binary table of contents is generated
+# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it
+# enables the Previous and Next buttons.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
BINARY_TOC = NO
-# The TOC_EXPAND flag can be set to YES to add extra items for group members
-# to the contents of the HTML help documentation and to the tree view.
+# The TOC_EXPAND flag can be set to YES to add extra items for group members to
+# the table of contents of the HTML help documentation and to the tree view.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
TOC_EXPAND = NO
-# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
-# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated
-# that can be used as input for Qt's qhelpgenerator to generate a
-# Qt Compressed Help (.qch) of the generated HTML documentation.
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
+# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
+# (.qch) of the generated HTML documentation.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_QHP = NO
-# If the QHG_LOCATION tag is specified, the QCH_FILE tag can
-# be used to specify the file name of the resulting .qch file.
-# The path specified is relative to the HTML output folder.
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
+# the file name of the resulting .qch file. The path specified is relative to
+# the HTML output folder.
+# This tag requires that the tag GENERATE_QHP is set to YES.
QCH_FILE =
-# The QHP_NAMESPACE tag specifies the namespace to use when generating
-# Qt Help Project output. For more information please see
-# http://doc.trolltech.com/qthelpproject.html#namespace
+# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
+# Project output. For more information please see Qt Help Project / Namespace
+# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace).
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_NAMESPACE = org.doxygen.Project
-# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating
-# Qt Help Project output. For more information please see
-# http://doc.trolltech.com/qthelpproject.html#virtual-folders
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
+# Help Project output. For more information please see Qt Help Project / Virtual
+# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual-
+# folders).
+# The default value is: doc.
+# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_VIRTUAL_FOLDER = doc
-# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to
-# add. For more information please see
-# http://doc.trolltech.com/qthelpproject.html#custom-filters
+# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
+# filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_CUST_FILTER_NAME =
-# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the
-# custom filter to add. For more information please see
-# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters">
-# Qt Help Project / Custom Filters</a>.
+# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_CUST_FILTER_ATTRS =
-# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
-# project's
-# filter section matches.
-# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes">
-# Qt Help Project / Filter Attributes</a>.
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
+# project's filter section matches. Qt Help Project / Filter Attributes (see:
+# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes).
+# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_SECT_FILTER_ATTRS =
-# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can
-# be used to specify the location of Qt's qhelpgenerator.
-# If non-empty doxygen will try to run qhelpgenerator on the generated
-# .qhp file.
+# The QHG_LOCATION tag can be used to specify the location of Qt's
+# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the
+# generated .qhp file.
+# This tag requires that the tag GENERATE_QHP is set to YES.
QHG_LOCATION =
-# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files
-# will be generated, which together with the HTML files, form an Eclipse help
-# plugin. To install this plugin and make it available under the help contents
-# menu in Eclipse, the contents of the directory containing the HTML and XML
-# files needs to be copied into the plugins directory of eclipse. The name of
-# the directory within the plugins directory should be the same as
-# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before
-# the help appears.
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
+# generated, together with the HTML files, they form an Eclipse help plugin. To
+# install this plugin and make it available under the help contents menu in
+# Eclipse, the contents of the directory containing the HTML and XML files needs
+# to be copied into the plugins directory of eclipse. The name of the directory
+# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
+# After copying Eclipse needs to be restarted before the help appears.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_ECLIPSEHELP = NO
-# A unique identifier for the eclipse help plugin. When installing the plugin
-# the directory name containing the HTML and XML files should also have
-# this name.
+# A unique identifier for the Eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have this
+# name. Each documentation set should have its own identifier.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
ECLIPSE_DOC_ID = org.doxygen.Project
-# The DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs)
-# at top of each HTML page. The value NO (the default) enables the index and
-# the value YES disables it. Since the tabs have the same information as the
-# navigation tree you can set this option to NO if you already set
-# GENERATE_TREEVIEW to YES.
+# If you want full control over the layout of the generated HTML pages it might
+# be necessary to disable the index and replace it with your own. The
+# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
+# of each HTML page. A value of NO enables the index and the value YES disables
+# it. Since the tabs in the index contain the same information as the navigation
+# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
DISABLE_INDEX = NO
-# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
-# structure should be generated to display hierarchical information.
-# If the tag value is set to YES, a side panel will be generated
-# containing a tree-like index structure (just like the one that
-# is generated for HTML Help). For this to work a browser that supports
-# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser).
-# Windows users are probably better off using the HTML help feature.
-# Since the tree basically has the same information as the tab index you
-# could consider to set DISABLE_INDEX to NO when enabling this option.
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information. If the tag
+# value is set to YES, a side panel will be generated containing a tree-like
+# index structure (just like the one that is generated for HTML Help). For this
+# to work a browser that supports JavaScript, DHTML, CSS and frames is required
+# (i.e. any modern browser). Windows users are probably better off using the
+# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
+# further fine-tune the look of the index. As an example, the default style
+# sheet generated by doxygen has an example that shows how to put an image at
+# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
+# the same information as the tab index, you could consider setting
+# DISABLE_INDEX to YES when enabling this option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_TREEVIEW = YES
-# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values
-# (range [0,1..20]) that doxygen will group on one line in the generated HTML
-# documentation. Note that a value of 0 will completely suppress the enum
-# values from appearing in the overview section.
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
+# doxygen will group on one line in the generated HTML documentation.
+#
+# Note that a value of 0 will completely suppress the enum values from appearing
+# in the overview section.
+# Minimum value: 0, maximum value: 20, default value: 4.
+# This tag requires that the tag GENERATE_HTML is set to YES.
ENUM_VALUES_PER_LINE = 4
-# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
-# used to set the initial width (in pixels) of the frame in which the tree
-# is shown.
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
+# to set the initial width (in pixels) of the frame in which the tree is shown.
+# Minimum value: 0, maximum value: 1500, default value: 250.
+# This tag requires that the tag GENERATE_HTML is set to YES.
TREEVIEW_WIDTH = 250
-# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open
-# links to external symbols imported via tag files in a separate window.
+# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to
+# external symbols imported via tag files in a separate window.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
EXT_LINKS_IN_WINDOW = NO
-# Use this tag to change the font size of Latex formulas included
-# as images in the HTML documentation. The default is 10. Note that
-# when you change the font size after a successful doxygen run you need
-# to manually remove any form_*.png images from the HTML output directory
-# to force them to be regenerated.
+# Use this tag to change the font size of LaTeX formulas included as images in
+# the HTML documentation. When you change the font size after a successful
+# doxygen run you need to manually remove any form_*.png images from the HTML
+# output directory to force them to be regenerated.
+# Minimum value: 8, maximum value: 50, default value: 10.
+# This tag requires that the tag GENERATE_HTML is set to YES.
FORMULA_FONTSIZE = 10
-# Use the FORMULA_TRANPARENT tag to determine whether or not the images
-# generated for formulas are transparent PNGs. Transparent PNGs are
-# not supported properly for IE 6.0, but are supported on all modern browsers.
-# Note that when changing this option you need to delete any form_*.png files
-# in the HTML output before the changes have effect.
+# Use the FORMULA_TRANPARENT tag to determine whether or not the images
+# generated for formulas are transparent PNGs. Transparent PNGs are not
+# supported properly for IE 6.0, but are supported on all modern browsers.
+#
+# Note that when changing this option you need to delete any form_*.png files in
+# the HTML output directory before the changes have effect.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
FORMULA_TRANSPARENT = YES
-# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax
-# (see http://www.mathjax.org) which uses client side Javascript for the
-# rendering instead of using prerendered bitmaps. Use this if you do not
-# have LaTeX installed or if you want to formulas look prettier in the HTML
-# output. When enabled you may also need to install MathJax separately and
-# configure the path to it using the MATHJAX_RELPATH option.
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
+# http://www.mathjax.org) which uses client side Javascript for the rendering
+# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX
+# installed or if you want to formulas look prettier in the HTML output. When
+# enabled you may also need to install MathJax separately and configure the path
+# to it using the MATHJAX_RELPATH option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
USE_MATHJAX = NO
-# When MathJax is enabled you can set the default output format to be used for
-# thA MathJax output. Supported types are HTML-CSS, NativeMML (i.e. MathML) and
-# SVG. The default value is HTML-CSS, which is slower, but has the best
-# compatibility.
+# When MathJax is enabled you can set the default output format to be used for
+# the MathJax output. See the MathJax site (see:
+# http://docs.mathjax.org/en/latest/output.html) for more details.
+# Possible values are: HTML-CSS (which is slower, but has the best
+# compatibility), NativeMML (i.e. MathML) and SVG.
+# The default value is: HTML-CSS.
+# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_FORMAT = HTML-CSS
-# When MathJax is enabled you need to specify the location relative to the
-# HTML output directory using the MATHJAX_RELPATH option. The destination
-# directory should contain the MathJax.js script. For instance, if the mathjax
-# directory is located at the same level as the HTML output directory, then
-# MATHJAX_RELPATH should be ../mathjax. The default value points to
-# the MathJax Content Delivery Network so you can quickly see the result without
-# installing MathJax. However, it is strongly recommended to install a local
-# copy of MathJax from http://www.mathjax.org before deployment.
+# When MathJax is enabled you need to specify the location relative to the HTML
+# output directory using the MATHJAX_RELPATH option. The destination directory
+# should contain the MathJax.js script. For instance, if the mathjax directory
+# is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
+# Content Delivery Network so you can quickly see the result without installing
+# MathJax. However, it is strongly recommended to install a local copy of
+# MathJax from http://www.mathjax.org before deployment.
+# The default value is: http://cdn.mathjax.org/mathjax/latest.
+# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest
-# The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension
-# names that should be enabled during MathJax rendering.
+# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
+# extension names that should be enabled during MathJax rendering. For example
+# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
+# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_EXTENSIONS =
-# When the SEARCHENGINE tag is enabled doxygen will generate a search box
-# for the HTML output. The underlying search engine uses javascript
-# and DHTML and should work on any modern browser. Note that when using
-# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets
-# (GENERATE_DOCSET) there is already a search function so this one should
-# typically be disabled. For large projects the javascript based search engine
-# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.
+# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
+# of code that will be used on startup of the MathJax code. See the MathJax site
+# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
+# example see the documentation.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_CODEFILE =
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
+# the HTML output. The underlying search engine uses javascript and DHTML and
+# should work on any modern browser. Note that when using HTML help
+# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
+# there is already a search function so this one should typically be disabled.
+# For large projects the javascript based search engine can be slow, then
+# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
+# search using the keyboard; to jump to the search box use <access key> + S
+# (what the <access key> is depends on the OS and browser, but it is typically
+# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
+# key> to jump into the search results window, the results can be navigated
+# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
+# the search. The filter options can be selected when the cursor is inside the
+# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
+# to select a filter and <Enter> or <escape> to activate or cancel the filter
+# option.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
SEARCHENGINE = YES
-# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
-# implemented using a web server instead of a web client using Javascript.
-# There are two flavours of web server based search depending on the
-# EXTERNAL_SEARCH setting. When disabled, doxygen will generate a PHP script for
-# searching and an index file used by the script. When EXTERNAL_SEARCH is
-# enabled the indexing and searching needs to be provided by external tools.
-# See the manual for details.
+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
+# implemented using a web server instead of a web client using Javascript. There
+# are two flavors of web server based searching depending on the EXTERNAL_SEARCH
+# setting. When disabled, doxygen will generate a PHP script for searching and
+# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing
+# and searching needs to be provided by external tools. See the section
+# "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
SERVER_BASED_SEARCH = NO
-# When EXTERNAL_SEARCH is enabled doxygen will no longer generate the PHP
-# script for searching. Instead the search results are written to an XML file
-# which needs to be processed by an external indexer. Doxygen will invoke an
-# external search engine pointed to by the SEARCHENGINE_URL option to obtain
-# the search results. Doxygen ships with an example indexer (doxyindexer) and
-# search engine (doxysearch.cgi) which are based on the open source search engine
-# library Xapian. See the manual for configuration details.
+# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
+# script for searching. Instead the search results are written to an XML file
+# which needs to be processed by an external indexer. Doxygen will invoke an
+# external search engine pointed to by the SEARCHENGINE_URL option to obtain the
+# search results.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: http://xapian.org/).
+#
+# See the section "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
EXTERNAL_SEARCH = NO
-# The SEARCHENGINE_URL should point to a search engine hosted by a web server
-# which will returned the search results when EXTERNAL_SEARCH is enabled.
-# Doxygen ships with an example search engine (doxysearch) which is based on
-# the open source search engine library Xapian. See the manual for configuration
-# details.
+# The SEARCHENGINE_URL should point to a search engine hosted by a web server
+# which will return the search results when EXTERNAL_SEARCH is enabled.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: http://xapian.org/). See the section "External Indexing and
+# Searching" for details.
+# This tag requires that the tag SEARCHENGINE is set to YES.
SEARCHENGINE_URL =
-# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
-# search data is written to a file for indexing by an external tool. With the
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
+# search data is written to a file for indexing by an external tool. With the
# SEARCHDATA_FILE tag the name of this file can be specified.
+# The default file is: searchdata.xml.
+# This tag requires that the tag SEARCHENGINE is set to YES.
SEARCHDATA_FILE = searchdata.xml
-# When SERVER_BASED_SEARCH AND EXTERNAL_SEARCH are both enabled the
-# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
-# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the
+# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
+# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
# projects and redirect the results back to the right project.
+# This tag requires that the tag SEARCHENGINE is set to YES.
EXTERNAL_SEARCH_ID =
-# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
-# projects other than the one defined by this configuration file, but that are
-# all added to the same external search index. Each project needs to have a
-# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id
-# of to a relative location where the documentation can be found.
-# The format is: EXTRA_SEARCH_MAPPINGS = id1=loc1 id2=loc2 ...
+# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
+# projects other than the one defined by this configuration file, but that are
+# all added to the same external search index. Each project needs to have a
+# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of
+# to a relative location where the documentation can be found. The format is:
+# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
+# This tag requires that the tag SEARCHENGINE is set to YES.
EXTRA_SEARCH_MAPPINGS =
#---------------------------------------------------------------------------
-# configuration options related to the LaTeX output
+# Configuration options related to the LaTeX output
#---------------------------------------------------------------------------
-# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
-# generate Latex output.
+# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
+# The default value is: YES.
GENERATE_LATEX = NO
-# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `latex' will be used as the default path.
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_OUTPUT = latex
-# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
-# invoked. If left blank `latex' will be used as the default command name.
-# Note that when enabling USE_PDFLATEX this option is only used for
-# generating bitmaps for formulas in the HTML output, but not in the
-# Makefile that is written to the output directory.
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+# invoked.
+#
+# Note that when enabling USE_PDFLATEX this option is only used for generating
+# bitmaps for formulas in the HTML output, but not in the Makefile that is
+# written to the output directory.
+# The default file is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_CMD_NAME = latex
-# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
-# generate index for LaTeX. If left blank `makeindex' will be used as the
-# default command name.
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
+# index for LaTeX.
+# The default file is: makeindex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
MAKEINDEX_CMD_NAME = makeindex
-# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
-# LaTeX documents. This may be useful for small projects and may help to
-# save some trees in general.
+# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
COMPACT_LATEX = NO
-# The PAPER_TYPE tag can be used to set the paper type that is used
-# by the printer. Possible values are: a4, letter, legal and
-# executive. If left blank a4wide will be used.
+# The PAPER_TYPE tag can be used to set the paper type that is used by the
+# printer.
+# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
+# 14 inches) and executive (7.25 x 10.5 inches).
+# The default value is: a4.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
PAPER_TYPE = a4wide
-# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
-# packages that should be included in the LaTeX output.
+# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
+# that should be included in the LaTeX output. The package can be specified just
+# by its name or with the correct syntax as to be used with the LaTeX
+# \usepackage command. To get the times font for instance you can specify :
+# EXTRA_PACKAGES=times or EXTRA_PACKAGES={times}
+# To use the option intlimits with the amsmath package you can specify:
+# EXTRA_PACKAGES=[intlimits]{amsmath}
+# If left blank no extra packages will be included.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
EXTRA_PACKAGES = amsmath
-# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
-# the generated latex document. The header should contain everything until
-# the first chapter. If it is left blank doxygen will generate a
-# standard header. Notice: only use this tag if you know what you are doing!
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
+# generated LaTeX document. The header should contain everything until the first
+# chapter. If it is left blank doxygen will generate a standard header. See
+# section "Doxygen usage" for information on how to let doxygen write the
+# default header to a separate file.
+#
+# Note: Only use a user-defined header if you know what you are doing! The
+# following commands have a special meaning inside the header: $title,
+# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
+# $projectbrief, $projectlogo. Doxygen will replace $title with the empty
+# string, for the replacement values of the other commands the user is referred
+# to HTML_HEADER.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_HEADER =
-# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for
-# the generated latex document. The footer should contain everything after
-# the last chapter. If it is left blank doxygen will generate a
-# standard footer. Notice: only use this tag if you know what you are doing!
+# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
+# generated LaTeX document. The footer should contain everything after the last
+# chapter. If it is left blank doxygen will generate a standard footer. See
+# LATEX_HEADER for more information on how to generate a default footer and what
+# special commands can be used inside the footer.
+#
+# Note: Only use a user-defined footer if you know what you are doing!
+# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_FOOTER =
-# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images
-# or other source files which should be copied to the LaTeX output directory.
-# Note that the files will be copied as-is; there are no commands or markers
-# available.
+# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# LaTeX style sheets that are included after the standard style sheets created
+# by doxygen. Using this option one can overrule certain style aspects. Doxygen
+# will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list).
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_STYLESHEET =
+
+# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the LATEX_OUTPUT output
+# directory. Note that the files will be copied as-is; there are no commands or
+# markers available.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_EXTRA_FILES =
-# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
-# is prepared for conversion to pdf (using ps2pdf). The pdf file will
-# contain links (just like the HTML output) instead of page references
-# This makes the output suitable for online browsing using a pdf viewer.
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
+# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
+# contain links (just like the HTML output) instead of page references. This
+# makes the output suitable for online browsing using a PDF viewer.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
PDF_HYPERLINKS = NO
-# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
-# plain latex in the generated Makefile. Set this option to YES to get a
+# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
+# the PDF file directly from the LaTeX files. Set this option to YES, to get a
# higher quality PDF documentation.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
USE_PDFLATEX = NO
-# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
-# command to the generated LaTeX files. This will instruct LaTeX to keep
-# running if errors occur, instead of asking the user for help.
-# This option is also used when generating formulas in HTML.
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
+# command to the generated LaTeX files. This will instruct LaTeX to keep running
+# if errors occur, instead of asking the user for help. This option is also used
+# when generating formulas in HTML.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_BATCHMODE = NO
-# If LATEX_HIDE_INDICES is set to YES then doxygen will not
-# include the index chapters (such as File Index, Compound Index, etc.)
-# in the output.
+# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
+# index chapters (such as File Index, Compound Index, etc.) in the output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_HIDE_INDICES = NO
-# If LATEX_SOURCE_CODE is set to YES then doxygen will include
-# source code with syntax highlighting in the LaTeX output.
-# Note that which sources are shown also depends on other settings
-# such as SOURCE_BROWSER.
+# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
+# code with syntax highlighting in the LaTeX output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_SOURCE_CODE = NO
-# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
-# bibliography, e.g. plainnat, or ieeetr. The default style is "plain". See
-# http://en.wikipedia.org/wiki/BibTeX for more info.
+# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
+# bibliography, e.g. plainnat, or ieeetr. See
+# http://en.wikipedia.org/wiki/BibTeX and \cite for more info.
+# The default value is: plain.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_BIB_STYLE = plain
+# If the LATEX_TIMESTAMP tag is set to YES then the footer of each generated
+# page will contain the date and time when the page was generated. Setting this
+# to NO can help when comparing the output of multiple runs.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_TIMESTAMP = NO
+
#---------------------------------------------------------------------------
-# configuration options related to the RTF output
+# Configuration options related to the RTF output
#---------------------------------------------------------------------------
-# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
-# The RTF output is optimized for Word 97 and may not look very pretty with
-# other RTF readers or editors.
+# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The
+# RTF output is optimized for Word 97 and may not look too pretty with other RTF
+# readers/editors.
+# The default value is: NO.
GENERATE_RTF = NO
-# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `rtf' will be used as the default path.
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: rtf.
+# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_OUTPUT = rtf
-# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
-# RTF documents. This may be useful for small projects and may help to
-# save some trees in general.
+# If the COMPACT_RTF tag is set to YES, doxygen generates more compact RTF
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
COMPACT_RTF = NO
-# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
-# will contain hyperlink fields. The RTF file will
-# contain links (just like the HTML output) instead of page references.
-# This makes the output suitable for online browsing using WORD or other
-# programs which support those fields.
-# Note: wordpad (write) and others do not support links.
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
+# contain hyperlink fields. The RTF file will contain links (just like the HTML
+# output) instead of page references. This makes the output suitable for online
+# browsing using Word or some other Word compatible readers that support those
+# fields.
+#
+# Note: WordPad (write) and others do not support links.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_HYPERLINKS = NO
-# Load style sheet definitions from file. Syntax is similar to doxygen's
-# config file, i.e. a series of assignments. You only have to provide
-# replacements, missing definitions are set to their default value.
+# Load stylesheet definitions from file. Syntax is similar to doxygen's config
+# file, i.e. a series of assignments. You only have to provide replacements,
+# missing definitions are set to their default value.
+#
+# See also section "Doxygen usage" for information on how to generate the
+# default style sheet that doxygen normally uses.
+# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_STYLESHEET_FILE =
-# Set optional variables used in the generation of an rtf document.
-# Syntax is similar to doxygen's config file.
+# Set optional variables used in the generation of an RTF document. Syntax is
+# similar to doxygen's config file. A template extensions file can be generated
+# using doxygen -e rtf extensionFile.
+# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_EXTENSIONS_FILE =
+# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code
+# with syntax highlighting in the RTF output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_SOURCE_CODE = NO
+
#---------------------------------------------------------------------------
-# configuration options related to the man page output
+# Configuration options related to the man page output
#---------------------------------------------------------------------------
-# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
-# generate man pages
+# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for
+# classes and files.
+# The default value is: NO.
GENERATE_MAN = NO
-# The MAN_OUTPUT tag is used to specify where the man pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `man' will be used as the default path.
+# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it. A directory man3 will be created inside the directory specified by
+# MAN_OUTPUT.
+# The default directory is: man.
+# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_OUTPUT = man
-# The MAN_EXTENSION tag determines the extension that is added to
-# the generated man pages (default is the subroutine's section .3)
+# The MAN_EXTENSION tag determines the extension that is added to the generated
+# man pages. In case the manual section does not start with a number, the number
+# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
+# optional.
+# The default value is: .3.
+# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_EXTENSION = .3
-# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
-# then it will generate one additional man file for each entity
-# documented in the real man page(s). These additional files
-# only source the real man page, but without them the man command
-# would be unable to find the correct page. The default is NO.
+# The MAN_SUBDIR tag determines the name of the directory created within
+# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by
+# MAN_EXTENSION with the initial . removed.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_SUBDIR =
+
+# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
+# will generate one additional man file for each entity documented in the real
+# man page(s). These additional files only source the real man page, but without
+# them the man command would be unable to find the correct page.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_LINKS = NO
#---------------------------------------------------------------------------
-# configuration options related to the XML output
+# Configuration options related to the XML output
#---------------------------------------------------------------------------
-# If the GENERATE_XML tag is set to YES Doxygen will
-# generate an XML file that captures the structure of
-# the code including all documentation.
+# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that
+# captures the structure of the code including all documentation.
+# The default value is: NO.
GENERATE_XML = NO
-# The XML_OUTPUT tag is used to specify where the XML pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `xml' will be used as the default path.
+# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: xml.
+# This tag requires that the tag GENERATE_XML is set to YES.
XML_OUTPUT = xml
-# The XML_SCHEMA tag can be used to specify an XML schema,
-# which can be used by a validating XML parser to check the
-# syntax of the XML files.
-
-XML_SCHEMA =
-
-# The XML_DTD tag can be used to specify an XML DTD,
-# which can be used by a validating XML parser to check the
-# syntax of the XML files.
-
-XML_DTD =
-
-# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
-# dump the program listings (including syntax highlighting
-# and cross-referencing information) to the XML output. Note that
-# enabling this will significantly increase the size of the XML output.
+# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program
+# listings (including syntax highlighting and cross-referencing information) to
+# the XML output. Note that enabling this will significantly increase the size
+# of the XML output.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_XML is set to YES.
XML_PROGRAMLISTING = YES
#---------------------------------------------------------------------------
-# configuration options related to the DOCBOOK output
+# Configuration options related to the DOCBOOK output
#---------------------------------------------------------------------------
-# If the GENERATE_DOCBOOK tag is set to YES Doxygen will generate DOCBOOK files
+# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files
# that can be used to generate PDF.
+# The default value is: NO.
GENERATE_DOCBOOK = NO
-# The DOCBOOK_OUTPUT tag is used to specify where the DOCBOOK pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
-# front of it. If left blank docbook will be used as the default path.
+# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
+# front of it.
+# The default directory is: docbook.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
DOCBOOK_OUTPUT = docbook
+# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the
+# program listings (including syntax highlighting and cross-referencing
+# information) to the DOCBOOK output. Note that enabling this will significantly
+# increase the size of the DOCBOOK output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_PROGRAMLISTING = NO
+
#---------------------------------------------------------------------------
-# configuration options for the AutoGen Definitions output
+# Configuration options for the AutoGen Definitions output
#---------------------------------------------------------------------------
-# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
-# generate an AutoGen Definitions (see autogen.sf.net) file
-# that captures the structure of the code including all
-# documentation. Note that this feature is still experimental
-# and incomplete at the moment.
+# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an
+# AutoGen Definitions (see http://autogen.sf.net) file that captures the
+# structure of the code including all documentation. Note that this feature is
+# still experimental and incomplete at the moment.
+# The default value is: NO.
GENERATE_AUTOGEN_DEF = NO
#---------------------------------------------------------------------------
-# configuration options related to the Perl module output
+# Configuration options related to the Perl module output
#---------------------------------------------------------------------------
-# If the GENERATE_PERLMOD tag is set to YES Doxygen will
-# generate a Perl module file that captures the structure of
-# the code including all documentation. Note that this
-# feature is still experimental and incomplete at the
-# moment.
+# If the GENERATE_PERLMOD tag is set to YES, doxygen will generate a Perl module
+# file that captures the structure of the code including all documentation.
+#
+# Note that this feature is still experimental and incomplete at the moment.
+# The default value is: NO.
GENERATE_PERLMOD = NO
-# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
-# the necessary Makefile rules, Perl scripts and LaTeX code to be able
-# to generate PDF and DVI output from the Perl module output.
+# If the PERLMOD_LATEX tag is set to YES, doxygen will generate the necessary
+# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI
+# output from the Perl module output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_LATEX = NO
-# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
-# nicely formatted so it can be parsed by a human reader. This is useful
-# if you want to understand what is going on. On the other hand, if this
-# tag is set to NO the size of the Perl module output will be much smaller
-# and Perl will parse it just the same.
+# If the PERLMOD_PRETTY tag is set to YES, the Perl module output will be nicely
+# formatted so it can be parsed by a human reader. This is useful if you want to
+# understand what is going on. On the other hand, if this tag is set to NO, the
+# size of the Perl module output will be much smaller and Perl will parse it
+# just the same.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_PRETTY = YES
-# The names of the make variables in the generated doxyrules.make file
-# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
-# This is useful so different doxyrules.make files included by the same
-# Makefile don't overwrite each other's variables.
+# The names of the make variables in the generated doxyrules.make file are
+# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
+# so different doxyrules.make files included by the same Makefile don't
+# overwrite each other's variables.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_MAKEVAR_PREFIX =
@@ -1557,111 +1986,130 @@ PERLMOD_MAKEVAR_PREFIX =
# Configuration options related to the preprocessor
#---------------------------------------------------------------------------
-# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
-# evaluate all C-preprocessor directives found in the sources and include
-# files.
+# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all
+# C-preprocessor directives found in the sources and include files.
+# The default value is: YES.
ENABLE_PREPROCESSING = YES
-# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
-# names in the source code. If set to NO (the default) only conditional
-# compilation will be performed. Macro expansion can be done in a controlled
-# way by setting EXPAND_ONLY_PREDEF to YES.
+# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
+# in the source code. If set to NO, only conditional compilation will be
+# performed. Macro expansion can be done in a controlled way by setting
+# EXPAND_ONLY_PREDEF to YES.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
MACRO_EXPANSION = NO
-# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
-# then the macro expansion is limited to the macros specified with the
-# PREDEFINED and EXPAND_AS_DEFINED tags.
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
+# the macro expansion is limited to the macros specified with the PREDEFINED and
+# EXPAND_AS_DEFINED tags.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
EXPAND_ONLY_PREDEF = NO
-# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
-# pointed to by INCLUDE_PATH will be searched when a #include is found.
+# If the SEARCH_INCLUDES tag is set to YES, the include files in the
+# INCLUDE_PATH will be searched if a #include is found.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
SEARCH_INCLUDES = YES
-# The INCLUDE_PATH tag can be used to specify one or more directories that
-# contain include files that are not input files but should be processed by
-# the preprocessor.
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by the
+# preprocessor.
+# This tag requires that the tag SEARCH_INCLUDES is set to YES.
INCLUDE_PATH =
-# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
-# patterns (like *.h and *.hpp) to filter out the header-files in the
-# directories. If left blank, the patterns specified with FILE_PATTERNS will
-# be used.
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will be
+# used.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
INCLUDE_FILE_PATTERNS =
-# The PREDEFINED tag can be used to specify one or more macro names that
-# are defined before the preprocessor is started (similar to the -D option of
-# gcc). The argument of the tag is a list of macros of the form: name
-# or name=definition (no spaces). If the definition and the = are
-# omitted =1 is assumed. To prevent a macro definition from being
-# undefined via #undef or recursively expanded use the := operator
-# instead of the = operator.
+# The PREDEFINED tag can be used to specify one or more macro names that are
+# defined before the preprocessor is started (similar to the -D option of e.g.
+# gcc). The argument of the tag is a list of macros of the form: name or
+# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
+# is assumed. To prevent a macro definition from being undefined via #undef or
+# recursively expanded use the := operator instead of the = operator.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
PREDEFINED =
-# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
-# this tag can be used to specify a list of macro names that should be expanded.
-# The macro definition that is found in the sources will be used.
-# Use the PREDEFINED tag if you want to use a different macro definition that
-# overrules the definition found in the source code.
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
+# tag can be used to specify a list of macro names that should be expanded. The
+# macro definition that is found in the sources will be used. Use the PREDEFINED
+# tag if you want to use a different macro definition that overrules the
+# definition found in the source code.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
EXPAND_AS_DEFINED =
-# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
-# doxygen's preprocessor will remove all references to function-like macros
-# that are alone on a line, have an all uppercase name, and do not end with a
-# semicolon, because these will confuse the parser if not removed.
+# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
+# remove all references to function-like macros that are alone on a line, have
+# an all uppercase name, and do not end with a semicolon. Such function macros
+# are typically used for boiler-plate code, and will confuse the parser if not
+# removed.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
SKIP_FUNCTION_MACROS = YES
#---------------------------------------------------------------------------
-# Configuration::additions related to external references
+# Configuration options related to external references
#---------------------------------------------------------------------------
-# The TAGFILES option can be used to specify one or more tagfiles. For each
-# tag file the location of the external documentation should be added. The
-# format of a tag file without this location is as follows:
-# TAGFILES = file1 file2 ...
-# Adding location for the tag files is done as follows:
-# TAGFILES = file1=loc1 "file2 = loc2" ...
-# where "loc1" and "loc2" can be relative or absolute paths
-# or URLs. Note that each tag file must have a unique name (where the name does
-# NOT include the path). If a tag file is not located in the directory in which
-# doxygen is run, you must also specify the path to the tagfile here.
+# The TAGFILES tag can be used to specify one or more tag files. For each tag
+# file the location of the external documentation should be added. The format of
+# a tag file without this location is as follows:
+# TAGFILES = file1 file2 ...
+# Adding location for the tag files is done as follows:
+# TAGFILES = file1=loc1 "file2 = loc2" ...
+# where loc1 and loc2 can be relative or absolute paths or URLs. See the
+# section "Linking to external documentation" for more information about the use
+# of tag files.
+# Note: Each tag file must have a unique name (where the name does NOT include
+# the path). If a tag file is not located in the directory in which doxygen is
+# run, you must also specify the path to the tagfile here.
TAGFILES = ../bpp-core/BppCore.tag=../../bpp-core/html \
../bpp-seq/BppSeq.tag=../../bpp-seq/html
-# When a file name is specified after GENERATE_TAGFILE, doxygen will create
-# a tag file that is based on the input files it reads.
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create a
+# tag file that is based on the input files it reads. See section "Linking to
+# external documentation" for more information about the usage of tag files.
GENERATE_TAGFILE = BppRaa.tag
-# If the ALLEXTERNALS tag is set to YES all external classes will be listed
-# in the class index. If set to NO only the inherited external classes
-# will be listed.
+# If the ALLEXTERNALS tag is set to YES, all external class will be listed in
+# the class index. If set to NO, only the inherited external classes will be
+# listed.
+# The default value is: NO.
ALLEXTERNALS = NO
-# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed
-# in the modules index. If set to NO, only the current project's groups will
-# be listed.
+# If the EXTERNAL_GROUPS tag is set to YES, all external groups will be listed
+# in the modules index. If set to NO, only the current project's groups will be
+# listed.
+# The default value is: YES.
EXTERNAL_GROUPS = YES
-# If the EXTERNAL_PAGES tag is set to YES all external pages will be listed
-# in the related pages index. If set to NO, only the current project's
-# pages will be listed.
+# If the EXTERNAL_PAGES tag is set to YES, all external pages will be listed in
+# the related pages index. If set to NO, only the current project's pages will
+# be listed.
+# The default value is: YES.
EXTERNAL_PAGES = YES
-# The PERL_PATH should be the absolute path and name of the perl script
-# interpreter (i.e. the result of `which perl').
+# The PERL_PATH should be the absolute path and name of the perl script
+# interpreter (i.e. the result of 'which perl').
+# The default file (with absolute path) is: /usr/bin/perl.
PERL_PATH = /usr/bin/perl
@@ -1669,222 +2117,314 @@ PERL_PATH = /usr/bin/perl
# Configuration options related to the dot tool
#---------------------------------------------------------------------------
-# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
-# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
-# or super classes. Setting the tag to NO turns the diagrams off. Note that
-# this option also works with HAVE_DOT disabled, but it is recommended to
-# install and use dot, since it yields more powerful graphs.
+# If the CLASS_DIAGRAMS tag is set to YES, doxygen will generate a class diagram
+# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to
+# NO turns the diagrams off. Note that this option also works with HAVE_DOT
+# disabled, but it is recommended to install and use dot, since it yields more
+# powerful graphs.
+# The default value is: YES.
CLASS_DIAGRAMS = NO
-# You can define message sequence charts within doxygen comments using the \msc
-# command. Doxygen will then run the mscgen tool (see
-# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the
-# documentation. The MSCGEN_PATH tag allows you to specify the directory where
-# the mscgen tool resides. If left empty the tool is assumed to be found in the
+# You can define message sequence charts within doxygen comments using the \msc
+# command. Doxygen will then run the mscgen tool (see:
+# http://www.mcternan.me.uk/mscgen/)) to produce the chart and insert it in the
+# documentation. The MSCGEN_PATH tag allows you to specify the directory where
+# the mscgen tool resides. If left empty the tool is assumed to be found in the
# default search path.
MSCGEN_PATH =
-# If set to YES, the inheritance and collaboration graphs will hide
-# inheritance and usage relations if the target is undocumented
-# or is not a class.
+# You can include diagrams made with dia in doxygen documentation. Doxygen will
+# then run dia to produce the diagram and insert it in the documentation. The
+# DIA_PATH tag allows you to specify the directory where the dia binary resides.
+# If left empty dia is assumed to be found in the default search path.
+
+DIA_PATH =
+
+# If set to YES the inheritance and collaboration graphs will hide inheritance
+# and usage relations if the target is undocumented or is not a class.
+# The default value is: YES.
HIDE_UNDOC_RELATIONS = YES
-# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
-# available from the path. This tool is part of Graphviz, a graph visualization
-# toolkit from AT&T and Lucent Bell Labs. The other options in this section
-# have no effect if this option is set to NO (the default)
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
+# available from the path. This tool is part of Graphviz (see:
+# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
+# Bell Labs. The other options in this section have no effect if this option is
+# set to NO
+# The default value is: YES.
HAVE_DOT = YES
-# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is
-# allowed to run in parallel. When set to 0 (the default) doxygen will
-# base this on the number of processors available in the system. You can set it
-# explicitly to a value larger than 0 to get control over the balance
-# between CPU load and processing speed.
+# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
+# to run in parallel. When set to 0 doxygen will base this on the number of
+# processors available in the system. You can set it explicitly to a value
+# larger than 0 to get control over the balance between CPU load and processing
+# speed.
+# Minimum value: 0, maximum value: 32, default value: 0.
+# This tag requires that the tag HAVE_DOT is set to YES.
DOT_NUM_THREADS = 0
-# By default doxygen will use the Helvetica font for all dot files that
-# doxygen generates. When you want a differently looking font you can specify
-# the font name using DOT_FONTNAME. You need to make sure dot is able to find
-# the font, which can be done by putting it in a standard location or by setting
-# the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the
-# directory containing the font.
+# When you want a differently looking font in the dot files that doxygen
+# generates you can specify the font name using DOT_FONTNAME. You need to make
+# sure dot is able to find the font, which can be done by putting it in a
+# standard location or by setting the DOTFONTPATH environment variable or by
+# setting DOT_FONTPATH to the directory containing the font.
+# The default value is: Helvetica.
+# This tag requires that the tag HAVE_DOT is set to YES.
-DOT_FONTNAME = FreeSans
+DOT_FONTNAME = Helvetica
-# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
-# The default size is 10pt.
+# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of
+# dot graphs.
+# Minimum value: 4, maximum value: 24, default value: 10.
+# This tag requires that the tag HAVE_DOT is set to YES.
DOT_FONTSIZE = 10
-# By default doxygen will tell dot to use the Helvetica font.
-# If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to
-# set the path where dot can find it.
+# By default doxygen will tell dot to use the default font as specified with
+# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set
+# the path where dot can find it using this tag.
+# This tag requires that the tag HAVE_DOT is set to YES.
DOT_FONTPATH =
-# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for each documented class showing the direct and
-# indirect inheritance relations. Setting this tag to YES will force the
-# CLASS_DIAGRAMS tag to NO.
+# If the CLASS_GRAPH tag is set to YES then doxygen will generate a graph for
+# each documented class showing the direct and indirect inheritance relations.
+# Setting this tag to YES will force the CLASS_DIAGRAMS tag to NO.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
CLASS_GRAPH = YES
-# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for each documented class showing the direct and
-# indirect implementation dependencies (inheritance, containment, and
-# class references variables) of the class with other documented classes.
+# If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a
+# graph for each documented class showing the direct and indirect implementation
+# dependencies (inheritance, containment, and class references variables) of the
+# class with other documented classes.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
COLLABORATION_GRAPH = YES
-# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for groups, showing the direct groups dependencies
+# If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for
+# groups, showing the direct groups dependencies.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
GROUP_GRAPHS = YES
-# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
-# collaboration diagrams in a style similar to the OMG's Unified Modeling
+# If the UML_LOOK tag is set to YES, doxygen will generate inheritance and
+# collaboration diagrams in a style similar to the OMG's Unified Modeling
# Language.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
UML_LOOK = NO
-# If the UML_LOOK tag is enabled, the fields and methods are shown inside
-# the class node. If there are many fields or methods and many nodes the
-# graph may become too big to be useful. The UML_LIMIT_NUM_FIELDS
-# threshold limits the number of items for each type to make the size more
-# managable. Set this to 0 for no limit. Note that the threshold may be
-# exceeded by 50% before the limit is enforced.
+# If the UML_LOOK tag is enabled, the fields and methods are shown inside the
+# class node. If there are many fields or methods and many nodes the graph may
+# become too big to be useful. The UML_LIMIT_NUM_FIELDS threshold limits the
+# number of items for each type to make the size more manageable. Set this to 0
+# for no limit. Note that the threshold may be exceeded by 50% before the limit
+# is enforced. So when you set the threshold to 10, up to 15 fields may appear,
+# but if the number exceeds 15, the total amount of fields shown is limited to
+# 10.
+# Minimum value: 0, maximum value: 100, default value: 10.
+# This tag requires that the tag HAVE_DOT is set to YES.
UML_LIMIT_NUM_FIELDS = 10
-# If set to YES, the inheritance and collaboration graphs will show the
-# relations between templates and their instances.
+# If the TEMPLATE_RELATIONS tag is set to YES then the inheritance and
+# collaboration graphs will show the relations between templates and their
+# instances.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
TEMPLATE_RELATIONS = YES
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
-# tags are set to YES then doxygen will generate a graph for each documented
-# file showing the direct and indirect include dependencies of the file with
-# other documented files.
+# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to
+# YES then doxygen will generate a graph for each documented file showing the
+# direct and indirect include dependencies of the file with other documented
+# files.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
INCLUDE_GRAPH = YES
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
-# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
-# documented header file showing the documented files that directly or
-# indirectly include this file.
+# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are
+# set to YES then doxygen will generate a graph for each documented file showing
+# the direct and indirect include dependencies of the file with other documented
+# files.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
INCLUDED_BY_GRAPH = YES
-# If the CALL_GRAPH and HAVE_DOT options are set to YES then
-# doxygen will generate a call dependency graph for every global function
-# or class method. Note that enabling this option will significantly increase
-# the time of a run. So in most cases it will be better to enable call graphs
-# for selected functions only using the \callgraph command.
+# If the CALL_GRAPH tag is set to YES then doxygen will generate a call
+# dependency graph for every global function or class method.
+#
+# Note that enabling this option will significantly increase the time of a run.
+# So in most cases it will be better to enable call graphs for selected
+# functions only using the \callgraph command. Disabling a call graph can be
+# accomplished by means of the command \hidecallgraph.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
CALL_GRAPH = NO
-# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then
-# doxygen will generate a caller dependency graph for every global function
-# or class method. Note that enabling this option will significantly increase
-# the time of a run. So in most cases it will be better to enable caller
-# graphs for selected functions only using the \callergraph command.
+# If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller
+# dependency graph for every global function or class method.
+#
+# Note that enabling this option will significantly increase the time of a run.
+# So in most cases it will be better to enable caller graphs for selected
+# functions only using the \callergraph command. Disabling a caller graph can be
+# accomplished by means of the command \hidecallergraph.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
CALLER_GRAPH = NO
-# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
-# will generate a graphical hierarchy of all classes instead of a textual one.
+# If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
+# hierarchy of all classes instead of a textual one.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
GRAPHICAL_HIERARCHY = YES
-# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
-# then doxygen will show the dependencies a directory has on other directories
-# in a graphical way. The dependency relations are determined by the #include
-# relations between the files in the directories.
+# If the DIRECTORY_GRAPH tag is set to YES then doxygen will show the
+# dependencies a directory has on other directories in a graphical way. The
+# dependency relations are determined by the #include relations between the
+# files in the directories.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
DIRECTORY_GRAPH = YES
-# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
-# generated by dot. Possible values are svg, png, jpg, or gif.
-# If left blank png will be used. If you choose svg you need to set
-# HTML_FILE_EXTENSION to xhtml in order to make the SVG files
-# visible in IE 9+ (other browsers do not have this requirement).
+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
+# generated by dot. For an explanation of the image formats see the section
+# output formats in the documentation of the dot tool (Graphviz (see:
+# http://www.graphviz.org/)).
+# Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order
+# to make the SVG files visible in IE 9+ (other browsers do not have this
+# requirement).
+# Possible values are: png, png:cairo, png:cairo:cairo, png:cairo:gd, png:gd,
+# png:gd:gd, jpg, jpg:cairo, jpg:cairo:gd, jpg:gd, jpg:gd:gd, gif, gif:cairo,
+# gif:cairo:gd, gif:gd, gif:gd:gd, svg, png:gd, png:gd:gd, png:cairo,
+# png:cairo:gd, png:cairo:cairo, png:cairo:gdiplus, png:gdiplus and
+# png:gdiplus:gdiplus.
+# The default value is: png.
+# This tag requires that the tag HAVE_DOT is set to YES.
DOT_IMAGE_FORMAT = png
-# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
-# enable generation of interactive SVG images that allow zooming and panning.
-# Note that this requires a modern browser other than Internet Explorer.
-# Tested and working are Firefox, Chrome, Safari, and Opera. For IE 9+ you
-# need to set HTML_FILE_EXTENSION to xhtml in order to make the SVG files
-# visible. Older versions of IE do not have SVG support.
+# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
+# enable generation of interactive SVG images that allow zooming and panning.
+#
+# Note that this requires a modern browser other than Internet Explorer. Tested
+# and working are Firefox, Chrome, Safari, and Opera.
+# Note: For IE 9+ you need to set HTML_FILE_EXTENSION to xhtml in order to make
+# the SVG files visible. Older versions of IE do not have SVG support.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
INTERACTIVE_SVG = NO
-# The tag DOT_PATH can be used to specify the path where the dot tool can be
+# The DOT_PATH tag can be used to specify the path where the dot tool can be
# found. If left blank, it is assumed the dot tool can be found in the path.
+# This tag requires that the tag HAVE_DOT is set to YES.
DOT_PATH =
-# The DOTFILE_DIRS tag can be used to specify one or more directories that
-# contain dot files that are included in the documentation (see the
-# \dotfile command).
+# The DOTFILE_DIRS tag can be used to specify one or more directories that
+# contain dot files that are included in the documentation (see the \dotfile
+# command).
+# This tag requires that the tag HAVE_DOT is set to YES.
DOTFILE_DIRS =
-# The MSCFILE_DIRS tag can be used to specify one or more directories that
-# contain msc files that are included in the documentation (see the
-# \mscfile command).
+# The MSCFILE_DIRS tag can be used to specify one or more directories that
+# contain msc files that are included in the documentation (see the \mscfile
+# command).
MSCFILE_DIRS =
-# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of
-# nodes that will be shown in the graph. If the number of nodes in a graph
-# becomes larger than this value, doxygen will truncate the graph, which is
-# visualized by representing a node as a red box. Note that doxygen if the
-# number of direct children of the root node in a graph is already larger than
-# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note
-# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+# The DIAFILE_DIRS tag can be used to specify one or more directories that
+# contain dia files that are included in the documentation (see the \diafile
+# command).
+
+DIAFILE_DIRS =
+
+# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the
+# path where java can find the plantuml.jar file. If left blank, it is assumed
+# PlantUML is not used or called during a preprocessing step. Doxygen will
+# generate a warning when it encounters a \startuml command in this case and
+# will not generate output for the diagram.
+
+PLANTUML_JAR_PATH =
+
+# When using plantuml, the specified paths are searched for files specified by
+# the !include statement in a plantuml block.
+
+PLANTUML_INCLUDE_PATH =
+
+# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes
+# that will be shown in the graph. If the number of nodes in a graph becomes
+# larger than this value, doxygen will truncate the graph, which is visualized
+# by representing a node as a red box. Note that doxygen if the number of direct
+# children of the root node in a graph is already larger than
+# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note that
+# the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+# Minimum value: 0, maximum value: 10000, default value: 50.
+# This tag requires that the tag HAVE_DOT is set to YES.
DOT_GRAPH_MAX_NODES = 50
-# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
-# graphs generated by dot. A depth value of 3 means that only nodes reachable
-# from the root by following a path via at most 3 edges will be shown. Nodes
-# that lay further from the root node will be omitted. Note that setting this
-# option to 1 or 2 may greatly reduce the computation time needed for large
-# code bases. Also note that the size of a graph can be further restricted by
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the graphs
+# generated by dot. A depth value of 3 means that only nodes reachable from the
+# root by following a path via at most 3 edges will be shown. Nodes that lay
+# further from the root node will be omitted. Note that setting this option to 1
+# or 2 may greatly reduce the computation time needed for large code bases. Also
+# note that the size of a graph can be further restricted by
# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+# Minimum value: 0, maximum value: 1000, default value: 0.
+# This tag requires that the tag HAVE_DOT is set to YES.
MAX_DOT_GRAPH_DEPTH = 0
-# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
-# background. This is disabled by default, because dot on Windows does not
-# seem to support this out of the box. Warning: Depending on the platform used,
-# enabling this option may lead to badly anti-aliased labels on the edges of
-# a graph (i.e. they become hard to read).
+# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
+# background. This is disabled by default, because dot on Windows does not seem
+# to support this out of the box.
+#
+# Warning: Depending on the platform used, enabling this option may lead to
+# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
+# read).
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
DOT_TRANSPARENT = NO
-# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
-# files in one run (i.e. multiple -o and -T options on the command line). This
-# makes dot run faster, but since only newer versions of dot (>1.8.10)
-# support this, this feature is disabled by default.
+# Set the DOT_MULTI_TARGETS tag to YES to allow dot to generate multiple output
+# files in one run (i.e. multiple -o and -T options on the command line). This
+# makes dot run faster, but since only newer versions of dot (>1.8.10) support
+# this, this feature is disabled by default.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
DOT_MULTI_TARGETS = YES
-# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
-# generate a legend page explaining the meaning of the various boxes and
-# arrows in the dot generated graphs.
+# If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page
+# explaining the meaning of the various boxes and arrows in the dot generated
+# graphs.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
GENERATE_LEGEND = YES
-# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will
-# remove the intermediate dot files that are used to generate
-# the various graphs.
+# If the DOT_CLEANUP tag is set to YES, doxygen will remove the intermediate dot
+# files that are used to generate the various graphs.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
DOT_CLEANUP = YES
diff --git a/INSTALL.txt b/INSTALL.txt
index c8859da..8c499db 100644
--- a/INSTALL.txt
+++ b/INSTALL.txt
@@ -1,12 +1,23 @@
-This software needs cmake >= 2.6 to build.
+This software needs cmake >= 2.8.11 and a C++11 capable compiler to build
After installing cmake, run it with the following command:
-cmake -DCMAKE_INSTALL_PREFIX=[where to install, for instance /usr/local or $HOME/.local] .
+$ cmake -DCMAKE_INSTALL_PREFIX=[where to install, for instance /usr/local or $HOME/.local] .
If available, you can also use ccmake instead of cmake for a more user-friendly interface.
-Then compile and install the software with
-make install
+Then compile and install the software with:
+$ make install
You may also consider installing and using the software checkinstall for easier system administration.
+If you install Bio++ in a non standard path (not /usr/), remember that:
+-> if you compile your project with CMake, give it the path with -DCMAKE_PREFIX_PATH=<path>
+-> if you compile with something else, give the path to the compiler (-I / -L options)
+-> if you use shared libraries, you must also tell programs where to find them at startup:
+ -> either by adding the path to LD_LIBRARY_PATH environment variable.
+ -> or by using RPATHs to hard code the path in the executable (generates NON PORTABLE executables !)
+ -> with CMake, see documentation in bpp-core/cmake/project-template
+ -> or see your compiler documentation ("-Wl,-rpath,<path>" for clang/gcc)
+ -> consider installing Bio++ with the "-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE" option
+
+Detailed documentation for using Bio++ with CMake are available in bpp-core/cmake/
diff --git a/bpp-raa.spec b/bpp-raa.spec
index 71752e0..87834ca 100644
--- a/bpp-raa.spec
+++ b/bpp-raa.spec
@@ -1,5 +1,5 @@
%define _basename bpp-raa
-%define _version 2.2.0
+%define _version 2.3.1
%define _release 1
%define _prefix /usr
@@ -17,11 +17,11 @@ Requires: bpp-core = %{_version}
Requires: bpp-seq = %{_version}
BuildRoot: %{_builddir}/%{_basename}-root
-BuildRequires: cmake >= 2.6.0
-BuildRequires: gcc-c++ >= 4.0.0
-BuildRequires: libbpp-core2 = %{_version}
+BuildRequires: cmake >= 2.8.11
+BuildRequires: gcc-c++ >= 4.7.0
+BuildRequires: libbpp-core3 = %{_version}
BuildRequires: libbpp-core-devel = %{_version}
-BuildRequires: libbpp-seq9 = %{_version}
+BuildRequires: libbpp-seq11 = %{_version}
BuildRequires: libbpp-seq-devel = %{_version}
BuildRequires: zlib >= 1.2.3
BuildRequires: zlib-devel >= 1.2.3
@@ -33,21 +33,21 @@ AutoProv: yes
This library contains utilitary and classes to query public database (GenBank, EMBL, SwissProt, etc) using acnuc.
It is part of the Bio++ project.
-%package -n libbpp-raa1
+%package -n libbpp-raa3
Summary: Bio++ Remote Acnuc Access library
Group: Development/Libraries/C and C++
-%description -n libbpp-raa1
+%description -n libbpp-raa3
This library contains utilitary and classes to query public database (GenBank, EMBL, SwissProt, etc) using acnuc.
It is part of the Bio++ project.
%package -n libbpp-raa-devel
Summary: Libraries, includes to develop applications with %{_basename}
Group: Development/Libraries/C and C++
-Requires: libbpp-raa1 = %{_version}
-Requires: libbpp-seq9 = %{_version}
+Requires: libbpp-raa3 = %{_version}
+Requires: libbpp-seq11 = %{_version}
Requires: libbpp-seq-devel = %{_version}
-Requires: libbpp-core2 = %{_version}
+Requires: libbpp-core3 = %{_version}
Requires: libbpp-core-devel = %{_version}
Requires: zlib >= 1.2.3
Requires: zlib-devel >= 1.2.3
@@ -62,9 +62,6 @@ building applications which use %{_basename}.
%build
CFLAGS="$RPM_OPT_FLAGS"
CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=%{_prefix} -DBUILD_TESTING=OFF"
-if [ %{_lib} == 'lib64' ] ; then
- CMAKE_FLAGS="$CMAKE_FLAGS -DLIB_SUFFIX=64"
-fi
cmake $CMAKE_FLAGS .
make
@@ -74,103 +71,11 @@ make DESTDIR=$RPM_BUILD_ROOT install
%clean
rm -rf $RPM_BUILD_ROOT
-%post -n libbpp-raa1 -p /sbin/ldconfig
-
-%post -n libbpp-raa-devel
-createGeneric() {
- echo "-- Creating generic include file: $1.all"
- #Make sure we run into subdirectories first:
- dirs=()
- for file in "$1"/*
- do
- if [ -d "$file" ]
- then
- # Recursion:
- dirs+=( "$file" )
- fi
- done
- for dir in ${dirs[@]}
- do
- createGeneric $dir
- done
- #Now list all files, including newly created .all files:
- if [ -f $1.all ]
- then
- rm $1.all
- fi
- dir=`basename $1`
- for file in "$1"/*
- do
- if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] )
- then
- file=`basename $file`
- echo "#include \"$dir/$file\"" >> $1.all
- fi
- done;
-}
-# Actualize .all files
-createGeneric %{_prefix}/include/Bpp
-exit 0
-
-%preun -n libbpp-raa-devel
-removeGeneric() {
- if [ -f $1.all ]
- then
- echo "-- Remove generic include file: $1.all"
- rm $1.all
- fi
- for file in "$1"/*
- do
- if [ -d "$file" ]
- then
- # Recursion:
- removeGeneric $file
- fi
- done
-}
-# Actualize .all files
-removeGeneric %{_prefix}/include/Bpp
-exit 0
-
-%postun -n libbpp-raa1 -p /sbin/ldconfig
-
-%postun -n libbpp-raa-devel
-createGeneric() {
- echo "-- Creating generic include file: $1.all"
- #Make sure we run into subdirectories first:
- dirs=()
- for file in "$1"/*
- do
- if [ -d "$file" ]
- then
- # Recursion:
- dirs+=( "$file" )
- fi
- done
- for dir in ${dirs[@]}
- do
- createGeneric $dir
- done
- #Now list all files, including newly created .all files:
- if [ -f $1.all ]
- then
- rm $1.all
- fi
- dir=`basename $1`
- for file in "$1"/*
- do
- if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] )
- then
- file=`basename $file`
- echo "#include \"$dir/$file\"" >> $1.all
- fi
- done;
-}
-# Actualize .all files
-createGeneric %{_prefix}/include/Bpp
-exit 0
-
-%files -n libbpp-raa1
+%post -n libbpp-raa3 -p /sbin/ldconfig
+
+%postun -n libbpp-raa3 -p /sbin/ldconfig
+
+%files -n libbpp-raa3
%defattr(-,root,root)
%doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog
%{_prefix}/%{_lib}/lib*.so.*
@@ -178,11 +83,18 @@ exit 0
%files -n libbpp-raa-devel
%defattr(-,root,root)
%doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog
+%dir %{_prefix}/%{_lib}/cmake/
+%dir %{_prefix}/%{_lib}/cmake/bpp-raa
%{_prefix}/%{_lib}/lib*.so
%{_prefix}/%{_lib}/lib*.a
+%{_prefix}/%{_lib}/cmake/bpp-raa/bpp-raa*.cmake
%{_prefix}/include/*
%changelog
+* Tue Jun 06 2017 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.3.1-1
+- Increased interface number
+* Wed May 10 2017 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.3.0-1
+- Compatibility update.
* Mon Sep 22 2014 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.2.0-1
- Compatibility update.
* Thu Mar 07 2013 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.1.0-1
diff --git a/debian/changelog b/debian/changelog
deleted file mode 100644
index 34b9331..0000000
--- a/debian/changelog
+++ /dev/null
@@ -1,42 +0,0 @@
-libbpp-raa (2.2.0-1) unstable; urgency=low
-
- * Recompilation because of dependencies.
-
- -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Mon, 22 Sep 2014 14:00:00 +0100
-
-libbpp-raa (2.1.0-1) unstable; urgency=low
-
- * Recompilation because of dependencies.
-
- -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Thu, 07 Mar 2013 11:46:00 +0100
-
-libbpp-raa (2.0.3-1) unstable; urgency=low
-
- * Recompilation because of dependencies.
-
- -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Thu, 09 Feb 2012 16:45:00 +0100
-
-libbpp-raa (2.0.2-1) unstable; urgency=low
-
- * RFP: Bio++ -- The Bio++ bioinformatics libraries. (Closes: #616373).
- * Packages are now non-native.
-
- -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Thu, 09 Jun 2011 11:00:00 +0100
-
-libbpp-raa (2.0.1) unstable; urgency=low
-
- * Fixed copyright and rules issue in package.
-
- -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Mon, 28 Feb 2011 09:00:00 +0100
-
-libbpp-raa (2.0.0) unstable; urgency=low
-
- * Compatibility with Bio++ 2.0.0.
-
- -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Mon, 07 Feb 2011 09:00:00 +0100
-
-libbpp-raa (1.0.0) unstable; urgency=low
-
- * Initial Release.
-
- -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Thu, 25 Mar 2010 15:30:13 +0100
diff --git a/debian/compat b/debian/compat
deleted file mode 100644
index 7ed6ff8..0000000
--- a/debian/compat
+++ /dev/null
@@ -1 +0,0 @@
-5
diff --git a/debian/control b/debian/control
deleted file mode 100644
index afdd804..0000000
--- a/debian/control
+++ /dev/null
@@ -1,29 +0,0 @@
-Source: libbpp-raa
-Section: libs
-Priority: optional
-Maintainer: Loic Dachary <loic at dachary.org>
-Uploaders: Julien Dutheil <julien.dutheil at univ-montp2.fr>
-Build-Depends: debhelper (>= 5), cmake (>= 2.6),
- zlib1g-dev (>= 1.2.3), libbpp-seq-dev (>= 2.2.0), zlib1g (>= 1.2.3)
-Standards-Version: 3.9.4
-
-Package: libbpp-raa-dev
-Section: libdevel
-Architecture: any
-Depends: libbpp-raa1 (= ${binary:Version}), ${misc:Depends},
- zlib1g-dev (>= 1.2.3), libbpp-seq-dev (>= 2.2.0)
-Description: Bio++ Remote Acnuc Access library development files.
- This library contains utilitary and classes to query public databases
- (GenBank, EMBL, SwissProt, etc) using acnuc.
- It is part of the Bio++ project.
-
-Package: libbpp-raa1
-Section: libs
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends},
- zlib1g (>= 1.2.3), libbpp-seq9 (>= 2.2.0)
-Description: Bio++ Remote Acnuc Access library.
- This library contains utilitary and classes to query public databases
- (GenBank, EMBL, SwissProt, etc) using acnuc.
- It is part of the Bio++ project.
-
diff --git a/debian/copyright b/debian/copyright
deleted file mode 100644
index f8e692e..0000000
--- a/debian/copyright
+++ /dev/null
@@ -1,66 +0,0 @@
-This package was debianized by Julien Dutheil <julien.dutheil at univ-montp2.fr> on
-Thu, 22 Sep 2014 14:00:00 +0100.
-
-It was downloaded from <http://kimura.univ-montp2.fr/Repositories/sources>
-
-Upstream Author:
-
- Julien Dutheil <julien.dutheil at univ-montp2.fr>
-
-Copyright:
-
- Copyright (C) 2014 Bio++ Development Team
-
-License:
-
- This package is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
-
- This package is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this package; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-
-On Debian systems, the complete text of the GNU General
-Public License can be found in `/usr/share/common-licenses/GPL'.
-
-The Debian packaging is (C) 2014, Julien Dutheil <julien.dutheil at univ-montp2.fr> and
-is licensed under the GPL, see above.
-
-The provided software is distributed under the CeCILL license:
-
- This software is governed by the CeCILL license under French law and
- abiding by the rules of distribution of free software. You can use,
- modify and/ or redistribute the software under the terms of the CeCILL
- license as circulated by CEA, CNRS and INRIA at the following URL
- "http://www.cecill.info".
-
- As a counterpart to the access to the source code and rights to copy,
- modify and redistribute granted by the license, users are provided only
- with a limited warranty and the software's author, the holder of the
- economic rights, and the successive licensors have only limited
- liability.
-
- In this respect, the user's attention is drawn to the risks associated
- with loading, using, modifying and/or developing or reproducing the
- software by the user in light of its specific status of free software,
- that may mean that it is complicated to manipulate, and that also
- therefore means that it is reserved for developers and experienced
- professionals having in-depth computer knowledge. Users are therefore
- encouraged to load and test the software's suitability as regards their
- requirements in conditions enabling the security of their systems and/or
- data to be ensured and, more generally, to use and operate it in the
- same conditions as regards security.
-
- The fact that you are presently reading this means that you have had
- knowledge of the CeCILL license and that you accept its terms.
-
-The complete text of the license may be found here:
-http://www.cecill.info/licences/Licence_CeCILL_V2-en.html
-
diff --git a/debian/libbpp-raa-dev.install b/debian/libbpp-raa-dev.install
deleted file mode 100644
index 7d74f2b..0000000
--- a/debian/libbpp-raa-dev.install
+++ /dev/null
@@ -1,3 +0,0 @@
-debian/tmp/usr/include/*
-debian/tmp/usr/lib/lib*.a
-debian/tmp/usr/lib/lib*.so
diff --git a/debian/libbpp-raa1.install b/debian/libbpp-raa1.install
deleted file mode 100644
index c45ebcf..0000000
--- a/debian/libbpp-raa1.install
+++ /dev/null
@@ -1 +0,0 @@
-debian/tmp/usr/lib/lib*.so.*
diff --git a/debian/postinst b/debian/postinst
deleted file mode 100755
index cff89b1..0000000
--- a/debian/postinst
+++ /dev/null
@@ -1,57 +0,0 @@
-#! /bin/bash
-
-# Abort if any command returns an error value
-set -e
-
-createGeneric() {
- echo "-- Creating generic include file: $1.all"
- #Make sure we run into subdirectories first:
- dirs=()
- for file in "$1"/*
- do
- if [ -d "$file" ]
- then
- # Recursion:
- dirs+=( "$file" )
- fi
- done
- for dir in ${dirs[@]}
- do
- createGeneric $dir
- done
- #Now list all files, including newly created .all files:
- if [ -f $1.all ]
- then
- rm $1.all
- fi
- dir=`basename $1`
- for file in "$1"/*
- do
- if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] )
- then
- file=`basename $file`
- echo "#include \"$dir/$file\"" >> $1.all
- fi
- done;
-}
-
-case "$1" in
- configure)
- # Actualize .all files
- createGeneric /usr/include/Bpp
- ;;
- abort-upgrade|abort-remove|abort-deconfigure)
- echo "$1"
- ;;
- *)
- echo "postinst called with unknown argument \`\$1'" >&2
- exit 0
- ;;
-esac
-
-# dh_installdeb will replace this with shell code automatically
-# generated by other debhelper scripts.
-
-#DEBHELPER#
-
-exit 0
diff --git a/debian/postrm b/debian/postrm
deleted file mode 100755
index 744f8b1..0000000
--- a/debian/postrm
+++ /dev/null
@@ -1,59 +0,0 @@
-#! /bin/bash
-
-# Abort if any command returns an error value
-set -e
-
-createGeneric() {
- echo "-- Creating generic include file: $1.all"
- #Make sure we run into subdirectories first:
- dirs=()
- for file in "$1"/*
- do
- if [ -d "$file" ]
- then
- # Recursion:
- dirs+=( "$file" )
- fi
- done
- for dir in ${dirs[@]}
- do
- createGeneric $dir
- done
- #Now list all files, including newly created .all files:
- if [ -f $1.all ]
- then
- rm $1.all
- fi
- dir=`basename $1`
- for file in "$1"/*
- do
- if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] )
- then
- file=`basename $file`
- echo "#include \"$dir/$file\"" >> $1.all
- fi
- done;
-}
-
-case "$1" in
- remove)
- # Automatically added by dh_makeshlibs
- ldconfig
- # Actualize .all files
- createGeneric /usr/include/Bpp
- ;;
- purge|upgrade|failed-upgrade|abort-install|abort-upgrade|disappear)
- echo $1
- ;;
- *)
- echo "postrm called with unknown argument \`\$1'" >&2
- exit 0
- ;;
-esac
-
-# dh_installdeb will replace this with shell code automatically
-# generated by other debhelper scripts.
-
-#DEBHELPER#
-
-exit 0
diff --git a/debian/prerm b/debian/prerm
deleted file mode 100755
index 8fab52e..0000000
--- a/debian/prerm
+++ /dev/null
@@ -1,41 +0,0 @@
-#! /bin/bash
-
-# Abort if any command returns an error value
-set -e
-
-removeGeneric() {
- if [ -f $1.all ]
- then
- echo "-- Remove generic include file: $1.all"
- rm $1.all
- fi
- for file in "$1"/*
- do
- if [ -d "$file" ]
- then
- # Recursion:
- removeGeneric $file
- fi
- done
-}
-
-case "$1" in
- remove|upgrade|deconfigure)
- # Actualize .all files
- removeGeneric /usr/include/Bpp
- ;;
- failed-upgrade)
- echo "$1"
- ;;
- *)
- echo "prerm called with unknown argument \`$1'" >&2
- exit 1
- ;;
-esac
-
-# dh_installdeb will replace this with shell code automatically
-# generated by other debhelper scripts.
-
-#DEBHELPER#
-
-exit 0
diff --git a/debian/rules b/debian/rules
deleted file mode 100755
index aa1aeed..0000000
--- a/debian/rules
+++ /dev/null
@@ -1,121 +0,0 @@
-#!/usr/bin/make -f
-# -*- makefile -*-
-# Sample debian/rules that uses debhelper.
-# This file was originally written by Joey Hess and Craig Small.
-# As a special exception, when this file is copied by dh-make into a
-# dh-make output file, you may use that output file without restriction.
-# This special exception was added by Craig Small in version 0.37 of dh-make.
-
-# 24/01/10 Modification for use with CMake by Julien Dutheil.
-
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-
-
-# These are used for cross-compiling and for saving the configure script
-# from having to guess our platform (since we know it already)
-DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
-DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
-
-
-CFLAGS = -Wall -g
-
-ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
- CFLAGS += -O0
-else
- CFLAGS += -O2
-endif
-
-# shared library versions
-version=`ls src/lib*.so.* | \
- awk '{if (match($$0,/[0-9]+\.[0-9]+\.[0-9]+$$/)) print substr($$0,RSTART)}'`
-major=`ls src/lib*.so.* | \
- awk '{if (match($$0,/\.so\.[0-9]+$$/)) print substr($$0,RSTART+4)}'`
-
-configure:
- cmake -DCMAKE_INSTALL_PREFIX=/usr .
-
-config.status: configure
- dh_testdir
-
-build: build-arch build-indep
-build-arch: build-stamp
-build-indep: build-stamp
-build-stamp: config.status
- dh_testdir
-
- # Add here commands to compile the package.
- $(MAKE)
-
- touch $@
-
-clean:
- dh_testdir
- dh_testroot
-
- # Add here commands to clean up after the build process.
- [ ! -f Makefile ] || $(MAKE) clean;
- [ ! -f Makefile ] || rm Makefile;
- [ ! -f src/Makefile ] || rm src/Makefile;
- rm -f config.sub config.guess
- rm -f build-stamp
- rm -f CMakeCache.txt
- rm -f *.cmake
- rm -f src/*.cmake
- #rm -f test/*.cmake
- rm -rf CMakeFiles
- rm -rf src/CMakeFiles
- #rm -rf test/CMakeFiles
- rm -rf _CPack_Packages
- #rm -rf Testing
- #rm -f DartConfiguration.tcl
-
- dh_clean
-
-install: build
- dh_testdir
- dh_testroot
- dh_prep
- dh_installdirs
-
- # Add here commands to install the package into debian/tmp
- $(MAKE) DESTDIR=$(CURDIR)/debian/tmp install
-
-
-# Build architecture-independent files here.
-binary-indep: build install
-# We have nothing to do by default.
-
-# Build architecture-dependent files here.
-binary-arch: build install
- dh_testdir
- dh_testroot
- dh_installchangelogs ChangeLog
- dh_installdocs
- dh_installexamples
- dh_install
-# dh_installmenu
-# dh_installdebconf
-# dh_installlogrotate
-# dh_installemacsen
-# dh_installpam
-# dh_installmime
-# dh_installinit
-# dh_installcron
-# dh_installinfo
- dh_installman
- dh_link
- dh_strip
- dh_compress
- dh_fixperms
-# dh_perl
-# dh_python
- dh_makeshlibs
- dh_installdeb
- dh_shlibdeps
- dh_gencontrol
- dh_md5sums
- dh_builddeb
-
-binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install
diff --git a/debian/source/format b/debian/source/format
deleted file mode 100644
index 163aaf8..0000000
--- a/debian/source/format
+++ /dev/null
@@ -1 +0,0 @@
-3.0 (quilt)
diff --git a/header.html b/header.html
new file mode 100644
index 0000000..a32a5fc
--- /dev/null
+++ b/header.html
@@ -0,0 +1,27 @@
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+ <head>
+ <meta http-equiv="Content-Type" content="text/xhtml;charset=utf-8" />
+ <meta http-equiv="Content-Style-Type" content="text/css" />
+ <meta http-equiv="Content-Language" content="en" />
+ <link href="doxygen.css" rel="stylesheet" type="text/css">
+ <link href="tabs.css" rel="stylesheet" type="text/css">
+ </head>
+
+ <body>
+ <div id="banner">
+ <h1><a href="http://kimura.univ-montp2.fr/BioPP/" accesskey="1" target="_top">Bio++</a> Class documentation</h1>
+ </div>
+
+ <div class="tabs">
+ <ul>
+ <li><a href="http://kimura.univ-montp2.fr/BioPP/Documents/ClassDocumentation/Utils/html/index.html" target="_top"><span>Utils</span></a></li>
+ <li><a href="http://kimura.univ-montp2.fr/BioPP/Documents/ClassDocumentation/NumCalc/html/index.html" target="_top"><span>NumCalc</span></a></li>
+ <li><a href="http://kimura.univ-montp2.fr/BioPP/Documents/ClassDocumentation/Seq/html/index.html" target="_top"><span>SeqLib</span></a></li>
+ <li><a href="http://kimura.univ-montp2.fr/BioPP/Documents/ClassDocumentation/Phyl/html/index.html" target="_top"><span>PhylLib</span></a></li>
+ <li><a href="http://kimura.univ-montp2.fr/BioPP/Documents/ClassDocumentation/Pop/html/index.html" target="_top"><span>PopGenLib</span></a></li>
+ <li><a href="http://kimura.univ-montp2.fr/BioPP/Documents/ClassDocumentation/Raa/html/index.html" target="_top"><span>Raa</span></a></li>
+ </ul>
+ </div>
+
+ <br />
+
diff --git a/package.cmake.in b/package.cmake.in
new file mode 100644
index 0000000..55440a3
--- /dev/null
+++ b/package.cmake.in
@@ -0,0 +1,26 @@
+# CMake package file for Bio++ Remote Acnuc Access
+# Authors:
+# Francois Gindraud (2017)
+# Created: 16/03/2017
+ at PACKAGE_INIT@
+
+if (NOT @PROJECT_NAME at _FOUND)
+ # Deps
+ find_package (bpp-seq @bpp-seq_VERSION@ REQUIRED)
+ # Add targets
+ include ("${CMAKE_CURRENT_LIST_DIR}/@PROJECT_NAME at -targets.cmake")
+ # Append targets to convenient lists
+ set (BPP_LIBS_STATIC "${BPP_LIBS_STATIC}" @PROJECT_NAME at -static)
+ set (BPP_LIBS_SHARED "${BPP_LIBS_SHARED}" @PROJECT_NAME at -shared)
+ # Print some path info for targets
+ get_property (static-location TARGET @PROJECT_NAME at -static PROPERTY LOCATION)
+ get_property (shared-location TARGET @PROJECT_NAME at -shared PROPERTY LOCATION)
+ get_property (header-location TARGET @PROJECT_NAME at -static PROPERTY INTERFACE_INCLUDE_DIRECTORIES)
+ message (STATUS "@PROJECT_NAME@ @PROJECT_VERSION@ found:")
+ message (STATUS " static lib: ${static-location}")
+ message (STATUS " shared lib: ${shared-location}")
+ message (STATUS " includes: ${header-location}")
+ unset (static-location)
+ unset (shared-location)
+ unset (header-location)
+endif (NOT @PROJECT_NAME at _FOUND)
diff --git a/src/Bpp/Raa.all b/src/Bpp/Raa.all
deleted file mode 100644
index 08ab51b..0000000
--- a/src/Bpp/Raa.all
+++ /dev/null
@@ -1,6 +0,0 @@
-#include "Raa/RaaSpeciesTree.h"
-#include "Raa/parser.h"
-#include "Raa/RaaList.h"
-#include "Raa/RaaSeqAttributes.h"
-#include "Raa/RAA_acnuc.h"
-#include "Raa/RAA.h"
diff --git a/src/Bpp/Raa/RAA.cpp b/src/Bpp/Raa/RAA.cpp
index 4127f9c..9d5594a 100644
--- a/src/Bpp/Raa/RAA.cpp
+++ b/src/Bpp/Raa/RAA.cpp
@@ -1,6 +1,6 @@
/*
* RAA.cpp
- *
+ *
*
*/
@@ -8,548 +8,638 @@
#include "RAA.h"
extern "C" {
- int get_ncbi_gc_number(int gc);
- int sock_printf(raa_db_access *raa_current_db, const char *fmt, ...);
- }
+int get_ncbi_gc_number(int gc);
+int sock_printf(raa_db_access* raa_current_db, const char* fmt, ...);
+}
using namespace std;
using namespace bpp;
-RAA::RAA(const string &dbname, int port, const string &server) throw (int)
+RAA::RAA(const string& dbname, int port, const string& server) throw (int)
{
- kw_pattern = NULL;
- current_address.div = -1;
- int error = raa_acnucopen_alt((char *)server.c_str(), port, (char *)dbname.c_str(), (char *)"Bio++", &raa_data);
- if(error) {
- throw error;
- }
+ kw_pattern = NULL;
+ current_address.div = -1;
+ int error = raa_acnucopen_alt((char*)server.c_str(), port, (char*)dbname.c_str(), (char*)"Bio++", &raa_data);
+ if (error)
+ {
+ throw error;
+ }
}
-RAA::RAA(int port, const string &server) throw(int)
+RAA::RAA(int port, const string& server) throw (int)
{
- kw_pattern = NULL;
- int error = raa_open_socket((char *)server.c_str(), port, (char *)"Bio++", &raa_data);
- if(error) {
- throw error;
- }
+ kw_pattern = NULL;
+ int error = raa_open_socket((char*)server.c_str(), port, (char*)"Bio++", &raa_data);
+ if (error)
+ {
+ throw error;
+ }
}
RAA::~RAA()
{
- if(raa_data != NULL) raa_acnucclose(raa_data);
- if(kw_pattern) delete kw_pattern;
+ if (raa_data != NULL)
+ raa_acnucclose(raa_data);
+ if (kw_pattern)
+ delete kw_pattern;
}
-Sequence *RAA::getSeq_both(const string &name_or_accno, int rank, int maxlength)
+Sequence* RAA::getSeq_both(const string& name_or_accno, int rank, int maxlength)
{
- int length;
- char *name, *description;
- if(rank == 0) name = raa_getattributes(raa_data, name_or_accno.c_str(), &rank, &length, NULL, NULL, NULL,
- &description, NULL, NULL);
- else name = raa_seqrank_attributes(raa_data, rank, &length, NULL, NULL, NULL,
- &description, NULL, NULL);
- if(length > maxlength) return NULL;
- string sname = name;
- vector<string> comment(1, string(description) );
- string *cseq = new string(length + 1, ' ');
- if(cseq == NULL) return NULL;
- raa_gfrag(this->raa_data, rank, 1, length, (char *)cseq->data());
- cseq->resize(length);
- const Alphabet *alphab;
- if(raa_data->swissprot || raa_data->nbrf) alphab = &AlphabetTools::PROTEIN_ALPHABET;
- else alphab = &AlphabetTools::DNA_ALPHABET;
- Sequence *seq = new BasicSequence(sname, *cseq, comment, alphab);
- delete cseq;
- return seq;
+ int length;
+ char* name, * description;
+ if (rank == 0)
+ name = raa_getattributes(raa_data, name_or_accno.c_str(), &rank, &length, NULL, NULL, NULL,
+ &description, NULL, NULL);
+ else
+ name = raa_seqrank_attributes(raa_data, rank, &length, NULL, NULL, NULL,
+ &description, NULL, NULL);
+ if (length > maxlength)
+ return NULL;
+ string sname = name;
+ vector<string> comment(1, string(description) );
+ string* cseq = new string(length + 1, ' ');
+ if (cseq == NULL)
+ return NULL;
+ raa_gfrag(this->raa_data, rank, 1, length, (char*)cseq->data());
+ cseq->resize(length);
+ const Alphabet* alphab;
+ if (raa_data->swissprot || raa_data->nbrf)
+ alphab = &AlphabetTools::PROTEIN_ALPHABET;
+ else
+ alphab = &AlphabetTools::DNA_ALPHABET;
+ Sequence* seq = new BasicSequence(sname, *cseq, comment, alphab);
+ delete cseq;
+ return seq;
}
-Sequence *RAA::getSeq(const string &name_or_accno, int maxlength)
+Sequence* RAA::getSeq(const string& name_or_accno, int maxlength)
+{
+ return getSeq_both(name_or_accno, 0, maxlength);
+}
+
+
+Sequence* RAA::getSeq(int seqrank, int maxlength)
{
- return getSeq_both(name_or_accno, 0, maxlength);
+ if (seqrank < 2 || seqrank > raa_data->nseq)
+ return NULL;
+ return getSeq_both(string(""), seqrank, maxlength);
}
-Sequence *RAA::getSeq(int seqrank, int maxlength)
+int RAA::getSeqFrag(int seqrank, int first, int length, string& sequence)
{
- if(seqrank < 2 || seqrank > raa_data->nseq) return NULL;
- return getSeq_both(string(""), seqrank, maxlength);
+ if (seqrank < 2 || seqrank > raa_data->nseq)
+ return 0;
+ sequence = "";
+ char* p = (char*)malloc(length + 1);
+ if (p == NULL)
+ return 0;
+ int l = raa_gfrag(this->raa_data, seqrank, first, length, p);
+ if (l > 0)
+ {
+ majuscules(p);
+ sequence = p;
+ }
+ free(p);
+ return l;
}
-int RAA::getSeqFrag(int seqrank, int first, int length, string &sequence)
+int RAA::getSeqFrag(const string& name_or_accno, int first, int length, string& sequence)
{
- if(seqrank < 2 || seqrank > raa_data->nseq) return 0;
- sequence = "";
- char *p = (char *)malloc(length + 1);
- if(p == NULL) return 0;
- int l = raa_gfrag(this->raa_data, seqrank, first, length, p);
- if(l > 0) {
- majuscules(p);
- sequence = p;
- }
- free(p);
- return l;
+ int seqrank;
+ raa_getattributes(raa_data, name_or_accno.c_str(), &seqrank, NULL, NULL, NULL, NULL, NULL, NULL, NULL);
+ if (seqrank == 0)
+ return 0;
+ return getSeqFrag(seqrank, first, length, sequence);
}
-int RAA::getSeqFrag(const string &name_or_accno, int first, int length, string &sequence)
+RaaSeqAttributes* RAA::getAttributes(const string& name_or_accno)
{
- int seqrank;
- raa_getattributes(raa_data, name_or_accno.c_str(), &seqrank, NULL, NULL, NULL, NULL, NULL, NULL, NULL);
- if(seqrank == 0) return 0;
- return getSeqFrag(seqrank, first, length, sequence);
+ char* description, * species, * access;
+ int acnuc_gc, rank, length, frame;
+ char* name = raa_getattributes(this->raa_data, name_or_accno.c_str(), &rank, &length,
+ &frame, &acnuc_gc, &access, &description, &species, NULL);
+ if (!name)
+ {
+ return NULL;
+ }
+ RaaSeqAttributes* myattr = new RaaSeqAttributes();
+ myattr->raa = this;
+ myattr->rank = rank;
+ myattr->length = length;
+ myattr->frame = frame;
+ myattr->name = name;
+ myattr->description = description;
+ myattr->accno = access;
+ myattr->species = species;
+ myattr->ncbi_gc = get_ncbi_gc_number(acnuc_gc);
+ return myattr;
}
-RaaSeqAttributes *RAA::getAttributes(const string &name_or_accno)
+RaaSeqAttributes* RAA::getAttributes(int seqrank)
{
- char *description, *species, *access;
- int acnuc_gc;
- RaaSeqAttributes *myattr = new RaaSeqAttributes();
- char *name = raa_getattributes(this->raa_data, name_or_accno.c_str(), &myattr->rank, &myattr->length,
- &myattr->frame, &acnuc_gc, &access, &description, &species, NULL);
- myattr->raa = this;
- myattr->name = name;
- myattr->description = description;
- myattr->accno = access;
- myattr->species = species;
- myattr->ncbi_gc = get_ncbi_gc_number(acnuc_gc);
- return myattr;
+ char* description, * species, * access;
+ int acnuc_gc;
+ if (seqrank < 2 || seqrank > raa_data->nseq)
+ return NULL;
+ RaaSeqAttributes* myattr = new RaaSeqAttributes();
+ char* name = raa_seqrank_attributes(this->raa_data, seqrank, &myattr->length,
+ &myattr->frame, &acnuc_gc, &access, &description, &species, NULL);
+ if (name == NULL)
+ return NULL;
+ myattr->rank = seqrank;
+ myattr->raa = this;
+ myattr->name = name;
+ myattr->description = description;
+ myattr->accno = access;
+ myattr->species = species;
+ myattr->ncbi_gc = get_ncbi_gc_number(acnuc_gc);
+ return myattr;
}
-RaaSeqAttributes *RAA::getAttributes(int seqrank)
+int RAA::knownDatabases(vector<string>& name, vector<string>& description)
{
- char *description, *species, *access;
- int acnuc_gc;
- if(seqrank < 2 || seqrank > raa_data->nseq) return NULL;
- RaaSeqAttributes *myattr = new RaaSeqAttributes();
- char *name = raa_seqrank_attributes(this->raa_data, seqrank, &myattr->length,
- &myattr->frame, &acnuc_gc, &access, &description, &species, NULL);
- if(name == NULL) return NULL;
- myattr->rank =seqrank;
- myattr->raa = this;
- myattr->name= name;
- myattr->description = description;
- myattr->accno = access;
- myattr->species = species;
- myattr->ncbi_gc = get_ncbi_gc_number(acnuc_gc);
- return myattr;
-}
-
+ char** cname, ** cdescription;
-int RAA::knownDatabases(vector<string> &name, vector<string> &description)
-{
- char **cname, **cdescription;
-
- int count = raa_knowndbs(raa_data, &cname, &cdescription);
- name.resize(count);
- description.resize(count);
- for(int i = 0; i < count; i++) {
- name[i] = cname[i]; free(cname[i]);
- description[i] = cdescription[i]; free(cdescription[i]);
- }
- if(count > 0) { free(cname); free(cdescription); }
- return count;
+ int count = raa_knowndbs(raa_data, &cname, &cdescription);
+ name.resize(count);
+ description.resize(count);
+ for (int i = 0; i < count; i++)
+ {
+ name[i] = cname[i]; free(cname[i]);
+ description[i] = cdescription[i]; free(cdescription[i]);
+ }
+ if (count > 0)
+ {
+ free(cname); free(cdescription);
+ }
+ return count;
}
-int RAA::openDatabase(const string &dbname, char *(*getpasswordf)(void *), void *p)
+int RAA::openDatabase(const string& dbname, char*(*getpasswordf)(void*), void* p)
{
- current_address.div = -1;
- return raa_opendb_pw(raa_data, (char *)dbname.c_str(), p, getpasswordf);
+ current_address.div = -1;
+ return raa_opendb_pw(raa_data, (char*)dbname.c_str(), p, getpasswordf);
}
void RAA::closeDatabase()
{
- sock_fputs(this->raa_data, (char *)"acnucclose\n");
- read_sock(this->raa_data);
+ sock_fputs(this->raa_data, (char*)"acnucclose\n");
+ read_sock(this->raa_data);
}
string RAA::getFirstAnnotLine(int seqrank)
{
- if(seqrank < 2 || seqrank > raa_data->nseq) return "";
- raa_seq_to_annots(raa_data, seqrank, ¤t_address.faddr, ¤t_address.div);
- char *p = raa_read_annots(raa_data, current_address.faddr, current_address.div);
- string retval(p);
- return retval;
+ if (seqrank < 2 || seqrank > raa_data->nseq)
+ return "";
+ raa_seq_to_annots(raa_data, seqrank, ¤t_address.faddr, ¤t_address.div);
+ char* p = raa_read_annots(raa_data, current_address.faddr, current_address.div);
+ string retval(p);
+ return retval;
}
string RAA::getNextAnnotLine()
{
- if(current_address.div == -1) return NULL;
- char *p = raa_next_annots(raa_data, ¤t_address.faddr);
- if(p != NULL) {
- string retval(p);
- return retval;
- }
- else return NULL;
+ if (current_address.div == -1)
+ return NULL;
+ char* p = raa_next_annots(raa_data, ¤t_address.faddr);
+ if (p != NULL)
+ {
+ string retval(p);
+ return retval;
+ }
+ else
+ return NULL;
}
RaaAddress RAA::getCurrentAnnotAddress()
{
- return current_address;
+ return current_address;
}
string RAA::getAnnotLineAtAddress(RaaAddress address)
{
- current_address = address;
- char *p = raa_read_annots(raa_data, current_address.faddr, current_address.div);
- string retval(p);
- return retval;
-}
-
-
-Sequence *RAA::translateCDS(int seqrank) throw(BadCharException)
-{
- char *descript;
- if(seqrank < 2 || seqrank > raa_data->nseq) return NULL;
- char *prot = raa_translate_cds(raa_data, seqrank);
- if(prot == NULL) return NULL;
- int l = strlen(prot) - 1;
- if(l >= 0 && prot[l] == '*') prot[l] = 0;
- char *name = raa_seqrank_attributes(raa_data, seqrank, NULL, NULL, NULL, NULL, &descript, NULL, NULL);
- string *sname = new string(name);
- string *pstring = new string(prot);
- if(sname == NULL || pstring == NULL) return NULL;
- Sequence *Sprot;
- try {
- Sprot = new BasicSequence(*sname, *pstring, &AlphabetTools::PROTEIN_ALPHABET );
- }
- catch (BadCharException e){
- delete sname;
+ current_address = address;
+ char* p = raa_read_annots(raa_data, current_address.faddr, current_address.div);
+ string retval(p);
+ return retval;
+}
+
+
+Sequence* RAA::translateCDS(int seqrank) throw (BadCharException)
+{
+ char* descript;
+ if (seqrank < 2 || seqrank > raa_data->nseq)
+ return NULL;
+ char* prot = raa_translate_cds(raa_data, seqrank);
+ if (prot == NULL)
+ return NULL;
+ int l = strlen(prot) - 1;
+ if (l >= 0 && prot[l] == '*')
+ prot[l] = 0;
+ char* name = raa_seqrank_attributes(raa_data, seqrank, NULL, NULL, NULL, NULL, &descript, NULL, NULL);
+ string* sname = new string(name);
+ string* pstring = new string(prot);
+ if (sname == NULL || pstring == NULL)
+ return NULL;
+ Sequence* Sprot;
+ try
+ {
+ Sprot = new BasicSequence(*sname, *pstring, &AlphabetTools::PROTEIN_ALPHABET );
+ }
+ catch (BadCharException e)
+ {
+ delete sname;
delete pstring;
- throw e;
- }
- delete sname;
+ throw e;
+ }
+ delete sname;
delete pstring;
- vector<string> comment(1, string(descript) );
- Sprot->setComments(comment);
- return Sprot;
+ vector<string> comment(1, string(descript) );
+ Sprot->setComments(comment);
+ return Sprot;
}
-Sequence *RAA::translateCDS(const string &name) throw(BadCharException)
+Sequence* RAA::translateCDS(const string& name) throw (BadCharException)
{
- int rank;
- rank = raa_isenum(raa_data, (char *)name.c_str());
- if(rank == 0) return NULL;
- Sequence *Sprot;
- try {
- Sprot = translateCDS(rank);
- }
- catch (BadCharException e){
- throw e;
- }
- return Sprot;
+ int rank;
+ rank = raa_isenum(raa_data, (char*)name.c_str());
+ if (rank == 0)
+ return NULL;
+ Sequence* Sprot;
+ try
+ {
+ Sprot = translateCDS(rank);
+ }
+ catch (BadCharException e)
+ {
+ throw e;
+ }
+ return Sprot;
}
char RAA::translateInitCodon(int seqrank)
{
- if(seqrank < 2 || seqrank > raa_data->nseq) return 0;
- return raa_translate_init_codon(raa_data, seqrank);
+ if (seqrank < 2 || seqrank > raa_data->nseq)
+ return 0;
+ return raa_translate_init_codon(raa_data, seqrank);
}
-RaaList *RAA::processQuery(const string &query, const string &listname) throw(string)
+RaaList* RAA::processQuery(const string& query, const string& listname) throw (string)
{
- char *message;
- int type, rank;
- int err = raa_proc_query(raa_data, (char *)query.c_str(), &message, (char *)listname.c_str(), &rank, NULL,
- NULL, &type);
- if(err) {
- string errmess = message;
- free(message);
- throw errmess;
- }
- RaaList *mylist = new RaaList();
- mylist->myraa = this;
- mylist->rank = rank;
- mylist->name = listname;
- if(type=='S') mylist->type = &RaaList::LIST_SEQUENCES;
- else if(type=='K') mylist->type = &RaaList::LIST_KEYWORDS;
- else mylist->type = &RaaList::LIST_SPECIES;
- return mylist;
+ char* message;
+ int type, rank;
+ int err = raa_proc_query(raa_data, (char*)query.c_str(), &message, (char*)listname.c_str(), &rank, NULL,
+ NULL, &type);
+ if (err)
+ {
+ string errmess = message;
+ free(message);
+ throw errmess;
+ }
+ RaaList* mylist = new RaaList();
+ mylist->myraa = this;
+ mylist->rank = rank;
+ mylist->name = listname;
+ if (type == 'S')
+ mylist->type = &RaaList::LIST_SEQUENCES;
+ else if (type == 'K')
+ mylist->type = &RaaList::LIST_KEYWORDS;
+ else
+ mylist->type = &RaaList::LIST_SPECIES;
+ return mylist;
}
-RaaList *RAA::createEmptyList(const string &listname, const string &kind) throw(int)
+RaaList* RAA::createEmptyList(const string& listname, const string& kind) throw (int)
{
- int err, lrank;
- char type, *p, *q;
- sock_printf(raa_data, (char *)"getemptylist&name=%s\n", listname.c_str() );
- char *reponse = read_sock(raa_data);
- p = strchr(reponse, '=');
- if(p) q = strchr(p+1, '=');
- sscanf(p+1, "%d", &err);
-
- if(err != 0) {
- throw err;
- }
- sscanf(q+1, "%d", &lrank);
- if(kind == RaaList::LIST_SEQUENCES) type='S';
- else if(kind == RaaList::LIST_KEYWORDS) type='K';
- else type='E';
- sock_printf(raa_data, "setliststate&lrank=%d&type=%c\n", lrank, type);
- read_sock(raa_data);
- RaaList *mylist = new RaaList();
- mylist->myraa = this;
- mylist->rank = lrank;
- mylist->name = listname;
- mylist->type = &kind;
- return mylist;
-}
-
-
-void RAA::deleteList(RaaList *list)
+ int err, lrank;
+ char type, * p = 0, * q = 0;
+ sock_printf(raa_data, (char*)"getemptylist&name=%s\n", listname.c_str() );
+ char* reponse = read_sock(raa_data);
+ p = strchr(reponse, '=');
+ if (p)
+ q = strchr(p + 1, '=');
+ sscanf(p + 1, "%d", &err);
+
+ if (err != 0)
+ {
+ throw err;
+ }
+ sscanf(q + 1, "%d", &lrank);
+ if (kind == RaaList::LIST_SEQUENCES)
+ type = 'S';
+ else if (kind == RaaList::LIST_KEYWORDS)
+ type = 'K';
+ else
+ type = 'E';
+ sock_printf(raa_data, "setliststate&lrank=%d&type=%c\n", lrank, type);
+ read_sock(raa_data);
+ RaaList* mylist = new RaaList();
+ mylist->myraa = this;
+ mylist->rank = lrank;
+ mylist->name = listname;
+ mylist->type = &kind;
+ return mylist;
+}
+
+
+void RAA::deleteList(RaaList* list)
+{
+ raa_releaselist(raa_data, list->rank);
+ delete list;
+}
+
+
+int RAA::keywordPattern(const string& pattern)
+{
+ current_kw_match = 2;
+ if (kw_pattern)
+ delete kw_pattern;
+ kw_pattern = new string(pattern);
+ return raa_data->WIDTH_KW;
+}
+
+
+int RAA::nextMatchingKeyword(string& matching)
+{
+ char* keyword;
+ if (current_kw_match == 2)
+ current_kw_match = raa_nextmatchkey(raa_data, 2, (char*)kw_pattern->c_str(), &keyword);
+ else
+ current_kw_match = raa_nextmatchkey(raa_data, current_kw_match, NULL, &keyword);
+ if (current_kw_match)
+ matching = keyword;
+ return current_kw_match;
+}
+
+
+static int treeloadprogress(int percent, void* data)
+{
+ bool* first = (bool*)data;
+ if (*first)
+ {
+ cout << "Starting species tree download\n";
+ *first = false;
+ }
+ cout << '.'; fflush(stdout);
+ return false;
+}
+
+
+RaaSpeciesTree* RAA::loadSpeciesTree(bool showprogress)
+{
+ bool init_load_mess = true;
+ int err = raa_loadtaxonomy(raa_data, (char*)"ROOT", showprogress ? treeloadprogress : NULL, &init_load_mess, NULL, NULL);
+ if (err)
+ return NULL;
+ if (showprogress && (!init_load_mess) )
+ cout << "\nSpecies tree download completed\n";
+ RaaSpeciesTree* tree = new RaaSpeciesTree();
+ tree->raa_data = raa_data;
+ tree->sp_tree = raa_data->sp_tree;
+ tree->tid_to_rank = raa_data->tid_to_rank;
+ tree->max_tid = raa_data->max_tid;
+ tree->max_sp = raa_read_first_rec(raa_data, raa_spec);
+ return tree;
+}
+
+
+void RAA::freeSpeciesTree(RaaSpeciesTree* tree)
{
- raa_releaselist(raa_data, list->rank);
- delete list;
+ int i;
+ struct raa_pair* p, * q;
+ for (i = 2; i <= tree->max_sp; i++)
+ {
+ if (raa_data->sp_tree[i] == NULL)
+ continue;
+ free(raa_data->sp_tree[i]->name);
+ if (raa_data->sp_tree[i]->libel != NULL)
+ free(raa_data->sp_tree[i]->libel);
+ if (raa_data->sp_tree[i]->libel_upcase != NULL)
+ free(raa_data->sp_tree[i]->libel_upcase);
+ p = raa_data->sp_tree[i]->list_desc;
+ while (p)
+ {
+ q = p->next;
+ free(p);
+ p = q;
+ }
+ free(raa_data->sp_tree[i]);
+ }
+ if (raa_data->tid_to_rank != NULL)
+ free(raa_data->tid_to_rank);
+ if (raa_data->sp_tree != NULL)
+ free(raa_data->sp_tree);
+ raa_data->sp_tree = NULL;
+ raa_data->tid_to_rank = NULL;
+ delete tree;
}
-int RAA::keywordPattern(const string &pattern)
-{
- current_kw_match = 2;
- if(kw_pattern) delete kw_pattern;
- kw_pattern = new string(pattern);
- return raa_data->WIDTH_KW;
-}
-
-
-int RAA::nextMatchingKeyword(string &matching)
-{
- char *keyword;
- if(current_kw_match==2) current_kw_match = raa_nextmatchkey(raa_data, 2, (char*)kw_pattern->c_str(), &keyword);
- else current_kw_match = raa_nextmatchkey(raa_data, current_kw_match, NULL, &keyword);
- if(current_kw_match) matching = keyword;
- return current_kw_match;
-}
-
-
-static int treeloadprogress(int percent, void *data)
-{
- bool *first =(bool *)data;
- if(*first) {
- cout << "Starting species tree download\n";
- *first = false;
- }
- cout << '.'; fflush(stdout);
- return false;
-}
-
-
-RaaSpeciesTree *RAA::loadSpeciesTree(bool showprogress)
+vector<string> RAA::listDirectFeatureKeys()
{
- bool init_load_mess = true;
- int err = raa_loadtaxonomy(raa_data, (char *)"ROOT", showprogress ? treeloadprogress : NULL, &init_load_mess, NULL, NULL);
- if(err) return NULL;
- if( showprogress && (!init_load_mess) ) cout << "\nSpecies tree download completed\n";
- RaaSpeciesTree *tree = new RaaSpeciesTree();
- tree->raa_data = raa_data;
- tree->sp_tree = raa_data->sp_tree;
- tree->tid_to_rank = raa_data->tid_to_rank;
- tree->max_tid = raa_data->max_tid;
- tree->max_sp = raa_read_first_rec(raa_data, raa_spec);
- return tree;
-}
+ int total, num;
+ vector<string> ftkeys;
-
-void RAA::freeSpeciesTree(RaaSpeciesTree *tree)
-{
- int i;
- struct raa_pair *p, *q;
- for(i = 2; i <= tree->max_sp; i++) {
- if(raa_data->sp_tree[i] == NULL) continue;
- free(raa_data->sp_tree[i]->name);
- if(raa_data->sp_tree[i]->libel != NULL) free(raa_data->sp_tree[i]->libel);
- if(raa_data->sp_tree[i]->libel_upcase != NULL) free(raa_data->sp_tree[i]->libel_upcase);
- p = raa_data->sp_tree[i]->list_desc;
- while(p) {
- q = p->next;
- free(p);
- p = q;
- }
- free(raa_data->sp_tree[i]);
- }
- if(raa_data->tid_to_rank != NULL) free(raa_data->tid_to_rank);
- if(raa_data->sp_tree != NULL) free(raa_data->sp_tree);
- raa_data->sp_tree = NULL;
- raa_data->tid_to_rank = NULL;
- delete tree;
+ total = raa_read_first_rec(raa_data, raa_smj);
+ for (num = 2; num <= total; num++)
+ {
+ char* name = raa_readsmj(raa_data, num, NULL, NULL);
+ if (strncmp(name, "04", 2) != 0)
+ continue;
+ if (strcmp(name, "04ID") == 0)
+ continue;
+ if (strcmp(name, "04LOCUS") == 0)
+ continue;
+ ftkeys.push_back(name + 2);
+ }
+ return ftkeys;
}
-vector<string> RAA::listDirectFeatureKeys()
+static void godownkey(raa_db_access* raa_data, unsigned int p3, vector<string>& ftkeys)
{
- int total, num;
- vector<string> ftkeys;
-
- total = raa_read_first_rec(raa_data, raa_smj);
- for(num = 2; num <= total; num++) {
- char *name = raa_readsmj(raa_data, num, NULL, NULL);
- if(strncmp(name, "04", 2) != 0) continue;
- if(strcmp(name, "04ID") == 0) continue;
- if(strcmp(name, "04LOCUS") == 0) continue;
- ftkeys.push_back(name + 2);
- }
- return ftkeys;
-}
+ unsigned next;
+ int value;
+ char* name;
+ next = raa_readshrt(raa_data, p3, &value);
+ name = raa_readkey(raa_data, abs(value), NULL, NULL, NULL, NULL);
+ ftkeys.push_back(name);
-static void godownkey(raa_db_access *raa_data, unsigned int p3, vector<string>& ftkeys)
-{
- unsigned next;
- int value;
- char *name;
-
- next = raa_readshrt(raa_data, p3, &value);
- name = raa_readkey(raa_data, abs(value), NULL, NULL, NULL, NULL);
- ftkeys.push_back(name);
-
- while(next != 0) {
- next = raa_readshrt(raa_data, next, &value);
- godownkey(raa_data, value, ftkeys);
- }
+ while (next != 0)
+ {
+ next = raa_readshrt(raa_data, next, &value);
+ godownkey(raa_data, value, ftkeys);
+ }
}
vector<string> RAA::listAllFeatureKeys()
{
- vector<string> ftkeys;
- int rank, pdesc;
-
- rank = raa_iknum(raa_data, (char *)"misc_feature", raa_key);
- raa_readkey(raa_data, rank, NULL, NULL, &pdesc, NULL);
- godownkey(raa_data, pdesc, ftkeys);
- return ftkeys;
-}
-
-
-RaaList *RAA::getDirectFeature(const string &seqname, const string &featurekey, const string &listname, const string &matching)
-{
- char query[80];
- RaaList *list1;
- int matchinglist, err;
- sprintf(query, "n=%s and t=%s", seqname.c_str(), featurekey.c_str());
- string squery = query;
- try {
- list1 = processQuery(squery, listname);
- }
- catch (string s) {
- return NULL;
- }
- if(matching.empty() || list1->getCount() == 0) return list1;
- sock_printf(raa_data, "prep_getannots&nl=1\n%s|%s\n", raa_data->embl ? "FT" : "FEATURES", featurekey.c_str());
- char *p = read_sock(raa_data);
- if(strncmp(p, "code=0", 6) != 0) return NULL;
- err = raa_modifylist(raa_data, list1->getRank(), (char *)"scan", (char *)matching.c_str(), &matchinglist, NULL, NULL);
- if(err != 0 || raa_bcount(raa_data, matchinglist) == 0) {
- delete list1;
- if(err == 0) raa_releaselist(raa_data, matchinglist);
- return NULL;
- }
- raa_setlistname(raa_data, matchinglist, (char *)listname.c_str());
- RaaList *list2 = new RaaList();
- list2->rank = matchinglist;
- list2->myraa = this;
- list2->name = listname;
- list2->type = &RaaList::LIST_SEQUENCES;
- delete list1;
- return list2;
-}
-
-
-struct extract_data {
- char line[100];
+ vector<string> ftkeys;
+ int rank, pdesc;
+
+ rank = raa_iknum(raa_data, (char*)"misc_feature", raa_key);
+ raa_readkey(raa_data, rank, NULL, NULL, &pdesc, NULL);
+ godownkey(raa_data, pdesc, ftkeys);
+ return ftkeys;
+}
+
+
+RaaList* RAA::getDirectFeature(const string& seqname, const string& featurekey, const string& listname, const string& matching)
+{
+ char query[80];
+ RaaList* list1;
+ int matchinglist, err;
+ sprintf(query, "n=%s and t=%s", seqname.c_str(), featurekey.c_str());
+ string squery = query;
+ try
+ {
+ list1 = processQuery(squery, listname);
+ }
+ catch (string s)
+ {
+ return NULL;
+ }
+ if (matching.empty() || list1->getCount() == 0)
+ return list1;
+ sock_printf(raa_data, "prep_getannots&nl=1\n%s|%s\n", raa_data->embl ? "FT" : "FEATURES", featurekey.c_str());
+ char* p = read_sock(raa_data);
+ if (strncmp(p, "code=0", 6) != 0)
+ return NULL;
+ err = raa_modifylist(raa_data, list1->getRank(), (char*)"scan", (char*)matching.c_str(), &matchinglist, NULL, NULL);
+ if (err != 0 || raa_bcount(raa_data, matchinglist) == 0)
+ {
+ delete list1;
+ if (err == 0)
+ raa_releaselist(raa_data, matchinglist);
+ return NULL;
+ }
+ raa_setlistname(raa_data, matchinglist, (char*)listname.c_str());
+ RaaList* list2 = new RaaList();
+ list2->rank = matchinglist;
+ list2->myraa = this;
+ list2->name = listname;
+ list2->type = &RaaList::LIST_SEQUENCES;
+ delete list1;
+ return list2;
+}
+
+
+struct extract_data
+{
+ char line[100];
};
-void *RAA::prepareGetAnyFeature(int seqrank, const string &featurekey) throw(string)
-{
- char *p, *line;
- int l;
-
- if(seqrank < 2 || seqrank > raa_data->nseq) throw "Incorrect first argument";
- struct extract_data *data = new struct extract_data;
- sock_printf(raa_data, "extractseqs&seqnum=%d&format=fasta&operation=feature&feature=%s&zlib=F\n", seqrank, featurekey.c_str());
- line = read_sock(raa_data);
- if(strcmp(line, "code=0") == 0) {
- p = read_sock(raa_data);
- strcpy(data->line, p);
- return (void *)data;
- }
- delete data;
- p = strstr(line, "message=");
- if(p == NULL) return NULL;
- p += 8;
- if(*p == '"') p++;
- l = strlen(p);
- if(p[l-1] == '"') p[l-1] = 0;
- string message = p;
- throw message;
-}
-
-
-Sequence *RAA::getNextFeature(void *v)
-{
- char *p;
- Sequence *seq;
- string name;
- struct extract_data *data = (struct extract_data *)v;
-
- while( data->line[0] == 27 /* esc */ ) {
- p = read_sock(raa_data);
- strcpy(data->line, p);
- }
- if(strcmp(data->line, "extractseqs END.") == 0) {
- delete data;
- return NULL;
- }
- p = strchr(data->line, ' ');
- if(p != NULL)*p = 0;
- name = data->line + 1;
- p = read_sock(raa_data);
- string seqdata = "";
- while( p != NULL && strcmp(p, "extractseqs END.") != 0 && *p != 27 /* esc */ && *p != '>') {
- seqdata += p;
- p = read_sock(raa_data);
- }
- if(p == NULL) strcpy(data->line, "extractseqs END.");
- else {
- if( *p == 27 /* esc */ ) p = read_sock(raa_data);
- strcpy(data->line, p);
- }
- seq = new BasicSequence(name, seqdata, &AlphabetTools::DNA_ALPHABET);
- return seq;
-}
-
-
-void RAA::interruptGetAnyFeature(void *v)
-{
- struct extract_data *data = (struct extract_data *)v;
- char *p;
-
- if(data == NULL) return;
- sock_fputs(raa_data, (char *)"\033" /* esc */);
- sock_flush(raa_data);
- p = data->line;
- while( strcmp(p, "extractseqs END.") != 0) {
- p = read_sock(raa_data);
- }
- delete data;
- /* just to consume ESC that may have arrived after extractseqs END. */
- sock_fputs(raa_data, (char *)"null_command\n");
- read_sock(raa_data);
+void* RAA::prepareGetAnyFeature(int seqrank, const string& featurekey) throw (string)
+{
+ char* p, * line;
+ int l;
+
+ if (seqrank < 2 || seqrank > raa_data->nseq)
+ throw "Incorrect first argument";
+ struct extract_data* data = new struct extract_data;
+ sock_printf(raa_data, "extractseqs&seqnum=%d&format=fasta&operation=feature&feature=%s&zlib=F\n", seqrank, featurekey.c_str());
+ line = read_sock(raa_data);
+ if (strcmp(line, "code=0") == 0)
+ {
+ p = read_sock(raa_data);
+ strcpy(data->line, p);
+ return (void*)data;
+ }
+ delete data;
+ p = strstr(line, "message=");
+ if (p == NULL)
+ return NULL;
+ p += 8;
+ if (*p == '"')
+ p++;
+ l = strlen(p);
+ if (p[l - 1] == '"')
+ p[l - 1] = 0;
+ string message = p;
+ throw message;
+}
+
+
+Sequence* RAA::getNextFeature(void* v)
+{
+ char* p;
+ Sequence* seq;
+ string name;
+ struct extract_data* data = (struct extract_data*)v;
+
+ while (data->line[0] == 27 /* esc */)
+ {
+ p = read_sock(raa_data);
+ strcpy(data->line, p);
+ }
+ if (strcmp(data->line, "extractseqs END.") == 0)
+ {
+ delete data;
+ return NULL;
+ }
+ p = strchr(data->line, ' ');
+ if (p != NULL)
+ *p = 0;
+ name = data->line + 1;
+ p = read_sock(raa_data);
+ string seqdata = "";
+ while (p != NULL && strcmp(p, "extractseqs END.") != 0 && *p != 27 /* esc */ && *p != '>')
+ {
+ seqdata += p;
+ p = read_sock(raa_data);
+ }
+ if (p == NULL)
+ strcpy(data->line, "extractseqs END.");
+ else
+ {
+ if (*p == 27 /* esc */)
+ p = read_sock(raa_data);
+ strcpy(data->line, p);
+ }
+ seq = new BasicSequence(name, seqdata, &AlphabetTools::DNA_ALPHABET);
+ return seq;
+}
+
+
+void RAA::interruptGetAnyFeature(void* v)
+{
+ struct extract_data* data = (struct extract_data*)v;
+ char* p;
+
+ if (data == NULL)
+ return;
+ sock_fputs(raa_data, (char*)"\033" /* esc */);
+ sock_flush(raa_data);
+ p = data->line;
+ while (strcmp(p, "extractseqs END.") != 0)
+ {
+ p = read_sock(raa_data);
+ }
+ delete data;
+ /* just to consume ESC that may have arrived after extractseqs END. */
+ sock_fputs(raa_data, (char*)"null_command\n");
+ read_sock(raa_data);
}
-
diff --git a/src/Bpp/Raa/RAA.h b/src/Bpp/Raa/RAA.h
index f260e7a..adba6c7 100644
--- a/src/Bpp/Raa/RAA.h
+++ b/src/Bpp/Raa/RAA.h
@@ -11,7 +11,7 @@
*
* These classes provides network access to several nucleotide and protein sequence databases
* structured for multi-criteria retrieval under the ACNUC system as described in
- * <a href=http://dx.doi.org/10.1016/j.biochi.2007.07.003>Remote access to ACNUC nucleotide
+ * <a href=http://dx.doi.org/10.1016/j.biochi.2007.07.003>Remote access to ACNUC nucleotide
* and protein sequence databases at PBIL</a>.
*
* The list of available databases is <a href=http://pbil.univ-lyon1.fr/databases/acnuc/banques_raa.php>here</a>.
@@ -24,11 +24,11 @@
extern "C" {
#include "RAA_acnuc.h"
- }
+}
#include <string>
#include <Bpp/Seq/Sequence.h>
-#include <Bpp/Seq/Alphabet.all>
+#include <Bpp/Seq/Alphabet/AlphabetTools.h>
#include "RaaList.h"
#include "RaaSpeciesTree.h"
@@ -36,24 +36,24 @@ extern "C" {
namespace bpp
{
-
-
/**
* @brief Identifies an annotation line in a database.
*/
-class RaaAddress {
- friend class RAA;
- int div;
- raa_long faddr;
+class RaaAddress
+{
+ friend class RAA;
+ int div;
+ raa_long faddr;
+
public:
- /**
- * @brief Gives the rank of the database file containing this annotation line.
- */
- int getDiv() {return div; };
- /**
- * @brief Gives, as a 64-bit int value, the offset of this annotation line within its database file.
- */
- raa_long getAddr() {return faddr; };
+ /**
+ * @brief Gives the rank of the database file containing this annotation line.
+ */
+ int getDiv() {return div; }
+ /**
+ * @brief Gives, as a 64-bit int value, the offset of this annotation line within its database file.
+ */
+ raa_long getAddr() {return faddr; }
};
@@ -65,425 +65,436 @@ public:
* Access can be done to single sequences from their name or accession number
* or to lists of sequences matching a query combining several retrieval criteria.
* Any fragment of any sequence defined by coordinates or by feature table entries
- * can be retrieved. Access to sequence annotations is possible. Concurrent access
+ * can be retrieved. Access to sequence annotations is possible. Concurrent access
* to several databases is possible.
*
- * Access is possible to database entries and also to subsequences, i.e., one or more fragments
+ * Access is possible to database entries and also to subsequences, i.e., one or more fragments
* of one or more parent sequences defined by a feature table entry.
* Subsequences are named by adding an extension (e.g., .PE1) to the name of their parent sequence.
*/
-class RAA {
- friend class RaaList;
+class RAA
+{
+ friend class RaaList;
+
public:
-
- /**
- * @name Opening/closing database connections.
- *
- * @{
- */
-
- /**
- * @brief Direct constructor: opens a network connection to a database.
- *
- * @param dbname The database name (e.g., "embl", "genbank", "swissprot").
- * @param port The IP port number of the server (the default value is a safe choice; make sure that no
- * firewall blocks outbound connections on this port).
- * @param server The IP name of the server (the default value is a safe choice).
- * @throw int An error code as follows:\n
- * 1: incorrect server name\n
- * 2: cannot create connection with server\n
- * 3: unknown database name\n
- * 4: database is currently not available for remote connection\n
- * 7: not enough memory
- */
- RAA(const std::string &dbname, int port = 5558, const std::string &server = "pbil.univ-lyon1.fr") throw(int);
-
- /**
- * @brief Direct constructor: opens a network connection to a database server, without specifying a database.
- *
- * Typical usage is to ask with knownDatabases() for the list of served databases, and then to open the chosen
- * database with openDatabase().
- *
- * @param port The IP port number of the server (the default value is a safe choice; make sure that no
- * firewall blocks outbound connections on this port).
- * @param server The IP name of the server (the default value is a safe choice).
- * @throw int An error code as follows:\n
- * 1: incorrect server name\n
- * 2: cannot create connection with server\n
- * 7: not enough memory
- */
- RAA(int port=5558, const std::string &server = "pbil.univ-lyon1.fr") throw(int);
-
- /**
- * @brief Destructor: closes both the database access, if any, and the network connection.
- */
- ~RAA();
-
- /**
- * @brief Opens a database from its name.
- *
- * @param dbname The database name (e.g., "embl", "genbank", "swissprot").
- * @param getpasswordf NULL, or, for a password-protected database, pointer to a password-providing function
- * that returns the password as a writable static char string.
- * @param p NULL, or pointer to data transmitted as argument of getpasswordf.
- * @return 0 if OK, or an error code as follows:\n
- * 3: unknown database name\n
- * 4: database is currently not available for remote connection\n
- * 5: a database was previously opened on this RAA object and not closed\n
- * 6: incorrect password for password-protected database\n
- * 7: not enough memory
- */
- int openDatabase(const std::string &dbname, char *(*getpasswordf)(void *) = NULL, void *p = NULL);
-
- /**
- * @brief Closes a database connection.
-
- * Allows to later open another database with openDatabase() using the same RAA object.
- */
- void closeDatabase();
-
- /**
- * @brief Computes the list of names and descriptions of databases served by the server.
-
- * Typically used after creation of an RAA object without database and before openDatabase() call.
- *
- * @return The number of served databases.
- * @param name Vector of database names. Any of these names can be used
- * in openDatabase() calls.
- * @param description Vector of database descriptions. A description can
- * begin with "(offline)" to mean the database is currently not available.
- */
- int knownDatabases(std::vector<std::string> &name, std::vector<std::string> &description);
-
- /** @} */
-
- /**
- * @name Access to sequence data and annotations.
- *
- * @{
- */
-
- /**
- * @brief Returns several attributes of a sequence from its name or accession number.
- *
- * @param name_or_accno A sequence name or accession number. Case is not significant.
- * @return Several attributes (length, species, etc..., see: RaaSeqAttributes) of a sequence.
- */
- RaaSeqAttributes *getAttributes(const std::string &name_or_accno);
-
- /**
- * @brief Returns several attributes of a sequence from its database rank.
- *
- * @param seqrank The database rank of a sequence.
- * @return Several attributes (length, species, etc..., see: RaaSeqAttributes) of a sequence,
- * or NULL if seqrank is not a valid database sequence rank.
- */
- RaaSeqAttributes *getAttributes(int seqrank);
-
- /**
- * @brief Returns a database sequence identified by name or accession number.
- *
- * Because nucleotide database sequences can be several megabases in length, the maxlength argument
- * avoids unexpected huge sequence downloads.
- *
- * @param name_or_accno A sequence name or accession number. Case is not significant.
- * @param maxlength The maximum sequence length beyond which the function returns NULL.
- * @return The database sequence including a one-line comment, or NULL if name_or_accno
- * does not match any sequence or if the sequence length exceeds maxlength.
- */
- Sequence *getSeq(const std::string &name_or_accno, int maxlength=100000);
-
- /**
- * @brief Returns a sequence identified by its database rank.
- *
- * Because nucleotide database sequences can be several megabases in length, the maxlength argument
- * avoids unexpected huge sequence downloads.
- *
- * @param seqrank The database rank of a sequence.
- * @param maxlength The maximum sequence length beyond which the function returns NULL.
- * @return The database sequence including a one-line comment, or NULL if seqrank
- * does not match any sequence or if the sequence length exceeds maxlength.
- */
- Sequence *getSeq(int seqrank, int maxlength=100000);
-
- /**
- * @brief Returns any part of a sequence identified by its database rank.
- *
- * @param seqrank The database rank of a sequence.
- * @param first The first desired position within the sequence (1 is the smallest valid value).
- * @param length The desired number of residues (can be larger than what exists in the sequence).
- * @param sequence Filled upon return with requested sequence data.
- * @return The length of returned sequence data, or 0 if impossible.
- */
- int getSeqFrag(int seqrank, int first, int length, std::string &sequence);
-
- /**
- * @brief Returns any part of a sequence identified by its name or accession number.
- *
- * @param name_or_accno The name or accession number of a sequence. Case is not significant.
- * @param first The first desired position within the sequence (1 is the smallest valid value).
- * @param length The desired number of residues (can be larger than what exists in the sequence).
- * @param sequence Filled upon return with requested sequence data.
- * @return The length of returned sequence data, or 0 if impossible.
- */
- int getSeqFrag(const std::string &name_or_accno, int first, int length, std::string &sequence);
-
- /**
- * @brief Returns the first annotation line of the sequence of given database rank.
- *
- * @param seqrank Database rank of a sequence.
- * @return The first annotation line of this sequence (without terminal \\n).
- */
- std::string getFirstAnnotLine(int seqrank);
-
- /**
- * @brief Returns the next annotation line after that previously read, or NULL if the end of the
- * database file was reached.
- *
- * @return The next annotation line after that previously read (without terminal \\n).
- */
- std::string getNextAnnotLine();
-
- /**
- * @brief Returns information identifying the position of the last read annotation line.
- *
- * @return Information identifying the position of the last read annotation line.
- */
- RaaAddress getCurrentAnnotAddress();
-
- /**
- * @brief Returns the annotation line at the given address.
- *
- * @param address Information identifying the position of an annotation line
- * typically obtained from a previous call to getCurrentAnnotAddress().
- * @return The annotation line at that position (in static memory, without terminal \\n).
- */
- std::string getAnnotLineAtAddress(RaaAddress address);
-
- /**
- * @brief Returns the full protein translation of a protein-coding nucleotide database (sub)sequence.
- *
- * @param seqrank The database rank of a protein-coding sequence. It can be either a subsequence
- * corresponding to a CDS feature table entry, or a sequence if all of it belongs to the CDS.
- * @return The complete protein translation of this CDS, using the genetic code suggested
- * by the sequence annotations and with a one-line comment, or NULL if seqrank does not match a CDS
- * or if not enough memory.
- * @throw BadCharException In rare cases, the CDS may contain an internal stop codon that raises an
- * exception when translated to protein.
- */
- Sequence *translateCDS(int seqrank) throw(BadCharException);//TODO add comment to Sequence
-
- /**
- * @brief Returns the full protein translation of a protein-coding nucleotide database (sub)sequence.
- *
- * @param name The name of a protein-coding sequence. It can be either a subsequence
- * corresponding to a CDS feature table entry, or a sequence if all of it belongs to the CDS.
- * @return The complete protein translation of this CDS, using the genetic code suggested
- * by the sequence annotations and with a one-line comment, or NULL if name does not match a CDS or
- * if not enough memory.
- * @throw BadCharException In rare cases, the CDS may contain an internal stop codon that raises an
- * exception when translated to protein.
- */
- Sequence *translateCDS(const std::string &name) throw(BadCharException);
-
- /**
- * @brief Returns the amino acid translation of the first codon of a protein-coding (sub)sequence.
- *
- * @param seqrank The database rank of a protein-coding sequence. It can be either a subsequence
- * corresponding to a CDS feature table entry, or a sequence if all of it belongs to the CDS.
- * @return The amino acid corresponding to the start codon of this sequence, using the
- * adequate initiation-codon-specific genetic code.
- */
- char translateInitCodon(int seqrank);
-
- /** @} */
-
- /**
- * @name Creation of lists of sequences, species or keywords.
- *
- * @{
- */
-
- /**
- * @brief Returns the list of database elements (often sequences) matching a query.
- *
- * Query examples:\n k=ribosomal protein L14 \n sp=felis catus and t=cds
- * @param query A retrieval query following the syntax described
- * <a href=http://pbil.univ-lyon1.fr/databases/acnuc/cfonctions.html#QUERYLANGUAGE>here</a>.
- * @param listname A name to be given to the resulting list. Case is not significant. If a list with same
- * name already exists, it is replaced by the new list.
- * @return The resulting list of matching database elements.
- * @throw string If error, the string is a message describing the error cause.
- */
- RaaList *processQuery(const std::string &query, const std::string &listname) throw(std::string);
-
- /**
- * @brief Creates an empty list with specified name.
- *
- * @param listname A name to be given to the resulting list. Case is not significant.
- * @param kind Nature of the resulting list. One of RaaList::LIST_SEQUENCES, RaaList::LIST_KEYWORDS,
- * RaaList::LIST_SPECIES.
- * @return The resulting list, unless an exception was raised.
- * @throw int 3: a list with same name already existed; it is left unchanged.\n
- * 4: the server cannot create more lists.
- */
- RaaList *createEmptyList(const std::string &listname, const std::string &kind=RaaList::LIST_SEQUENCES) throw(int);
-
- /**
- * @brief Deletes a list and calls its destructor.
- *
- * @param list An RaaList object.
- */
- void deleteList(RaaList *list);
-
-
- /** @} */
-
-
- /**
- * @name Access to feature table-defined sequences (nucleotide databases only).
- *
- * @{
- */
-
- /**
- * @brief Computes the list of subsequences of a given sequence corresponding to a given feature key with
- * optional annotation string matching.
- *
- * This function allows to retrieve all features of the given sequence corresponding to a given feature key
- * and whose annotation optionally contains a given string. \n
- * Example:\n
- * getDirectFeature("AE005174", "tRNA", "mytrnas", "anticodon: TTG")\n
- * retrieves all tRNA features present in the feature table of sequence AE005174 that contain the string
- * "anticodon: TTG" in their annotations, and puts that in a sequence list called "mytrnas". This function is
- * meaningful with nucleotide sequence databases only (not with protein databases).
- *
- * @param seqname The name of a database sequence. Case is not significant.
- * @param featurekey A feature key (e.g., CDS, tRNA, ncRNA) that must be directly accessible, that is, one of those
- * returned by listDirectFeatureKeys(). Case is not significant.
- * @param listname The name to give to the resulting sequence list.
- * @param matching An optional string required to be present in the feature's annotations. Case is not significant.
- * @return The list of subsequences of <i>seqname</i> that correspond to the specified feature key and, optionally, whose
- * annotation contains the matching string, or NULL if no matching sequence exists.
- */
- RaaList *getDirectFeature(const std::string &seqname, const std::string &featurekey, const std::string &listname,
- const std::string &matching = "");
-
- /**
- * @brief Gives all feature keys of the database that can be directly accessed.
- *
- * These feature keys (e.g., CDS, rRNA, tRNA) can be used with function getDirectFeature(). This function is
- * meaningful with nucleotide sequence databases only (not with protein databases).
- *
- * @return A string vector listing all feature keys of the database that can be directly accessed.
- */
+ /**
+ * @name Opening/closing database connections.
+ *
+ * @{
+ */
+
+ /**
+ * @brief Direct constructor: opens a network connection to a database.
+ *
+ * @param dbname The database name (e.g., "embl", "genbank", "swissprot").
+ * @param port The IP port number of the server (the default value is a safe choice; make sure that no
+ * firewall blocks outbound connections on this port).
+ * @param server The IP name of the server (the default value is a safe choice).
+ * @throw int An error code as follows:\n
+ * 1: incorrect server name\n
+ * 2: cannot create connection with server\n
+ * 3: unknown database name\n
+ * 4: database is currently not available for remote connection\n
+ * 7: not enough memory
+ */
+ RAA(const std::string& dbname, int port = 5558, const std::string& server = "pbil.univ-lyon1.fr") throw (int);
+
+ /**
+ * @brief Direct constructor: opens a network connection to a database server, without specifying a database.
+ *
+ * Typical usage is to ask with knownDatabases() for the list of served databases, and then to open the chosen
+ * database with openDatabase().
+ *
+ * @param port The IP port number of the server (the default value is a safe choice; make sure that no
+ * firewall blocks outbound connections on this port).
+ * @param server The IP name of the server (the default value is a safe choice).
+ * @throw int An error code as follows:\n
+ * 1: incorrect server name\n
+ * 2: cannot create connection with server\n
+ * 7: not enough memory
+ */
+ RAA(int port = 5558, const std::string& server = "pbil.univ-lyon1.fr") throw (int);
+
+ /**
+ * @brief Destructor: closes both the database access, if any, and the network connection.
+ */
+ ~RAA();
+
+ /**
+ * @brief Opens a database from its name.
+ *
+ * @param dbname The database name (e.g., "embl", "genbank", "swissprot").
+ * @param getpasswordf NULL, or, for a password-protected database, pointer to a password-providing function
+ * that returns the password as a writable static char string.
+ * @param p NULL, or pointer to data transmitted as argument of getpasswordf.
+ * @return 0 if OK, or an error code as follows:\n
+ * 3: unknown database name\n
+ * 4: database is currently not available for remote connection\n
+ * 5: a database was previously opened on this RAA object and not closed\n
+ * 6: incorrect password for password-protected database\n
+ * 7: not enough memory
+ */
+ int openDatabase(const std::string& dbname, char*(*getpasswordf)(void*) = NULL, void* p = NULL);
+
+ /**
+ * @brief Closes a database connection.
+
+ * Allows to later open another database with openDatabase() using the same RAA object.
+ */
+ void closeDatabase();
+
+ /**
+ * @brief Computes the list of names and descriptions of databases served by the server.
+
+ * Typically used after creation of an RAA object without database and before openDatabase() call.
+ *
+ * @return The number of served databases.
+ * @param name Vector of database names. Any of these names can be used
+ * in openDatabase() calls.
+ * @param description Vector of database descriptions. A description can
+ * begin with "(offline)" to mean the database is currently not available.
+ */
+ int knownDatabases(std::vector<std::string>& name, std::vector<std::string>& description);
+
+ /** @} */
+
+ /**
+ * @name Access to sequence data and annotations.
+ *
+ * @{
+ */
+
+ /**
+ * @brief Returns several attributes of a sequence from its name or accession number.
+ *
+ * @param name_or_accno A sequence name or accession number. Case is not significant.
+ * @return Several attributes (length, species, etc..., see: RaaSeqAttributes) of a sequence.
+ */
+ RaaSeqAttributes* getAttributes(const std::string& name_or_accno);
+
+ /**
+ * @brief Returns several attributes of a sequence from its database rank.
+ *
+ * @param seqrank The database rank of a sequence.
+ * @return Several attributes (length, species, etc..., see: RaaSeqAttributes) of a sequence,
+ * or NULL if seqrank is not a valid database sequence rank.
+ */
+ RaaSeqAttributes* getAttributes(int seqrank);
+
+ /**
+ * @brief Returns a database sequence identified by name or accession number.
+ *
+ * Because nucleotide database sequences can be several megabases in length, the maxlength argument
+ * avoids unexpected huge sequence downloads.
+ *
+ * @param name_or_accno A sequence name or accession number. Case is not significant.
+ * @param maxlength The maximum sequence length beyond which the function returns NULL.
+ * @return The database sequence including a one-line comment, or NULL if name_or_accno
+ * does not match any sequence or if the sequence length exceeds maxlength.
+ */
+ Sequence* getSeq(const std::string& name_or_accno, int maxlength = 100000);
+
+ /**
+ * @brief Returns a sequence identified by its database rank.
+ *
+ * Because nucleotide database sequences can be several megabases in length, the maxlength argument
+ * avoids unexpected huge sequence downloads.
+ *
+ * @param seqrank The database rank of a sequence.
+ * @param maxlength The maximum sequence length beyond which the function returns NULL.
+ * @return The database sequence including a one-line comment, or NULL if seqrank
+ * does not match any sequence or if the sequence length exceeds maxlength.
+ */
+ Sequence* getSeq(int seqrank, int maxlength = 100000);
+
+ /**
+ * @brief Returns any part of a sequence identified by its database rank.
+ *
+ * @param seqrank The database rank of a sequence.
+ * @param first The first desired position within the sequence (1 is the smallest valid value).
+ * @param length The desired number of residues (can be larger than what exists in the sequence).
+ * @param sequence Filled upon return with requested sequence data.
+ * @return The length of returned sequence data, or 0 if impossible.
+ */
+ int getSeqFrag(int seqrank, int first, int length, std::string& sequence);
+
+ /**
+ * @brief Returns any part of a sequence identified by its name or accession number.
+ *
+ * @param name_or_accno The name or accession number of a sequence. Case is not significant.
+ * @param first The first desired position within the sequence (1 is the smallest valid value).
+ * @param length The desired number of residues (can be larger than what exists in the sequence).
+ * @param sequence Filled upon return with requested sequence data.
+ * @return The length of returned sequence data, or 0 if impossible.
+ */
+ int getSeqFrag(const std::string& name_or_accno, int first, int length, std::string& sequence);
+
+ /**
+ * @brief Returns the first annotation line of the sequence of given database rank.
+ *
+ * @param seqrank Database rank of a sequence.
+ * @return The first annotation line of this sequence (without terminal \\n).
+ */
+ std::string getFirstAnnotLine(int seqrank);
+
+ /**
+ * @brief Returns the next annotation line after that previously read, or NULL if the end of the
+ * database file was reached.
+ *
+ * @return The next annotation line after that previously read (without terminal \\n).
+ */
+ std::string getNextAnnotLine();
+
+ /**
+ * @brief Returns information identifying the position of the last read annotation line.
+ *
+ * @return Information identifying the position of the last read annotation line.
+ */
+ RaaAddress getCurrentAnnotAddress();
+
+ /**
+ * @brief Returns the annotation line at the given address.
+ *
+ * @param address Information identifying the position of an annotation line
+ * typically obtained from a previous call to getCurrentAnnotAddress().
+ * @return The annotation line at that position (in static memory, without terminal \\n).
+ */
+ std::string getAnnotLineAtAddress(RaaAddress address);
+
+ /**
+ * @brief Returns the full protein translation of a protein-coding nucleotide database (sub)sequence.
+ *
+ * @param seqrank The database rank of a protein-coding sequence. It can be either a subsequence
+ * corresponding to a CDS feature table entry, or a sequence if all of it belongs to the CDS.
+ * @return The complete protein translation of this CDS, using the genetic code suggested
+ * by the sequence annotations and with a one-line comment, or NULL if seqrank does not match a CDS
+ * or if not enough memory.
+ * @throw BadCharException In rare cases, the CDS may contain an internal stop codon that raises an
+ * exception when translated to protein.
+ */
+ Sequence* translateCDS(int seqrank) throw (BadCharException); // TODO add comment to Sequence
+
+ /**
+ * @brief Returns the full protein translation of a protein-coding nucleotide database (sub)sequence.
+ *
+ * @param name The name of a protein-coding sequence. It can be either a subsequence
+ * corresponding to a CDS feature table entry, or a sequence if all of it belongs to the CDS.
+ * @return The complete protein translation of this CDS, using the genetic code suggested
+ * by the sequence annotations and with a one-line comment, or NULL if name does not match a CDS or
+ * if not enough memory.
+ * @throw BadCharException In rare cases, the CDS may contain an internal stop codon that raises an
+ * exception when translated to protein.
+ */
+ Sequence* translateCDS(const std::string& name) throw (BadCharException);
+
+ /**
+ * @brief Returns the amino acid translation of the first codon of a protein-coding (sub)sequence.
+ *
+ * @param seqrank The database rank of a protein-coding sequence. It can be either a subsequence
+ * corresponding to a CDS feature table entry, or a sequence if all of it belongs to the CDS.
+ * @return The amino acid corresponding to the start codon of this sequence, using the
+ * adequate initiation-codon-specific genetic code.
+ */
+ char translateInitCodon(int seqrank);
+
+ /** @} */
+
+ /**
+ * @name Creation of lists of sequences, species or keywords.
+ *
+ * @{
+ */
+
+ /**
+ * @brief Returns the list of database elements (often sequences) matching a query.
+ *
+ * Query examples:\n k=ribosomal protein L14 \n sp=felis catus and t=cds
+ * @param query A retrieval query following the syntax described
+ * <a href=http://pbil.univ-lyon1.fr/databases/acnuc/cfonctions.html#QUERYLANGUAGE>here</a>.
+ * @param listname A name to be given to the resulting list. Case is not significant. If a list with same
+ * name already exists, it is replaced by the new list.
+ * @return The resulting list of matching database elements.
+ * @throw string If error, the string is a message describing the error cause.
+ */
+ RaaList* processQuery(const std::string& query, const std::string& listname) throw (std::string);
+
+ /**
+ * @brief Creates an empty list with specified name.
+ *
+ * @param listname A name to be given to the resulting list. Case is not significant.
+ * @param kind Nature of the resulting list. One of RaaList::LIST_SEQUENCES, RaaList::LIST_KEYWORDS,
+ * RaaList::LIST_SPECIES.
+ * @return The resulting list, unless an exception was raised.
+ * @throw int 3: a list with same name already existed; it is left unchanged.\n
+ * 4: the server cannot create more lists.
+ */
+ RaaList* createEmptyList(const std::string& listname, const std::string& kind = RaaList::LIST_SEQUENCES) throw (int);
+
+ /**
+ * @brief Deletes a list and calls its destructor.
+ *
+ * @param list An RaaList object.
+ */
+ void deleteList(RaaList* list);
+
+
+ /** @} */
+
+
+ /**
+ * @name Access to feature table-defined sequences (nucleotide databases only).
+ *
+ * @{
+ */
+
+ /**
+ * @brief Computes the list of subsequences of a given sequence corresponding to a given feature key with
+ * optional annotation string matching.
+ *
+ * This function allows to retrieve all features of the given sequence corresponding to a given feature key
+ * and whose annotation optionally contains a given string. \n
+ * Example:\n
+ * getDirectFeature("AE005174", "tRNA", "mytrnas", "anticodon: TTG")\n
+ * retrieves all tRNA features present in the feature table of sequence AE005174 that contain the string
+ * "anticodon: TTG" in their annotations, and puts that in a sequence list called "mytrnas". This function is
+ * meaningful with nucleotide sequence databases only (not with protein databases).
+ *
+ * @param seqname The name of a database sequence. Case is not significant.
+ * @param featurekey A feature key (e.g., CDS, tRNA, ncRNA) that must be directly accessible, that is, one of those
+ * returned by listDirectFeatureKeys(). Case is not significant.
+ * @param listname The name to give to the resulting sequence list.
+ * @param matching An optional string required to be present in the feature's annotations. Case is not significant.
+ * @return The list of subsequences of <i>seqname</i> that correspond to the specified feature key and, optionally, whose
+ * annotation contains the matching string, or NULL if no matching sequence exists.
+ */
+ RaaList* getDirectFeature(const std::string& seqname, const std::string& featurekey, const std::string& listname,
+ const std::string& matching = "");
+
+ /**
+ * @brief Gives all feature keys of the database that can be directly accessed.
+ *
+ * These feature keys (e.g., CDS, rRNA, tRNA) can be used with function getDirectFeature(). This function is
+ * meaningful with nucleotide sequence databases only (not with protein databases).
+ *
+ * @return A string vector listing all feature keys of the database that can be directly accessed.
+ */
std::vector<std::string> listDirectFeatureKeys();
-
- /**
- * @brief Gives all feature keys of the database.
- *
- * These feature keys (e.g., CDS, conflict, misc_feature) can be used with function prepareGetAnyFeature(). This function is
- * meaningful with nucleotide sequence databases only (not with protein databases).
- *
- * @return A string vector listing all feature keys of the database.
- */
+
+ /**
+ * @brief Gives all feature keys of the database.
+ *
+ * These feature keys (e.g., CDS, conflict, misc_feature) can be used with function prepareGetAnyFeature(). This function is
+ * meaningful with nucleotide sequence databases only (not with protein databases).
+ *
+ * @return A string vector listing all feature keys of the database.
+ */
std::vector<std::string> listAllFeatureKeys();
-
- /**
- * @brief Starts extraction of all features of a specified key present in the feature table of a database sequence.
- *
- * A database sequence can contain many instances of a given feature key in its feature table. Thus, feature extraction
- * is done by first preparing the desired feature extraction, and by then successively extracting features
- * by getNextFeature() calls until no more exist in the feature table or until a call to interruptGetAnyFeature() is done.
- * Any successful prepareGetAnyFeature() call must be followed by getNextFeature() calls until
- * it returns NULL or by a call to interruptGetAnyFeature(); any call to other RAA member functions in between is prohibited.
- *
- * @param seqrank The database rank of a sequence.
- * @param featurekey Any feature key (direct or not) defined in
- * <a href=http://www.ebi.ac.uk/embl/WebFeat/>EMBL/GenBank/DDBJ feature tables</a>. These are also returned by listAllFeatureKeys().
- * @return An opaque pointer to be transmitted to functions getNextFeature() or interruptGetAnyFeature().
- * @throw string A message indicating the cause of the error.
- */
- void *prepareGetAnyFeature(int seqrank, const std::string &featurekey) throw(std::string);
-
- /**
- * @brief Successively returns features specified in a previous prepareGetAnyFeature() call.
- *
- * This function must be called repetitively until it returns NULL or until function interruptGetAnyFeature() is called.
- * Features are processed in their order of appearance in the feature table.
- * @param opaque A pointer returned by a previous prepareGetAnyFeature() call.
- * @return A sequence corresponding to one of the features specified in the prepareGetAnyFeature() call, or NULL
- * if no more such feature exists.
- */
- Sequence *getNextFeature(void *opaque);
-
- /**
- * @brief Terminates a features extraction session initiated by a prepareGetAnyFeature() call before getNextFeature() call
- * returned NULL.
- *
- * @param opaque A pointer returned by a previous prepareGetAnyFeature() call.
- */
- void interruptGetAnyFeature(void *opaque);
-
- /** @} */
-
-
-
- /**
- * @name Browsing database species and keywords.
- *
- * @{
- */
-
- /**
- * @brief Loads the database's full species tree classification.
- *
- * This call takes a few seconds to run on large databases because much data get downloaded from the server.
- *
- * @param showprogress If true, progress information gets sent to stdout.
- * @return An object allowing work with the full species tree (see RaaSpeciesTree), or NULL if error.
- */
- RaaSpeciesTree *loadSpeciesTree(bool showprogress=true);
-
- /**
- * @brief Frees the memory occupied by the species tree classification.
- *
- * @param tree An object previously returned by a loadSpeciesTree() call. It is deleted upon return.
- */
- void freeSpeciesTree(RaaSpeciesTree *tree);
-
-
- /**
- * @brief Initializes pattern-matching in database keywords. Matching keywords are then returned by successive nextMatchingKeyword() calls.
- *
- * @param pattern A pattern-matching string using @ as wildcard (example: RNA\@polymerase\@).
- * Case is not significant.
- * @return The maximum length of any database keyword.
- */
- int keywordPattern(const std::string &pattern);
-
- /**
- * @brief Finds next matching keyword in database.
- *
- * @param matching Set to the next matching keyword upon return.
- * @return The database rank of the next matching keyword, or 0 if no more matching keyword.
- */
- int nextMatchingKeyword(std::string &matching);
-
- /** @} */
-
-
+
+ /**
+ * @brief Starts extraction of all features of a specified key present in the feature table of a database sequence.
+ *
+ * A database sequence can contain many instances of a given feature key in its feature table. Thus, feature extraction
+ * is done by first preparing the desired feature extraction, and by then successively extracting features
+ * by getNextFeature() calls until no more exist in the feature table or until a call to interruptGetAnyFeature() is done.
+ * Any successful prepareGetAnyFeature() call must be followed by getNextFeature() calls until
+ * it returns NULL or by a call to interruptGetAnyFeature(); any call to other RAA member functions in between is prohibited.
+ *
+ * @param seqrank The database rank of a sequence.
+ * @param featurekey Any feature key (direct or not) defined in
+ * <a href=http://www.ebi.ac.uk/embl/WebFeat/>EMBL/GenBank/DDBJ feature tables</a>. These are also returned by listAllFeatureKeys().
+ * @return An opaque pointer to be transmitted to functions getNextFeature() or interruptGetAnyFeature().
+ * @throw string A message indicating the cause of the error.
+ */
+ void* prepareGetAnyFeature(int seqrank, const std::string& featurekey) throw (std::string);
+
+ /**
+ * @brief Successively returns features specified in a previous prepareGetAnyFeature() call.
+ *
+ * This function must be called repetitively until it returns NULL or until function interruptGetAnyFeature() is called.
+ * Features are processed in their order of appearance in the feature table.
+ * @param opaque A pointer returned by a previous prepareGetAnyFeature() call.
+ * @return A sequence corresponding to one of the features specified in the prepareGetAnyFeature() call, or NULL
+ * if no more such feature exists.
+ */
+ Sequence* getNextFeature(void* opaque);
+
+ /**
+ * @brief Terminates a features extraction session initiated by a prepareGetAnyFeature() call before getNextFeature() call
+ * returned NULL.
+ *
+ * @param opaque A pointer returned by a previous prepareGetAnyFeature() call.
+ */
+ void interruptGetAnyFeature(void* opaque);
+
+ /** @} */
+
+
+ /**
+ * @name Browsing database species and keywords.
+ *
+ * @{
+ */
+
+ /**
+ * @brief Loads the database's full species tree classification.
+ *
+ * This call takes a few seconds to run on large databases because much data get downloaded from the server.
+ *
+ * @param showprogress If true, progress information gets sent to stdout.
+ * @return An object allowing work with the full species tree (see RaaSpeciesTree), or NULL if error.
+ */
+ RaaSpeciesTree* loadSpeciesTree(bool showprogress = true);
+
+ /**
+ * @brief Frees the memory occupied by the species tree classification.
+ *
+ * @param tree An object previously returned by a loadSpeciesTree() call. It is deleted upon return.
+ */
+ void freeSpeciesTree(RaaSpeciesTree* tree);
+
+
+ /**
+ * @brief Initializes pattern-matching in database keywords. Matching keywords are then returned by successive nextMatchingKeyword() calls.
+ *
+ * @param pattern A pattern-matching string using @ as wildcard (example: RNA\@polymerase\@).
+ * Case is not significant.
+ * @return The maximum length of any database keyword.
+ */
+ int keywordPattern(const std::string& pattern);
+
+ /**
+ * @brief Finds next matching keyword in database.
+ *
+ * @param matching Set to the next matching keyword upon return.
+ * @return The database rank of the next matching keyword, or 0 if no more matching keyword.
+ */
+ int nextMatchingKeyword(std::string& matching);
+
+ /** @} */
+
+ /**
+ * @brief returns a pointer to a structure containing various information about the database.
+ *
+ * See http://doua.prabi.fr/databases/acnuc_data/raa_acnuc#raa_db_access for a description of the raa_db_access structure.
+ * Usage example:
+ * @code
+ RAA *mydb = new RAA("swissprot");
+ cout << "mydb is" << (mydb->get_raa_data()->swissprot ? " " : " not ") << "a protein database." << endl;
+ * @endcode
+ * @return A pointer to a structure of type raa_db_access.
+ */
+ raa_db_access* get_raa_data() { return raa_data; }
+
protected:
- raa_db_access *raa_data;
+ raa_db_access* raa_data;
+
private:
- RaaAddress current_address;
- int current_kw_match;
- std::string *kw_pattern;
- Sequence *getSeq_both(const std::string &name_or_accno, int rank, int maxlength);
+ RaaAddress current_address;
+ int current_kw_match;
+ std::string* kw_pattern;
+ Sequence* getSeq_both(const std::string& name_or_accno, int rank, int maxlength);
};
-
-} //end of namespace bpp.
+} // end of namespace bpp.
#endif // _RAA_H_
-
diff --git a/src/Bpp/Raa/RAA_acnuc.c b/src/Bpp/Raa/RAA_acnuc.c
index 8599773..09d1047 100644
--- a/src/Bpp/Raa/RAA_acnuc.c
+++ b/src/Bpp/Raa/RAA_acnuc.c
@@ -14,707 +14,757 @@
#include <sys/time.h>
#include <termios.h>
#elif defined(WIN32)
-#include <Ws2tcpip.h>
-#include <Wspiapi.h>
+#if _WIN32_WINNT < 0x0501
+#define _WIN32_WINNT 0x0501
+#endif
+#include <Winsock2.h>
+#include <Ws2tcpip.h> // for getaddrinfo, freeaddrinfo, struct addrinfo
+// #include <Wspiapi.h>
#endif
#define SERVER_UPDATE_MESSAGE "acnuc stop for update\n"
/* seules fctions utilisables hors de ce fichier pour ecrire sur socket */
-int sock_fputs(raa_db_access *f, char *l);
-int sock_flush(raa_db_access *f);
+int sock_fputs(raa_db_access* f, const char* l);
+int sock_flush(raa_db_access* f);
/* some prototypes */
-void raa_acnucclose(raa_db_access *raa_current_db);
-void list_open_dbs_remove(raa_db_access *raa_current_db);
+void raa_acnucclose(raa_db_access* raa_current_db);
+static char* protect_quotes(char* name);
+static void raa_free_matchkeys(raa_db_access* raa_current_db);
/* needed functions */
-extern char init_codon_to_aa(char *codon, int gc);
-char codaa(char *codon, int code);
-void *prepare_sock_gz_r(FILE *sockr);
-char *z_read_sock(void *v);
-int close_sock_gz_r(void *v);
-char *unprotect_quotes(char *name);
+extern char init_codon_to_aa(char* codon, int gc);
+char codaa(char* codon, int code);
+void* prepare_sock_gz_r(FILE* sockr);
+char* z_read_sock(void* v);
+int close_sock_gz_r(void* v);
+char* unprotect_quotes(char* name);
/* global variables */
-void (*raa_error_mess_proc)(raa_db_access *, char *) = NULL;
+void (* raa_error_mess_proc)(raa_db_access*, char*) = NULL;
#define MAX_RDSHRT 50 /* max short list length read in one time */
-
-
-static raa_db_access *init_raa_db_access(void);
-static struct chain_void *raa_list_open_dbs = NULL;
-
#if defined(WIN32)
-static int socket_getc(raa_db_access *raa_current_db, SOCKET f)
+static int socket_getc(raa_db_access* raa_current_db, SOCKET f)
{
-int q;
+ int q;
-if(raa_current_db->sock_input_pos < raa_current_db->sock_input_end) {
- return *(raa_current_db->sock_input_pos++);
- }
-q = recv(f, raa_current_db->sock_input, SOCKBUFS, 0);
-if(q == 0 || q == SOCKET_ERROR) return EOF;
-raa_current_db->sock_input_end = raa_current_db->sock_input + q;
-raa_current_db->sock_input_pos = raa_current_db->sock_input;
-return *(raa_current_db->sock_input_pos++);
+ if (raa_current_db->sock_input_pos < raa_current_db->sock_input_end)
+ {
+ return *(raa_current_db->sock_input_pos++);
+ }
+ q = recv(f, raa_current_db->sock_input, SOCKBUFS, 0);
+ if (q == 0 || q == SOCKET_ERROR)
+ return EOF;
+ raa_current_db->sock_input_end = raa_current_db->sock_input + q;
+ raa_current_db->sock_input_pos = raa_current_db->sock_input;
+ return *(raa_current_db->sock_input_pos++);
}
-static char *sock_fgets(raa_db_access *raa_current_db, char *line, int len)
+static char* sock_fgets(raa_db_access* raa_current_db, char* line, int len)
{
-int c;
-char *p;
+ int c;
+ char* p;
-p = line;
-while(len > 1) {
- c = socket_getc(raa_current_db, (SOCKET)(raa_current_db->raa_sockfdr) );
- if(c == EOF) {
- if(p == line) return NULL;
- break;
- }
- *(p++) = c;
- if(c == '\n') break;
- len--;
- }
-*p = 0;
-return line;
+ p = line;
+ while (len > 1)
+ {
+ c = socket_getc(raa_current_db, (SOCKET)(raa_current_db->raa_sockfdr) );
+ if (c == EOF)
+ {
+ if (p == line)
+ return NULL;
+ break;
+ }
+ *(p++) = c;
+ if (c == '\n')
+ break;
+ len--;
+ }
+ *p = 0;
+ return line;
}
-static int mswin_sock_flush(raa_db_access *raa_current_db)
+static int mswin_sock_flush(raa_db_access* raa_current_db)
{
-int w;
-char *p;
+ int w;
+ char* p;
-p = raa_current_db->sock_output;
-while(raa_current_db->sock_output_lbuf > 0) {
- w = send((SOCKET)raa_current_db->raa_sockfdw, p, raa_current_db->sock_output_lbuf, 0);
- raa_current_db->sock_output_lbuf -= w;
- p += w;
- }
-return 0;
+ p = raa_current_db->sock_output;
+ while (raa_current_db->sock_output_lbuf > 0)
+ {
+ w = send((SOCKET)raa_current_db->raa_sockfdw, p, raa_current_db->sock_output_lbuf, 0);
+ raa_current_db->sock_output_lbuf -= w;
+ p += w;
+ }
+ return 0;
}
-int sock_flush(raa_db_access *raa_current_db)
+int sock_flush(raa_db_access* raa_current_db)
{
-if(raa_current_db == NULL) return 0;
-return mswin_sock_flush(raa_current_db);
+ if (raa_current_db == NULL)
+ return 0;
+ return mswin_sock_flush(raa_current_db);
}
-int sock_fputs(raa_db_access *raa_current_db, char *s)
+int sock_fputs(raa_db_access* raa_current_db, const char* s)
{
-int l, r;
+ int l, r;
-if(raa_current_db == NULL) return 0;
-l = strlen(s);
-while(raa_current_db->sock_output_lbuf + l > SOCKBUFS) {
- r = SOCKBUFS - raa_current_db->sock_output_lbuf;
- memcpy(raa_current_db->sock_output + raa_current_db->sock_output_lbuf, s, r);
- raa_current_db->sock_output_lbuf += r;
- l -= r;
- s += r;
- mswin_sock_flush(raa_current_db);
- }
-if(l > 0) {
- memcpy(raa_current_db->sock_output + raa_current_db->sock_output_lbuf, s, l);
- raa_current_db->sock_output_lbuf += l;
- }
-return 0;
+ if (raa_current_db == NULL)
+ return 0;
+ l = strlen(s);
+ while (raa_current_db->sock_output_lbuf + l > SOCKBUFS)
+ {
+ r = SOCKBUFS - raa_current_db->sock_output_lbuf;
+ memcpy(raa_current_db->sock_output + raa_current_db->sock_output_lbuf, s, r);
+ raa_current_db->sock_output_lbuf += r;
+ l -= r;
+ s += r;
+ mswin_sock_flush(raa_current_db);
+ }
+ if (l > 0)
+ {
+ memcpy(raa_current_db->sock_output + raa_current_db->sock_output_lbuf, s, l);
+ raa_current_db->sock_output_lbuf += l;
+ }
+ return 0;
}
-
#else
-int sock_fputs(raa_db_access *raa_current_db, char *s)
+int sock_fputs(raa_db_access* raa_current_db, const char* s)
{
-if(raa_current_db == NULL) return EOF;
-return fputs(s, raa_current_db->raa_sockfdw);
+ if (raa_current_db == NULL)
+ return EOF;
+ return fputs(s, raa_current_db->raa_sockfdw);
}
-int sock_flush(raa_db_access *raa_current_db)
+int sock_flush(raa_db_access* raa_current_db)
{
-if(raa_current_db == NULL) return EOF;
-return fflush(raa_current_db->raa_sockfdw);
+ if (raa_current_db == NULL)
+ return EOF;
+ return fflush(raa_current_db->raa_sockfdw);
}
-#endif /* WIN32 */
+#endif/* WIN32 */
-int sock_printf(raa_db_access *raa_current_db, const char *fmt, ...)
+int sock_printf(raa_db_access* raa_current_db, const char* fmt, ...)
{
-va_list ap;
-int retval;
-static char buffer[1000];
+ va_list ap;
+ int retval;
-va_start(ap, fmt);
-vsprintf(buffer, fmt, ap);
-retval = sock_fputs(raa_current_db, buffer);
-va_end(ap);
-return retval;
+ va_start(ap, fmt);
+ vsprintf(raa_current_db->buffer, fmt, ap);
+ retval = sock_fputs(raa_current_db, raa_current_db->buffer);
+ va_end(ap);
+ return retval;
}
-
/******************************************************************/
/* lit une ligne au plus de la socket et transfere le resultat dans une chaine char * */
-static char *read_sock_tell(raa_db_access *raa_current_db, int *wascompleteline) {
-#define RSOCKBUFS 5000
- int lnbuf, isfull;
- char *p ;
- static char buffer[RSOCKBUFS];
- static int was_here = FALSE;
-
- if(raa_current_db == NULL || was_here) return NULL;
+static char* read_sock_tell(raa_db_access* raa_current_db, int* wascompleteline)
+{
+ int lnbuf, isfull;
+ char* p;
+
+ if (raa_current_db == NULL || raa_current_db->was_here)
+ return NULL;
sock_flush(raa_current_db); /* tres important */
isfull = FALSE;
#if defined(WIN32)
- p = sock_fgets(raa_current_db, buffer, RSOCKBUFS);
+ p = sock_fgets(raa_current_db, raa_current_db->buffer, sizeof(raa_current_db->buffer));
#else
- p = fgets(buffer, RSOCKBUFS, raa_current_db->raa_sockfdr);
+ p = fgets(raa_current_db->buffer, sizeof(raa_current_db->buffer), raa_current_db->raa_sockfdr);
#endif
- if(p == NULL || strcmp(p, SERVER_UPDATE_MESSAGE) == 0) {
- if(!was_here) {
- was_here = TRUE;
- *buffer = 0;
- if(raa_current_db != NULL && raa_current_db->dbname != NULL) {
- sprintf(buffer, "%s: ", raa_current_db->dbname);
- }
- strcat(buffer, ( p == NULL ?
- "Error: connection to acnuc server is down. Please try again."
- :
- "Error: acnuc server is down for database update. Please try again later." )
- );
- if(raa_error_mess_proc == NULL) {
- fprintf(stderr, "%s: %s\n", raa_current_db->dbname, buffer);
- /*raa_acnucclose(raa_current_db);
- exit(ERREUR);*/
- return NULL;
- }
- else (*raa_error_mess_proc)(raa_current_db, buffer);/*this function sd call raa_acnucclose*/
- was_here = FALSE;
- }
- return NULL;
- }
-
- was_here = FALSE;
- lnbuf = strlen(buffer);
- p = buffer + lnbuf - 1;
- if(*p == '\n') isfull = TRUE;
- while(p >= buffer && (*p == '\n' || *p == '\r') ) *(p--) = 0;
- if(wascompleteline != NULL) *wascompleteline = isfull;
- return buffer;
-}
-
-
-char *read_sock(raa_db_access *raa_current_db) /* lit une ligne entiere, rend ligne dans memoire privee */
-{
-int wasfull, l2, l = 0;
-char *p;
-static char *reponse = NULL;
-static int lr = 0;
-
-do {
- p = read_sock_tell(raa_current_db, &wasfull);
- if(p == NULL) return NULL;
- l2 = strlen(p);
- if(l + l2 + 1 > lr) {
- lr = l + l2 + 1;
- reponse = (char *)realloc(reponse, lr);
- }
- memcpy(reponse + l, p, l2);
- l += l2;
- }
-while(! wasfull);
-reponse[l] = 0;
-return reponse;
-}
-
-
-char *read_sock_timeout(raa_db_access *raa_current_db, int timeout_ms)
-{
-fd_set readfds;
-struct timeval tout;
-int err;
+ if (p == NULL || strcmp(p, SERVER_UPDATE_MESSAGE) == 0)
+ {
+ if (!raa_current_db->was_here)
+ {
+ raa_current_db->was_here = TRUE;
+ *raa_current_db->buffer = 0;
+ if (raa_current_db != NULL && raa_current_db->dbname != NULL)
+ {
+ sprintf(raa_current_db->buffer, "%s: ", raa_current_db->dbname);
+ }
+ strcat(raa_current_db->buffer, ( p == NULL ?
+ "Error: connection to acnuc server is down. Please try again."
+ :
+ "Error: acnuc server is down for database update. Please try again later." )
+ );
+ if (raa_error_mess_proc == NULL)
+ {
+ fprintf(stderr, "%s\n", raa_current_db->buffer);
+ }
+ else
+ (*raa_error_mess_proc)(raa_current_db, raa_current_db->buffer);
+ }
+ return NULL;
+ }
+
+ raa_current_db->was_here = FALSE;
+ lnbuf = strlen(raa_current_db->buffer);
+ p = raa_current_db->buffer + lnbuf - 1;
+ if (*p == '\n')
+ isfull = TRUE;
+ while (p >= raa_current_db->buffer && (*p == '\n' || *p == '\r') )
+ *(p--) = 0;
+ if (wascompleteline != NULL)
+ *wascompleteline = isfull;
+ return raa_current_db->buffer;
+}
+
+
+char* read_sock(raa_db_access* raa_current_db) /* lit une ligne entiere, rend ligne dans memoire privee */
+{
+ int wasfull, l2, l = 0;
+ char* p;
+
+ do
+ {
+ p = read_sock_tell(raa_current_db, &wasfull);
+ if (p == NULL)
+ return NULL;
+ l2 = strlen(p);
+ if (l + l2 + 1 > raa_current_db->max_full_line)
+ {
+ raa_current_db->max_full_line = l + l2 + 100;
+ raa_current_db->full_line = (char*)realloc(raa_current_db->full_line, raa_current_db->max_full_line);
+ }
+ memcpy(raa_current_db->full_line + l, p, l2);
+ l += l2;
+ }
+ while (!wasfull);
+ raa_current_db->full_line[l] = 0;
+ return raa_current_db->full_line;
+}
+
+
+char* read_sock_timeout(raa_db_access* raa_current_db, int timeout_ms)
+{
+ fd_set readfds;
+ struct timeval tout;
+ int err;
#if defined(WIN32)
-SOCKET fd;
-if(raa_current_db == NULL) return NULL;
-fd = (SOCKET)(raa_current_db->raa_sockfdr);
+ SOCKET fd;
+ if (raa_current_db == NULL)
+ return NULL;
+ fd = (SOCKET)(raa_current_db->raa_sockfdr);
#else
-int fd;
-if(raa_current_db == NULL) return NULL;
-fd = fileno(raa_current_db->raa_sockfdr);
+ int fd;
+ if (raa_current_db == NULL)
+ return NULL;
+ fd = fileno(raa_current_db->raa_sockfdr);
#endif
-FD_ZERO(&readfds);
-FD_SET(fd, &readfds);
-tout.tv_sec = timeout_ms / 1000; tout.tv_usec = 1000*(timeout_ms % 1000);
-err = select(fd + 1, &readfds, NULL, NULL, &tout);
-if(err > 0 && FD_ISSET(fd, &readfds) ) {
- return read_sock(raa_current_db);
- }
-return NULL;
-}
-
-enum {errservname=1, /* bad server name */
-cantopensocket, /* 2 error opening socket */
-unknowndb, /* 3 not in list of known dbs */
-unavailabledb, /* 4 db is currently unavailable */
-dbisopen, /* 5 a db is already open and was not closed */
-badpsswd, /* 6 bad password for protected db */
-nomemory, /* 7 not enough memory */
-badracnuc, /* 8 enviroment variables racnuc or acnuc undefined or inadequate */
-nosocket /* 9 no socket was opened yet */
+ FD_ZERO(&readfds);
+ FD_SET(fd, &readfds);
+ tout.tv_sec = timeout_ms / 1000; tout.tv_usec = 1000 * (timeout_ms % 1000);
+ err = select(fd + 1, &readfds, NULL, NULL, &tout);
+ if (err > 0 && FD_ISSET(fd, &readfds) )
+ {
+ return read_sock(raa_current_db);
+ }
+ return NULL;
+}
+
+enum {errservname = 1, /* bad server name */
+ cantopensocket, /* 2 error opening socket */
+ unknowndb, /* 3 not in list of known dbs */
+ unavailabledb, /* 4 db is currently unavailable */
+ dbisopen, /* 5 a db is already open and was not closed */
+ badpsswd, /* 6 bad password for protected db */
+ nomemory, /* 7 not enough memory */
+ badracnuc, /* 8 enviroment variables racnuc or acnuc undefined or inadequate */
+ nosocket /* 9 no socket was opened yet */
};
-int raa_acnucopen (char *clientid, raa_db_access **psock)
+int raa_acnucopen (const char* clientid, raa_db_access** psock)
/* opens the acnuc db using the environment variable racnuc, or, if undefined, acnuc,
-that should be defined to an url of the form
-raa://pbil.univ-lyon1.fr:5558/embl
-clientid: NULL or a string identifying the client
-*/
+ that should be defined to an url of the form
+ raa://pbil.univ-lyon1.fr:5558/embl
+ clientid: NULL or a string identifying the client
+ */
{
-char *serveurName, *db_name, *p;
-int port, err;
+ char* serveurName, * db_name, * p;
+ int port, err;
-if( (p = getenv("racnuc")) == NULL) p = getenv("acnuc");
-if(p == NULL) return badracnuc;
-err = raa_decode_address(p, &serveurName, &port, &db_name);
-if(err) return badracnuc;
-err = raa_acnucopen_alt (serveurName, port, db_name, clientid, psock);
-return err;
+ if ( (p = getenv("racnuc")) == NULL)
+ p = getenv("acnuc");
+ if (p == NULL)
+ return badracnuc;
+ err = raa_decode_address(p, &serveurName, &port, &db_name);
+ if (err)
+ return badracnuc;
+ err = raa_acnucopen_alt (serveurName, port, db_name, clientid, psock);
+ free(serveurName);
+ if (db_name)
+ free(db_name);
+ return err;
}
-int raa_acnucopen_alt (char *serveurName, int port, char *db_name, char *clientid, raa_db_access **p)
+int raa_acnucopen_alt (const char* serveurName, int port, const char* db_name, const char* clientid, raa_db_access** p)
/*
-clientid: NULL or a string identifying the client
-*/
-{
-int err;
-
- err = raa_open_socket(serveurName, port, clientid, p);
- if(err != 0) return err;
- err = raa_opendb(*p, db_name);
- if(err != 0) {
- list_open_dbs_remove(*p);
- }
- return err;
- }
-
-
-int raa_open_socket(char *serveurName, int port, char *clientid, raa_db_access **psock)
+ clientid: NULL or a string identifying the client
+ */
+{
+ int err;
+
+ err = raa_open_socket(serveurName, port, clientid, p);
+ if (err != 0)
+ return err;
+ err = raa_opendb(*p, db_name);
+ if (err != 0)
+ {
+ free(*p);
+ }
+ return err;
+}
+
+
+int raa_open_socket(const char* serveurName, int port, const char* clientid, raa_db_access** psock)
/*
-clientid: NULL or a string identifying the client
-*/
+ clientid: NULL or a string identifying the client
+ */
{
- raa_db_access *raa_current_db;
- struct addrinfo *ai;
- char *reponse, portstring[10];
+ raa_db_access* raa_current_db;
+ struct addrinfo* ai;
+ char* reponse, portstring[10];
int err;
#ifdef WIN32
-WSADATA mywsadata;
-SOCKET raa_snum;
+ WSADATA mywsadata;
+ SOCKET raa_snum;
#else
-int raa_snum;
+ int raa_snum;
#endif
-raa_current_db = init_raa_db_access();
-if(raa_current_db == NULL) return nomemory; /* not enough memory */
+ raa_current_db = (raa_db_access*)calloc(1, sizeof(raa_db_access));
+ if (raa_current_db == NULL)
+ return nomemory; /* not enough memory */
/* cr�ation de la socket */
#ifdef WIN32
- err = WSAStartup(MAKEWORD(2,2), &mywsadata); /* indispensable avant utilisation socket */
- if (err == 0) raa_snum = WSASocket(AF_INET, SOCK_STREAM, IPPROTO_TCP, NULL, (GROUP)0, 0);
- if (err != 0 || raa_snum == INVALID_SOCKET) {
- list_open_dbs_remove(raa_current_db);
- return cantopensocket;
- }
+ err = WSAStartup(MAKEWORD(2, 2), &mywsadata); /* indispensable avant utilisation socket */
+ if (err == 0)
+ raa_snum = WSASocket(AF_INET, SOCK_STREAM, IPPROTO_TCP, NULL, (GROUP)0, 0);
+ if (err != 0 || raa_snum == INVALID_SOCKET)
+ {
+ free(raa_current_db);
+ return cantopensocket;
+ }
#else
raa_snum = socket(AF_INET, SOCK_STREAM, 0);
- if (raa_snum == -1) {
- list_open_dbs_remove(raa_current_db);
- return cantopensocket;
- }
+ if (raa_snum == -1)
+ {
+ free(raa_current_db);
+ return cantopensocket;
+ }
#endif
/* cr�ation de deux flux type FILE * */
#if defined(WIN32)
-raa_current_db->raa_sockfdr = (FILE *)raa_snum;
-raa_current_db->raa_sockfdw = (FILE *)raa_snum;
+ raa_current_db->raa_sockfdr = (FILE*)raa_snum;
+ raa_current_db->raa_sockfdw = (FILE*)raa_snum;
#else
-raa_current_db->raa_sockfdr = fdopen(raa_snum,"r");
-raa_current_db->raa_sockfdw = fdopen(raa_snum,"a");
+ raa_current_db->raa_sockfdr = fdopen(raa_snum, "r");
+ raa_current_db->raa_sockfdw = fdopen(raa_snum, "a");
#endif
sprintf(portstring, "%d", port);
err = getaddrinfo(serveurName, portstring, NULL, &ai);
- if (err) {
- list_open_dbs_remove(raa_current_db);
+ if (err)
+ {
+ free(raa_current_db);
return errservname;
- }
+ }
err = connect(raa_snum, ai->ai_addr, ai->ai_addrlen);
- freeaddrinfo(ai);
-
- if (err != 0) {
- list_open_dbs_remove(raa_current_db);
- return cantopensocket;
- }
+ freeaddrinfo(ai);
+
+ if (err != 0)
+ {
+ free(raa_current_db);
+ return cantopensocket;
+ }
// read first reply from the server
- reponse = read_sock_timeout(raa_current_db, 1000*60 /* 1 min */);
- if(reponse == NULL || strcmp(reponse, "OK acnuc socket started") != 0) {
- list_open_dbs_remove(raa_current_db);
- return cantopensocket;
- }
- if(clientid != NULL) {
- sock_printf(raa_current_db, "clientid&id=\"%s\"\n", clientid);
- reponse=read_sock(raa_current_db);
- if(reponse == NULL) {
- list_open_dbs_remove(raa_current_db);
- return cantopensocket;
- }
- }
-*psock = raa_current_db;
- return 0;
-}
-
-
-extern void raa_MD5String (char *in_string, char out_digest[33]);
-
-int raa_opendb_pw(raa_db_access *raa_current_db, char *db_name, void *ptr, char *(*getpasswordf)(void *) )
+ reponse = read_sock_timeout(raa_current_db, 1000 * 60 /* 1 min */);
+ if (reponse == NULL || strcmp(reponse, "OK acnuc socket started") != 0)
+ {
+ free(raa_current_db);
+ return cantopensocket;
+ }
+ if (clientid != NULL)
+ {
+ sock_printf(raa_current_db, "clientid&id=\"%s\"\n", clientid);
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ {
+ free(raa_current_db);
+ return cantopensocket;
+ }
+ }
+ *psock = raa_current_db;
+ return 0;
+}
+
+
+extern void raa_MD5String (char* in_string, char out_digest[33]);
+
+int raa_opendb_pw(raa_db_access* raa_current_db, const char* db_name, void* ptr, char*(*getpasswordf)(void*) )
/*
-getpasswordf: pointer to function that gets called if a password is needed
-ptr: pointer to data passed to the getpasswordf function
-return values :
+ getpasswordf: pointer to function that gets called if a password is needed
+ ptr: pointer to data passed to the getpasswordf function
+ return values :
3 not in list of known dbs
4 db is unavailable
5 a db is already open
6 failed password-based authorization
-*/
-{
-Reponse *rep;
-char *reponse, *code, *p, *challenge;
-int codret, totspecs, totkeys;
-
-if(raa_current_db == NULL) return nosocket;
- sock_printf(raa_current_db, "acnucopen&db=%s\n", db_name);
- reponse=read_sock(raa_current_db);
- if(reponse == NULL) return nosocket;
- rep=initreponse();
- parse(reponse,rep);
- code=val(rep,"code");
- codret=atoi(code);
- free(code);
- if(codret == 6) {
- static char reply[33], tmp[300];
- char *password = NULL;
- clear_reponse(rep);
- if(getpasswordf != NULL) password = getpasswordf(ptr);
- if(password == NULL) return badpsswd;
- challenge = reponse + 17;
- /* reply = MD5 of challenge:db_name:MD5(password) */
- raa_MD5String(password, reply);
- memset(password, 0, strlen(password));
- sprintf(tmp, "%s:%s:%s", challenge, db_name, reply);
- raa_MD5String(tmp, reply);
- memset(tmp, 0, strlen(tmp));
- sock_printf(raa_current_db, "reply=%s\n", reply);
- reponse = read_sock(raa_current_db);
- rep=initreponse();
- parse(reponse,rep);
- code=val(rep,"code");
- codret=atoi(code);
- free(code);
- }
-if (codret != 0) {
- clear_reponse(rep);
- return codret;
- }
-
-p = val(rep,"type");
-raa_current_db->dbname = strdup(db_name);
-raa_current_db->genbank = raa_current_db->embl = raa_current_db->swissprot =
- raa_current_db->nbrf = FALSE;
-if(p != NULL) {
- if(strcmp(p, "GENBANK") == 0) raa_current_db->genbank = TRUE;
- else if(strcmp(p, "EMBL") == 0) raa_current_db->embl = TRUE;
- else if(strcmp(p, "SWISSPROT") == 0) raa_current_db->swissprot = TRUE;
- else if(strcmp(p, "NBRF") == 0) raa_current_db->nbrf = TRUE;
- free(p);
- }
-p = val(rep,"totseqs");
-raa_current_db->nseq = atoi(p);
-free(p);
-p = val(rep,"totspecs");
-totspecs = atoi(p);
-free(p);
-p = val(rep,"totkeys");
-totkeys = atoi(p);
-free(p);
-raa_current_db->maxa=(totspecs > totkeys ? totspecs : totkeys);
-raa_current_db->longa=(raa_current_db->maxa-1)/(8 * sizeof(int))+1;
+ */
+{
+ Reponse* rep;
+ char* reponse, * code, * p, * challenge;
+ int codret, totspecs, totkeys, i;
-/* default values useful if talking to old server */
- raa_current_db->WIDTH_SMJ = 20;
- raa_current_db->L_MNEMO = 16;
- raa_current_db->WIDTH_BIB = 40;
- raa_current_db->WIDTH_AUT = 20;
- raa_current_db->WIDTH_SP = 40;
- raa_current_db->WIDTH_KW = 40;
- raa_current_db->lrtxt = 60;
- raa_current_db->SUBINLNG=63;
- raa_current_db->ACC_LENGTH=13; /* conservative value */
-p = val(rep,"L_MNEMO");
-if(p != NULL) { raa_current_db->L_MNEMO = atoi(p); free(p); }
-p = val(rep,"WIDTH_SP");
-if(p != NULL) { raa_current_db->WIDTH_SP = atoi(p); free(p); }
-p = val(rep,"WIDTH_KW");
-if(p != NULL) { raa_current_db->WIDTH_KW = atoi(p); free(p); }
-p = val(rep,"WIDTH_AUT");
-if(p != NULL) { raa_current_db->WIDTH_AUT = atoi(p); free(p); }
-p = val(rep,"WIDTH_BIB");
-if(p != NULL) { raa_current_db->WIDTH_BIB = atoi(p); free(p); }
-p = val(rep,"WIDTH_SMJ");
-if(p != NULL) { raa_current_db->WIDTH_SMJ = atoi(p); free(p); }
-p = val(rep,"ACC_LENGTH");
-if(p != NULL) { raa_current_db->ACC_LENGTH = atoi(p); free(p); }
-p = val(rep,"lrtxt");
-if(p != NULL) { raa_current_db->lrtxt = atoi(p); free(p); }
-p = val(rep,"SUBINLNG");
-if(p != NULL) {
- raa_current_db->SUBINLNG = atoi(p);
- free(p);
- raa_current_db->rlng_buffer = (struct rlng *)realloc(raa_current_db->rlng_buffer,
- (raa_current_db->SUBINLNG + 1) * sizeof(int));
- }
-
-clear_reponse(rep);
-return 0;
-}
-
-
-int raa_opendb(raa_db_access *raa_current_db, char *db_name)
-{
-return raa_opendb_pw(raa_current_db, db_name, NULL, NULL);
-}
-
-
-int raa_decode_address(char *url, char **p_ip_name, int *socket, char **p_remote_db)
-/* decode syntax such as raa://pbil.univ-lyon1.fr:5557/embl
-return !=0 if error
-*/
-{
-char *p, *q;
-static char ip_name[200];
-static char remote_db[100];
-
-p = url;
-if(p == NULL) return 1;
-if( (q = strstr(url, "://") ) != NULL ) p = q + 3;
-q = strchr(p, ':');
-if(q == NULL) return 1;
-memcpy(ip_name, p, q - p); ip_name[q - p] = 0;
-if(p_ip_name != NULL) *p_ip_name = ip_name;
-if(socket != NULL) *socket = atoi(q+1);
-if(p_remote_db == NULL) return 0;
-q = strchr(p, '/');
-if(q != NULL) {
- q++;
- while(*q == ' ') q++;
- if(*q == 0) *p_remote_db = NULL;
- else {
- strcpy(remote_db, q);
- *p_remote_db = remote_db;
- }
- }
-else *p_remote_db = NULL;
-return 0;
-}
-
-
-#define maxSUBINLNG 512
-static raa_db_access *init_raa_db_access(void)
-{
-raa_db_access *data;
-struct chain_void *elt;
-
-data = (raa_db_access *)calloc(1, sizeof(raa_db_access));
-elt = (struct chain_void *)malloc(sizeof(struct chain_void));
-if(data == NULL || elt == NULL) return NULL;
-data->rlng_buffer = (struct rlng *)malloc((maxSUBINLNG+1)*sizeof(int));
-if(data->rlng_buffer == NULL) return NULL;
-/* ajouter un elt a liste ds db ouvertes */
-elt->data = data;
-elt->next = raa_list_open_dbs;
-raa_list_open_dbs = elt;
-
-/* initialiser les champs non nuls */
-data->gfrag_data.l_nseq_buf = INT_MAX;
-data->nextelt_data.current_rank = -1;
-data->nextelt_data.previous = -2;
-data->readshrt_data.shrt_begin = S_BUF_SHRT - 1;
+ if (raa_current_db == NULL)
+ return nosocket;
+ sock_printf(raa_current_db, "acnucopen&db=%s\n", db_name);
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ return nosocket;
+ rep = initreponse();
+ parse(reponse, rep);
+ code = val(rep, "code");
+ codret = atoi(code);
+ free(code);
+ if (codret == 6)
+ {
+ char reply[33], tmp[300];
+ char* password = NULL;
+ clear_reponse(rep);
+ if (getpasswordf != NULL)
+ password = getpasswordf(ptr);
+ if (password == NULL)
+ return badpsswd;
+ challenge = reponse + 17;
+ /* reply = MD5 of challenge:db_name:MD5(password) */
+ raa_MD5String(password, reply);
+ memset(password, 0, strlen(password));
+ sprintf(tmp, "%s:%s:%s", challenge, db_name, reply);
+ raa_MD5String(tmp, reply);
+ memset(tmp, 0, strlen(tmp));
+ sock_printf(raa_current_db, "reply=%s\n", reply);
+ reponse = read_sock(raa_current_db);
+ rep = initreponse();
+ parse(reponse, rep);
+ code = val(rep, "code");
+ codret = atoi(code);
+ free(code);
+ }
+ if (codret != 0)
+ {
+ clear_reponse(rep);
+ return codret;
+ }
+
+ /* initialiser les champs non nuls */
+ raa_current_db->gfrag_data.l_nseq_buf = INT_MAX;
+ raa_current_db->nextelt_data.current_rank = -1;
+ raa_current_db->nextelt_data.previous = -2;
+ raa_current_db->readshrt_data.shrt_begin = S_BUF_SHRT - 1;
#ifdef WIN32
-data->sock_input_pos = data->sock_input; data->sock_input_end = data->sock_input;
+ raa_current_db->sock_input_pos = raa_current_db->sock_input; raa_current_db->sock_input_end = raa_current_db->sock_input;
#endif
-return data;
+ p = val(rep, "type");
+ raa_current_db->dbname = strdup(db_name);
+ raa_current_db->genbank = raa_current_db->embl = raa_current_db->swissprot =
+ raa_current_db->nbrf = FALSE;
+ if (p != NULL)
+ {
+ if (strcmp(p, "GENBANK") == 0)
+ raa_current_db->genbank = TRUE;
+ else if (strcmp(p, "EMBL") == 0)
+ raa_current_db->embl = TRUE;
+ else if (strcmp(p, "SWISSPROT") == 0)
+ raa_current_db->swissprot = TRUE;
+ else if (strcmp(p, "NBRF") == 0)
+ raa_current_db->nbrf = TRUE;
+ free(p);
+ }
+ p = val(rep, "totseqs");
+ raa_current_db->nseq = atoi(p);
+ free(p);
+ p = val(rep, "totspecs");
+ totspecs = atoi(p);
+ free(p);
+ p = val(rep, "totkeys");
+ totkeys = atoi(p);
+ free(p);
+ raa_current_db->maxa = (totspecs > totkeys ? totspecs : totkeys);
+ raa_current_db->longa = (raa_current_db->maxa - 1) / (8 * sizeof(int)) + 1;
+
+/* default values useful if talking to old server */
+ raa_current_db->WIDTH_SMJ = 20;
+ raa_current_db->L_MNEMO = 16;
+ raa_current_db->WIDTH_BIB = 40;
+ raa_current_db->WIDTH_AUT = 20;
+ raa_current_db->WIDTH_SP = 40;
+ raa_current_db->WIDTH_KW = 40;
+ raa_current_db->lrtxt = 60;
+ raa_current_db->SUBINLNG = 63;
+ raa_current_db->VALINSHRT2 = 0;
+ raa_current_db->ACC_LENGTH = 13; /* conservative value */
+ p = val(rep, "L_MNEMO");
+ if (p != NULL)
+ {
+ raa_current_db->L_MNEMO = atoi(p); free(p);
+ }
+ p = val(rep, "WIDTH_SP");
+ if (p != NULL)
+ {
+ raa_current_db->WIDTH_SP = atoi(p); free(p);
+ }
+ p = val(rep, "WIDTH_KW");
+ if (p != NULL)
+ {
+ raa_current_db->WIDTH_KW = atoi(p); free(p);
+ }
+ p = val(rep, "WIDTH_AUT");
+ if (p != NULL)
+ {
+ raa_current_db->WIDTH_AUT = atoi(p); free(p);
+ }
+ p = val(rep, "WIDTH_BIB");
+ if (p != NULL)
+ {
+ raa_current_db->WIDTH_BIB = atoi(p); free(p);
+ }
+ p = val(rep, "WIDTH_SMJ");
+ if (p != NULL)
+ {
+ raa_current_db->WIDTH_SMJ = atoi(p); free(p);
+ }
+ p = val(rep, "ACC_LENGTH");
+ if (p != NULL)
+ {
+ raa_current_db->ACC_LENGTH = atoi(p); free(p);
+ }
+ p = val(rep, "lrtxt");
+ if (p != NULL)
+ {
+ raa_current_db->lrtxt = atoi(p); free(p);
+ }
+ p = val(rep, "SUBINLNG");
+ if (p != NULL)
+ {
+ raa_current_db->SUBINLNG = atoi(p);
+ free(p);
+ raa_current_db->rlng_buffer = (struct rlng*)calloc((raa_current_db->SUBINLNG + 1), sizeof(int));
+ }
+ p = val(rep, "VALINSHRT2");
+ if (p != NULL)
+ {
+ raa_current_db->VALINSHRT2 = atoi(p); free(p);
+ }
+ if (raa_current_db->VALINSHRT2)
+ {
+ for (i = raa_sub_of_bib; i <= raa_acc_of_loc; i++)
+ {
+ int size = 100 * raa_current_db->VALINSHRT2;
+ raa_current_db->readshrt2_data[i] = (struct shrt2_list*)malloc(sizeof(int) * (size + 4));
+ raa_current_db->readshrt2_data[i]->size = size;
+ raa_current_db->readshrt2_data[i]->length = 0;
+ raa_current_db->readshrt2_data[i]->point = 0;
+ raa_current_db->readshrt2_data[i]->next = 0;
+ }
+ }
+
+ clear_reponse(rep);
+ return 0;
+}
+
+
+int raa_opendb(raa_db_access* raa_current_db, const char* db_name)
+{
+ return raa_opendb_pw(raa_current_db, db_name, NULL, NULL);
+}
+
+
+int raa_decode_address(char* url, char** p_ip_name, int* socket, char** p_remote_db)
+/* decode syntax such as raa://pbil.univ-lyon1.fr:5557/embl
+ return !=0 if error
+ */
+{
+ char* p, * q;
+ char* ip_name;
+ char* remote_db;
+
+ p = url;
+ if (p == NULL)
+ return 1;
+ if ( (q = strstr(url, "://") ) != NULL)
+ p = q + 3;
+ q = strchr(p, ':');
+ if (q == NULL)
+ return 1;
+ ip_name = (char*)malloc(q - p + 1);
+ memcpy(ip_name, p, q - p); ip_name[q - p] = 0;
+ if (p_ip_name != NULL)
+ *p_ip_name = ip_name;
+ if (socket != NULL)
+ *socket = atoi(q + 1);
+ if (p_remote_db == NULL)
+ return 0;
+ q = strchr(p, '/');
+ if (q != NULL)
+ {
+ q++;
+ while (*q == ' ')
+ q++;
+ if (*q == 0)
+ *p_remote_db = NULL;
+ else
+ {
+ remote_db = strdup(q);
+ *p_remote_db = remote_db;
+ }
+ }
+ else
+ *p_remote_db = NULL;
+ return 0;
}
-static int fill_gfrag_buf(raa_db_access *raa_current_db, int nsub, int first)
+static int fill_gfrag_buf(raa_db_access* raa_current_db, int nsub, int first)
{
-char *p, *line;
-int lu, l, length, wasfull;
+ char* p, * line;
+ int lu, l, wasfull;
-sock_printf(raa_current_db,"gfrag&number=%d&start=%d&length=%d\n", nsub, first, RAA_GFRAG_BSIZE);
+ sock_printf(raa_current_db, "gfrag&number=%d&start=%d&length=%d\n", nsub, first, RAA_GFRAG_BSIZE);
/* retour: length=xx&...the seq...\n */
-line = read_sock_tell(raa_current_db, &wasfull);
-if(line == NULL) return 0;
-if(strncmp(line, "length=", 7) != 0 || (p = strchr(line, '&')) == NULL ) {
- return 0;
- }
-length = atoi(line + 7);
-lu = strlen(++p);
-memcpy(raa_current_db->gfrag_data.buffer, p, lu);
-while(! wasfull) {
- line = read_sock_tell(raa_current_db, &wasfull);
- if(line == NULL) break;
- l = strlen(line);
- if(lu+l <= RAA_GFRAG_BSIZE) memcpy(raa_current_db->gfrag_data.buffer + lu, line, l);
- lu += l;
- }
-raa_current_db->gfrag_data.buffer[lu] = 0;
-return lu;
-}
-
-
-
-int raa_gfrag(raa_db_access *raa_current_db, int nsub, int first, int lfrag, char *dseq)
-{
-int lu, piece;
-char *debut;
-
-if(raa_current_db == NULL) return 0;
-if(raa_current_db->gfrag_data.lbuf == 0 || nsub != raa_current_db->gfrag_data.nseq_buf ||
- first >= raa_current_db->gfrag_data.first_buf + raa_current_db->gfrag_data.lbuf ||
- first < raa_current_db->gfrag_data.first_buf) {
- if( nsub == raa_current_db->gfrag_data.nseq_buf && first > raa_current_db->gfrag_data.l_nseq_buf)
- lu = 0;
- else
- lu = fill_gfrag_buf(raa_current_db, nsub, first);
-
- if(lu == 0) return 0;
- raa_current_db->gfrag_data.lbuf = lu;
- if(raa_current_db->gfrag_data.lbuf < RAA_GFRAG_BSIZE)
- raa_current_db->gfrag_data.l_nseq_buf = first + raa_current_db->gfrag_data.lbuf - 1;
- else raa_current_db->gfrag_data.l_nseq_buf = INT_MAX;
- raa_current_db->gfrag_data.first_buf = first;
- raa_current_db->gfrag_data.nseq_buf = nsub;
- }
-debut = raa_current_db->gfrag_data.buffer + (first - raa_current_db->gfrag_data.first_buf);
-lu = raa_current_db->gfrag_data.lbuf + raa_current_db->gfrag_data.first_buf-1 - first+1;
-if( lu > lfrag) lu = lfrag;
-memcpy(dseq, debut, lu);
-while(lfrag > lu) {
- piece = raa_gfrag(raa_current_db, nsub, first + lu, lfrag - lu, dseq + lu);
- if(piece == 0) break;
- lu += piece;
- }
-dseq[lu] = 0;
-return lu;
-}
-
-
-void list_open_dbs_remove(raa_db_access *raa_current_db)
-/* enlever de liste des db ouvertes */
-{
-struct chain_void *elt, *elt2;
-int i;
-
-if(raa_current_db == NULL) return; /* should not happen */
-if(raa_current_db->dbname != NULL) free(raa_current_db->dbname);
-if(raa_current_db->rlng_buffer != NULL) free(raa_current_db->rlng_buffer);
-if(raa_current_db->readsub_data.name != NULL) free(raa_current_db->readsub_data.name);
-for(i = 0; i < raa_current_db->annot_data.annotcount; i++)
- free(raa_current_db->annot_data.annotline[i]);
-for(i = 0; i < BLOCK_ELTS_IN_LIST; i++) if(raa_current_db->nextelt_data.tabname[i] != NULL)
- free(raa_current_db->nextelt_data.tabname[i]);
-if(raa_current_db->readsmj_data.lastrec > 0) {
- free(raa_current_db->readsmj_data.plongs);
- for(i=2; i <= raa_current_db->readsmj_data.lastrec; i++) {
- if(raa_current_db->readsmj_data.names[i] != NULL) free(raa_current_db->readsmj_data.names[i]);
- if(raa_current_db->readsmj_data.libels[i] != NULL) free(raa_current_db->readsmj_data.libels[i]);
- }
- free(raa_current_db->readsmj_data.names); free(raa_current_db->readsmj_data.libels);
- raa_current_db->readsmj_data.lastrec = 0;
- }
-
-if(raa_list_open_dbs == NULL) return; /* should not happen */
-if(raa_list_open_dbs->data == raa_current_db) {
- elt = raa_list_open_dbs;
- raa_list_open_dbs = raa_list_open_dbs->next;
- free(elt);
- }
-else {
- elt = raa_list_open_dbs;
- while(elt->next != NULL) {
- if(elt->next->data == raa_current_db) {
- elt2 = elt->next;
- elt->next = elt2->next;
- free(elt2);
- break;
- }
- elt = elt->next;
- }
- }
-free(raa_current_db);
-}
-
-
-static void raa_free_sp_tree(raa_node *pere)
-{
-raa_node *next, *tmp_n;
-struct raa_pair *liste, *tmp_p;
-
-liste = pere->list_desc;
-while(liste != NULL) {
- tmp_p = liste->next;
- raa_free_sp_tree(liste->value);
- free(liste);
- liste = tmp_p;
- }
-next = pere->syno;
-while(next != NULL && next != pere) {
- tmp_n = next->syno;
- free(next->name);
- free(next);
- next = tmp_n;
- }
-free(pere->name);
-if(pere->libel != NULL) free(pere->libel);
-if(pere->libel_upcase != NULL) free(pere->libel_upcase);
-free(pere);
-}
-
-
-void raa_acnucclose(raa_db_access *raa_current_db) {
-char *reponse;
-int i;
-
-if(raa_current_db == NULL) return;
-
-sock_fputs(raa_current_db, "acnucclose\n");
-
-reponse=read_sock(raa_current_db);
-if(reponse != NULL) {
- sock_fputs(raa_current_db, "quit\n");
- sock_flush(raa_current_db);
- }
+ line = read_sock_tell(raa_current_db, &wasfull);
+ if (line == NULL)
+ return 0;
+ if (strncmp(line, "length=", 7) != 0 || (p = strchr(line, '&')) == NULL)
+ {
+ return 0;
+ }
+ lu = strlen(++p);
+ memcpy(raa_current_db->gfrag_data.buffer, p, lu);
+ while (!wasfull)
+ {
+ line = read_sock_tell(raa_current_db, &wasfull);
+ if (line == NULL)
+ break;
+ l = strlen(line);
+ if (lu + l <= RAA_GFRAG_BSIZE)
+ memcpy(raa_current_db->gfrag_data.buffer + lu, line, l);
+ lu += l;
+ }
+ raa_current_db->gfrag_data.buffer[lu] = 0;
+ return lu;
+}
+
+
+int raa_gfrag(raa_db_access* raa_current_db, int nsub, int first, int lfrag, char* dseq)
+{
+ int lu, piece;
+ char* debut;
+
+ if (raa_current_db == NULL)
+ return 0;
+ if (raa_current_db->gfrag_data.lbuf == 0 || nsub != raa_current_db->gfrag_data.nseq_buf ||
+ first >= raa_current_db->gfrag_data.first_buf + raa_current_db->gfrag_data.lbuf ||
+ first < raa_current_db->gfrag_data.first_buf)
+ {
+ if (nsub == raa_current_db->gfrag_data.nseq_buf && first > raa_current_db->gfrag_data.l_nseq_buf)
+ lu = 0;
+ else
+ lu = fill_gfrag_buf(raa_current_db, nsub, first);
+
+ if (lu == 0)
+ return 0;
+ raa_current_db->gfrag_data.lbuf = lu;
+ if (raa_current_db->gfrag_data.lbuf < RAA_GFRAG_BSIZE)
+ raa_current_db->gfrag_data.l_nseq_buf = first + raa_current_db->gfrag_data.lbuf - 1;
+ else
+ raa_current_db->gfrag_data.l_nseq_buf = INT_MAX;
+ raa_current_db->gfrag_data.first_buf = first;
+ raa_current_db->gfrag_data.nseq_buf = nsub;
+ }
+ debut = raa_current_db->gfrag_data.buffer + (first - raa_current_db->gfrag_data.first_buf);
+ lu = raa_current_db->gfrag_data.lbuf + raa_current_db->gfrag_data.first_buf - 1 - first + 1;
+ if (lu > lfrag)
+ lu = lfrag;
+ memcpy(dseq, debut, lu);
+ while (lfrag > lu)
+ {
+ piece = raa_gfrag(raa_current_db, nsub, first + lu, lfrag - lu, dseq + lu);
+ if (piece == 0)
+ break;
+ lu += piece;
+ }
+ dseq[lu] = 0;
+ return lu;
+}
+
+
+static void raa_free_sp_tree(raa_node* pere)
+{
+ raa_node* next, * tmp_n;
+ struct raa_pair* liste, * tmp_p;
+
+ liste = pere->list_desc;
+ while (liste != NULL)
+ {
+ tmp_p = liste->next;
+ raa_free_sp_tree(liste->value);
+ free(liste);
+ liste = tmp_p;
+ }
+ next = pere->syno;
+ while (next != NULL && next != pere)
+ {
+ tmp_n = next->syno;
+ free(next->name);
+ free(next);
+ next = tmp_n;
+ }
+ free(pere->name);
+ if (pere->libel != NULL)
+ free(pere->libel);
+ if (pere->libel_upcase != NULL)
+ free(pere->libel_upcase);
+ free(pere);
+}
+
+
+void raa_acnucclose(raa_db_access* raa_current_db)
+{
+ char* reponse;
+ int i;
+
+ if (raa_current_db == NULL)
+ return;
+
+ sock_fputs(raa_current_db, "acnucclose\n");
+
+ reponse = read_sock(raa_current_db);
+ if (reponse != NULL)
+ {
+ sock_fputs(raa_current_db, "quit\n");
+ sock_flush(raa_current_db);
+ }
#ifdef WIN32
closesocket( (SOCKET) (raa_current_db->raa_sockfdw) );
#else
@@ -722,2371 +772,2901 @@ if(reponse != NULL) {
fclose(raa_current_db->raa_sockfdw);
#endif
-if(raa_current_db->tot_key_annots > 0) {
- for(i = 0; i < raa_current_db->tot_key_annots; i++) {
- free(raa_current_db->key_annots[i]);
- free(raa_current_db->key_annots_min[i]);
- }
- free(raa_current_db->key_annots);
- free(raa_current_db->key_annots_min);
- free(raa_current_db->want_key_annots);
- raa_current_db->tot_key_annots = 0;
- }
-if(raa_current_db->tid_to_rank != NULL) free(raa_current_db->tid_to_rank);
-if(raa_current_db->sp_tree != NULL) {
- raa_free_sp_tree(raa_current_db->sp_tree[2]);
- free(raa_current_db->sp_tree);
- }
+ if (raa_current_db->tot_key_annots > 0)
+ {
+ for (i = 0; i < raa_current_db->tot_key_annots; i++)
+ {
+ free(raa_current_db->key_annots[i]);
+ free(raa_current_db->key_annots_min[i]);
+ }
+ free(raa_current_db->key_annots);
+ free(raa_current_db->key_annots_min);
+ free(raa_current_db->want_key_annots);
+ raa_current_db->tot_key_annots = 0;
+ }
+ if (raa_current_db->tid_to_rank != NULL)
+ free(raa_current_db->tid_to_rank);
+ if (raa_current_db->sp_tree != NULL)
+ {
+ raa_free_sp_tree(raa_current_db->sp_tree[2]);
+ free(raa_current_db->sp_tree);
+ }
+ if (raa_current_db->dbname != NULL)
+ free(raa_current_db->dbname);
+ if (raa_current_db->rlng_buffer != NULL)
+ free(raa_current_db->rlng_buffer);
+ if (raa_current_db->readsub_data.name != NULL)
+ free(raa_current_db->readsub_data.name);
+ for (i = 0; i < raa_current_db->annot_data.annotcount; i++)
+ {
+ free(raa_current_db->annot_data.annotline[i]);
+ }
+ for (i = 0; i < BLOCK_ELTS_IN_LIST; i++)
+ {
+ if (raa_current_db->nextelt_data.tabname[i] != NULL)
+ free(raa_current_db->nextelt_data.tabname[i]);
+ }
+ if (raa_current_db->readsmj_data.lastrec > 0)
+ {
+ free(raa_current_db->readsmj_data.plongs);
+ for (i = 2; i <= raa_current_db->readsmj_data.lastrec; i++)
+ {
+ if (raa_current_db->readsmj_data.names[i] != NULL)
+ free(raa_current_db->readsmj_data.names[i]);
+ if (raa_current_db->readsmj_data.libels[i] != NULL)
+ free(raa_current_db->readsmj_data.libels[i]);
+ }
+ free(raa_current_db->readsmj_data.names); free(raa_current_db->readsmj_data.libels);
+ raa_current_db->readsmj_data.lastrec = 0;
+ }
+ raa_free_matchkeys(raa_current_db);
+ if (raa_current_db->full_line)
+ free(raa_current_db->full_line);
+ if (raa_current_db->namestr)
+ free(raa_current_db->namestr);
+ if (raa_current_db->help)
+ free(raa_current_db->help);
+ if (raa_current_db->tmp_prelist)
+ free(raa_current_db->tmp_prelist);
+ if (raa_current_db->translate_buffer)
+ free(raa_current_db->translate_buffer);
-list_open_dbs_remove(raa_current_db);
+ free(raa_current_db);
}
-int raa_prep_acnuc_query(raa_db_access *raa_current_db) {
+int raa_prep_acnuc_query(raa_db_access* raa_current_db)
+{
/* returns -1 if error or number of free bit lists
-*/
- char *reponse, *p, *q, *annotlines;
+ */
+ char* reponse, * p, * q, * annotlines;
int codret, i;
- Reponse *rep;
+ Reponse* rep;
-if(raa_current_db == NULL) return -1;
+ if (raa_current_db == NULL)
+ return -1;
rep = initreponse();
sock_fputs(raa_current_db, "countfreelists\n");
- reponse=read_sock(raa_current_db);
-if(reponse == NULL) return -1;
- parse(reponse,rep);
- reponse=val(rep,"code");
- if(reponse == NULL) return -1;
- codret=atoi(reponse);
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ return -1;
+ parse(reponse, rep);
+ reponse = val(rep, "code");
+ if (reponse == NULL)
+ return -1;
+ codret = atoi(reponse);
free(reponse);
- if(codret != 0) return -1;
- reponse=val(rep,"free");
- if(reponse != NULL) {
- codret = atoi(reponse);
- free(reponse);
- }
-annotlines = val(rep, "annotlines");
-raa_current_db->tot_key_annots = 0;
-if(annotlines != NULL) {
- p = annotlines - 1;
- do {
- p++;
- raa_current_db->tot_key_annots++;
- }
- while((p = strchr(p, '|')) != NULL);
- raa_current_db->want_key_annots = (unsigned char *)malloc(raa_current_db->tot_key_annots *
- sizeof(unsigned char));
- raa_current_db->key_annots = (char **)malloc(raa_current_db->tot_key_annots * sizeof(char *));
- raa_current_db->key_annots_min = (char **)malloc(raa_current_db->tot_key_annots * sizeof(char *));
- p = annotlines;
- for(i = 0; i < raa_current_db->tot_key_annots; i++) {
- q = strchr(p, '|');
- if(q == NULL) q = p + strlen(p);
- raa_current_db->key_annots[i] = malloc(q - p + 1);
- raa_current_db->key_annots_min[i] = malloc(q - p + 1);
- memcpy(raa_current_db->key_annots_min[i], p, q - p);
- raa_current_db->key_annots_min[i][q - p] = 0;
- strcpy(raa_current_db->key_annots[i], raa_current_db->key_annots_min[i]);
- majuscules(raa_current_db->key_annots[i]);
- compact(raa_current_db->key_annots[i]);
- p = q + 1;
- }
- free(annotlines);
- }
-else codret = -1;
+ if (codret != 0)
+ return -1;
+ reponse = val(rep, "free");
+ if (reponse != NULL)
+ {
+ codret = atoi(reponse);
+ free(reponse);
+ }
+ annotlines = val(rep, "annotlines");
+ raa_current_db->tot_key_annots = 0;
+ if (annotlines != NULL)
+ {
+ p = annotlines - 1;
+ do
+ {
+ p++;
+ raa_current_db->tot_key_annots++;
+ }
+ while ((p = strchr(p, '|')) != NULL);
+ raa_current_db->want_key_annots = (unsigned char*)malloc(raa_current_db->tot_key_annots *
+ sizeof(unsigned char));
+ raa_current_db->key_annots = (char**)malloc(raa_current_db->tot_key_annots * sizeof(char*));
+ raa_current_db->key_annots_min = (char**)malloc(raa_current_db->tot_key_annots * sizeof(char*));
+ p = annotlines;
+ for (i = 0; i < raa_current_db->tot_key_annots; i++)
+ {
+ q = strchr(p, '|');
+ if (q == NULL)
+ q = p + strlen(p);
+ raa_current_db->key_annots[i] = malloc(q - p + 1);
+ raa_current_db->key_annots_min[i] = malloc(q - p + 1);
+ memcpy(raa_current_db->key_annots_min[i], p, q - p);
+ raa_current_db->key_annots_min[i][q - p] = 0;
+ strcpy(raa_current_db->key_annots[i], raa_current_db->key_annots_min[i]);
+ majuscules(raa_current_db->key_annots[i]);
+ compact(raa_current_db->key_annots[i]);
+ p = q + 1;
+ }
+ free(annotlines);
+ }
+ else
+ codret = -1;
clear_reponse(rep);
return codret;
}
-static char *raa_requete_remote_file(raa_db_access *raa_current_db, char *oldrequete, int **plist, char **);
+static char* raa_requete_remote_file(raa_db_access* raa_current_db, char* oldrequete, int** plist, char**);
+
+int raa_proc_query(raa_db_access* raa_current_db, char* requete, char** message,
+ char* nomliste, int* numlist, int* count, int* locus, int* type)
+{
+ char* reponse, * code, * numlistchr, * countchr, * locuschr, * typechr, * badfname, * p;
+ int codret, * tmp_blists;
+ Reponse* rep;
-int raa_proc_query(raa_db_access *raa_current_db, char *requete, char **message,
- char *nomliste, int *numlist, int *count, int *locus, int *type) {
- char *reponse, *code, *numlistchr, *countchr, *locuschr, *typechr, *badfname;
- int codret, *tmp_blists;
- Reponse *rep;
-
-if(raa_current_db == NULL) return -1;
+ if (raa_current_db == NULL)
+ return -1;
requete = raa_requete_remote_file(raa_current_db, requete, &tmp_blists, &badfname);
- if(requete == NULL) {
- if(message != NULL) {
- static char fmt[] = "problem accessing file: %s";
- *message = (char *)malloc(strlen(fmt) + strlen(badfname) + 1);
- sprintf(*message, fmt, badfname);
- }
- return 1;
- }
- sock_printf(raa_current_db,"proc_query&query=\"%s\"&name=\"%s\"\n",
- protect_quotes(requete), nomliste);
+ if (requete == NULL)
+ {
+ if (message != NULL)
+ {
+ char fmt[] = "problem accessing file: %s";
+ *message = (char*)malloc(strlen(fmt) + strlen(badfname) + 1);
+ sprintf(*message, fmt, badfname);
+ }
+ return 1;
+ }
+ p = protect_quotes(requete);
+ sock_printf(raa_current_db, "proc_query&query=\"%s\"&name=\"%s\"\n", p, nomliste);
+ free(p);
free(requete);
- reponse=read_sock(raa_current_db);
- if(reponse == NULL) {
- if(message != NULL) *message = strdup("connection with server is down");
- return -1;
- }
- rep=initreponse();
- parse(reponse,rep);
- code=val(rep,"code");
- codret=atoi(code);
- if(codret == 0) {
- numlistchr=val(rep,"lrank");
- *numlist=atoi(numlistchr);
- countchr=val(rep,"count");
- if(count != NULL) *count=atoi(countchr);
- typechr=val(rep,"type");
- locuschr=val(rep,"locus");
- if(type != NULL) {
- if (strcmp(typechr,"SQ")==0) *type='S';
- else if (strcmp(typechr,"KW")==0) *type='K';
- else if (strcmp(typechr,"SP")==0) *type='E';
- }
- if(locus != NULL) *locus = strcmp(locuschr,"T") == 0;
- free(countchr);
- free(locuschr);
- free(typechr);
- free(numlistchr);
- }
- else if(message != NULL) {
- *message = val(rep, "message");
- }
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ {
+ if (message != NULL)
+ *message = strdup("connection with server is down");
+ return -1;
+ }
+ rep = initreponse();
+ parse(reponse, rep);
+ code = val(rep, "code");
+ codret = atoi(code);
+ if (codret == 0)
+ {
+ numlistchr = val(rep, "lrank");
+ *numlist = atoi(numlistchr);
+ countchr = val(rep, "count");
+ if (count != NULL)
+ *count = atoi(countchr);
+ typechr = val(rep, "type");
+ locuschr = val(rep, "locus");
+ if (type != NULL)
+ {
+ if (strcmp(typechr, "SQ") == 0)
+ *type = 'S';
+ else if (strcmp(typechr, "KW") == 0)
+ *type = 'K';
+ else if (strcmp(typechr, "SP") == 0)
+ *type = 'E';
+ }
+ if (locus != NULL)
+ *locus = strcmp(locuschr, "T") == 0;
+ free(countchr);
+ free(locuschr);
+ free(typechr);
+ free(numlistchr);
+ }
+ else if (message != NULL)
+ {
+ *message = val(rep, "message");
+ }
free(code);
clear_reponse(rep);
- if(tmp_blists != NULL) {
- while(*tmp_blists != 0) raa_releaselist(raa_current_db, *(tmp_blists++) );
- }
+ if (tmp_blists != NULL)
+ {
+ while (*tmp_blists != 0)
+ raa_releaselist(raa_current_db, *(tmp_blists++) );
+ }
return codret;
}
-int raa_nexteltinlist(raa_db_access *raa_current_db, int first, int lrank, char **pname, int *plength)
+int raa_nexteltinlist(raa_db_access* raa_current_db, int first, int lrank, char** pname, int* plength)
{
-return raa_nexteltinlist_annots(raa_current_db, first, lrank, pname, plength, NULL, NULL);
+ return raa_nexteltinlist_annots(raa_current_db, first, lrank, pname, plength, NULL, NULL);
}
-int raa_nexteltinlist_annots(raa_db_access *raa_current_db, int first, int lrank, char **pname, int *plength,
- raa_long *paddr, int *pdiv)
+int raa_nexteltinlist_annots(raa_db_access* raa_current_db, int first, int lrank, char** pname, int* plength,
+ raa_long* paddr, int* pdiv)
{
-int num, next, count;
-char *p;
-Reponse *rep;
+ int num, next, count;
+ char* p;
+ Reponse* rep;
-if(raa_current_db == NULL) return 0;
-if(lrank == raa_current_db->nextelt_data.current_rank &&
- raa_current_db->nextelt_data.previous < raa_current_db->nextelt_data.total - 1 &&
- (raa_current_db->nextelt_data.previous == -1 ||
- first == raa_current_db->nextelt_data.tabnum[raa_current_db->nextelt_data.previous] ) ) {
- raa_current_db->nextelt_data.previous++;
- next = raa_current_db->nextelt_data.tabnum[raa_current_db->nextelt_data.previous];
- if(next != 0) {
- if(pname != NULL) *pname = raa_current_db->nextelt_data.tabname[raa_current_db->nextelt_data.previous];
- if(plength != NULL) *plength = raa_current_db->nextelt_data.tablength[raa_current_db->nextelt_data.previous];
- if(paddr != NULL) *paddr = raa_current_db->nextelt_data.taboffset[raa_current_db->nextelt_data.previous];
- if(pdiv != NULL) *pdiv = raa_current_db->nextelt_data.tabdiv[raa_current_db->nextelt_data.previous];
- }
- return next;
- }
+ if (raa_current_db == NULL)
+ return 0;
+ if (lrank == raa_current_db->nextelt_data.current_rank &&
+ raa_current_db->nextelt_data.previous < raa_current_db->nextelt_data.total - 1 &&
+ (raa_current_db->nextelt_data.previous == -1 ||
+ first == raa_current_db->nextelt_data.tabnum[raa_current_db->nextelt_data.previous] ) )
+ {
+ raa_current_db->nextelt_data.previous++;
+ next = raa_current_db->nextelt_data.tabnum[raa_current_db->nextelt_data.previous];
+ if (next != 0)
+ {
+ if (pname != NULL)
+ *pname = raa_current_db->nextelt_data.tabname[raa_current_db->nextelt_data.previous];
+ if (plength != NULL)
+ *plength = raa_current_db->nextelt_data.tablength[raa_current_db->nextelt_data.previous];
+ if (paddr != NULL)
+ *paddr = raa_current_db->nextelt_data.taboffset[raa_current_db->nextelt_data.previous];
+ if (pdiv != NULL)
+ *pdiv = raa_current_db->nextelt_data.tabdiv[raa_current_db->nextelt_data.previous];
+ }
+ return next;
+ }
-count = BLOCK_ELTS_IN_LIST;
-for(num = 0; num < count; num++) {
- if(raa_current_db->nextelt_data.tabname[num] != NULL) free(raa_current_db->nextelt_data.tabname[num]);
- }
-memset(raa_current_db->nextelt_data.tabname, 0, count * sizeof(char *));
-sock_printf(raa_current_db,"nexteltinlist&lrank=%d&first=%d&count=%d\n",lrank,first, count);
-num = 0; raa_current_db->nextelt_data.current_rank = lrank;
-raa_current_db->nextelt_data.total = 0;
-do {
- p = read_sock(raa_current_db);
- if(p == NULL) return 0;
- rep = initreponse();
- parse(p, rep);
- p = val(rep,"next");
- if(p == NULL) {
- clear_reponse(rep);
- return 0;
- }
- next = atoi(p);
- free(p);
- raa_current_db->nextelt_data.total++;
- raa_current_db->nextelt_data.tabnum[num] = next;
- if(next != 0) {
- raa_current_db->nextelt_data.tabname[num] = val(rep, "name");
- if( (p= val(rep, "length")) != NULL) {
- raa_current_db->nextelt_data.tablength[num] = atoi(p);
- free(p);
- }
- if((p= val(rep, "offset")) != NULL) {
- raa_current_db->nextelt_data.taboffset[num] = scan_raa_long(p);
- free(p);
- }
- if((p= val(rep, "div")) != NULL) {
- raa_current_db->nextelt_data.tabdiv[num] = atoi(p);
- free(p);
- }
- }
- clear_reponse(rep);
- num++;
+ count = BLOCK_ELTS_IN_LIST;
+ for (num = 0; num < count; num++)
+ {
+ if (raa_current_db->nextelt_data.tabname[num] != NULL)
+ free(raa_current_db->nextelt_data.tabname[num]);
+ }
+ memset(raa_current_db->nextelt_data.tabname, 0, count * sizeof(char*));
+ sock_printf(raa_current_db, "nexteltinlist&lrank=%d&first=%d&count=%d\n", lrank, first, count);
+ num = 0; raa_current_db->nextelt_data.current_rank = lrank;
+ raa_current_db->nextelt_data.total = 0;
+ do
+ {
+ p = read_sock(raa_current_db);
+ if (p == NULL)
+ return 0;
+ rep = initreponse();
+ parse(p, rep);
+ p = val(rep, "next");
+ if (p == NULL)
+ {
+ clear_reponse(rep);
+ return 0;
+ }
+ next = atoi(p);
+ free(p);
+ raa_current_db->nextelt_data.total++;
+ raa_current_db->nextelt_data.tabnum[num] = next;
+ if (next != 0)
+ {
+ raa_current_db->nextelt_data.tabname[num] = val(rep, "name");
+ if ( (p = val(rep, "length")) != NULL)
+ {
+ raa_current_db->nextelt_data.tablength[num] = atoi(p);
+ free(p);
+ }
+ if ((p = val(rep, "offset")) != NULL)
+ {
+ raa_current_db->nextelt_data.taboffset[num] = scan_raa_long(p);
+ free(p);
+ }
+ if ((p = val(rep, "div")) != NULL)
+ {
+ raa_current_db->nextelt_data.tabdiv[num] = atoi(p);
+ free(p);
+ }
+ }
+ clear_reponse(rep);
+ num++;
}
-while(next != 0 && --count > 0);
-raa_current_db->nextelt_data.previous = -1;
-return raa_nexteltinlist_annots(raa_current_db, first, lrank, pname, plength, paddr, pdiv);
+ while (next != 0 && --count > 0);
+ raa_current_db->nextelt_data.previous = -1;
+ return raa_nexteltinlist_annots(raa_current_db, first, lrank, pname, plength, paddr, pdiv);
}
-raa_long scan_raa_long(char *txt)
+raa_long scan_raa_long(char* txt)
{
-raa_long val;
+ raa_long val;
-sscanf(txt, RAA_LONG_FORMAT, &val);
-return val;
+ sscanf(txt, RAA_LONG_FORMAT, &val);
+ return val;
}
-char *print_raa_long(raa_long val)
+char* print_raa_long(raa_long val, char* buffer)
{
-static char buffer[50];
-sprintf(buffer, RAA_LONG_FORMAT, val);
-return buffer;
+ sprintf(buffer, RAA_LONG_FORMAT, val);
+ return buffer;
}
-
-
-static char *load_annots_buf(raa_db_access *raa_current_db, raa_long faddr, int div, int was_nextannots)
+static char* load_annots_buf(raa_db_access* raa_current_db, raa_long faddr, int div, int was_nextannots)
/* appeler juste apr�s avoir envoye sur socket
-read_annots&... ou next_annots&... :
-retour attendu sur socket : nl=xx[&offset=xx]&...nl lines each with \n */
+ read_annots&... ou next_annots&... :
+ retour attendu sur socket : nl=xx[&offset=xx]&...nl lines each with \n */
{
-int i, nl;
-char *firstline, *p, *q;
+ int i, nl;
+ char* firstline, * p, * q;
- if(raa_current_db == NULL) return NULL;
- for(i=0; i < raa_current_db->annot_data.annotcount; i++)
- free(raa_current_db->annot_data.annotline[i]);
+ if (raa_current_db == NULL)
+ return NULL;
+ for (i = 0; i < raa_current_db->annot_data.annotcount; i++)
+ {
+ free(raa_current_db->annot_data.annotline[i]);
+ }
raa_current_db->annot_data.annotcount = 0;
raa_current_db->annot_data.annotaddrlast = faddr;
firstline = read_sock(raa_current_db);
- if(firstline == NULL) return NULL;
- if(strncmp(firstline, "nl=", 3) != 0 || (p = strchr(firstline, '&')) == NULL ) return NULL;
+ if (firstline == NULL)
+ return NULL;
+ if (strncmp(firstline, "nl=", 3) != 0 || (p = strchr(firstline, '&')) == NULL)
+ return NULL;
nl = atoi(firstline + 3);
- if(nl == 0) return NULL;
+ if (nl == 0)
+ return NULL;
p++;
- if(was_nextannots && strncmp(p, "offset=", 7) == 0) {
- p = strchr(p, '&');
- if(p == NULL) return NULL;
- p++;
- }
+ if (was_nextannots && strncmp(p, "offset=", 7) == 0)
+ {
+ p = strchr(p, '&');
+ if (p == NULL)
+ return NULL;
+ p++;
+ }
i = strlen(p);
- raa_current_db->annot_data.annotline[0] = (char *)malloc(i+1);
+ raa_current_db->annot_data.annotline[0] = (char*)malloc(i + 1);
strcpy(raa_current_db->annot_data.annotline[0], p);
raa_current_db->annot_data.annotaddrlast += strlen(raa_current_db->annot_data.annotline[0]) + 1;
- for(i = 1; i < nl; i++) {
- q = read_sock(raa_current_db);
- if(q == NULL) return NULL;
- raa_current_db->annot_data.annotline[i] = strdup( q );
- raa_current_db->annot_data.annotaddrlast += strlen(raa_current_db->annot_data.annotline[i]) + 1;
- }
- raa_current_db->annot_data.annotcurrent = 1; raa_current_db->annot_data.annotcount = nl;
- raa_current_db->annot_data.annotaddr = faddr; raa_current_db->annot_data.annotdiv = div;
+ for (i = 1; i < nl; i++)
+ {
+ q = read_sock(raa_current_db);
+ if (q == NULL)
+ return NULL;
+ raa_current_db->annot_data.annotline[i] = strdup( q );
+ raa_current_db->annot_data.annotaddrlast += strlen(raa_current_db->annot_data.annotline[i]) + 1;
+ }
+ raa_current_db->annot_data.annotcurrent = 1; raa_current_db->annot_data.annotcount = nl;
+ raa_current_db->annot_data.annotaddr = faddr; raa_current_db->annot_data.annotdiv = div;
raa_current_db->annot_data.annotaddrfirst = faddr;
strcpy(raa_current_db->annot_data.annotsbuffer, raa_current_db->annot_data.annotline[0]);
return raa_current_db->annot_data.annotsbuffer;
}
-char *raa_read_annots(raa_db_access *raa_current_db, raa_long faddr, int div)
+char* raa_read_annots(raa_db_access* raa_current_db, raa_long faddr, int div)
{
int i;
raa_long debut;
- char *p;
-
-if(raa_current_db == NULL) return NULL;
- if(raa_current_db->annot_data.annotcount > 0 &&
- div == raa_current_db->annot_data.annotdiv &&
- faddr >= raa_current_db->annot_data.annotaddrfirst &&
- faddr < raa_current_db->annot_data.annotaddrlast ) {
- debut = raa_current_db->annot_data.annotaddrfirst;
- for(i = 1; i <= raa_current_db->annot_data.annotcount; i++) {
- if(debut == faddr) {
- raa_current_db->annot_data.annotcurrent = i;
- raa_current_db->annot_data.annotaddr = debut;
- strcpy(raa_current_db->annot_data.annotsbuffer, raa_current_db->annot_data.annotline[raa_current_db->annot_data.annotcurrent - 1]);
- return raa_current_db->annot_data.annotsbuffer;
- }
- debut += strlen(raa_current_db->annot_data.annotline[i - 1]) + 1;
- }
- }
- sock_printf(raa_current_db,"read_annots&offset=%s&div=%d&nl=%d\n",
- print_raa_long(faddr), div, ANNOTCOUNT);
+ char* p, buffer[40];
+
+ if (raa_current_db == NULL)
+ return NULL;
+ if (raa_current_db->annot_data.annotcount > 0 &&
+ div == raa_current_db->annot_data.annotdiv &&
+ faddr >= raa_current_db->annot_data.annotaddrfirst &&
+ faddr < raa_current_db->annot_data.annotaddrlast)
+ {
+ debut = raa_current_db->annot_data.annotaddrfirst;
+ for (i = 1; i <= raa_current_db->annot_data.annotcount; i++)
+ {
+ if (debut == faddr)
+ {
+ raa_current_db->annot_data.annotcurrent = i;
+ raa_current_db->annot_data.annotaddr = debut;
+ strcpy(raa_current_db->annot_data.annotsbuffer, raa_current_db->annot_data.annotline[raa_current_db->annot_data.annotcurrent - 1]);
+ return raa_current_db->annot_data.annotsbuffer;
+ }
+ debut += strlen(raa_current_db->annot_data.annotline[i - 1]) + 1;
+ }
+ }
+ sock_printf(raa_current_db, "read_annots&offset=%s&div=%d&nl=%d\n",
+ print_raa_long(faddr, buffer), div, ANNOTCOUNT);
p = load_annots_buf(raa_current_db, faddr, div, FALSE);
return p;
}
-char *raa_next_annots(raa_db_access *raa_current_db, raa_long *paddr)
+char* raa_next_annots(raa_db_access* raa_current_db, raa_long* paddr)
{
raa_long faddr;
- char *p;
-
-if(raa_current_db == NULL) return NULL;
- if(raa_current_db->annot_data.annotcurrent < raa_current_db->annot_data.annotcount) {
- raa_current_db->annot_data.annotaddr +=
- strlen(raa_current_db->annot_data.annotline[raa_current_db->annot_data.annotcurrent - 1]) + 1;
- if(paddr != NULL) *paddr = raa_current_db->annot_data.annotaddr;
- raa_current_db->annot_data.annotcurrent++;
- strcpy(raa_current_db->annot_data.annotsbuffer,
- raa_current_db->annot_data.annotline[raa_current_db->annot_data.annotcurrent - 1]);
- return raa_current_db->annot_data.annotsbuffer;
- }
+ char* p;
+
+ if (raa_current_db == NULL)
+ return NULL;
+ if (raa_current_db->annot_data.annotcurrent < raa_current_db->annot_data.annotcount)
+ {
+ raa_current_db->annot_data.annotaddr +=
+ strlen(raa_current_db->annot_data.annotline[raa_current_db->annot_data.annotcurrent - 1]) + 1;
+ if (paddr != NULL)
+ *paddr = raa_current_db->annot_data.annotaddr;
+ raa_current_db->annot_data.annotcurrent++;
+ strcpy(raa_current_db->annot_data.annotsbuffer,
+ raa_current_db->annot_data.annotline[raa_current_db->annot_data.annotcurrent - 1]);
+ return raa_current_db->annot_data.annotsbuffer;
+ }
faddr = raa_current_db->annot_data.annotaddrlast;
- if(paddr != NULL) *paddr = faddr;
+ if (paddr != NULL)
+ *paddr = faddr;
sock_printf(raa_current_db, "next_annots&nl=%d\n", ANNOTCOUNT);
p = load_annots_buf(raa_current_db, faddr, raa_current_db->annot_data.annotdiv, TRUE);
return p;
}
-int raa_iknum(raa_db_access *raa_current_db, char *name, raa_file cas)
+int raa_iknum(raa_db_access* raa_current_db, char* name, raa_file cas)
{
-char *reponse, *p;
-int val;
+ char* reponse, * p;
+ int val;
-if(raa_current_db == NULL) return 0;
- sock_printf(raa_current_db,"iknum&name=\"%s\"&type=%s\n", protect_quotes(name),
- (cas == raa_key ? "KW" : "SP") );
+ if (raa_current_db == NULL)
+ return 0;
+ p = protect_quotes(name);
+ sock_printf(raa_current_db, "iknum&name=\"%s\"&type=%s\n", p, (cas == raa_key ? "KW" : "SP") );
+ free(p);
reponse = read_sock(raa_current_db);
- if(reponse == NULL) return 0;
+ if (reponse == NULL)
+ return 0;
p = strchr(reponse, '=');
- if(p == NULL) return 0;
+ if (p == NULL)
+ return 0;
p++;
sscanf(p, "%u", &val);
return val;
}
-int raa_isenum(raa_db_access *raa_current_db, char *name)
+int raa_isenum(raa_db_access* raa_current_db, char* name)
{
-char *reponse, *p;
-int val;
+ char* reponse, * p;
+ int val;
-if(raa_current_db == NULL) return 0;
- sock_printf(raa_current_db,"isenum&name=\"%s\"\n", protect_quotes(name) );
+ if (raa_current_db == NULL)
+ return 0;
+ p = protect_quotes(name);
+ sock_printf(raa_current_db, "isenum&name=\"%s\"\n", p );
+ free(p);
reponse = read_sock(raa_current_db);
- if(reponse == NULL) return 0;
+ if (reponse == NULL)
+ return 0;
p = strchr(reponse, '=');
- if(p == NULL) return 0;
+ if (p == NULL)
+ return 0;
p++;
sscanf(p, "%u", &val);
return val;
}
-int raa_bcount(raa_db_access *raa_current_db, int lrank)
+int raa_bcount(raa_db_access* raa_current_db, int lrank)
{
- Reponse *rep;
- char *reponse, *code, *countstr;
+ Reponse* rep;
+ char* reponse, * code, * countstr;
int count = 0;
-
-if(raa_current_db == NULL) return 0;
- rep=initreponse();
- sock_printf(raa_current_db,"bcount&lrank=%d\n",lrank);
- reponse=read_sock(raa_current_db);
- if(reponse == NULL) return 0;
+
+ if (raa_current_db == NULL)
+ return 0;
+ rep = initreponse();
+ sock_printf(raa_current_db, "bcount&lrank=%d\n", lrank);
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ return 0;
parse(reponse, rep);
- code = val(rep,"code");
- if(*code == '0') {
- countstr = val(rep,"count");
- count = atoi(countstr);
- free(countstr);
- }
+ code = val(rep, "code");
+ if (*code == '0')
+ {
+ countstr = val(rep, "count");
+ count = atoi(countstr);
+ free(countstr);
+ }
free(code);
clear_reponse(rep);
return count;
}
-void raa_bit1(raa_db_access *raa_current_db, int lrank, int num)
+void raa_bit1(raa_db_access* raa_current_db, int lrank, int num)
{
-char *reponse;
-
-if(raa_current_db == NULL) return;
- sock_printf(raa_current_db,"bit1&lrank=%d&num=%d\n", lrank, num);
- reponse=read_sock(raa_current_db);
+ if (raa_current_db == NULL)
+ return;
+ sock_printf(raa_current_db, "bit1&lrank=%d&num=%d\n", lrank, num);
+ read_sock(raa_current_db); //memory leak?
}
-void raa_bit0(raa_db_access *raa_current_db, int lrank, int num)
+void raa_bit0(raa_db_access* raa_current_db, int lrank, int num)
{
-char *reponse;
-
-if(raa_current_db == NULL) return;
- sock_printf(raa_current_db,"bit0&lrank=%d&num=%d\n", lrank, num);
- reponse=read_sock(raa_current_db);
+ if (raa_current_db == NULL)
+ return;
+ sock_printf(raa_current_db, "bit0&lrank=%d&num=%d\n", lrank, num);
+ read_sock(raa_current_db); //memory leak?
}
-int raa_btest(raa_db_access *raa_current_db, int lrank, int num)
+int raa_btest(raa_db_access* raa_current_db, int lrank, int num)
{
-char *reponse;
-
-if(raa_current_db == NULL) return 0;
- sock_printf(raa_current_db,"btest&lrank=%d&num=%d\n", lrank, num);
- reponse=read_sock(raa_current_db);
- if(reponse == NULL) return 0;
+ if (raa_current_db == NULL)
+ return 0;
+ sock_printf(raa_current_db, "btest&lrank=%d&num=%d\n", lrank, num);
+ char* reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ return 0;
return strcmp(reponse, "code=0&on") == 0;
}
-void raa_copylist(raa_db_access *raa_current_db, int from, int to)
+void raa_copylist(raa_db_access* raa_current_db, int from, int to)
{
-char *reponse;
-
-if(raa_current_db == NULL) return;
- sock_printf(raa_current_db,"copylist&lfrom=%d<o=%d\n", from, to);
- reponse=read_sock(raa_current_db);
+ if (raa_current_db == NULL)
+ return;
+ sock_printf(raa_current_db, "copylist&lfrom=%d<o=%d\n", from, to);
+ read_sock(raa_current_db); //memory leak?
}
-void raa_zerolist(raa_db_access *raa_current_db, int rank)
+void raa_zerolist(raa_db_access* raa_current_db, int rank)
{
-char *reponse;
-
-if(raa_current_db == NULL) return;
- sock_printf(raa_current_db,"zerolist&lrank=%d\n", rank);
- reponse=read_sock(raa_current_db);
+ if (raa_current_db == NULL)
+ return;
+ sock_printf(raa_current_db, "zerolist&lrank=%d\n", rank);
+ read_sock(raa_current_db); //memory leak?
}
-void raa_setliststate(raa_db_access *raa_current_db, int lrank, int locus, int type)
+void raa_setliststate(raa_db_access* raa_current_db, int lrank, int locus, int type)
{
-char *reponse, str_type[3];
+ char str_type[3];
-if(raa_current_db == NULL) return;
-if(type == 'S') strcpy(str_type, "SQ");
-else if(type == 'K') strcpy(str_type, "KW");
-else strcpy(str_type, "SP");
+ if (raa_current_db == NULL)
+ return;
+ if (type == 'S')
+ strcpy(str_type, "SQ");
+ else if (type == 'K')
+ strcpy(str_type, "KW");
+ else
+ strcpy(str_type, "SP");
- sock_printf(raa_current_db,"setliststate&lrank=%d&locus=%c&type=%s\n", lrank, (locus ? 'T' : 'F'),
- str_type );
- reponse=read_sock(raa_current_db);
+ sock_printf(raa_current_db, "setliststate&lrank=%d&locus=%c&type=%s\n", lrank, (locus ? 'T' : 'F'),
+ str_type );
+ read_sock(raa_current_db); //memory leak?
}
-char *raa_getliststate(raa_db_access *raa_current_db, int lrank, int *locus, int *type, int *count)
-/* list name is returned in static memory */
+char* raa_getliststate(raa_db_access* raa_current_db, int lrank, int* locus, int* type, int* count)
{
- Reponse *rep;
- char *reponse, *code, *countstr, *locusstr, *typestr, *retp = NULL;
- static char *namestr = NULL;
-
-if(raa_current_db == NULL) return NULL;
- rep=initreponse();
- sock_printf(raa_current_db,"getliststate&lrank=%d\n",lrank);
- reponse=read_sock(raa_current_db);
- if(reponse == NULL) return NULL;
+ Reponse* rep;
+ char* reponse, * code, * countstr, * locusstr, * typestr, * retp = NULL;
+
+ if (raa_current_db == NULL)
+ return NULL;
+ rep = initreponse();
+ sock_printf(raa_current_db, "getliststate&lrank=%d\n", lrank);
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ return NULL;
parse(reponse, rep);
- code = val(rep,"code");
- if(code != NULL && *code == '0') {
- typestr = val(rep,"type");
- if(type != NULL) {
- if(strcmp(typestr, "SQ") == 0) *type = 'S';
- else if(strcmp(typestr, "KW") == 0) *type = 'K';
- else *type = 'E';
- }
- if(namestr != NULL) free(namestr); /* allocation precedante */
- namestr = val(rep, "name");
- countstr = val(rep, "count");
- if(count != NULL) *count = atoi(countstr);
- locusstr = val(rep, "locus");
- if(locus != NULL) *locus = (*locusstr == 'T');
- free(countstr);
- free(locusstr);
- free(typestr);
- retp = namestr;
- }
- if(code != NULL) free(code);
+ code = val(rep, "code");
+ if (code != NULL && *code == '0')
+ {
+ typestr = val(rep, "type");
+ if (type != NULL)
+ {
+ if (strcmp(typestr, "SQ") == 0)
+ *type = 'S';
+ else if (strcmp(typestr, "KW") == 0)
+ *type = 'K';
+ else
+ *type = 'E';
+ }
+ if (raa_current_db->namestr != NULL)
+ free(raa_current_db->namestr); /* allocation precedante */
+ raa_current_db->namestr = val(rep, "name");
+ countstr = val(rep, "count");
+ if (count != NULL)
+ *count = atoi(countstr);
+ locusstr = val(rep, "locus");
+ if (locus != NULL)
+ *locus = (*locusstr == 'T');
+ free(countstr);
+ free(locusstr);
+ free(typestr);
+ retp = raa_current_db->namestr;
+ }
+ if (code != NULL)
+ free(code);
clear_reponse(rep);
return retp;
}
-char *raa_residuecount(raa_db_access *raa_current_db, int lrank)
+char* raa_residuecount(raa_db_access* raa_current_db, int lrank)
{
-Reponse *rep;
-char *reponse, *code;
-static char total[30];
+ Reponse* rep;
+ char* reponse, * code;
-if(raa_current_db == NULL) return 0;
- rep=initreponse();
- sock_printf(raa_current_db,"residuecount&lrank=%d\n",lrank);
- reponse=read_sock(raa_current_db);
- if(reponse == NULL) return 0;
+ if (raa_current_db == NULL)
+ return 0;
+ rep = initreponse();
+ sock_printf(raa_current_db, "residuecount&lrank=%d\n", lrank);
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ return 0;
parse(reponse, rep);
- code = val(rep,"code");
- strcpy(total, "0");
- if(code != NULL && *code == '0') {
- free(code);
- code = val(rep,"count");
- if(code != NULL) {
- strcpy(total, code);
- free(code);
- }
- }
-clear_reponse(rep);
-return total;
+ code = val(rep, "code");
+ strcpy(raa_current_db->residuecount, "0");
+ if (code != NULL && *code == '0')
+ {
+ free(code);
+ code = val(rep, "count");
+ if (code != NULL)
+ {
+ strcpy(raa_current_db->residuecount, code);
+ free(code);
+ }
+ }
+ clear_reponse(rep);
+ return raa_current_db->residuecount;
}
-int raa_getemptylist(raa_db_access *raa_current_db, char *name)
+int raa_getemptylist(raa_db_access* raa_current_db, char* name)
{
- Reponse *rep;
- char *reponse, *code, *rankstr;
+ Reponse* rep;
+ char* reponse, * code, * rankstr, * p;
int rank = 0;
-
-if(raa_current_db == NULL) return 0;
- rep=initreponse();
- sock_printf(raa_current_db, "getemptylist&name=\"%s\"\n", protect_quotes(name));
- reponse=read_sock(raa_current_db);
- if(reponse == NULL) return 0;
+
+ if (raa_current_db == NULL)
+ return 0;
+ rep = initreponse();
+ p = protect_quotes(name);
+ sock_printf(raa_current_db, "getemptylist&name=\"%s\"\n", p);
+ free(p);
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ return 0;
parse(reponse, rep);
- code = val(rep,"code");
- if(code != NULL && (*code == '0' || *code == '3') ) {
- rankstr = val(rep, "lrank");
- rank = atoi(rankstr);
- free(rankstr);
- }
- if(code != NULL) free(code);
+ code = val(rep, "code");
+ if (code != NULL && (*code == '0' || *code == '3') )
+ {
+ rankstr = val(rep, "lrank");
+ rank = atoi(rankstr);
+ free(rankstr);
+ }
+ if (code != NULL)
+ free(code);
clear_reponse(rep);
return rank;
}
-int raa_setlistname(raa_db_access *raa_current_db, int lrank, char *name)
+int raa_setlistname(raa_db_access* raa_current_db, int lrank, char* name)
{
- Reponse *rep;
-char *reponse, *code;
-int retval;
+ Reponse* rep;
+ char* reponse, * code;
+ int retval;
-if(raa_current_db == NULL) return -1;
- rep=initreponse();
+ if (raa_current_db == NULL)
+ return -1;
+ rep = initreponse();
sock_printf(raa_current_db, "setlistname&lrank=%d&name=\"%s\"\n", lrank, name);
- reponse=read_sock(raa_current_db);
- if(reponse == NULL) return -1;
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ return -1;
parse(reponse, rep);
- code = val(rep,"code");
- if(*code == '0') retval = 0;
- else if(*code == '3') retval = 1;
- else retval = -1;
+ code = val(rep, "code");
+ if (*code == '0')
+ retval = 0;
+ else if (*code == '3')
+ retval = 1;
+ else
+ retval = -1;
free(code);
clear_reponse(rep);
-return retval;
+ return retval;
}
-int raa_getlistrank(raa_db_access *raa_current_db, char *name)
+int raa_getlistrank(raa_db_access* raa_current_db, char* name)
{
- Reponse *rep;
-char *reponse, *rankstr;
-int rank;
+ Reponse* rep;
+ char* reponse, * rankstr;
+ int rank;
-if(raa_current_db == NULL) return 0;
- rep=initreponse();
+ if (raa_current_db == NULL)
+ return 0;
+ rep = initreponse();
sock_printf(raa_current_db, "getlistrank&name=\"%s\"\n", name);
- reponse=read_sock(raa_current_db);
- if(reponse == NULL) return 0;
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ return 0;
parse(reponse, rep);
- rankstr = val(rep,"lrank");
- if(rankstr == NULL) return 0;
+ rankstr = val(rep, "lrank");
+ if (rankstr == NULL)
+ return 0;
rank = atoi(rankstr);
free(rankstr);
clear_reponse(rep);
- return rank;
+ return rank;
}
-
-int raa_releaselist(raa_db_access *raa_current_db, int lrank)
+int raa_releaselist(raa_db_access* raa_current_db, int lrank)
{
- Reponse *rep;
-char *reponse, *rankstr;
-int rank;
+ Reponse* rep;
+ char* reponse, * rankstr;
+ int rank;
-if(raa_current_db == NULL) return 1;
- rep=initreponse();
+ if (raa_current_db == NULL)
+ return 1;
+ rep = initreponse();
sock_printf(raa_current_db, "releaselist&lrank=%d\n", lrank);
- reponse=read_sock(raa_current_db);
- if(reponse == NULL) return 1;
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ return 1;
parse(reponse, rep);
- rankstr = val(rep,"code");
- if(rankstr == NULL) return 1;
+ rankstr = val(rep, "code");
+ if (rankstr == NULL)
+ return 1;
rank = atoi(rankstr);
free(rankstr);
clear_reponse(rep);
- return rank;
+ return rank;
}
-
-int raa_countfilles(raa_db_access *raa_current_db, int lrank)
+int raa_countfilles(raa_db_access* raa_current_db, int lrank)
{
- Reponse *rep;
-char *reponse, *rankstr;
-int rank;
+ Reponse* rep;
+ char* reponse, * rankstr;
+ int rank;
-if(raa_current_db == NULL) return 0;
- rep=initreponse();
+ if (raa_current_db == NULL)
+ return 0;
+ rep = initreponse();
sock_printf(raa_current_db, "countsubseqs&lrank=%d\n", lrank);
- reponse=read_sock(raa_current_db);
- if(reponse == NULL) return 0;
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ return 0;
parse(reponse, rep);
- rankstr = val(rep,"count");
- if(rankstr == NULL) return 0;
+ rankstr = val(rep, "count");
+ if (rankstr == NULL)
+ return 0;
rank = atoi(rankstr);
free(rankstr);
clear_reponse(rep);
- return rank;
+ return rank;
}
-int raa_alllistranks(raa_db_access *raa_current_db, int **pranks)
+int raa_alllistranks(raa_db_access* raa_current_db, int** pranks)
{
- Reponse *rep;
-char *reponse, *rankstr, *p;
-int count, *ranks, i;
+ Reponse* rep;
+ char* reponse, * rankstr, * p;
+ int count, * ranks, i;
-if(raa_current_db == NULL) return 0;
- rep=initreponse();
+ if (raa_current_db == NULL)
+ return 0;
+ rep = initreponse();
sock_fputs(raa_current_db, "alllistranks\n");
- reponse=read_sock(raa_current_db);
- if(reponse == NULL) return 0;
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ return 0;
parse(reponse, rep);
- rankstr = val(rep,"count");
+ rankstr = val(rep, "count");
p = strchr(reponse, '&');
- if(rankstr == NULL || p == NULL) return 0;
+ if (rankstr == NULL || p == NULL)
+ return 0;
count = atoi(rankstr);
- ranks = (int *)malloc(count * sizeof(int));
- if(ranks == NULL ) return 0;
+ ranks = (int*)malloc(count * sizeof(int));
+ if (ranks == NULL)
+ return 0;
p++;
- for(i=0; i< count; i++) {
- sscanf(p, "%d", &ranks[i]);
- p = strchr(p, ',');
- if(p == NULL) break;
- p++;
- }
+ for (i = 0; i < count; i++)
+ {
+ sscanf(p, "%d", &ranks[i]);
+ p = strchr(p, ',');
+ if (p == NULL)
+ break;
+ p++;
+ }
*pranks = ranks;
free(rankstr);
clear_reponse(rep);
- return count;
+ return count;
}
-
-int raa_fcode(raa_db_access *raa_current_db, raa_file cas, char *name)
-{
-char *reponse, *p, type[5];
-int value;
-
-if(raa_current_db == NULL) return 0;
-if(cas == raa_aut) strcpy(type, "AUT");
-else if(cas == raa_bib) strcpy(type, "BIB");
-else if(cas == raa_acc) strcpy(type, "ACC");
-else if(cas == raa_smj) strcpy(type, "SMJ");
-else if(cas == raa_sub) strcpy(type, "SUB");
-else return 0;
- sock_printf(raa_current_db,"fcode&name=\"%s\"&type=%s\n", protect_quotes(name), type );
+int raa_fcode(raa_db_access* raa_current_db, raa_file cas, char* name)
+{
+ char* reponse, * p, type[5];
+ int value;
+
+ if (raa_current_db == NULL)
+ return 0;
+ if (cas == raa_aut)
+ strcpy(type, "AUT");
+ else if (cas == raa_bib)
+ strcpy(type, "BIB");
+ else if (cas == raa_acc)
+ strcpy(type, "ACC");
+ else if (cas == raa_smj)
+ strcpy(type, "SMJ");
+ else if (cas == raa_sub)
+ strcpy(type, "SUB");
+ else
+ return 0;
+ p = protect_quotes(name);
+ sock_printf(raa_current_db, "fcode&name=\"%s\"&type=%s\n", p, type );
+ free(p);
reponse = read_sock(raa_current_db);
- if(reponse == NULL) return 0;
+ if (reponse == NULL)
+ return 0;
p = strchr(reponse, '=');
- if(p == NULL) return 0;
+ if (p == NULL)
+ return 0;
p++;
sscanf(p, "%u", &value);
return value;
}
+int raa_read_first_rec(raa_db_access* raa_current_db, raa_file cas)
+{
+ int value;
+ char type[5], * p, * reponse;
+
+ if (raa_current_db == NULL)
+ return 1;
+ if (raa_current_db->first_recs[cas] != 0)
+ return raa_current_db->first_recs[cas];
+
+ if (cas == raa_aut)
+ strcpy(type, "AUT");
+ else if (cas == raa_bib)
+ strcpy(type, "BIB");
+ else if (cas == raa_acc)
+ strcpy(type, "ACC");
+ else if (cas == raa_smj)
+ strcpy(type, "SMJ");
+ else if (cas == raa_sub)
+ strcpy(type, "SUB");
+
+
+ else if (cas == raa_loc)
+ strcpy(type, "LOC");
+ else if (cas == raa_key)
+ strcpy(type, "KEY");
+ else if (cas == raa_spec)
+ strcpy(type, "SPEC");
+ else if (cas == raa_shrt)
+ strcpy(type, "SHRT");
+ else if (cas == raa_lng)
+ strcpy(type, "LNG");
+ else if (cas == raa_ext)
+ strcpy(type, "EXT");
+ else if (cas == raa_txt)
+ strcpy(type, "TXT");
+ else
+ return 0;
+ sock_printf(raa_current_db, "readfirstrec&type=%s\n", type );
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ return 1;
+ p = strstr(reponse, "count=");
+ if (p == NULL)
+ return 0;
+ sscanf(p + 6, "%u", &value);
+ raa_current_db->first_recs[cas] = value;
+ return value;
+}
+
-int raa_read_first_rec(raa_db_access *raa_current_db, raa_file cas)
+char* raa_readsub_pannots(raa_db_access* raa_current_db, int num, int* plength, int* ptype, int* pext, int* plkey, int* plocus,
+ int* pframe, int* pgencode, raa_long* paddr, int* pdiv)
+/* do both seq_to_annots and readsub and buffer result for one seq */
{
-int value;
-char type[5], *p, *reponse;
+ Reponse* rep;
+ char* p, * reponse;
+ int code, l;
+
+ if (raa_current_db == NULL)
+ return NULL;
+ if (num < 2 || num > raa_current_db->nseq)
+ return NULL;
+ if (num != raa_current_db->readsub_data.previous)
+ {
+ sock_printf(raa_current_db, "seq_to_annots&number=%d\nreadsub&num=%u\n", num, num);
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ return NULL;
+ /* process reply to seq_to_annots */
+ rep = initreponse();
+ parse(reponse, rep);
+ p = val(rep, "code");
+ code = atoi(p);
+ free(p);
+ if (code == 0)
+ {
+ p = val(rep, "offset");
+ raa_current_db->readsub_data.addr = scan_raa_long(p);
+ free(p);
+ p = val(rep, "div");
+ raa_current_db->readsub_data.div = atoi(p);
+ free(p);
+ }
+ clear_reponse(rep);
+ /* process reply to readsub */
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ return NULL;
+ rep = initreponse();
+ parse(reponse, rep);
+ p = val(rep, "code");
+ if (p == NULL)
+ return NULL;
+ code = atoi(p);
+ free(p);
+ if (code != 0)
+ {
+ clear_reponse(rep);
+ return NULL;
+ }
+ p = val(rep, "name");
+ l = strlen(p) + 1;
+ if (l > raa_current_db->readsub_data.lname)
+ {
+ raa_current_db->readsub_data.lname = l;
+ raa_current_db->readsub_data.name = (char*)realloc(raa_current_db->readsub_data.name,
+ raa_current_db->readsub_data.lname);
+ }
+ strcpy(raa_current_db->readsub_data.name, p);
+ free(p);
+ p = val(rep, "length");
+ raa_current_db->readsub_data.length = atoi(p);
+ free(p);
+ p = val(rep, "type");
+ raa_current_db->readsub_data.type = atoi_u(p);
+ free(p);
+ p = val(rep, "is_sub");
+ raa_current_db->readsub_data.locus = atoi_u(p);
+ free(p);
+ p = val(rep, "toext");
+ raa_current_db->readsub_data.toext = atoi_u(p);
+ if (raa_current_db->readsub_data.locus > 0)
+ raa_current_db->readsub_data.toext = -raa_current_db->readsub_data.toext;
+ free(p);
+ p = val(rep, "plkey");
+ raa_current_db->readsub_data.lkey = atoi_u(p);
+ free(p);
+ p = val(rep, "frame");
+ raa_current_db->readsub_data.frame = atoi_u(p);
+ free(p);
+ p = val(rep, "genet");
+ raa_current_db->readsub_data.gencode = atoi_u(p);
+ free(p);
+ raa_current_db->readsub_data.previous = num;
+ clear_reponse(rep);
+ }
+ if (plength != NULL)
+ *plength = raa_current_db->readsub_data.length;
+ if (ptype != NULL)
+ *ptype = raa_current_db->readsub_data.type;
+ if (plocus != NULL)
+ *plocus = raa_current_db->readsub_data.locus;
+ if (pext != NULL)
+ *pext = raa_current_db->readsub_data.toext;
+ if (plkey != NULL)
+ *plkey = raa_current_db->readsub_data.lkey;
+ if (pframe != NULL)
+ *pframe = raa_current_db->readsub_data.frame;
+ if (pgencode != NULL)
+ *pgencode = raa_current_db->readsub_data.gencode;
+ if (paddr != NULL)
+ *paddr = raa_current_db->readsub_data.addr;
+ if (pdiv != NULL)
+ *pdiv = raa_current_db->readsub_data.div;
+ return raa_current_db->readsub_data.name;
+}
-if(raa_current_db == NULL) return 1;
-if(raa_current_db->first_recs[cas] != 0) return raa_current_db->first_recs[cas];
-if(cas == raa_aut) strcpy(type, "AUT");
-else if(cas == raa_bib) strcpy(type, "BIB");
-else if(cas == raa_acc) strcpy(type, "ACC");
-else if(cas == raa_smj) strcpy(type, "SMJ");
-else if(cas == raa_sub) strcpy(type, "SUB");
+int raa_seq_to_annots(raa_db_access* raa_current_db, int numseq, raa_long* faddr, int* div)
+{
+ char* p;
+
+ p = raa_readsub_pannots(raa_current_db, numseq, NULL, NULL, NULL, NULL, NULL, NULL, NULL, faddr, div);
+ return p == NULL;
+}
-else if(cas == raa_loc) strcpy(type, "LOC");
-else if(cas == raa_key) strcpy(type, "KEY");
-else if(cas == raa_spec) strcpy(type, "SPEC");
-else if(cas == raa_shrt) strcpy(type, "SHRT");
-else if(cas == raa_lng) strcpy(type, "LNG");
-else if(cas == raa_ext) strcpy(type, "EXT");
-else if(cas == raa_txt) strcpy(type, "TXT");
-else return 0;
-sock_printf(raa_current_db,"readfirstrec&type=%s\n", type );
-reponse = read_sock(raa_current_db);
-if(reponse == NULL) return 1;
-p = strstr(reponse, "count=");
-if(p == NULL) return 0;
-sscanf(p + 6, "%u", &value);
-raa_current_db->first_recs[cas] = value;
-return value;
+char* raa_readsub(raa_db_access* raa_current_db, int num, int* plength, int* ptype, int* pext, int* plkey, int* plocus,
+ int* pframe, int* pgencode)
+{
+ return raa_readsub_pannots(raa_current_db, num, plength, ptype, pext, plkey, plocus, pframe, pgencode, NULL, NULL);
}
-char *raa_readsub_pannots(raa_db_access *raa_current_db, int num, int *plength, int *ptype, int *pext, int *plkey, int *plocus,
- int *pframe, int *pgencode, raa_long *paddr, int *pdiv)
-/* do both seq_to_annots and readsub and buffer result for one seq */
+char* raa_readloc(raa_db_access* raa_current_db, int num, int* sub, int* pnuc, int* spec, int* host, int* plref,
+ int* molec, int* placc, int* org)
{
- Reponse *rep;
- char *p, *reponse;
- int code, l;
-
-if(raa_current_db == NULL) return NULL;
- if(num < 2 || num > raa_current_db->nseq) return NULL;
- if(num != raa_current_db->readsub_data.previous) {
- sock_printf(raa_current_db,"seq_to_annots&number=%d\nreadsub&num=%u\n", num, num);
- reponse = read_sock(raa_current_db);
- if(reponse == NULL) return NULL;
- /* process reply to seq_to_annots */
- rep=initreponse();
- parse(reponse, rep);
- p = val(rep,"code");
- code = atoi(p);
- free(p);
- if(code == 0) {
- p = val(rep,"offset");
- raa_current_db->readsub_data.addr = scan_raa_long(p);
- free(p);
- p = val(rep,"div");
- raa_current_db->readsub_data.div = atoi(p);
- free(p);
- }
- clear_reponse(rep);
- /* process reply to readsub */
- reponse = read_sock(raa_current_db);
- if(reponse == NULL) return NULL;
- rep=initreponse();
- parse(reponse, rep);
- p = val(rep,"code");
- if(p == NULL) return NULL;
- code = atoi(p);
- free(p);
- if(code != 0) {
- clear_reponse(rep);
- return NULL;
- }
- p = val(rep, "name");
- l = strlen(p) + 1;
- if(l > raa_current_db->readsub_data.lname) {
- raa_current_db->readsub_data.lname = l;
- raa_current_db->readsub_data.name = (char *)realloc(raa_current_db->readsub_data.name,
- raa_current_db->readsub_data.lname);
- }
- strcpy(raa_current_db->readsub_data.name, p);
- free(p);
- p = val(rep, "length");
- raa_current_db->readsub_data.length = atoi(p);
- free(p);
- p = val(rep, "type");
- raa_current_db->readsub_data.type = atoi_u(p);
- free(p);
- p = val(rep, "is_sub");
- raa_current_db->readsub_data.locus = atoi_u(p);
- free(p);
- p = val(rep, "toext");
- raa_current_db->readsub_data.toext = atoi_u(p);
- if(raa_current_db->readsub_data.locus > 0)
- raa_current_db->readsub_data.toext = - raa_current_db->readsub_data.toext;
- free(p);
- p = val(rep, "plkey");
- raa_current_db->readsub_data.lkey = atoi_u(p);
- free(p);
- p = val(rep, "frame");
- raa_current_db->readsub_data.frame = atoi_u(p);
- free(p);
- p = val(rep, "genet");
- raa_current_db->readsub_data.gencode = atoi_u(p);
- free(p);
- raa_current_db->readsub_data.previous = num;
- clear_reponse(rep);
- }
- if(plength != NULL) *plength = raa_current_db->readsub_data.length;
- if(ptype != NULL) *ptype = raa_current_db->readsub_data.type;
- if(plocus != NULL) *plocus = raa_current_db->readsub_data.locus;
- if(pext != NULL) *pext = raa_current_db->readsub_data.toext;
- if(plkey != NULL) *plkey = raa_current_db->readsub_data.lkey;
- if(pframe != NULL) *pframe = raa_current_db->readsub_data.frame;
- if(pgencode != NULL) *pgencode = raa_current_db->readsub_data.gencode;
- if(paddr != NULL) *paddr = raa_current_db->readsub_data.addr;
- if(pdiv != NULL) *pdiv = raa_current_db->readsub_data.div;
- return raa_current_db->readsub_data.name;
-}
-
-
-int raa_seq_to_annots(raa_db_access *raa_current_db, int numseq, raa_long *faddr, int *div)
-{
-char *p;
-
-p = raa_readsub_pannots(raa_current_db, numseq,NULL,NULL,NULL,NULL,NULL,NULL,NULL,faddr,div);
-return p == NULL;
-}
-
-
-char *raa_readsub(raa_db_access *raa_current_db, int num, int *plength, int *ptype, int *pext, int *plkey, int *plocus,
- int *pframe, int *pgencode)
-{
-return raa_readsub_pannots(raa_current_db, num,plength,ptype,pext,plkey,plocus,pframe,pgencode,NULL,NULL);
-}
-
-
-char *raa_readloc(raa_db_access *raa_current_db, int num, int *sub, int *pnuc, int *spec, int *host, int *plref,
- int *molec, int *placc, int *org)
-{
- Reponse *rep;
- char *p, *reponse;
+ Reponse* rep;
+ char* p, * reponse;
int code;
- static char date[50];
-if(raa_current_db == NULL) return NULL;
- rep=initreponse();
- sock_printf(raa_current_db,"readloc&num=%u\n", num);
+ if (raa_current_db == NULL)
+ return NULL;
+ rep = initreponse();
+ sock_printf(raa_current_db, "readloc&num=%u\n", num);
reponse = read_sock(raa_current_db);
- if(reponse == NULL) return NULL;
+ if (reponse == NULL)
+ return NULL;
parse(reponse, rep);
- p = val(rep,"code");
- if(p == NULL) return NULL;
+ p = val(rep, "code");
+ if (p == NULL)
+ return NULL;
code = atoi(p);
free(p);
- if(code == 0) {
- if(sub != NULL) {
- p = val(rep, "sub");
- *sub = atoi_u(p);
- free(p);
- }
- if(pnuc != NULL) {
- p = val(rep, "pnuc");
- *pnuc = atoi_u(p);
- free(p);
- }
- if(spec != NULL) {
- p = val(rep, "spec");
- *spec = atoi_u(p);
- free(p);
- }
- if(host != NULL) {
- p = val(rep, "host");
- *host = atoi_u(p);
- free(p);
- }
- if(plref != NULL) {
- p = val(rep, "plref");
- *plref = atoi_u(p);
- free(p);
- }
- if(molec != NULL) {
- p = val(rep, "molec");
- *molec = atoi_u(p);
- free(p);
- }
- if(placc != NULL) {
- p = val(rep, "placc");
- *placc = atoi_u(p);
- free(p);
- }
- if(org != NULL) {
- p = val(rep, "org");
- *org = atoi_u(p);
- free(p);
- }
- p = val(rep, "date");
- strcpy(date, p);
- free(p);
- p = date;
- }
- else p = NULL;
+ if (code == 0)
+ {
+ if (sub != NULL)
+ {
+ p = val(rep, "sub");
+ *sub = atoi_u(p);
+ free(p);
+ }
+ if (pnuc != NULL)
+ {
+ p = val(rep, "pnuc");
+ *pnuc = atoi_u(p);
+ free(p);
+ }
+ if (spec != NULL)
+ {
+ p = val(rep, "spec");
+ *spec = atoi_u(p);
+ free(p);
+ }
+ if (host != NULL)
+ {
+ p = val(rep, "host");
+ *host = atoi_u(p);
+ free(p);
+ }
+ if (plref != NULL)
+ {
+ p = val(rep, "plref");
+ *plref = atoi_u(p);
+ free(p);
+ }
+ if (molec != NULL)
+ {
+ p = val(rep, "molec");
+ *molec = atoi_u(p);
+ free(p);
+ }
+ if (placc != NULL)
+ {
+ p = val(rep, "placc");
+ *placc = atoi_u(p);
+ free(p);
+ }
+ if (org != NULL)
+ {
+ p = val(rep, "org");
+ *org = atoi_u(p);
+ free(p);
+ }
+ p = val(rep, "date");
+ strcpy(raa_current_db->date, p);
+ free(p);
+ p = raa_current_db->date;
+ }
+ else
+ p = NULL;
clear_reponse(rep);
- return p;
+ return p;
}
-char *raa_readspec(raa_db_access *raa_current_db, int num, char **plibel, int *plsub, int *pdesc, int *psyno, int *plhost)
+char* raa_readspec(raa_db_access* raa_current_db, int num, char** plibel, int* plsub, int* pdesc, int* psyno, int* plhost)
{
- Reponse *rep;
- char *p, *reponse;
+ Reponse* rep;
+ char* p, * reponse;
int code;
-
-if(raa_current_db == NULL) return NULL;
- if(num == raa_current_db->readspec_data.previous && raa_current_db->readspec_data.previous != 0) {
- if(plibel != NULL) {
- if(*(raa_current_db->readspec_data.libel) != 0) *plibel = raa_current_db->readspec_data.libel;
- else *plibel = NULL;
- }
- if(plsub != NULL) *plsub = raa_current_db->readspec_data.lsub;
- if(pdesc != NULL) *pdesc = raa_current_db->readspec_data.desc;
- if(psyno != NULL) *psyno = raa_current_db->readspec_data.syno;
- if(plhost != NULL) *plhost = raa_current_db->readspec_data.host;
- return raa_current_db->readspec_data.name;
- }
-
- rep=initreponse();
+
+ if (raa_current_db == NULL)
+ return NULL;
+ if (num == raa_current_db->readspec_data.previous && raa_current_db->readspec_data.previous != 0)
+ {
+ if (plibel != NULL)
+ {
+ if (*(raa_current_db->readspec_data.libel) != 0)
+ *plibel = raa_current_db->readspec_data.libel;
+ else
+ *plibel = NULL;
+ }
+ if (plsub != NULL)
+ *plsub = raa_current_db->readspec_data.lsub;
+ if (pdesc != NULL)
+ *pdesc = raa_current_db->readspec_data.desc;
+ if (psyno != NULL)
+ *psyno = raa_current_db->readspec_data.syno;
+ if (plhost != NULL)
+ *plhost = raa_current_db->readspec_data.host;
+ return raa_current_db->readspec_data.name;
+ }
+
+ rep = initreponse();
sock_printf(raa_current_db, "readspec&num=%u\n", num);
reponse = read_sock(raa_current_db);
- if(reponse == NULL) return NULL;
+ if (reponse == NULL)
+ return NULL;
parse(reponse, rep);
- p = val(rep,"code");
- if(p == NULL) return NULL;
+ p = val(rep, "code");
+ if (p == NULL)
+ return NULL;
code = atoi(p);
free(p);
- if(code != 0) {
- clear_reponse(rep);
- return NULL;
- }
+ if (code != 0)
+ {
+ clear_reponse(rep);
+ return NULL;
+ }
raa_current_db->readspec_data.previous = num;
- p = val(rep, "plsub");
- raa_current_db->readspec_data.lsub = atoi_u(p);
- free(p);
- p = val(rep, "desc");
- raa_current_db->readspec_data.desc = atoi_u(p);
- free(p);
- p = val(rep, "syno");
- raa_current_db->readspec_data.syno = atoi_u(p);
- free(p);
- p = val(rep, "host");
- raa_current_db->readspec_data.host = atoi_u(p);
- free(p);
- p = val(rep, "libel");
- if(p != NULL) {
- strcpy(raa_current_db->readspec_data.libel, p);
- free(p);
- }
- else *(raa_current_db->readspec_data.libel) = 0;
- p = val(rep, "name");
- strcpy(raa_current_db->readspec_data.name, p );
- free(p);
+ p = val(rep, "plsub");
+ raa_current_db->readspec_data.lsub = atoi_u(p);
+ free(p);
+ p = val(rep, "desc");
+ raa_current_db->readspec_data.desc = atoi_u(p);
+ free(p);
+ p = val(rep, "syno");
+ raa_current_db->readspec_data.syno = atoi_u(p);
+ free(p);
+ p = val(rep, "host");
+ raa_current_db->readspec_data.host = atoi_u(p);
+ free(p);
+ p = val(rep, "libel");
+ if (p != NULL)
+ {
+ strcpy(raa_current_db->readspec_data.libel, p);
+ free(p);
+ }
+ else
+ *(raa_current_db->readspec_data.libel) = 0;
+ p = val(rep, "name");
+ strcpy(raa_current_db->readspec_data.name, p );
+ free(p);
clear_reponse(rep);
- return raa_readspec(raa_current_db, num, plibel, plsub, pdesc, psyno, plhost);
+ return raa_readspec(raa_current_db, num, plibel, plsub, pdesc, psyno, plhost);
}
-char *raa_readkey(raa_db_access *raa_current_db, int num, char **plibel, int *plsub, int *pdesc, int *psyno)
+char* raa_readkey(raa_db_access* raa_current_db, int num, char** plibel, int* plsub, int* pdesc, int* psyno)
{
- Reponse *rep;
- char *p, *reponse;
+ Reponse* rep;
+ char* p, * reponse;
int code;
-
-if(raa_current_db == NULL) return NULL;
- if(num == raa_current_db->readkey_data.previous && raa_current_db->readkey_data.previous != 0) {
- if(plibel != NULL) {
- if(*(raa_current_db->readkey_data.libel) != 0) *plibel = raa_current_db->readkey_data.libel;
- else *plibel = NULL;
- }
- if(plsub != NULL) *plsub = raa_current_db->readkey_data.lsub;
- if(pdesc != NULL) *pdesc = raa_current_db->readkey_data.desc;
- if(psyno != NULL) *psyno = raa_current_db->readkey_data.syno;
- return raa_current_db->readkey_data.name;
- }
-
- rep=initreponse();
+
+ if (raa_current_db == NULL)
+ return NULL;
+ if (num == raa_current_db->readkey_data.previous && raa_current_db->readkey_data.previous != 0)
+ {
+ if (plibel != NULL)
+ {
+ if (*(raa_current_db->readkey_data.libel) != 0)
+ *plibel = raa_current_db->readkey_data.libel;
+ else
+ *plibel = NULL;
+ }
+ if (plsub != NULL)
+ *plsub = raa_current_db->readkey_data.lsub;
+ if (pdesc != NULL)
+ *pdesc = raa_current_db->readkey_data.desc;
+ if (psyno != NULL)
+ *psyno = raa_current_db->readkey_data.syno;
+ return raa_current_db->readkey_data.name;
+ }
+
+ rep = initreponse();
sock_printf(raa_current_db, "readkey&num=%u\n", num);
reponse = read_sock(raa_current_db);
- if(reponse == NULL) return NULL;
+ if (reponse == NULL)
+ return NULL;
parse(reponse, rep);
- p = val(rep,"code");
- if(p == NULL) return NULL;
+ p = val(rep, "code");
+ if (p == NULL)
+ return NULL;
code = atoi(p);
free(p);
- if(code != 0) {
- clear_reponse(rep);
- return NULL;
- }
-
- raa_current_db->readkey_data.previous = num;
- p = val(rep, "plsub");
- raa_current_db->readkey_data.lsub = atoi_u(p);
- free(p);
- p = val(rep, "desc");
- raa_current_db->readkey_data.desc = atoi_u(p);
- free(p);
- p = val(rep, "syno");
- raa_current_db->readkey_data.syno = atoi_u(p);
- free(p);
- p = val(rep, "libel");
- if(p != NULL) {
- strcpy(raa_current_db->readkey_data.libel, p);
- free(p);
- }
- else *(raa_current_db->readkey_data.libel) = 0;
- p = val(rep, "name");
- strcpy(raa_current_db->readkey_data.name, p);
- free(p);
- clear_reponse(rep);
- return raa_readkey(raa_current_db, num, plibel, plsub, pdesc, psyno);
-}
-
+ if (code != 0)
+ {
+ clear_reponse(rep);
+ return NULL;
+ }
+
+ raa_current_db->readkey_data.previous = num;
+ p = val(rep, "plsub");
+ raa_current_db->readkey_data.lsub = atoi_u(p);
+ free(p);
+ p = val(rep, "desc");
+ raa_current_db->readkey_data.desc = atoi_u(p);
+ free(p);
+ p = val(rep, "syno");
+ raa_current_db->readkey_data.syno = atoi_u(p);
+ free(p);
+ p = val(rep, "libel");
+ if (p != NULL)
+ {
+ strcpy(raa_current_db->readkey_data.libel, p);
+ free(p);
+ }
+ else
+ *(raa_current_db->readkey_data.libel) = 0;
+ p = val(rep, "name");
+ strcpy(raa_current_db->readkey_data.name, p);
+ free(p);
+ clear_reponse(rep);
+ return raa_readkey(raa_current_db, num, plibel, plsub, pdesc, psyno);
+}
-static int load_smj(raa_db_access *raa_current_db, char ***names, unsigned **plongs, char ***libels)
-{
- Reponse *rep;
- char *reponse, *p;
- int nl, i, code, totsmj, recnum;
-if(raa_current_db == NULL) return 0;
-totsmj = raa_read_first_rec(raa_current_db, raa_smj);
- rep=initreponse();
- sock_printf(raa_current_db,"readsmj&num=2&nl=%d\n", totsmj - 1);
+static int load_smj(raa_db_access* raa_current_db, char*** names, unsigned** plongs, char*** libels)
+{
+ Reponse* rep;
+ char* reponse, * p;
+ int nl, i, code, totsmj, recnum;
+
+ if (raa_current_db == NULL)
+ return 0;
+ totsmj = raa_read_first_rec(raa_current_db, raa_smj);
+ rep = initreponse();
+ sock_printf(raa_current_db, "readsmj&num=2&nl=%d\n", totsmj - 1);
/* ==>readsmj&num=..&nl=..
-code=0&nl=..
-recnum=..&name=".."&plong=..{&libel=".."} nl times
-*/
+ code=0&nl=..
+ recnum=..&name=".."&plong=..{&libel=".."} nl times
+ */
reponse = read_sock(raa_current_db);
- if(reponse == NULL) return 0;
+ if (reponse == NULL)
+ return 0;
parse(reponse, rep);
- p = val(rep,"code");
- if(p == NULL) return 0;
+ p = val(rep, "code");
+ if (p == NULL)
+ return 0;
code = atoi(p);
free(p);
- if(code != 0) return 0;
- p = val(rep,"nl");
- if(p == NULL) return 0;
+ if (code != 0)
+ return 0;
+ p = val(rep, "nl");
+ if (p == NULL)
+ return 0;
nl = atoi(p);
free(p);
clear_reponse(rep);
- if(nl == 0) return 0;
- *names = (char **)calloc(totsmj + 1 , sizeof(char *));
- *plongs = (unsigned *)calloc(totsmj + 1 , sizeof(unsigned));
- *libels = (char **)calloc(totsmj + 1 , sizeof(char *));
- for(i = 0; i < nl; i++) {
- reponse = read_sock(raa_current_db);
- if(reponse == NULL) return 0;
- rep=initreponse();
- parse(reponse, rep);
- p = val(rep, "recnum");
- recnum = atoi(p);
- free(p);
- p = val(rep, "plong");
- (*plongs)[recnum] = atoi_u(p);
- free(p);
- p = val(rep, "name");
- (*names)[recnum] = p;
- p = val(rep, "libel");
- (*libels)[recnum] = p;
- clear_reponse(rep);
- }
-return totsmj;
-}
-
-
-char *raa_readsmj(raa_db_access *raa_current_db, int num, char **plibel, int *plong)
-{
-if(raa_current_db == NULL) return NULL;
-if(raa_current_db->readsmj_data.lastrec == 0) {
- raa_current_db->readsmj_data.lastrec = load_smj(raa_current_db,
- &raa_current_db->readsmj_data.names, &raa_current_db->readsmj_data.plongs,
- &raa_current_db->readsmj_data.libels);
- }
-if(num <= 1 || num > raa_current_db->readsmj_data.lastrec) return NULL;
-if(plong != NULL) *plong = raa_current_db->readsmj_data.plongs[num];
-if(plibel != NULL) *plibel = raa_current_db->readsmj_data.libels[num];
-return raa_current_db->readsmj_data.names[num];
-}
-
-
-char *raa_readacc(raa_db_access *raa_current_db, int num, int *plsub)
-{
- Reponse *rep;
- char *p, *reponse;
+ if (nl == 0)
+ return 0;
+ *names = (char**)calloc(totsmj + 1, sizeof(char*));
+ *plongs = (unsigned*)calloc(totsmj + 1, sizeof(unsigned));
+ *libels = (char**)calloc(totsmj + 1, sizeof(char*));
+ for (i = 0; i < nl; i++)
+ {
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ return 0;
+ rep = initreponse();
+ parse(reponse, rep);
+ p = val(rep, "recnum");
+ recnum = atoi(p);
+ free(p);
+ p = val(rep, "plong");
+ (*plongs)[recnum] = atoi_u(p);
+ free(p);
+ p = val(rep, "name");
+ (*names)[recnum] = p;
+ p = val(rep, "libel");
+ (*libels)[recnum] = p;
+ clear_reponse(rep);
+ }
+ return totsmj;
+}
+
+
+char* raa_readsmj(raa_db_access* raa_current_db, int num, char** plibel, int* plong)
+{
+ if (raa_current_db == NULL)
+ return NULL;
+ if (raa_current_db->readsmj_data.lastrec == 0)
+ {
+ raa_current_db->readsmj_data.lastrec = load_smj(raa_current_db,
+ &raa_current_db->readsmj_data.names, &raa_current_db->readsmj_data.plongs,
+ &raa_current_db->readsmj_data.libels);
+ }
+ if (num <= 1 || num > raa_current_db->readsmj_data.lastrec)
+ return NULL;
+ if (plong != NULL)
+ *plong = raa_current_db->readsmj_data.plongs[num];
+ if (plibel != NULL)
+ *plibel = raa_current_db->readsmj_data.libels[num];
+ return raa_current_db->readsmj_data.names[num];
+}
+
+
+char* raa_readacc(raa_db_access* raa_current_db, int num, int* plsub)
+{
+ Reponse* rep;
+ char* p, * reponse;
int code;
- static char name[100];
-if(raa_current_db == NULL) return NULL;
- rep=initreponse();
- sock_printf(raa_current_db,"readacc&num=%u\n", num);
+ if (raa_current_db == NULL)
+ return NULL;
+ rep = initreponse();
+ sock_printf(raa_current_db, "readacc&num=%u\n", num);
reponse = read_sock(raa_current_db);
- if(reponse == NULL) return NULL;
+ if (reponse == NULL)
+ return NULL;
parse(reponse, rep);
- p = val(rep,"code");
- if(p == NULL) return NULL;
+ p = val(rep, "code");
+ if (p == NULL)
+ return NULL;
code = atoi(p);
free(p);
- if(code == 0) {
- if(plsub != NULL) {
- p = val(rep, "plsub");
- *plsub = atoi_u(p);
- free(p);
- }
- p = val(rep, "name");
- strcpy(name, p);
- free(p);
- p = name;
- }
- else p = NULL;
+ if (code == 0)
+ {
+ if (plsub != NULL)
+ {
+ p = val(rep, "plsub");
+ *plsub = atoi_u(p);
+ free(p);
+ }
+ p = val(rep, "name");
+ strcpy(raa_current_db->access, p);
+ free(p);
+ p = raa_current_db->access;
+ }
+ else
+ p = NULL;
clear_reponse(rep);
- return p;
+ return p;
}
-int raa_readext(raa_db_access *raa_current_db, int num, int *mere, int *deb, int *fin)
+int raa_readext(raa_db_access* raa_current_db, int num, int* mere, int* deb, int* fin)
{
- Reponse *rep;
- char *p, *reponse;
+ Reponse* rep;
+ char* p, * reponse;
int code, next;
-if(raa_current_db == NULL) return 0;
- rep=initreponse();
- sock_printf(raa_current_db,"readext&num=%u\n", num);
+ if (raa_current_db == NULL)
+ return 0;
+ rep = initreponse();
+ sock_printf(raa_current_db, "readext&num=%u\n", num);
reponse = read_sock(raa_current_db);
- if(reponse == NULL) return 0;
+ if (reponse == NULL)
+ return 0;
parse(reponse, rep);
- p = val(rep,"code");
- if(p == NULL) return 0;
+ p = val(rep, "code");
+ if (p == NULL)
+ return 0;
code = atoi(p);
free(p);
- if(code == 0) {
- if(mere != NULL) {
- p = val(rep, "mere");
- *mere = atoi_u(p);
- free(p);
- }
- if(deb != NULL) {
- p = val(rep, "debut");
- *deb = atoi_u(p);
- free(p);
- }
- if(fin != NULL) {
- p = val(rep, "fin");
- *fin = atoi_u(p);
- free(p);
- }
- p = val(rep, "next");
- next = atoi_u(p);
- free(p);
- }
- else next = 0;
+ if (code == 0)
+ {
+ if (mere != NULL)
+ {
+ p = val(rep, "mere");
+ *mere = atoi_u(p);
+ free(p);
+ }
+ if (deb != NULL)
+ {
+ p = val(rep, "debut");
+ *deb = atoi_u(p);
+ free(p);
+ }
+ if (fin != NULL)
+ {
+ p = val(rep, "fin");
+ *fin = atoi_u(p);
+ free(p);
+ }
+ p = val(rep, "next");
+ next = atoi_u(p);
+ free(p);
+ }
+ else
+ next = 0;
clear_reponse(rep);
- return next;
+ return next;
}
-int raa_readlng(raa_db_access *raa_current_db, int num)
+int raa_readlng(raa_db_access* raa_current_db, int num)
/* fills the rlng_buffer structure */
{
- char *p, *reponse;
+ char* p, * reponse;
int count, i;
-if(raa_current_db == NULL) return 0;
- memset(raa_current_db->rlng_buffer, 0, (raa_current_db->SUBINLNG+1)*sizeof(int));
- sock_printf(raa_current_db,"readlng&num=%u\n", num);
+ if (raa_current_db == NULL)
+ return 0;
+ memset(raa_current_db->rlng_buffer, 0, (raa_current_db->SUBINLNG + 1) * sizeof(int));
+ sock_printf(raa_current_db, "readlng&num=%u\n", num);
/* retour code=0&n=xx&x1,x2,...{&next=xx} */
reponse = read_sock(raa_current_db);
- if(reponse == NULL) return 0;
- if(strncmp(reponse, "code=0&n=", 9) != 0 || (count = atoi(reponse+9)) == 0) {
- return 0;
- }
- p = strchr(reponse+9, '&');
- for(i=0; i < count && i < raa_current_db->SUBINLNG; i++) {
- raa_current_db->rlng_buffer->sub[i] = atoi_u(p+1);
- p = strchr(p+1, ',');
- if(p == NULL) break;
- }
+ if (reponse == NULL)
+ return 0;
+ if (strncmp(reponse, "code=0&n=", 9) != 0 || (count = atoi(reponse + 9)) == 0)
+ {
+ return 0;
+ }
+ p = strchr(reponse + 9, '&');
+ for (i = 0; i < count && i < raa_current_db->SUBINLNG; i++)
+ {
+ raa_current_db->rlng_buffer->sub[i] = atoi_u(p + 1);
+ p = strchr(p + 1, ',');
+ if (p == NULL)
+ break;
+ }
p = strstr(reponse, "next=");
- if(p!= NULL) raa_current_db->rlng_buffer->next = atoi_u(p+5);
- else raa_current_db->rlng_buffer->next=0;
- return raa_current_db->rlng_buffer->next;
+ if (p != NULL)
+ raa_current_db->rlng_buffer->next = atoi_u(p + 5);
+ else
+ raa_current_db->rlng_buffer->next = 0;
+ return raa_current_db->rlng_buffer->next;
}
-
-static void load_shrt_buffer(raa_db_access *raa_current_db, unsigned point)
+static void load_shrt_buffer(raa_db_access* raa_current_db, unsigned point)
{
-char *reponse, *p, *q;
-int n, i;
-unsigned val, next, previous;
+ char* reponse, * p, * q;
+ int n, i;
+ unsigned val, next, previous;
-if(raa_current_db == NULL) return;
-sock_printf(raa_current_db, "readshrt&num=%u&max=%d\n", point, MAX_RDSHRT);
+ if (raa_current_db == NULL)
+ return;
+ sock_printf(raa_current_db, "readshrt&num=%u&max=%d\n", point, MAX_RDSHRT);
/* reponse is: code=0&n=xx&val,next,.... n times ...\n */
-reponse = read_sock(raa_current_db);
-
-if(reponse == NULL || strncmp(reponse, "code=0&n=", 9) != 0) {
- return;
- }
-n = atoi(reponse + 9);
-if (n == 0) return;
-p = strchr(reponse+9, '&');
-if(p == NULL) return;
-q = p + 1;
-previous = point;
-for(i = 0; i < n; i++) {
- p = strtok(q, ",");
- q = NULL;
- sscanf(p, "%u", &val);
- p = strtok(NULL, ",");
- sscanf(p, "%u", &next);
- raa_current_db->readshrt_data.shrt_begin = (raa_current_db->readshrt_data.shrt_begin + 1) % S_BUF_SHRT;
- raa_current_db->readshrt_data.shrt_buffer[raa_current_db->readshrt_data.shrt_begin][0] = previous;
- raa_current_db->readshrt_data.shrt_buffer[raa_current_db->readshrt_data.shrt_begin][1] = val;
- raa_current_db->readshrt_data.shrt_buffer[raa_current_db->readshrt_data.shrt_begin][2] = next;
- previous = next;
- }
-if(raa_current_db->readshrt_data.shrt_begin > raa_current_db->readshrt_data.shrt_max - 1) {
- raa_current_db->readshrt_data.shrt_max = raa_current_db->readshrt_data.shrt_begin + 1;
- }
-return;
-}
-
-
-unsigned raa_readshrt(raa_db_access *raa_current_db, unsigned point, int *pval)
-{
-int i;
-
-if(raa_current_db == NULL) return 0;
-if(raa_current_db->readshrt_data.total == 0)
- raa_current_db->readshrt_data.total = (unsigned)raa_read_first_rec(raa_current_db, raa_shrt);
-if(point < 2 || point > raa_current_db->readshrt_data.total) return 0;
-
-for(i = 0; i < raa_current_db->readshrt_data.shrt_max; i++) {
- if(raa_current_db->readshrt_data.shrt_buffer[i][0] == point) {
- if(pval != NULL) *pval = raa_current_db->readshrt_data.shrt_buffer[i][1];
- return raa_current_db->readshrt_data.shrt_buffer[i][2];
- }
- }
-load_shrt_buffer(raa_current_db, point);
-return raa_readshrt(raa_current_db, point, pval);
-}
-
-
-
-char *raa_ghelp(raa_db_access *raa_current_db, char *fname, char *topic)
+ reponse = read_sock(raa_current_db);
+
+ if (reponse == NULL || strncmp(reponse, "code=0&n=", 9) != 0)
+ {
+ return;
+ }
+ n = atoi(reponse + 9);
+ if (n == 0)
+ return;
+ p = strchr(reponse + 9, '&');
+ if (p == NULL)
+ return;
+ q = p + 1;
+ previous = point;
+ for (i = 0; i < n; i++)
+ {
+ p = strtok(q, ",");
+ q = NULL;
+ sscanf(p, "%u", &val);
+ p = strtok(NULL, ",");
+ sscanf(p, "%u", &next);
+ raa_current_db->readshrt_data.shrt_begin = (raa_current_db->readshrt_data.shrt_begin + 1) % S_BUF_SHRT;
+ raa_current_db->readshrt_data.shrt_buffer[raa_current_db->readshrt_data.shrt_begin][0] = previous;
+ raa_current_db->readshrt_data.shrt_buffer[raa_current_db->readshrt_data.shrt_begin][1] = val;
+ raa_current_db->readshrt_data.shrt_buffer[raa_current_db->readshrt_data.shrt_begin][2] = next;
+ previous = next;
+ }
+ if (raa_current_db->readshrt_data.shrt_begin > raa_current_db->readshrt_data.shrt_max - 1)
+ {
+ raa_current_db->readshrt_data.shrt_max = raa_current_db->readshrt_data.shrt_begin + 1;
+ }
+ return;
+}
+
+
+unsigned raa_readshrt(raa_db_access* raa_current_db, unsigned point, int* pval)
+{
+ int i;
+
+ if (raa_current_db == NULL)
+ return 0;
+ if (raa_current_db->readshrt_data.total == 0)
+ raa_current_db->readshrt_data.total = (unsigned)raa_read_first_rec(raa_current_db, raa_shrt);
+ if (point < 2 || point > raa_current_db->readshrt_data.total)
+ return 0;
+
+ for (i = 0; i < raa_current_db->readshrt_data.shrt_max; i++)
+ {
+ if (raa_current_db->readshrt_data.shrt_buffer[i][0] == point)
+ {
+ if (pval != NULL)
+ *pval = raa_current_db->readshrt_data.shrt_buffer[i][1];
+ return raa_current_db->readshrt_data.shrt_buffer[i][2];
+ }
+ }
+ load_shrt_buffer(raa_current_db, point);
+ return raa_readshrt(raa_current_db, point, pval);
+}
+
+
+static void load_shrt2_aux(raa_db_access* raa_current_db, unsigned point, raa_shortl2_kind kind)
+{
+ static const char kind_name[][11] = {"sub_of_bib", "spc_of_loc", "bib_of_loc", "aut_of_bib", "bib_of_aut",
+ "sub_of_acc", "key_of_sub", "acc_of_loc"};
+ char* p, * reponse;
+ int i;
+
+ if (raa_current_db == NULL)
+ return;
+ sock_printf(raa_current_db, "followshrt2&num=%u&kind=%s&rank=0&max=%d\n", point, kind_name[kind],
+ raa_current_db->readshrt2_data[kind]->size);
+ /* reponse is: code=0&num=xx&rank=xx&n=xx&val,.... n times ...\n */
+ reponse = read_sock(raa_current_db);
+
+ if (reponse == NULL || strncmp(reponse, "code=0&", 7) != 0)
+ {
+ return;
+ }
+ raa_current_db->readshrt2_data[kind]->point = point;
+ p = strstr(reponse, "num=");
+ raa_current_db->readshrt2_data[kind]->next = atoi(p + 4);
+ p = strstr(reponse, "n=");
+ raa_current_db->readshrt2_data[kind]->length = atoi(p + 2);
+ p = strchr(p, '&') + 1;
+ for (i = 0; i < raa_current_db->readshrt2_data[kind]->length; i++)
+ {
+ sscanf(p, "%u", raa_current_db->readshrt2_data[kind]->vals + i);
+ p = strchr(p, ',') + 1;
+ }
+}
+
+
+unsigned raa_followshrt2(raa_db_access* raa_current_db, int* p_point, int* p_rank, raa_shortl2_kind kind)
+{
+ int rank = *p_rank;
+ unsigned retval;
+
+ if (raa_current_db->readshrt2_data[kind]->point == *p_point &&
+ rank < raa_current_db->readshrt2_data[kind]->length)
+ {
+ retval = raa_current_db->readshrt2_data[kind]->vals[rank++];
+ if (rank >= raa_current_db->readshrt2_data[kind]->length)
+ {
+ *p_rank = 0;
+ *p_point = raa_current_db->readshrt2_data[kind]->next;
+ }
+ else
+ *p_rank = rank;
+ return retval;
+ }
+ load_shrt2_aux(raa_current_db, *p_point, kind);
+ return raa_followshrt2(raa_current_db, p_point, p_rank, kind);
+}
+
+
+char* raa_ghelp(raa_db_access* raa_current_db, char* fname, char* topic)
/* returns all help topic in one string in private memory
-*/
+ */
{
-char *reponse, *p, *fintext, *tmp;
-int nl, l, i;
-static char *text = NULL;
-static int ltext = 0;
+ char* reponse, * p, * fintext, * tmp;
+ int nl, l, i;
-if(raa_current_db == NULL) return NULL;
- sock_printf(raa_current_db,"ghelp&file=%s&item=%s\n", fname, topic);
+ if (raa_current_db == NULL)
+ return NULL;
+ sock_printf(raa_current_db, "ghelp&file=%s&item=%s\n", fname, topic);
reponse = read_sock(raa_current_db);
- if(reponse == NULL) return NULL;
+ if (reponse == NULL)
+ return NULL;
nl = 0;
- if(strncmp(reponse, "nl=", 3) == 0) nl = atoi(reponse+3);
+ if (strncmp(reponse, "nl=", 3) == 0)
+ nl = atoi(reponse + 3);
p = strchr(reponse, '&');
- if(nl <= 0 || p == NULL) return NULL;
- fintext = text; p++;
- for(i = 0; i < nl; i++) {
- l = strlen(p) + 1; /* +1 pour ajouter \n */
- if( (fintext - text) + l > ltext) {
- ltext += 1000;
- tmp = (char *)realloc(text, ltext + 1);
- if(tmp == NULL) {
- if(text != NULL) free(text);
- text = NULL; ltext = 0;
- return NULL;
- }
- fintext = tmp + (fintext - text);
- text = tmp;
- }
- memcpy(fintext, p, l -1);
- fintext += l;
- *(fintext - 1) = '\n';
- if(i + 1 < nl) reponse = read_sock(raa_current_db);
- if(reponse == NULL) return NULL;
- p = reponse;
- }
+ if (nl <= 0 || p == NULL)
+ return NULL;
+ fintext = raa_current_db->help; p++;
+ for (i = 0; i < nl; i++)
+ {
+ l = strlen(p) + 1; /* +1 pour ajouter \n */
+ if ( (fintext - raa_current_db->help) + l > raa_current_db->lhelp)
+ {
+ raa_current_db->lhelp += 1000;
+ tmp = (char*)realloc(raa_current_db->help, raa_current_db->lhelp + 1);
+ if (tmp == NULL)
+ {
+ if (raa_current_db->help != NULL)
+ free(raa_current_db->help);
+ raa_current_db->help = NULL; raa_current_db->lhelp = 0;
+ return NULL;
+ }
+ fintext = tmp + (fintext - raa_current_db->help);
+ raa_current_db->help = tmp;
+ }
+ memcpy(fintext, p, l - 1);
+ fintext += l;
+ *(fintext - 1) = '\n';
+ if (i + 1 < nl)
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ return NULL;
+ p = reponse;
+ }
*fintext = 0;
- return text;
-}
-
-
-struct raa_matchkey {
- int *ranks;
- char **names;
- int count;
- int current;
- int no_more;
- };
-
-static void raa_free_matchkeys(raa_db_access *raa_current_db)
-{
-int i;
-struct raa_matchkey *data = (struct raa_matchkey *)(raa_current_db->matchkey_data);
-
-if(data == NULL) return;
-if(data->count > 0) {
- for(i = 0; i < data->count; i++) free(data->names[i]);
- free(data->names);
- free(data->ranks);
- }
-free(data);
-raa_current_db->matchkey_data = NULL;
-}
-
-
-static void next_block_matchkeys(raa_db_access *raa_current_db, int num, char *pattern)
-{
-const int blocksize = 2001;
-char *reponse, *p;
-int count, i;
-struct raa_matchkey *data;
-
-if(raa_current_db == NULL) return;
-raa_free_matchkeys(raa_current_db);
-sock_printf(raa_current_db, "nextmatchkey&num=%d", num );
-if(num == 2) sock_printf(raa_current_db, "&pattern=\"%s\"", protect_quotes(pattern) );
-sock_printf(raa_current_db, "&count=%d\n", blocksize);
-reponse = read_sock(raa_current_db);
-if(reponse == NULL || strncmp(reponse, "code=0&count=", 13) != 0) return;
-sscanf(reponse + 13, "%d", &count);
-data = (struct raa_matchkey *)calloc(1, sizeof(struct raa_matchkey));
-raa_current_db->matchkey_data = data;
-if(data == NULL || count == 0) return;
-data->ranks = (int *)malloc(count * sizeof(int));
-data->names = (char **)malloc(count * sizeof(char *));
-data->current = 0;
-data->no_more = (count < blocksize);
-data->count = count;
-if(data->ranks == NULL || data->names == NULL) data->count = 0;
-for(i = 0; i < data->count; i++) {
- reponse = read_sock(raa_current_db);
- sscanf(reponse + 4, "%d", &(data->ranks[i]) );
- p = strchr(reponse, '&');
- p = strchr(p, '=') + 1;
- data->names[i] = strdup(unprotect_quotes(p));
- if(data->names[i] == NULL) {
- data->count = i;
- break;
- }
- }
-for(i = data->count; i < count; i++) {
- read_sock(raa_current_db);
- }
-return;
-}
-
-
-int raa_nextmatchkey(raa_db_access *raa_current_db, int num, char *pattern, char **matching)
+ return raa_current_db->help;
+}
+
+
+struct raa_matchkey
+{
+ int* ranks;
+ char** names;
+ int count;
+ int current;
+ int no_more;
+};
+
+static void raa_free_matchkeys(raa_db_access* raa_current_db)
+{
+ int i;
+ struct raa_matchkey* data = (struct raa_matchkey*)(raa_current_db->matchkey_data);
+
+ if (data == NULL)
+ return;
+ if (data->count > 0)
+ {
+ for (i = 0; i < data->count; i++)
+ {
+ free(data->names[i]);
+ }
+ free(data->names);
+ free(data->ranks);
+ }
+ free(data);
+ raa_current_db->matchkey_data = NULL;
+}
+
+
+static void next_block_matchkeys(raa_db_access* raa_current_db, int num, char* pattern)
+{
+ const int blocksize = 2001;
+ char* reponse, * p;
+ int count, i;
+ struct raa_matchkey* data;
+
+ if (raa_current_db == NULL)
+ return;
+ raa_free_matchkeys(raa_current_db);
+ sock_printf(raa_current_db, "nextmatchkey&num=%d", num );
+ p = protect_quotes(pattern);
+ if (num == 2)
+ sock_printf(raa_current_db, "&pattern=\"%s\"", p );
+ free(p);
+ sock_printf(raa_current_db, "&count=%d\n", blocksize);
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL || strncmp(reponse, "code=0&count=", 13) != 0)
+ return;
+ sscanf(reponse + 13, "%d", &count);
+ data = (struct raa_matchkey*)calloc(1, sizeof(struct raa_matchkey));
+ raa_current_db->matchkey_data = data;
+ if (data == NULL || count == 0)
+ return;
+ data->ranks = (int*)malloc(count * sizeof(int));
+ data->names = (char**)malloc(count * sizeof(char*));
+ data->current = 0;
+ data->no_more = (count < blocksize);
+ data->count = count;
+ if (data->ranks == NULL || data->names == NULL)
+ data->count = 0;
+ for (i = 0; i < data->count; i++)
+ {
+ reponse = read_sock(raa_current_db);
+ sscanf(reponse + 4, "%d", &(data->ranks[i]) );
+ p = strchr(reponse, '&');
+ p = strchr(p, '=') + 1;
+ data->names[i] = strdup(unprotect_quotes(p));
+ if (data->names[i] == NULL)
+ {
+ data->count = i;
+ break;
+ }
+ }
+ for (i = data->count; i < count; i++)
+ {
+ read_sock(raa_current_db);
+ }
+ return;
+}
+
+
+int raa_nextmatchkey(raa_db_access* raa_current_db, int num, char* pattern, char** matching)
/* *matching returned in static memory */
{
-struct raa_matchkey *data;
-int no_more, count;
+ struct raa_matchkey* data;
+ int no_more = 0, count;
-if(raa_current_db == NULL) return 0;
-if(num == 2) {
- next_block_matchkeys(raa_current_db, 2, pattern);
- }
-data = (struct raa_matchkey *)(raa_current_db->matchkey_data);
-if(data == NULL) return 0;
-if(data->current < data->count) {
- if(matching != NULL) *matching = data->names[data->current];
- return data->ranks[(data->current)++];
- }
-count = data->count;
-if(count > 0) {
- no_more = data->no_more;
- }
-raa_free_matchkeys(raa_current_db);
-if(count == 0 || no_more) return 0;
-next_block_matchkeys(raa_current_db, num, NULL);
-return raa_nextmatchkey(raa_current_db, num, NULL, matching);
+ if (raa_current_db == NULL)
+ return 0;
+ if (num == 2)
+ {
+ next_block_matchkeys(raa_current_db, 2, pattern);
+ }
+ data = (struct raa_matchkey*)(raa_current_db->matchkey_data);
+ if (data == NULL)
+ return 0;
+ if (data->current < data->count)
+ {
+ if (matching != NULL)
+ *matching = data->names[data->current];
+ return data->ranks[(data->current)++];
+ }
+ count = data->count;
+ if (count > 0)
+ {
+ no_more = data->no_more;
+ }
+ raa_free_matchkeys(raa_current_db);
+ if (count == 0 || no_more)
+ return 0;
+ next_block_matchkeys(raa_current_db, num, NULL);
+ return raa_nextmatchkey(raa_current_db, num, NULL, matching);
}
-int atoi_u(const char *p)
+int atoi_u(const char* p)
{
-unsigned value;
+ unsigned value;
-sscanf(p, "%u", &value);
-return (int)value;
+ sscanf(p, "%u", &value);
+ return (int)value;
}
-char *protect_quotes(char *name)
+static char* protect_quotes(char* name)
/* remplacer tous les " par \"
-name : une chaine inchangee
-retourne un pointeur vers la chaine rendue privee pour cette fonction
-*/
-{
-char *p, *q;
-int l, count;
-static char *bis = NULL;
-static int lbis = 0;
-
-count = 0; p = name - 1;
-while( (p=strchr(p+1, '"')) != NULL) count++;
-if(count == 0) return name;
-
-l = strlen(name);
-if(l + count > lbis) {
- lbis = l + count;
- bis = (char *)realloc(bis, lbis + 1);
- }
-p = name; q = bis;
-while(TRUE) {
- if(*p == '"') *(q++) = '\\';
- *q = *p;
- if(*p == 0) break;
- q++; p++;
- }
-return bis;
-}
-
-
-static char *prepare_remote_file(raa_db_access *raa_current_db, char *oldrequete, char *debut, char *type, int *plrank,
- char **badfname)
-{
-char *p, *q, *reponse, *fin;
-static char line[200];
-int nl, l, code;
-FILE *in;
-Reponse *rep;
-
-*plrank = 0; *badfname = line;
-p = strchr(debut, '=') + 1;
-while(isspace(*p)) p++;
-if(*p == '"') { /* if filename is bracketed by " */
- *(p++) = ' ';
- fin = strchr(p, '"');
- if(fin == NULL) return NULL;
- *fin = ' ';
- }
-else {
- fin = p;
- do ++fin; while( *fin != 0 && *fin != ')' && !isspace(*fin) );
- }
-l = fin - p;
-if(l >= sizeof(line)) l = sizeof(line) - 1;
-memcpy(line, p, l); line[l] = 0;
-if(fin - p >= sizeof(line)) return NULL;
-in = fopen(line, "r");
-if(in == NULL) return NULL;
-nl = 0;
-while( fgets(line, sizeof(line), in) != NULL) nl++;
-rewind(in);
-sock_printf(raa_current_db, "crelistfromclientdata&type=%s&nl=%d\n", type, nl);
-if(nl > 0) {
- while( fgets(line, sizeof(line), in) != NULL) {
- l = strlen(line);
- if(line[l - 1] != '\n') strcpy(line + l, "\n");
- sock_fputs(raa_current_db, line);
- }
- }
-fclose(in);
-
-reponse = read_sock(raa_current_db);
-if(reponse == NULL) {
- strcpy(line, "connection with server is down");
- return NULL;
- }
-rep = initreponse();
-parse(reponse, rep);
-q = val(rep,"code");
-code = atoi(q);
-free(q);
-if(code != 0) {
- if(code == 3) strcpy(line, "too many lists, delete a few");
- else sprintf(line, "code=%d", code);
- return NULL;
- }
-q = val(rep,"name");
-l = strlen(q);
-reponse = (char *)malloc( (debut - oldrequete) + 1 + l + 1 + strlen(fin) + 1);
-p = reponse;
-memcpy(p, oldrequete, debut - oldrequete);
-p += debut - oldrequete;
-*(p++) = ' ';
-memcpy(p, q, l);
-p += l;
-*(p++) = ' ';
-free(q);
-strcpy(p, fin);
-free(oldrequete);
-q = val(rep,"lrank");
-if(q != NULL) {
- *plrank = atoi(q);
- free(q);
- }
-
-clear_reponse(rep);
-return reponse;
-}
-
-
-static int *add_tmp_blist(int lrank, int *list)
-{
-static int total = 0, current, *prelist = NULL; /* need not be specific to each opened db */
-
-if(list == NULL) { /* initialisation */
- if(prelist != NULL) free(prelist);
- total = 10; current = 0;
- list = (int *)malloc(total*sizeof(int));
- prelist = list;
- return list;
- }
-if(current >= total) {
- int *tmp;
- tmp = (int *)realloc(list, (total + 10)*sizeof(int));
- if(tmp == NULL) return list;
- total += 10;
- list = tmp;
- }
-list[current++] = lrank;
-prelist = list;
-return list;
-}
-
-
-char *maj_strstr(char *in, char *target)
-{
-static char *buffer = NULL;
-static int lbuf = 0;
-int l;
-char *p;
-
-l = strlen(in);
-if(l > lbuf) {
- lbuf = l;
- buffer = (char *)realloc(buffer, lbuf + 1);
- }
-strcpy(buffer, in);
-majuscules(buffer);
-p = strstr(buffer, target);
-if(p != NULL) p = in + (p - buffer);
-return p;
-}
-
-
-static char *raa_requete_remote_file(raa_db_access *raa_current_db, char *oldrequete, int **plist, char **pbadfname)
+ name : une chaine inchangee
+ retourne un pointeur vers la chaine rendue allouee par malloc
+ */
+{
+ char* p, * q;
+ int count;
+ char* bis;
+
+ count = 0; p = name - 1;
+ while ( (p = strchr(p + 1, '"')) != NULL)
+ count++;
+ if (count == 0)
+ return strdup(name);
+
+ bis = (char*)malloc(strlen(name) + count + 1);
+ p = name; q = bis;
+ while (TRUE)
+ {
+ if (*p == '"')
+ *(q++) = '\\';
+ *q = *p;
+ if (*p == 0)
+ break;
+ q++; p++;
+ }
+ return bis;
+}
+
+
+static char* prepare_remote_file(raa_db_access* raa_current_db, char* oldrequete, char* debut, char* type, int* plrank,
+ char** badfname)
+{
+ char* p, * q, * reponse, * fin;
+ char* line = raa_current_db->remote_file;
+ int nl, l, code;
+ FILE* in;
+ Reponse* rep;
+
+ *plrank = 0; *badfname = line;
+ p = strchr(debut, '=') + 1;
+ while (isspace(*p))
+ p++;
+ if (*p == '"') /* if filename is bracketed by " */
+ {
+ *(p++) = ' ';
+ fin = strchr(p, '"');
+ if (fin == NULL)
+ return NULL;
+ *fin = ' ';
+ }
+ else
+ {
+ fin = p;
+ do
+ ++fin;
+ while (*fin != 0 && *fin != ')' && !isspace(*fin) );
+ }
+ l = fin - p;
+ if (l >= sizeof(raa_current_db->remote_file))
+ l = sizeof(raa_current_db->remote_file) - 1;
+ memcpy(line, p, l); line[l] = 0;
+ if (fin - p >= sizeof(raa_current_db->remote_file))
+ return NULL;
+ in = fopen(line, "r");
+ if (in == NULL)
+ return NULL;
+ nl = 0;
+ while (fgets(line, sizeof(raa_current_db->remote_file), in) != NULL)
+ nl++;
+ rewind(in);
+ sock_printf(raa_current_db, "crelistfromclientdata&type=%s&nl=%d\n", type, nl);
+ if (nl > 0)
+ {
+ while (fgets(line, sizeof(raa_current_db->remote_file), in) != NULL)
+ {
+ l = strlen(line);
+ if (line[l - 1] != '\n')
+ strcpy(line + l, "\n");
+ sock_fputs(raa_current_db, line);
+ }
+ }
+ fclose(in);
+
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ {
+ strcpy(line, "connection with server is down");
+ return NULL;
+ }
+ rep = initreponse();
+ parse(reponse, rep);
+ q = val(rep, "code");
+ code = atoi(q);
+ free(q);
+ if (code != 0)
+ {
+ if (code == 3)
+ strcpy(line, "too many lists, delete a few");
+ else
+ sprintf(line, "code=%d", code);
+ return NULL;
+ }
+ q = val(rep, "name");
+ l = strlen(q);
+ reponse = (char*)malloc( (debut - oldrequete) + 1 + l + 1 + strlen(fin) + 1);
+ p = reponse;
+ memcpy(p, oldrequete, debut - oldrequete);
+ p += debut - oldrequete;
+ *(p++) = ' ';
+ memcpy(p, q, l);
+ p += l;
+ *(p++) = ' ';
+ free(q);
+ strcpy(p, fin);
+ free(oldrequete);
+ q = val(rep, "lrank");
+ if (q != NULL)
+ {
+ *plrank = atoi(q);
+ free(q);
+ }
+
+ clear_reponse(rep);
+ return reponse;
+}
+
+
+static int* add_tmp_blist(raa_db_access* raa_current_db, int lrank, int* list)
+{
+ if (list == NULL) /* initialisation */
+ {
+ if (raa_current_db->tmp_prelist != NULL)
+ free(raa_current_db->tmp_prelist);
+ raa_current_db->tmp_total = 10; raa_current_db->tmp_current = 0;
+ list = (int*)malloc(raa_current_db->tmp_total * sizeof(int));
+ raa_current_db->tmp_prelist = list;
+ return list;
+ }
+ if (raa_current_db->tmp_current >= raa_current_db->tmp_total)
+ {
+ int* tmp;
+ tmp = (int*)realloc(list, (raa_current_db->tmp_total + 10) * sizeof(int));
+ if (tmp == NULL)
+ return list;
+ raa_current_db->tmp_total += 10;
+ list = tmp;
+ }
+ list[raa_current_db->tmp_current++] = lrank;
+ raa_current_db->tmp_prelist = list;
+ return list;
+}
+
+
+static char* maj_strstr(char* in, char* target)
+{
+ char* p, * buffer;
+
+ buffer = strdup(in);
+ majuscules(buffer);
+ p = strstr(buffer, target);
+ if (p != NULL)
+ p = in + (p - buffer);
+ free(buffer);
+ return p;
+}
+
+
+static char* raa_requete_remote_file(raa_db_access* raa_current_db, char* oldrequete, int** plist, char** pbadfname)
/*
-rend NULL ou une requete dont les F= FA= FS= FK= ont ete changes en list-name
-et qui a ete creee par malloc
-*/
-{
-char *oldori, *p;
-int lrank, *list;
-
-oldori = strdup(oldrequete);
-if(maj_strstr(oldori, "F=") == NULL && maj_strstr(oldori, "FA=") == NULL &&
- maj_strstr(oldori, "FK=") == NULL && maj_strstr(oldori, "FS=") == NULL) {
- *plist = NULL;
- return oldori;
- }
-list = add_tmp_blist(0, NULL); /* initialisation a vide */
-while(oldori != NULL && (p = maj_strstr(oldori, "F=")) != NULL) {
- oldori = prepare_remote_file(raa_current_db, oldori, p, "SQ", &lrank, pbadfname);
- if(lrank != 0) list = add_tmp_blist(lrank, list);
- }
-while(oldori != NULL && (p = maj_strstr(oldori, "FA=")) != NULL) {
- oldori = prepare_remote_file(raa_current_db, oldori, p, "AC", &lrank, pbadfname);
- if(lrank != 0) list = add_tmp_blist(lrank, list);
- }
-while(oldori != NULL && (p = maj_strstr(oldori, "FS=")) != NULL) {
- oldori = prepare_remote_file(raa_current_db, oldori, p, "SP", &lrank, pbadfname);
- if(lrank != 0) list = add_tmp_blist(lrank, list);
- }
-while(oldori != NULL && (p = maj_strstr(oldori, "FK=")) != NULL) {
- oldori = prepare_remote_file(raa_current_db, oldori, p, "KW", &lrank, pbadfname);
- if(lrank != 0) list = add_tmp_blist(lrank, list);
- }
-list = add_tmp_blist(0, list); /* marquage fin de liste par zero */
-if(oldori == NULL && list != NULL) {
- while(*list != 0) raa_releaselist(raa_current_db, *(list++) );
- list = NULL;
- }
-*plist = list;
-return oldori;
-}
-
-
-int raa_savelist(raa_db_access *raa_current_db, int lrank, FILE *out, int use_acc, char *prefix)
-{
-char *reponse;
-int err;
-
-if(raa_current_db == NULL) return 1;
-sock_printf(raa_current_db, "savelist&lrank=%d&type=%c\n", lrank, (use_acc ? 'A' : 'N') );
-reponse = read_sock(raa_current_db);
-if(reponse == NULL) return 1;
-err = strcmp(reponse, "code=0");
-if(err != 0) {
- return 1;
- }
-while(TRUE) {
- reponse = read_sock(raa_current_db);
- if(reponse == NULL) return 1;
- if(strcmp(reponse, "savelist END.") == 0) break;
- if(prefix != NULL) fputs(prefix, out);
- fprintf(out, "%s\n", reponse);
- }
-return 0;
-}
-
-
-int raa_modifylist(raa_db_access *raa_current_db, int lrank, char *type, char *operation, int *pnewlist, int (*check_interrupt)(void),
- int *p_processed )
-{
-Reponse *rep;
-char *p, *reponse;
-int code;
-
-if(raa_current_db == NULL) return 3;
-sock_printf(raa_current_db, "modifylist&lrank=%d&type=%s&operation=\"%s\"\n", lrank,
- type, operation );
-sock_flush(raa_current_db); /* tres important */
-if(check_interrupt == NULL) {
- reponse = read_sock(raa_current_db);
- if(reponse == NULL) return 3;
- }
-else {
- while(TRUE) {
- reponse = read_sock_timeout(raa_current_db, 500 /* msec */);
- if(raa_current_db == NULL) return 3;
- if(reponse != NULL) break;
- if( check_interrupt() ) {
- sock_fputs(raa_current_db, "\033" /* esc */ );
- sock_flush(raa_current_db);
- }
- }
- }
-
-rep = initreponse();
-parse(reponse, rep);
-p = val(rep,"code");
-code = atoi(p);
-free(p);
-if(code != 0) return code;
-p = val(rep,"lrank");
-*pnewlist = atoi(p);
-free(p);
-p = val(rep,"processed");
-if(p != NULL && p_processed != NULL) *p_processed = atoi(p);
-if(p != NULL) free(p);
-clear_reponse(rep);
-return 0;
-}
-
-
-int raa_knowndbs(raa_db_access *raa_current_db, char ***pnames, char ***pdescriptions)
-{
-int nl;
-char **names = NULL, **descriptions = NULL;
-char *reponse, *p, *q, *r;
-int l, i;
-
-if(raa_current_db == NULL) return 0;
-sock_printf(raa_current_db, "knowndbs\n" );
-reponse = read_sock(raa_current_db);
-if(reponse == NULL || strncmp(reponse, "nl=", 3) != 0) {
- return 0;
- }
-nl = atoi(reponse + 3);
-if(nl == 0) return 0;
-names = (char **) malloc(nl * sizeof(char *));
-descriptions = (char **) malloc(nl * sizeof(char *));
-for(i = 0; i < nl; i++) {
- reponse = read_sock(raa_current_db);
- if(reponse == NULL) return 0;
- p = strchr(reponse, '|');
- if(p != NULL) {
- *(p++) = 0;
- q = strchr(p, '|');
- if(q != NULL) *(q++) = 0;
- }
- l = strlen(reponse);
- names[i] = (char *)malloc(l+1);
- strcpy(names[i], reponse);
- compact(names[i]);
- if(p != NULL && q != NULL) {
- while( (r=strchr(p, '\t')) != NULL) *r = ' ';
- majuscules(p); compact(p);
- l = strlen(q);
- descriptions[i] = (char *)malloc(l+20);
- descriptions[i][0] = 0;
- if(strcmp(p, "OFF") == 0) strcpy(descriptions[i], "(offline) ");
- strcat(descriptions[i], q);
- }
- else descriptions[i] = NULL;
- }
-*pnames = names; *pdescriptions = descriptions;
-return nl;
-}
-
-
-char *raa_short_descr(raa_db_access *raa_current_db, int seqnum, char *text, int maxlen, raa_long pinf, int div, char *name)
+ rend NULL ou une requete dont les F= FA= FS= FK= ont ete changes en list-name
+ et qui a ete creee par malloc
+ */
+{
+ char* oldori, * p;
+ int lrank, * list;
+
+ oldori = strdup(oldrequete);
+ if (maj_strstr(oldori, "F=") == NULL && maj_strstr(oldori, "FA=") == NULL &&
+ maj_strstr(oldori, "FK=") == NULL && maj_strstr(oldori, "FS=") == NULL)
+ {
+ *plist = NULL;
+ return oldori;
+ }
+ list = add_tmp_blist(raa_current_db, 0, NULL); /* initialisation a vide */
+ while (oldori != NULL && (p = maj_strstr(oldori, "F=")) != NULL)
+ {
+ oldori = prepare_remote_file(raa_current_db, oldori, p, "SQ", &lrank, pbadfname);
+ if (lrank != 0)
+ list = add_tmp_blist(raa_current_db, lrank, list);
+ }
+ while (oldori != NULL && (p = maj_strstr(oldori, "FA=")) != NULL)
+ {
+ oldori = prepare_remote_file(raa_current_db, oldori, p, "AC", &lrank, pbadfname);
+ if (lrank != 0)
+ list = add_tmp_blist(raa_current_db, lrank, list);
+ }
+ while (oldori != NULL && (p = maj_strstr(oldori, "FS=")) != NULL)
+ {
+ oldori = prepare_remote_file(raa_current_db, oldori, p, "SP", &lrank, pbadfname);
+ if (lrank != 0)
+ list = add_tmp_blist(raa_current_db, lrank, list);
+ }
+ while (oldori != NULL && (p = maj_strstr(oldori, "FK=")) != NULL)
+ {
+ oldori = prepare_remote_file(raa_current_db, oldori, p, "KW", &lrank, pbadfname);
+ if (lrank != 0)
+ list = add_tmp_blist(raa_current_db, lrank, list);
+ }
+ list = add_tmp_blist(raa_current_db, 0, list); /* marquage fin de liste par zero */
+ if (oldori == NULL && list != NULL)
+ {
+ while (*list != 0)
+ raa_releaselist(raa_current_db, *(list++) );
+ list = NULL;
+ }
+ *plist = list;
+ return oldori;
+}
+
+
+int raa_savelist(raa_db_access* raa_current_db, int lrank, FILE* out, int use_acc, char* prefix)
+{
+ char* reponse;
+ int err;
+
+ if (raa_current_db == NULL)
+ return 1;
+ sock_printf(raa_current_db, "savelist&lrank=%d&type=%c\n", lrank, (use_acc ? 'A' : 'N') );
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ return 1;
+ err = strcmp(reponse, "code=0");
+ if (err != 0)
+ {
+ return 1;
+ }
+ while (TRUE)
+ {
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ return 1;
+ if (strcmp(reponse, "savelist END.") == 0)
+ break;
+ if (prefix != NULL)
+ fputs(prefix, out);
+ fprintf(out, "%s\n", reponse);
+ }
+ return 0;
+}
+
+
+int raa_modifylist(raa_db_access* raa_current_db, int lrank, char* type, char* operation, int* pnewlist, int (* check_interrupt)(void),
+ int* p_processed )
+{
+ Reponse* rep;
+ char* p, * reponse;
+ int code;
+
+ if (raa_current_db == NULL)
+ return 3;
+ sock_printf(raa_current_db, "modifylist&lrank=%d&type=%s&operation=\"%s\"\n", lrank,
+ type, operation );
+ sock_flush(raa_current_db); /* tres important */
+ if (check_interrupt == NULL)
+ {
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ return 3;
+ }
+ else
+ {
+ while (TRUE)
+ {
+ reponse = read_sock_timeout(raa_current_db, 500 /* msec */);
+ if (raa_current_db == NULL)
+ return 3;
+ if (reponse != NULL)
+ break;
+ if (check_interrupt() )
+ {
+ sock_fputs(raa_current_db, "\033" /* esc */ );
+ sock_flush(raa_current_db);
+ }
+ }
+ }
+
+ rep = initreponse();
+ parse(reponse, rep);
+ p = val(rep, "code");
+ code = atoi(p);
+ free(p);
+ if (code != 0)
+ return code;
+ p = val(rep, "lrank");
+ *pnewlist = atoi(p);
+ free(p);
+ p = val(rep, "processed");
+ if (p != NULL && p_processed != NULL)
+ *p_processed = atoi(p);
+ if (p != NULL)
+ free(p);
+ clear_reponse(rep);
+ return 0;
+}
+
+
+int raa_knowndbs(raa_db_access* raa_current_db, char*** pnames, char*** pdescriptions)
+{
+ int nl;
+ char** names = NULL, ** descriptions = NULL;
+ char* reponse, * p, * q, * r;
+ int l, i;
+
+ if (raa_current_db == NULL)
+ return 0;
+ sock_printf(raa_current_db, "knowndbs\n" );
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL || strncmp(reponse, "nl=", 3) != 0)
+ {
+ return 0;
+ }
+ nl = atoi(reponse + 3);
+ if (nl == 0)
+ return 0;
+ names = (char**) malloc(nl * sizeof(char*));
+ descriptions = (char**) malloc(nl * sizeof(char*));
+ for (i = 0; i < nl; i++)
+ {
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ return 0;
+ p = strchr(reponse, '|');
+ if (p != NULL)
+ {
+ *(p++) = 0;
+ q = strchr(p, '|');
+ if (q != NULL)
+ *(q++) = 0;
+ }
+ l = strlen(reponse);
+ names[i] = (char*)malloc(l + 1);
+ strcpy(names[i], reponse);
+ compact(names[i]);
+ if (p != NULL && q != NULL)
+ {
+ while ( (r = strchr(p, '\t')) != NULL)
+ *r = ' ';
+ majuscules(p); compact(p);
+ l = strlen(q);
+ descriptions[i] = (char*)malloc(l + 20);
+ descriptions[i][0] = 0;
+ if (strcmp(p, "OFF") == 0)
+ strcpy(descriptions[i], "(offline) ");
+ strcat(descriptions[i], q);
+ }
+ else
+ descriptions[i] = NULL;
+ }
+ *pnames = names; *pdescriptions = descriptions;
+ return nl;
+}
+
+
+char* raa_short_descr(raa_db_access* raa_current_db, int seqnum, char* text, int maxlen, raa_long pinf, int div, char* name)
/*
-to get a description of a sequence or of a subsequence
-seqnum the sequence number
-text the string to be loaded with description
-maxlen the max # of chars allowed in text (\0 is put but not counted in maxlen)
-return value a pointer to text
-*/
-{
-int l, deb;
-char *p;
-
-text[maxlen]=0;
-strcpy(text, name);
-l=strlen(text);
-if(strchr(name, '.') != NULL) { /* subsequence */
- if( (p = raa_read_annots(raa_current_db, pinf, div)) == NULL) return text;
- p[20]=0;
- strcat(text,p+4);
- l=strlen(text);
- while(text[l-1]==' ') l--;
- text[l]=0;
- if( ( p = strchr(p + 21, '/') ) != NULL) {
- strncat(text, p, maxlen - l);
- l = strlen(text);
- if(l > 75) return text;
- }
- do {
- p = raa_next_annots(raa_current_db, NULL);
- if( strcmptrail(p,20,NULL,0) &&
- strncmp(p,"FT ",10) ) return text;
- }
- while(p[21]!='/');
- do {
- strncat(text,p+20,maxlen-l);
- l=strlen(text);
- if(l>75) return text;
- p = raa_next_annots(raa_current_db, NULL);
- }
- while ( !strcmptrail(p,20,NULL,0) ||
- !strncmp(p,"FT ",10) );
- }
-else { /* parent sequence */
- if( (p = raa_read_annots(raa_current_db, pinf, div)) == NULL) return text;
- p = raa_next_annots(raa_current_db, NULL);
- if(raa_current_db->nbrf) {
- deb=17;
- }
- else {
- deb=13;
- if(raa_current_db->embl || raa_current_db->swissprot) {
- while (strncmp(p,"DE",2)) {
- p = raa_next_annots(raa_current_db, NULL);
- }
- deb=6;
- }
- }
- do {
- strncat(text,p+deb-2,maxlen-l);
- l=strlen(text);
- if(l>=77) return text;
- p = raa_next_annots(raa_current_db, NULL);
- }
- while( !strncmp(p," ",2) || !strncmp(p,"DE",2) );
- }
-return text;
-}
-
-
-struct chain_void *raa_get_list_open_dbs(void)
-{
-return raa_list_open_dbs;
+ to get a description of a sequence or of a subsequence
+ seqnum the sequence number
+ text the string to be loaded with description
+ maxlen the max # of chars allowed in text (\0 is put but not counted in maxlen)
+ return value a pointer to text
+ */
+{
+ int l, deb;
+ char* p;
+
+ text[maxlen] = 0;
+ strcpy(text, name);
+ l = strlen(text);
+ if (strchr(name, '.') != NULL) /* subsequence */
+ {
+ if ( (p = raa_read_annots(raa_current_db, pinf, div)) == NULL)
+ return text;
+ p[20] = 0;
+ strcat(text, p + 4);
+ l = strlen(text);
+ while (text[l - 1] == ' ')
+ l--;
+ text[l] = 0;
+ if ( ( p = strchr(p + 21, '/') ) != NULL)
+ {
+ strncat(text, p, maxlen - l);
+ l = strlen(text);
+ if (l > 75)
+ return text;
+ }
+ do
+ {
+ p = raa_next_annots(raa_current_db, NULL);
+ if (strcmptrail(p, 20, NULL, 0) &&
+ strncmp(p, "FT ", 10) )
+ return text;
+ }
+ while (p[21] != '/');
+ do
+ {
+ strncat(text, p + 20, maxlen - l);
+ l = strlen(text);
+ if (l > 75)
+ return text;
+ p = raa_next_annots(raa_current_db, NULL);
+ }
+ while (!strcmptrail(p, 20, NULL, 0) ||
+ !strncmp(p, "FT ", 10) );
+ }
+ else /* parent sequence */
+ {
+ if (raa_read_annots(raa_current_db, pinf, div) == NULL)
+ return text;
+ p = raa_next_annots(raa_current_db, NULL);
+ if (raa_current_db->nbrf)
+ {
+ deb = 17;
+ }
+ else
+ {
+ deb = 13;
+ if (raa_current_db->embl || raa_current_db->swissprot)
+ {
+ while (strncmp(p, "DE", 2))
+ {
+ p = raa_next_annots(raa_current_db, NULL);
+ }
+ deb = 6;
+ }
+ }
+ do
+ {
+ strncat(text, p + deb - 2, maxlen - l);
+ l = strlen(text);
+ if (l >= 77)
+ return text;
+ p = raa_next_annots(raa_current_db, NULL);
+ }
+ while (!strncmp(p, " ", 2) || !strncmp(p, "DE", 2) );
+ }
+ return text;
}
#define END_COORDINATE_TEST(line) strncmp(line, "extractseqs END.", 16)
-static int *next_1_coordinate_set(raa_db_access *raa_current_db)
-{
-char *p, *line, *q;
-int start, last, seqnum, elt, i, count;
-int *table = NULL;
-
-line = read_sock(raa_current_db);
-if(END_COORDINATE_TEST(line) == 0) return NULL;
-count = 0; p = line;
-while(TRUE) {
- p = strchr(p+1, '|');
- if( p == NULL) break;
- count++;
- }
-table = (int *)malloc( (3 * count + 1) * sizeof(int));
-if(table == NULL) {
- do line = read_sock(raa_current_db);
- while(END_COORDINATE_TEST(line) != 0) ;
- return NULL;
- }
-table[0] = count;
-elt = 1;
-for(i = 0; i < count; i++) {
- p = strchr(line, '|');
- if(p == NULL) break;
- q = strchr(line, '=');
- if(q == NULL || q > p) break;
- sscanf(q+1, "%d", &seqnum);
- q = strchr(q+1, '=');
- if(q == NULL || q > p) break;
- sscanf(q+1, "%d", &start);
- q = strchr(q+1, '=');
- if(q == NULL || q > p) break;
- sscanf(q+1, "%d", &last);
- table[elt++] = seqnum;
- table[elt++] = start;
- table[elt++] = last;
- line = p + 1;
- }
-return table;
-}
-
-
-struct coord_series_struct {
- int count;
- int **table;
- int next;
- } ;
-
-void *raa_prep_coordinates(raa_db_access *raa_current_db, int lrank, int seqnum,
- char *operation, /* "simple","fragment","feature","region" */
- char *feature_name, char *bounds, char *min_bounds)
+static int* next_1_coordinate_set(raa_db_access* raa_current_db)
+{
+ char* p, * line, * q;
+ int start, last, seqnum, elt, i, count;
+ int* table = NULL;
+
+ line = read_sock(raa_current_db);
+ if (END_COORDINATE_TEST(line) == 0)
+ return NULL;
+ count = 0; p = line;
+ while (TRUE)
+ {
+ p = strchr(p + 1, '|');
+ if (p == NULL)
+ break;
+ count++;
+ }
+ table = (int*)malloc( (3 * count + 1) * sizeof(int));
+ if (table == NULL)
+ {
+ do
+ line = read_sock(raa_current_db);
+ while (END_COORDINATE_TEST(line) != 0);
+ return NULL;
+ }
+ table[0] = count;
+ elt = 1;
+ for (i = 0; i < count; i++)
+ {
+ p = strchr(line, '|');
+ if (p == NULL)
+ break;
+ q = strchr(line, '=');
+ if (q == NULL || q > p)
+ break;
+ sscanf(q + 1, "%d", &seqnum);
+ q = strchr(q + 1, '=');
+ if (q == NULL || q > p)
+ break;
+ sscanf(q + 1, "%d", &start);
+ q = strchr(q + 1, '=');
+ if (q == NULL || q > p)
+ break;
+ sscanf(q + 1, "%d", &last);
+ table[elt++] = seqnum;
+ table[elt++] = start;
+ table[elt++] = last;
+ line = p + 1;
+ }
+ return table;
+}
+
+
+struct coord_series_struct
+{
+ int count;
+ int** table;
+ int next;
+};
+
+void* raa_prep_coordinates(raa_db_access* raa_current_db, int lrank, int seqnum,
+ char* operation, /* "simple","fragment","feature","region" */
+ char* feature_name, char* bounds, char* min_bounds)
/*
-only one of lrank and seqnum is != 0 to work on a sequence list or on an individual sequence
-feature_name: used for operations feature and region, NULL otherwise
-bounds: used for operations fragment and region, NULL otherwise
+ only one of lrank and seqnum is != 0 to work on a sequence list or on an individual sequence
+ feature_name: used for operations feature and region, NULL otherwise
+ bounds: used for operations fragment and region, NULL otherwise
syntax by examples "45,155" "-100,100" "-10,e+100" "E-10,e+100"
-min_bounds: NULL for operations other than fragment and region
+ min_bounds: NULL for operations other than fragment and region
can be NULL for fragment and region and means min_bounds same as bounds
if not NULL, same syntax as bounds
-pcount: upon return, set to number of coordinate series
-
-return value: NULL if error, or pointer to opaque data
-*/
-{
-char message[200];
-char *line;
-int *v, maxi, **table, rank;
-struct coord_series_struct *retval;
-
-sprintf(message, "extractseqs&%s=%d&format=coordinates&operation=%s",
- seqnum == 0 ? "lrank" : "seqnum",
- seqnum == 0 ? lrank : seqnum,
- operation);
-sock_fputs(raa_current_db, message);
-if(strcmp(operation, "feature") == 0 || strcmp(operation, "region") == 0) {
- sprintf(message, "&feature=%s", feature_name);
- sock_fputs(raa_current_db, message);
- }
-if(strcmp(operation, "fragment") == 0 || strcmp(operation, "region") == 0) {
- sprintf(message, "&bounds=%s", bounds);
- sock_fputs(raa_current_db, message);
- }
-if(min_bounds != NULL) {
- sprintf(message, "&minbounds=%s", min_bounds);
- sock_fputs(raa_current_db, message);
- }
-sock_fputs(raa_current_db, "\n"); sock_flush(raa_current_db);
-line = read_sock(raa_current_db);
-if(strcmp(line, "code=0") != 0) {
- return NULL;
- }
-
-maxi = 100; rank = 0;
-table = (int **)malloc(maxi*sizeof(int *));
-if(table == NULL) {
- do line = read_sock(raa_current_db);
- while(END_COORDINATE_TEST(line) != 0) ;
- return NULL;
- }
-while( (v = next_1_coordinate_set(raa_current_db)) != NULL) {
- if(rank >= maxi) {
- int **vv;
- vv = (int **)realloc(table, 2*maxi*sizeof(int *));
- if(vv == NULL) {
- do line = read_sock(raa_current_db);
- while(END_COORDINATE_TEST(line) != 0) ;
- break;
- }
- maxi = 2*maxi;
- table = vv;
- }
- table[rank++] = v;
- }
-table = realloc(table, rank*sizeof(int *));
-retval = (struct coord_series_struct *)malloc(sizeof(struct coord_series_struct));
-if(retval == NULL) return NULL;
-retval->count = rank;
-retval->table = table;
-retval->next = 0;
-return retval;
-}
-
-
-int *raa_1_coordinate_set(void *v)
+ pcount: upon return, set to number of coordinate series
+
+ return value: NULL if error, or pointer to opaque data
+ */
+{
+ char message[200];
+ char* line;
+ int* v, maxi, ** table, rank;
+ struct coord_series_struct* retval;
+
+ sprintf(message, "extractseqs&%s=%d&format=coordinates&operation=%s",
+ seqnum == 0 ? "lrank" : "seqnum",
+ seqnum == 0 ? lrank : seqnum,
+ operation);
+ sock_fputs(raa_current_db, message);
+ if (strcmp(operation, "feature") == 0 || strcmp(operation, "region") == 0)
+ {
+ sprintf(message, "&feature=%s", feature_name);
+ sock_fputs(raa_current_db, message);
+ }
+ if (strcmp(operation, "fragment") == 0 || strcmp(operation, "region") == 0)
+ {
+ sprintf(message, "&bounds=%s", bounds);
+ sock_fputs(raa_current_db, message);
+ }
+ if (min_bounds != NULL)
+ {
+ sprintf(message, "&minbounds=%s", min_bounds);
+ sock_fputs(raa_current_db, message);
+ }
+ sock_fputs(raa_current_db, "\n"); sock_flush(raa_current_db);
+ line = read_sock(raa_current_db);
+ if (strcmp(line, "code=0") != 0)
+ {
+ return NULL;
+ }
+
+ maxi = 100; rank = 0;
+ table = (int**)malloc(maxi * sizeof(int*));
+ if (table == NULL)
+ {
+ do
+ line = read_sock(raa_current_db);
+ while (END_COORDINATE_TEST(line) != 0);
+ return NULL;
+ }
+ while ( (v = next_1_coordinate_set(raa_current_db)) != NULL)
+ {
+ if (rank >= maxi)
+ {
+ int** vv;
+ vv = (int**)realloc(table, 2 * maxi * sizeof(int*));
+ if (vv == NULL)
+ {
+ do
+ line = read_sock(raa_current_db);
+ while (END_COORDINATE_TEST(line) != 0);
+ break;
+ }
+ maxi = 2 * maxi;
+ table = vv;
+ }
+ table[rank++] = v;
+ }
+ table = realloc(table, rank * sizeof(int*));
+ retval = (struct coord_series_struct*)malloc(sizeof(struct coord_series_struct));
+ if (retval == NULL)
+ return NULL;
+ retval->count = rank;
+ retval->table = table;
+ retval->next = 0;
+ return retval;
+}
+
+
+int* raa_1_coordinate_set(void* v)
/*
-to be called repetitively as
-table = raa_1_coordinate_set(v);
-until returns NULL
-with the opaque pointer returned by the raa_prep_coordinates call
-
-returns int array table in private memory containing 1 + 3*table[0] elements
-count = table[0] ;
-j = 0;
-for(i=0; i < count; i++) {
- table[j+1] is the acnuc number of the sequence
- table[j+2] is the start position in this sequence
- table[j+3] is the end position in this sequence
- j += 3;
- }
-start position > end position <==> fragment is on the complementary strand of the acnuc seq
-returns NULL when all coordinate series have been processed
-*/
-{
-int *retval, i;
-struct coord_series_struct *s = (struct coord_series_struct *)v;
-
-if(s->next >= s->count) {
- for(i=0; i < s->count; i++) free(s->table[i]);
- free(s->table);
- free(s);
- return NULL;
- }
-retval = s->table[(s->next)++];
-return retval;
-}
-
-
-char *raa_translate_cds(raa_db_access *raa_current_db, int seqnum)
+ to be called repetitively as
+ table = raa_1_coordinate_set(v);
+ until returns NULL
+ with the opaque pointer returned by the raa_prep_coordinates call
+
+ returns int array table in private memory containing 1 + 3*table[0] elements
+ count = table[0] ;
+ j = 0;
+ for(i=0; i < count; i++) {
+ table[j+1] is the acnuc number of the sequence
+ table[j+2] is the start position in this sequence
+ table[j+3] is the end position in this sequence
+ j += 3;
+ }
+ start position > end position <==> fragment is on the complementary strand of the acnuc seq
+ returns NULL when all coordinate series have been processed
+ */
+{
+ int* retval, i;
+ struct coord_series_struct* s = (struct coord_series_struct*)v;
+
+ if (s->next >= s->count)
+ {
+ for (i = 0; i < s->count; i++)
+ {
+ free(s->table[i]);
+ }
+ free(s->table);
+ free(s);
+ return NULL;
+ }
+ retval = s->table[(s->next)++];
+ return retval;
+}
+
+
+char* raa_translate_cds(raa_db_access* raa_current_db, int seqnum)
/* traduction d'un cds avec codon initiateur traite et * internes ==> X
-rendue dans memoire allouee ici qu'il ne faut pas modifier
-retour NULL si pb lecture de la seq
-*/
-{
-static char *buffer = NULL;
-static int lbuffer = 0;
-int debut_codon, longueur, pos, code, phase;
-char codon[4], *p;
-
-raa_readsub(raa_current_db, seqnum,&longueur,NULL,NULL,NULL,NULL,&phase,&code);
-debut_codon = phase + 1;
-longueur = (longueur - debut_codon + 1)/3;
-if(longueur > lbuffer) {
- if(buffer != NULL) free(buffer);
- buffer = (char *)malloc(longueur + 1);
- lbuffer = longueur;
- }
-if(buffer == NULL) {lbuffer = 0; return NULL; }
-buffer[0] = raa_translate_init_codon(raa_current_db, seqnum);
-debut_codon += 3;
-for(pos = 1; pos < longueur; pos++) {
- if( raa_gfrag(raa_current_db, seqnum, debut_codon, 3, codon) == 0) return NULL;
- buffer[pos] = codaa(codon,code);
- debut_codon += 3;
- }
-buffer[longueur] = 0;
-while( (p = strchr(buffer, '*') ) != NULL && p - buffer < longueur - 1 )
- *p = 'X';
-return buffer;
-}
-
-
-char raa_translate_init_codon(raa_db_access *raa_current_db, int numseq)
-{
-char codon[4];
-int point, special_init = TRUE, val, gc, phase;
-static int num_5_partial = 0;
-
-if(num_5_partial == 0) num_5_partial = raa_iknum(raa_current_db, "5'-PARTIAL", raa_key);
-raa_readsub(raa_current_db, numseq, NULL, NULL,NULL, &point, NULL, &phase, &gc);
-if(phase != 0) special_init = FALSE;
-else { /* la seq est-elle 5'-PARTIAL ? */
- while(point != 0) {
- point = raa_readshrt(raa_current_db, point, &val);
- if(val == num_5_partial) {
- special_init = FALSE;
- break;
- }
- }
- }
-raa_gfrag(raa_current_db, numseq, phase + 1, 3, codon);
-if(special_init) /* traduction speciale du codon initiateur */
- return init_codon_to_aa(codon, gc);
-else return codaa(codon, gc);
-}
-
-
-static void ajout_synonyme(raa_node *secondaire, raa_node *principal)
-{
-raa_node *next;
-
-if(principal->syno == NULL) {
- principal->syno = secondaire;
- secondaire->syno = principal;
- }
-else {
- next = principal->syno;
- principal->syno = secondaire;
- secondaire->syno = next;
- }
-}
-
-static void redresse_branches(raa_node *pere)
+ rendue dans memoire allouee ici qu'il ne faut pas modifier
+ retour NULL si pb lecture de la seq
+ */
+{
+ int debut_codon, longueur, pos, code, phase;
+ char codon[4], * p;
+
+ raa_readsub(raa_current_db, seqnum, &longueur, NULL, NULL, NULL, NULL, &phase, &code);
+ debut_codon = phase + 1;
+ longueur = (longueur - debut_codon + 1) / 3;
+ raa_current_db->translate_buffer = (char*)realloc(raa_current_db->translate_buffer, longueur + 1);
+ if (raa_current_db->translate_buffer == NULL)
+ {
+ return NULL;
+ }
+ raa_current_db->translate_buffer[0] = raa_translate_init_codon(raa_current_db, seqnum);
+ debut_codon += 3;
+ for (pos = 1; pos < longueur; pos++)
+ {
+ if (raa_gfrag(raa_current_db, seqnum, debut_codon, 3, codon) == 0)
+ return NULL;
+ raa_current_db->translate_buffer[pos] = codaa(codon, code);
+ debut_codon += 3;
+ }
+ raa_current_db->translate_buffer[longueur] = 0;
+ while ( (p = strchr(raa_current_db->translate_buffer, '*') ) != NULL && p - raa_current_db->translate_buffer < longueur - 1)
+ *p = 'X';
+ return raa_current_db->translate_buffer;
+}
+
+
+char raa_translate_init_codon(raa_db_access* raa_current_db, int numseq)
+{
+ char codon[4];
+ int point, special_init = TRUE, val, gc, phase, rank = 0;
+
+ if (raa_current_db->num_5_partial == 0)
+ raa_current_db->num_5_partial = raa_iknum(raa_current_db, "5'-PARTIAL", raa_key);
+ raa_readsub(raa_current_db, numseq, NULL, NULL, NULL, &point, NULL, &phase, &gc);
+ if (phase != 0)
+ special_init = FALSE;
+ else /* la seq est-elle 5'-PARTIAL ? */
+ {
+ while (point != 0)
+ {
+ val = raa_followshrt2(raa_current_db, &point, &rank, raa_key_of_sub);
+ if (val == raa_current_db->num_5_partial)
+ {
+ special_init = FALSE;
+ break;
+ }
+ }
+ }
+ raa_gfrag(raa_current_db, numseq, phase + 1, 3, codon);
+ if (special_init) /* traduction speciale du codon initiateur */
+ return init_codon_to_aa(codon, gc);
+ else
+ return codaa(codon, gc);
+}
+
+
+static void ajout_synonyme(raa_node* secondaire, raa_node* principal)
+{
+ raa_node* next;
+
+ if (principal->syno == NULL)
+ {
+ principal->syno = secondaire;
+ secondaire->syno = principal;
+ }
+ else
+ {
+ next = principal->syno;
+ principal->syno = secondaire;
+ secondaire->syno = next;
+ }
+}
+
+static void redresse_branches(raa_node* pere)
/* Recursively reverse the order of descendants because it has been reversed
*/
{
- struct raa_pair *point, *next1, *next2, *last;
+ struct raa_pair* point, * next1, * next2, * last;
point = pere->list_desc;
- if (!point) return;
+ if (!point)
+ return;
next1 = point->next;
- if (next1) point->next = NULL;
- while (TRUE) {
+ if (next1)
+ point->next = NULL;
+ while (TRUE)
+ {
last = point;
redresse_branches(point->value);
- if (!next1) break;
+ if (!next1)
+ break;
next2 = next1->next;
next1->next = point;
point = next1;
next1 = next2;
- }
+ }
pere->list_desc = last;
}
-static void ajout_branche(raa_node *pere, raa_node *fils)
+static void ajout_branche(raa_node* pere, raa_node* fils)
/* adds a pere->fils branch. The last added branch is the first child of pere.
*/
{
-struct raa_pair *point, *nouveau;
+ struct raa_pair* nouveau;
-nouveau = (struct raa_pair *)calloc(1,sizeof(struct raa_pair));
-nouveau->value = fils;
-if( (point = pere->list_desc) == NULL) {
- pere->list_desc = nouveau;
- }
-else {
- nouveau->next = pere->list_desc;
- pere->list_desc = nouveau;
- }
+ nouveau = (struct raa_pair*)calloc(1, sizeof(struct raa_pair));
+ nouveau->value = fils;
+ if (pere->list_desc == NULL)
+ {
+ pere->list_desc = nouveau;
+ }
+ else
+ {
+ nouveau->next = pere->list_desc;
+ pere->list_desc = nouveau;
+ }
}
-static void raa_decode_desc_arbre(char *reponse, raa_node **tab_noeud)
+static void raa_decode_desc_arbre(char* reponse, raa_node** tab_noeud)
/* reponse contient
-rank&pere&count&"...name..."&"...libel..."
-synonyme est identifie par pere < 0 et -pere = son principal
-*/
-{
-int num, pere, count, l;
-char *p, *q, *name, *libel;
-
-num = atoi(reponse);
-p = strchr(reponse, '&');
-pere = atoi(p + 1);
-p = strchr(p+1, '&');
-count = atoi(p + 1);
+ rank&pere&count&"...name..."&"...libel..."
+ synonyme est identifie par pere < 0 et -pere = son principal
+ */
+{
+ int num, pere, count, l;
+ char* p, * q, * name, * libel;
+
+ num = atoi(reponse);
+ p = strchr(reponse, '&');
+ pere = atoi(p + 1);
+ p = strchr(p + 1, '&');
+ count = atoi(p + 1);
/* ne pas brancher un noeud deja branche ailleurs auparavant */
-if(tab_noeud[num] != NULL ) return;
-tab_noeud[num] = (raa_node *)calloc(1, sizeof(raa_node));
-tab_noeud[num]->rank = num;
-if(pere < 0) { /* un synonyme */
- ajout_synonyme(tab_noeud[num], tab_noeud[-pere]);
- }
-else {
- tab_noeud[num]->count = count;
- tab_noeud[num]->parent = tab_noeud[pere];
- if(num != 2) ajout_branche(tab_noeud[pere], tab_noeud[num]);
- }
-
-p = strchr(p+1, '&') + 1;
-q = p;
-do {
- q++;
- if(*q == 0) break;
- }
-while(*q != '"' || *(q-1) == '\\');
-l = q-p+1;
-name = (char *)malloc(l+1);
-strncpy(name, p, l); name[l] = 0;
-unprotect_quotes(name);
-tab_noeud[num]->name = name;
-q++;
-if(*q == '&') {
- p = q+1;
- q = p;
- do {
- q++;
- if(*q == 0) break;
- }
- while(*q != '"' || *(q-1) == '\\');
- l = q-p+1;
- libel = (char *)malloc(l+1);
- strncpy(libel, p, l); libel[l] = 0;
- unprotect_quotes(libel);
- tab_noeud[num]->libel = libel;
- p = (char *)malloc(l+1);
- strcpy(p, libel);
- majuscules(p);
- tab_noeud[num]->libel_upcase = p;
- if(strncmp(p, "ID:", 3) == 0 || (p = strstr(p, "|ID:")) != NULL) {
- p += 2; if(*p != ':') p++;
- sscanf(p + 1, "%d", &(tab_noeud[num]->tid) );
- }
- }
-}
-
-
-static void raa_calc_taxo_count(raa_node *racine)
-{
-struct raa_pair *paire;
-int count = 0;
-
-paire = racine->list_desc;
-while(paire != NULL) {
- raa_calc_taxo_count(paire->value);
- count += paire->value->count;
- paire = paire->next;
- }
-racine->count += count;
-}
-
-
-int raa_loadtaxonomy(raa_db_access *raa_current_db, char *rootname,
- int (*progress_function)(int, void *), void *progress_arg,
- int (*need_interrupt_f)(void *), void *interrupt_arg)
+ if (tab_noeud[num] != NULL)
+ return;
+ tab_noeud[num] = (raa_node*)calloc(1, sizeof(raa_node));
+ tab_noeud[num]->rank = num;
+ if (pere < 0) /* un synonyme */
+ {
+ ajout_synonyme(tab_noeud[num], tab_noeud[-pere]);
+ }
+ else
+ {
+ tab_noeud[num]->count = count;
+ tab_noeud[num]->parent = tab_noeud[pere];
+ if (num != 2)
+ ajout_branche(tab_noeud[pere], tab_noeud[num]);
+ }
+
+ p = strchr(p + 1, '&') + 1;
+ q = p;
+ do
+ {
+ q++;
+ if (*q == 0)
+ break;
+ }
+ while (*q != '"' || *(q - 1) == '\\');
+ l = q - p + 1;
+ name = (char*)malloc(l + 1);
+ strncpy(name, p, l); name[l] = 0;
+ unprotect_quotes(name);
+ tab_noeud[num]->name = name;
+ q++;
+ if (*q == '&')
+ {
+ p = q + 1;
+ q = p;
+ do
+ {
+ q++;
+ if (*q == 0)
+ break;
+ }
+ while (*q != '"' || *(q - 1) == '\\');
+ l = q - p + 1;
+ libel = (char*)malloc(l + 1);
+ strncpy(libel, p, l); libel[l] = 0;
+ unprotect_quotes(libel);
+ tab_noeud[num]->libel = libel;
+ p = (char*)malloc(l + 1);
+ strcpy(p, libel);
+ majuscules(p);
+ tab_noeud[num]->libel_upcase = p;
+ if (strncmp(p, "ID:", 3) == 0 || (p = strstr(p, "|ID:")) != NULL)
+ {
+ p += 2; if (*p != ':')
+ p++;
+ sscanf(p + 1, "%d", &(tab_noeud[num]->tid) );
+ }
+ }
+}
+
+
+static void raa_calc_taxo_count(raa_node* racine)
+{
+ struct raa_pair* paire;
+ int count = 0;
+
+ paire = racine->list_desc;
+ while (paire != NULL)
+ {
+ raa_calc_taxo_count(paire->value);
+ count += paire->value->count;
+ paire = paire->next;
+ }
+ racine->count += count;
+}
+
+
+int raa_loadtaxonomy(raa_db_access* raa_current_db, char* rootname,
+ int (* progress_function)(int, void*), void* progress_arg,
+ int (* need_interrupt_f)(void*), void* interrupt_arg)
/* charge la taxo complete dans raa_current_db->sp_tree et rend 0 ssi OK */
{
-int totspec, i, maxtid;
-raa_node **tab_noeud;
-struct raa_pair *pair, *pair2;
-char *reponse;
-int count, pourcent, prev_pourcent = 0;
-void *opaque;
-int interrupted;
-
-if(raa_current_db == NULL) return 1;
-if(raa_current_db->sp_tree != NULL) return 0;
-interrupted = FALSE;
-sock_fputs(raa_current_db, "zlibloadtaxonomy\n");
-sock_flush(raa_current_db);
-/* reply:
-<start of compressed data using zlib >
-code=0&total=xx
-rank&pere&count&"...name..."&"...libel..."
-loadtaxonomy END.
-<end of compressed data, back to normal data >
-*/
-opaque = prepare_sock_gz_r( raa_current_db->raa_sockfdr );
-reponse = z_read_sock(opaque);
-if(reponse == NULL || strncmp(reponse, "code=0&total=", 13) != 0) {
- return 1;
- }
-totspec = atoi(reponse + 13);
-tab_noeud = (raa_node **)calloc(totspec + 1, sizeof(raa_node *));
-count = 0;
-while(TRUE) {
- reponse = z_read_sock(opaque);
- if(strcmp(reponse, "loadtaxonomy END.") == 0) {
- if(interrupted && (tab_noeud != NULL) ) {
- for(i = 2; i <= totspec; i++) {
- if(tab_noeud[i] == NULL) continue;
- if(tab_noeud[i]->name != NULL) free(tab_noeud[i]->name);
- if(tab_noeud[i]->libel != NULL) free(tab_noeud[i]->libel);
- if(tab_noeud[i]->libel_upcase != NULL) free(tab_noeud[i]->libel_upcase);
- pair = tab_noeud[i]->list_desc;
- while(pair != NULL) {
- pair2 = pair->next;
- free(pair);
- pair = pair2;
- }
- free(tab_noeud[i]);
- }
- free(tab_noeud);
- tab_noeud = NULL;
- /* just to consume ESC that may have arrived after loadtaxonomy END. */
- sock_fputs(raa_current_db, "null_command\n");
- read_sock(raa_current_db);
- }
- break;
- }
- if(tab_noeud != NULL) raa_decode_desc_arbre(reponse, tab_noeud);
- pourcent = ((++count) * 100) / totspec;
- if(pourcent > prev_pourcent) {
- prev_pourcent = pourcent;
- if( progress_function != NULL && progress_function(pourcent, progress_arg) ) {
- if( need_interrupt_f != NULL && (! interrupted) && need_interrupt_f(interrupt_arg) ) {
- sock_fputs(raa_current_db, "\033" /* esc */);
- sock_flush(raa_current_db);
- interrupted = TRUE;
- }
- }
- }
- }
-close_sock_gz_r(opaque);
-if(tab_noeud != NULL) {
- redresse_branches(tab_noeud[2]);
- raa_calc_taxo_count(tab_noeud[2]);
- free(tab_noeud[2]->name);
- tab_noeud[2]->name = strdup(rootname);
- maxtid = 0;
- for(i = 2; i <= totspec; i++) if(tab_noeud[i] != NULL && tab_noeud[i]->tid > maxtid) maxtid = tab_noeud[i]->tid;
- raa_current_db->tid_to_rank = (int *)calloc(maxtid + 1, sizeof(int));
- if(raa_current_db->tid_to_rank != NULL) {
- raa_current_db->max_tid = maxtid;
- for(i = 2; i <= totspec; i++) {
- if(tab_noeud[i] != NULL && tab_noeud[i]->tid != 0) raa_current_db->tid_to_rank[tab_noeud[i]->tid] =
- tab_noeud[i]->rank;
- }
- }
- raa_current_db->sp_tree = tab_noeud;
- }
-return (tab_noeud == NULL ? 1 : 0);
-}
-
-
-char *raa_get_taxon_info(raa_db_access *raa_current_db, char *name, int rank, int tid, int *p_rank,
- int *p_tid, int *p_parent, struct raa_pair **p_desc_list)
+ int totspec, i, maxtid;
+ raa_node** tab_noeud;
+ struct raa_pair* pair, * pair2;
+ char* reponse;
+ int count, pourcent, prev_pourcent = 0;
+ void* opaque;
+ int interrupted;
+
+ if (raa_current_db == NULL)
+ return 1;
+ if (raa_current_db->sp_tree != NULL)
+ return 0;
+ interrupted = FALSE;
+ sock_fputs(raa_current_db, "zlibloadtaxonomy\n");
+ sock_flush(raa_current_db);
+/* reply:
+ <start of compressed data using zlib >
+ code=0&total=xx
+ rank&pere&count&"...name..."&"...libel..."
+ loadtaxonomy END.
+ <end of compressed data, back to normal data >
+ */
+ opaque = prepare_sock_gz_r( raa_current_db->raa_sockfdr );
+ reponse = z_read_sock(opaque);
+ if (reponse == NULL || strncmp(reponse, "code=0&total=", 13) != 0)
+ {
+ return 1;
+ }
+ totspec = atoi(reponse + 13);
+ tab_noeud = (raa_node**)calloc(totspec + 1, sizeof(raa_node*));
+ count = 0;
+ while (TRUE)
+ {
+ reponse = z_read_sock(opaque);
+ if (strcmp(reponse, "loadtaxonomy END.") == 0)
+ {
+ if (interrupted && (tab_noeud != NULL) )
+ {
+ for (i = 2; i <= totspec; i++)
+ {
+ if (tab_noeud[i] == NULL)
+ continue;
+ if (tab_noeud[i]->name != NULL)
+ free(tab_noeud[i]->name);
+ if (tab_noeud[i]->libel != NULL)
+ free(tab_noeud[i]->libel);
+ if (tab_noeud[i]->libel_upcase != NULL)
+ free(tab_noeud[i]->libel_upcase);
+ pair = tab_noeud[i]->list_desc;
+ while (pair != NULL)
+ {
+ pair2 = pair->next;
+ free(pair);
+ pair = pair2;
+ }
+ free(tab_noeud[i]);
+ }
+ free(tab_noeud);
+ tab_noeud = NULL;
+ /* just to consume ESC that may have arrived after loadtaxonomy END. */
+ sock_fputs(raa_current_db, "null_command\n");
+ read_sock(raa_current_db);
+ }
+ break;
+ }
+ if (tab_noeud != NULL)
+ raa_decode_desc_arbre(reponse, tab_noeud);
+ pourcent = ((++count) * 100) / totspec;
+ if (pourcent > prev_pourcent)
+ {
+ prev_pourcent = pourcent;
+ if (progress_function != NULL && progress_function(pourcent, progress_arg) )
+ {
+ if (need_interrupt_f != NULL && (!interrupted) && need_interrupt_f(interrupt_arg) )
+ {
+ sock_fputs(raa_current_db, "\033" /* esc */);
+ sock_flush(raa_current_db);
+ interrupted = TRUE;
+ }
+ }
+ }
+ }
+ close_sock_gz_r(opaque);
+ if (tab_noeud != NULL)
+ {
+ redresse_branches(tab_noeud[2]);
+ raa_calc_taxo_count(tab_noeud[2]);
+ free(tab_noeud[2]->name);
+ tab_noeud[2]->name = strdup(rootname);
+ maxtid = 0;
+ for (i = 2; i <= totspec; i++)
+ {
+ if (tab_noeud[i] != NULL && tab_noeud[i]->tid > maxtid)
+ maxtid = tab_noeud[i]->tid;
+ }
+ raa_current_db->tid_to_rank = (int*)calloc(maxtid + 1, sizeof(int));
+ if (raa_current_db->tid_to_rank != NULL)
+ {
+ raa_current_db->max_tid = maxtid;
+ for (i = 2; i <= totspec; i++)
+ {
+ if (tab_noeud[i] != NULL && tab_noeud[i]->tid != 0)
+ raa_current_db->tid_to_rank[tab_noeud[i]->tid] =
+ tab_noeud[i]->rank;
+ }
+ }
+ raa_current_db->sp_tree = tab_noeud;
+ }
+ return tab_noeud == NULL ? 1 : 0;
+}
+
+
+char* raa_get_taxon_info(raa_db_access* raa_current_db, char* name, int rank, int tid, int* p_rank,
+ int* p_tid, int* p_parent, struct raa_pair** p_desc_list)
/*
-from a taxon identified by its name or, if name is NULL, by its rank or, if rank is 0, by its taxon ID (tid)
-computes :
-- if p_rank != NULL, the taxon rank in *p_rank
-- if p_tid != NULL, the taxon ID in *p_tid
-- if p_parent != NULL, the taxon's parent rank in *p_parent (2 indicates that taxon is at top level)
-- if p_desc_list != NULL, the start of the linked chain of taxon's descending taxa in *p_desc_list
-returns the taxon name, or NULL if any error
-*/
-{
-int totspec;
-
-if(raa_current_db == NULL) return NULL;
-if(raa_current_db->sp_tree == NULL) raa_loadtaxonomy(raa_current_db, "root", NULL, NULL, NULL, NULL);
-if(raa_current_db->sp_tree == NULL) return NULL;
-totspec = raa_read_first_rec(raa_current_db, raa_spec);
-if(name != NULL) {
- name = strdup(name);
- if(name == NULL) return NULL;
- trim_key(name); majuscules(name);
- for(rank = 3; rank <= totspec; rank++) {
- if(raa_current_db->sp_tree[rank] != NULL && strcmp(name, raa_current_db->sp_tree[rank]->name) == 0) break;
- }
- free(name);
- }
-if(name == NULL && rank == 0 && tid >= 1 && tid <= raa_current_db->max_tid) rank = raa_current_db->tid_to_rank[tid];
-if(rank > totspec || rank < 2 || raa_current_db->sp_tree[rank] == NULL) return NULL;
-if(rank != 2) {
- while(raa_current_db->sp_tree[rank]->parent == NULL) {
- rank = raa_current_db->sp_tree[rank]->syno->rank;
- }
- }
-if(p_rank != NULL) *p_rank = rank;
-if(p_tid != NULL) *p_tid = raa_current_db->sp_tree[rank]->tid;
-if(p_parent != NULL) *p_parent = ( raa_current_db->sp_tree[rank]->parent != NULL ?
- raa_current_db->sp_tree[rank]->parent->rank : 0);
-if(p_desc_list != NULL) *p_desc_list = raa_current_db->sp_tree[rank]->list_desc;
-return raa_current_db->sp_tree[rank]->name;
-}
-
-
-char *raa_getattributes_both(raa_db_access *raa_current_db, const char *id, int rank,
- int *prank, int *plength, int *pframe, int *pgc, char **pacc, char **pdesc, char **pspecies, char **pseq)
+ from a taxon identified by its name or, if name is NULL, by its rank or, if rank is 0, by its taxon ID (tid)
+ computes :
+ - if p_rank != NULL, the taxon rank in *p_rank
+ - if p_tid != NULL, the taxon ID in *p_tid
+ - if p_parent != NULL, the taxon's parent rank in *p_parent (2 indicates that taxon is at top level)
+ - if p_desc_list != NULL, the start of the linked chain of taxon's descending taxa in *p_desc_list
+ returns the taxon name, or NULL if any error
+ */
+{
+ int totspec;
+
+ if (raa_current_db == NULL)
+ return NULL;
+ if (raa_current_db->sp_tree == NULL)
+ raa_loadtaxonomy(raa_current_db, "root", NULL, NULL, NULL, NULL);
+ if (raa_current_db->sp_tree == NULL)
+ return NULL;
+ totspec = raa_read_first_rec(raa_current_db, raa_spec);
+ if (name != NULL)
+ {
+ name = strdup(name);
+ if (name == NULL)
+ return NULL;
+ trim_key(name); majuscules(name);
+ for (rank = 3; rank <= totspec; rank++)
+ {
+ if (raa_current_db->sp_tree[rank] != NULL && strcmp(name, raa_current_db->sp_tree[rank]->name) == 0)
+ break;
+ }
+ free(name);
+ }
+ if (name == NULL && rank == 0 && tid >= 1 && tid <= raa_current_db->max_tid)
+ rank = raa_current_db->tid_to_rank[tid];
+ if (rank > totspec || rank < 2 || raa_current_db->sp_tree[rank] == NULL)
+ return NULL;
+ if (rank != 2)
+ {
+ while (raa_current_db->sp_tree[rank]->parent == NULL)
+ {
+ rank = raa_current_db->sp_tree[rank]->syno->rank;
+ }
+ }
+ if (p_rank != NULL)
+ *p_rank = rank;
+ if (p_tid != NULL)
+ *p_tid = raa_current_db->sp_tree[rank]->tid;
+ if (p_parent != NULL)
+ *p_parent = ( raa_current_db->sp_tree[rank]->parent != NULL ?
+ raa_current_db->sp_tree[rank]->parent->rank : 0);
+ if (p_desc_list != NULL)
+ *p_desc_list = raa_current_db->sp_tree[rank]->list_desc;
+ return raa_current_db->sp_tree[rank]->name;
+}
+
+
+static char* raa_getattributes_both(raa_db_access* raa_current_db, const char* id, int rank,
+ int* prank, int* plength, int* pframe, int* pgc, char** pacc, char** pdesc, char** pspecies, char** pseq)
/*
-for a sequence identified by name or acc. no. (id != NULL) or by rank
-returns rank, name, accession, length, frame, acnuc genetic code ID,
-one-line description, species, and full sequence.
-return value: NULL if not found or name (in private memory)
-pacc, pdesc, pspecies and pseq point to private memory upon return
-prank, plength, pframe, pgc, pacc, pdesc, pspecies, pseq can be NULL is no such information is needed
-*/
-{
-Reponse *rep;
-char *p, *reponse;
-int err;
-static char mnemo[WIDTH_MAX], species[WIDTH_MAX], access[WIDTH_MAX], descript[WIDTH_MAX];
-
-if(raa_current_db == NULL) return NULL;
-if(id != NULL) sock_printf(raa_current_db, "getattributes&id=%s&seq=%c\n", id, pseq == NULL ? 'F' : 'T');
-else sock_printf(raa_current_db, "getattributes&rank=%d&seq=%c\n", rank, pseq == NULL ? 'F' : 'T');
-reponse = read_sock(raa_current_db);
-if(reponse == NULL) {
- return NULL;
- }
-rep=initreponse();
-parse(reponse,rep);
-p=val(rep,"code");
-err = atoi(p);
-free(p);
-if(err == 0) {
- if(prank != NULL) {
- p=val(rep,"rank");
- *prank = atoi(p);
- free(p);
- }
- if(plength != NULL) {
- p=val(rep,"length");
- *plength = atoi(p);
- free(p);
- }
- if(pframe != NULL) {
- p=val(rep,"fr");
- if(p != NULL) {
- *pframe = atoi(p);
- free(p);
- }
- else *pframe = 0;
- }
- if(pgc != NULL) {
- p=val(rep,"gc");
- if(p != NULL) {
- *pgc = atoi(p);
- free(p);
- }
- else *pgc = 0;
- }
- p = val(rep, "name");
- strcpy(mnemo, p);
- free(p);
- if(pacc != NULL) {
- p = val(rep, "acc");
- strcpy(access, p);
- free(p);
- *pacc = access;
- }
- if(pspecies != NULL) {
- p = val(rep, "spec");
- strcpy(species, p);
- free(p);
- *pspecies = species;
- p = species;
- while(*(++p) != 0) *p = tolower(*p);
- }
- if(pdesc != NULL) {
- p = val(rep, "descr");
- strcpy(descript, p);
- free(p);
- *pdesc = descript;
- }
- if(pseq != NULL) {
- *pseq = read_sock(raa_current_db);
- if(*pseq != NULL) {
- *pseq += 4; /* seq=xxxx */
- }
- }
- err = 0;
- }
-clear_reponse(rep);
-return (err ? NULL : mnemo);
-}
-
-
-char *raa_getattributes(raa_db_access *raa_current_db, const char *id,
- int *prank, int *plength, int *pframe, int *pgc, char **pacc, char **pdesc, char **pspecies, char **pseq)
-{
- return raa_getattributes_both(raa_current_db, id, 0, prank, plength, pframe, pgc, pacc, pdesc, pspecies, pseq);
-}
-
-
-char *raa_seqrank_attributes(raa_db_access *raa_current_db, int rank,
- int *plength, int *pframe, int *pgc, char **pacc, char **pdesc, char **pspecies, char **pseq)
-{
- return raa_getattributes_both(raa_current_db, NULL, rank, NULL, plength, pframe, pgc, pacc, pdesc, pspecies, pseq);
+ for a sequence identified by name or acc. no. (id != NULL) or by rank
+ returns rank, name, accession, length, frame, acnuc genetic code ID,
+ one-line description, species, and full sequence.
+ return value: NULL if not found or name (in private memory)
+ pacc, pdesc, pspecies and pseq point to private memory upon return
+ prank, plength, pframe, pgc, pacc, pdesc, pspecies, pseq can be NULL is no such information is needed
+ */
+{
+ Reponse* rep;
+ char* p, * reponse;
+ int err;
+
+ if (raa_current_db == NULL)
+ return NULL;
+ if (id != NULL)
+ sock_printf(raa_current_db, "getattributes&id=%s&seq=%c\n", id, pseq == NULL ? 'F' : 'T');
+ else
+ sock_printf(raa_current_db, "getattributes&rank=%d&seq=%c\n", rank, pseq == NULL ? 'F' : 'T');
+ reponse = read_sock(raa_current_db);
+ if (reponse == NULL)
+ {
+ return NULL;
+ }
+ rep = initreponse();
+ parse(reponse, rep);
+ p = val(rep, "code");
+ err = atoi(p);
+ free(p);
+ if (err == 0)
+ {
+ if (prank != NULL)
+ {
+ p = val(rep, "rank");
+ *prank = atoi(p);
+ free(p);
+ }
+ if (plength != NULL)
+ {
+ p = val(rep, "length");
+ *plength = atoi(p);
+ free(p);
+ }
+ if (pframe != NULL)
+ {
+ p = val(rep, "fr");
+ if (p != NULL)
+ {
+ *pframe = atoi(p);
+ free(p);
+ }
+ else
+ *pframe = 0;
+ }
+ if (pgc != NULL)
+ {
+ p = val(rep, "gc");
+ if (p != NULL)
+ {
+ *pgc = atoi(p);
+ free(p);
+ }
+ else
+ *pgc = 0;
+ }
+ p = val(rep, "name");
+ strcpy(raa_current_db->mnemo, p);
+ free(p);
+ if (pacc != NULL)
+ {
+ p = val(rep, "acc");
+ strcpy(raa_current_db->access, p);
+ free(p);
+ *pacc = raa_current_db->access;
+ }
+ if (pspecies != NULL)
+ {
+ p = val(rep, "spec");
+ strcpy(raa_current_db->species, p);
+ free(p);
+ *pspecies = raa_current_db->species;
+ p = raa_current_db->species;
+ while (*(++p) != 0)
+ *p = tolower(*p);
+ }
+ if (pdesc != NULL)
+ {
+ p = val(rep, "descr");
+ strcpy(raa_current_db->descript, p);
+ free(p);
+ *pdesc = raa_current_db->descript;
+ }
+ if (pseq != NULL)
+ {
+ *pseq = read_sock(raa_current_db);
+ if (*pseq != NULL)
+ {
+ *pseq += 4; /* seq=xxxx */
+ }
+ }
+ err = 0;
+ }
+ clear_reponse(rep);
+ return err ? NULL : raa_current_db->mnemo;
}
+char* raa_getattributes(raa_db_access* raa_current_db, const char* id,
+ int* prank, int* plength, int* pframe, int* pgc, char** pacc, char** pdesc, char** pspecies, char** pseq)
+{
+ return raa_getattributes_both(raa_current_db, id, 0, prank, plength, pframe, pgc, pacc, pdesc, pspecies, pseq);
+}
+
+char* raa_seqrank_attributes(raa_db_access* raa_current_db, int rank,
+ int* plength, int* pframe, int* pgc, char** pacc, char** pdesc, char** pspecies, char** pseq)
+{
+ return raa_getattributes_both(raa_current_db, NULL, rank, NULL, plength, pframe, pgc, pacc, pdesc, pspecies, pseq);
+}
diff --git a/src/Bpp/Raa/RAA_acnuc.h b/src/Bpp/Raa/RAA_acnuc.h
index 30efaa6..c59d773 100644
--- a/src/Bpp/Raa/RAA_acnuc.h
+++ b/src/Bpp/Raa/RAA_acnuc.h
@@ -7,7 +7,6 @@
#include <ctype.h>
#if defined(WIN32)
#define SOCKBUFS 8192
-#include <winsock2.h>
#endif
#ifdef __alpha
typedef long raa_long;
@@ -25,209 +24,247 @@ typedef long long raa_long;
#define ERREUR 1
#endif
-struct rlng { /* LONGL series of linked records containing lists of SUBSEQ ranks */
- int next; /* to LONGL for next element of the long list, or 0 when list is finished */
- int sub[1]; /* array (length given by global SUBINLNG) of ranks of SUBSEQ records or of 0s */
- };
+struct rlng /* LONGL series of linked records containing lists of SUBSEQ ranks */
+{int next; /* to LONGL for next element of the long list, or 0 when list is finished */
+ int sub[1]; /* array (length given by global SUBINLNG) of ranks of SUBSEQ records or of 0s */
+};
#define RAA_GFRAG_BSIZE 10000
-struct gfrag_aux {
- char buffer[RAA_GFRAG_BSIZE + 1];
- int lbuf, nseq_buf, first_buf, l_nseq_buf;
- };
+struct gfrag_aux
+{
+ char buffer[RAA_GFRAG_BSIZE + 1];
+ int lbuf, nseq_buf, first_buf, l_nseq_buf;
+};
-struct readsub_aux {
- char *name;
- int lname, previous, length, type, toext, lkey, locus, frame, gencode, div;
- raa_long addr;
- };
+struct readsub_aux
+{
+ char* name;
+ int lname, previous, length, type, toext, lkey, locus, frame, gencode, div;
+ raa_long addr;
+};
#define ANNOTCOUNT 40
-struct annot_aux {
- char *annotline[ANNOTCOUNT + 1];
- int annotcurrent, annotcount, annotdiv;
- raa_long annotaddr, annotaddrfirst, annotaddrlast;
- char annotsbuffer[ 300 ];
- };
-
-struct readsp_kw_aux {
- char name[150], libel[200];
- int lsub, desc, syno, host, previous;
- };
+struct annot_aux
+{
+ char* annotline[ANNOTCOUNT + 1];
+ int annotcurrent, annotcount, annotdiv;
+ raa_long annotaddr, annotaddrfirst, annotaddrlast;
+ char annotsbuffer[ 300 ];
+};
+
+struct readsp_kw_aux
+{
+ char name[150], libel[200];
+ int lsub, desc, syno, host, previous;
+};
#define BLOCK_ELTS_IN_LIST 500
-struct nextelt_aux {
- int current_rank, previous, total;
- int tabnum[BLOCK_ELTS_IN_LIST];
- char *tabname[BLOCK_ELTS_IN_LIST];
- int tablength[BLOCK_ELTS_IN_LIST];
- raa_long taboffset[BLOCK_ELTS_IN_LIST];
- int tabdiv[BLOCK_ELTS_IN_LIST];
- };
-
+struct nextelt_aux
+{
+ int current_rank, previous, total;
+ int tabnum[BLOCK_ELTS_IN_LIST];
+ char* tabname[BLOCK_ELTS_IN_LIST];
+ int tablength[BLOCK_ELTS_IN_LIST];
+ raa_long taboffset[BLOCK_ELTS_IN_LIST];
+ int tabdiv[BLOCK_ELTS_IN_LIST];
+};
+
#define S_BUF_SHRT 5000 /* number of memorized SHORTL records */
-struct readshrt_aux {
- unsigned shrt_buffer[S_BUF_SHRT][3]; /* [0]=SHORTL_rank [1]=val [2]=next */
- int shrt_max, shrt_begin, total;
- };
-
-struct readsmj_aux {
- int lastrec;
- char **names, **libels;
- unsigned *plongs;
- };
-
-typedef struct raa_node {
- char *name;
- char *libel;
- char *libel_upcase;
- int rank;
- int tid;
- int count;
- struct raa_node *parent;
- struct raa_pair *list_desc;
- struct raa_node *syno;
- } raa_node;
-struct raa_pair {
- raa_node *value;
- struct raa_pair *next;
- };
-
-typedef struct _raa_db_access {
- char *dbname;
- FILE *raa_sockfdr, *raa_sockfdw;
- int genbank, embl, swissprot, nbrf;
- int nseq, longa, maxa;
- int L_MNEMO, WIDTH_SP, WIDTH_KW, WIDTH_SMJ, WIDTH_AUT, WIDTH_BIB, ACC_LENGTH, SUBINLNG, lrtxt;
- raa_node **sp_tree; /* NULL or the full taxonomy tree */
- int max_tid; /* largest correct taxon ID value */
- int *tid_to_rank; /* NULL or tid-to-rank table */
- struct rlng *rlng_buffer;
- struct gfrag_aux gfrag_data;
- struct readsub_aux readsub_data;
- int first_recs[20];
- struct annot_aux annot_data;
- struct readsp_kw_aux readspec_data, readkey_data;
- struct nextelt_aux nextelt_data;
- struct readshrt_aux readshrt_data;
- struct readsmj_aux readsmj_data;
- void *matchkey_data;
- /* mostly for raa_query/raa_query_win usage */
- int tot_key_annots;
- char **key_annots, **key_annots_min;
- unsigned char *want_key_annots;
+struct readshrt_aux
+{
+ unsigned shrt_buffer[S_BUF_SHRT][3]; /* [0]=SHORTL_rank [1]=val [2]=next */
+ int shrt_max, shrt_begin, total;
+};
+
+typedef struct shrt2_list
+{
+ int length;
+ int size;
+ unsigned point;
+ unsigned next;
+ unsigned vals[1];
+} shrt2_list;
+
+struct readsmj_aux
+{
+ int lastrec;
+ char** names, ** libels;
+ unsigned* plongs;
+};
+
+typedef struct raa_node
+{
+ char* name;
+ char* libel;
+ char* libel_upcase;
+ int rank;
+ int tid;
+ int count;
+ struct raa_node* parent;
+ struct raa_pair* list_desc;
+ struct raa_node* syno;
+} raa_node;
+struct raa_pair
+{
+ raa_node* value;
+ struct raa_pair* next;
+};
+
+#define WIDTH_MAX 150
+
+typedef enum { raa_sub_of_bib = 0, raa_spec_of_loc, raa_bib_of_loc, raa_aut_of_bib, raa_bib_of_aut,
+ raa_sub_of_acc, raa_key_of_sub, raa_acc_of_loc } raa_shortl2_kind;
+
+typedef struct _raa_db_access
+{
+ char* dbname;
+ FILE* raa_sockfdr, * raa_sockfdw;
+ int genbank, embl, swissprot, nbrf;
+ int nseq, longa, maxa;
+ int L_MNEMO, WIDTH_SP, WIDTH_KW, WIDTH_SMJ, WIDTH_AUT, WIDTH_BIB, ACC_LENGTH, SUBINLNG, lrtxt, VALINSHRT2;
+ raa_node** sp_tree; /* NULL or the full taxonomy tree */
+ int max_tid; /* largest correct taxon ID value */
+ int* tid_to_rank; /* NULL or tid-to-rank table */
+ struct rlng* rlng_buffer;
+ struct gfrag_aux gfrag_data;
+ struct readsub_aux readsub_data;
+ int first_recs[20];
+ struct annot_aux annot_data;
+ struct readsp_kw_aux readspec_data, readkey_data;
+ struct nextelt_aux nextelt_data;
+ struct readshrt_aux readshrt_data;
+ struct shrt2_list* readshrt2_data[raa_acc_of_loc + 1];
+ struct readsmj_aux readsmj_data;
+ void* matchkey_data;
+ /* mostly for raa_query/raa_query_win usage */
+ int tot_key_annots;
+ char** key_annots, ** key_annots_min;
+ unsigned char* want_key_annots;
#ifdef WIN32
- char sock_input[SOCKBUFS]; /* WIN32 socket input buffer */
- char *sock_input_pos, *sock_input_end;
- char sock_output[SOCKBUFS]; /* WIN32 socket output buffer */
- DWORD sock_output_lbuf;
+ char sock_input[SOCKBUFS]; /* WIN32 socket input buffer */
+ char* sock_input_pos, * sock_input_end;
+ char sock_output[SOCKBUFS]; /* WIN32 socket output buffer */
+ unsigned sock_output_lbuf;
#endif
- } raa_db_access;
+ char buffer[5000];
+ char remote_file[300];
+ char* full_line;
+ int max_full_line;
+ int was_here;
+ char* namestr;
+ char residuecount[30];
+ char* help;
+ int lhelp;
+ int tmp_total;
+ int tmp_current;
+ int* tmp_prelist;
+ char* translate_buffer;
+ int num_5_partial;
+ char mnemo[WIDTH_MAX];
+ char species[WIDTH_MAX];
+ char access[WIDTH_MAX];
+ char descript[WIDTH_MAX];
+ char date[12];
+} raa_db_access;
-#define WIDTH_MAX 150
typedef enum { raa_sub = 0, raa_loc, raa_key, raa_spec, raa_shrt, raa_lng, raa_ext, raa_smj,
- raa_aut, raa_bib, raa_txt, raa_acc } raa_file;
-typedef void (*raa_char_void_function)(raa_db_access *, char *);
-struct chain_void {
- void *data;
- struct chain_void *next;
- };
+ raa_aut, raa_bib, raa_txt, raa_acc } raa_file;
+typedef void (*raa_char_void_function)(raa_db_access*, char*);
/* global variables */
-extern raa_char_void_function raa_error_mess_proc;/*this function sd call raa_acnucclose*/
-
-
-extern int raa_acnucopen (char *clientid, raa_db_access **psock) ;
-extern int raa_decode_address(char *url, char **p_ip_name, int *socket, char **p_remote_db);
-extern int raa_acnucopen_alt (char *serveurName, int port, char *db_name, char *clientid, raa_db_access **psock);
-extern int raa_open_socket(char *serveurName, int port, char *clientid, raa_db_access **psock);
-extern int raa_opendb(raa_db_access *raa_current_db, char *db_name);
-int raa_opendb_pw(raa_db_access *raa_current_db, char *db_name, void *ptr, char *(*getpasswordf)(void *) );
-extern int raa_gfrag(raa_db_access *raa_current_db, int nsub, int first, int lfrag, char *dseq) ;
-extern void raa_acnucclose(raa_db_access *raa_current_db) ;
-extern int raa_prep_acnuc_query(raa_db_access *raa_current_db) ;
-extern int raa_proc_query(raa_db_access *raa_current_db, char *query, char **message, char *nomliste, int *numlist,
- int *count, int *locus, int *type) ;
-int raa_nexteltinlist(raa_db_access *raa_current_db, int first, int lrank, char **pname, int *plength) ;
-int raa_nexteltinlist_annots(raa_db_access *raa_current_db, int first, int lrank, char **pname, int *plength,
- raa_long *paddr, int *pdiv);
-raa_long scan_raa_long(char *txt);
-int raa_seq_to_annots(raa_db_access *raa_current_db, int numseq, raa_long *faddr, int *div);
-char *print_raa_long(raa_long val);
-char *raa_read_annots(raa_db_access *raa_current_db, raa_long faddr, int div);
-char *raa_next_annots(raa_db_access *raa_current_db, raa_long *faddr);
-char *raa_translate_cds(raa_db_access *raa_current_db, int seqnum);
-char raa_translate_init_codon(raa_db_access *raa_current_db, int numseq);
-int raa_iknum(raa_db_access *raa_current_db, char *name, raa_file cas);
-int raa_isenum(raa_db_access *raa_current_db, char *name);
-int raa_bcount(raa_db_access *raa_current_db, int lrank);
-void raa_bit1(raa_db_access *raa_current_db, int lrank, int num);
-void raa_bit0(raa_db_access *raa_current_db, int lrank, int num);
-int raa_btest(raa_db_access *raa_current_db, int lrank, int num);
-void raa_copylist(raa_db_access *raa_current_db, int from, int to);
-void raa_zerolist(raa_db_access *raa_current_db, int rank);
-void raa_setliststate(raa_db_access *raa_current_db, int lrank, int locus, int type);
-char *raa_getliststate(raa_db_access *raa_current_db, int lrank, int *locus, int *type, int *count);
-char *raa_residuecount(raa_db_access *raa_current_db, int lrank);
-int raa_getemptylist(raa_db_access *raa_current_db, char *name);
-int raa_setlistname(raa_db_access *raa_current_db, int lrank, char *name);
-int raa_getlistrank(raa_db_access *raa_current_db, char *name);
-int raa_releaselist(raa_db_access *raa_current_db, int lrank);
-int raa_countfilles(raa_db_access *raa_current_db, int lrank);
-int raa_alllistranks(raa_db_access *raa_current_db, int **pranks);
-int raa_fcode(raa_db_access *raa_current_db, raa_file cas, char *name);
-int raa_read_first_rec(raa_db_access *raa_current_db, raa_file cas);
-char *raa_readsub(raa_db_access *raa_current_db, int num, int *plength, int *ptype, int *pext, int *plkey, int *plocus,
- int *pframe, int *pgencode);
-char *raa_readsub_pannots(raa_db_access *raa_current_db, int num, int *plength, int *ptype, int *pext, int *plkey, int *plocus,
- int *pframe, int *pgencode, raa_long *paddr, int *pdiv);
-char *raa_readloc(raa_db_access *raa_current_db, int num, int *sub, int *pnuc, int *spec, int *host, int *plref,
- int *molec, int *placc, int *org);
-char *raa_readspec(raa_db_access *raa_current_db, int num, char **plibel, int *plsub, int *desc, int *syno, int *plhost);
-char *raa_readkey(raa_db_access *raa_current_db, int num, char **plibel, int *plsub, int *desc, int *syno);
-char *raa_readsmj(raa_db_access *raa_current_db, int num, char **plibel, int *plong);
-char *raa_readacc(raa_db_access *raa_current_db, int num, int *plsub);
-int raa_readext(raa_db_access *raa_current_db, int num, int *mere, int *deb, int *fin);
-int raa_readlng(raa_db_access *raa_current_db, int num);
-unsigned raa_readshrt(raa_db_access *raa_current_db, unsigned point, int *val);
-char *raa_ghelp(raa_db_access *raa_current_db, char *fname, char *topic);
-int raa_nextmatchkey(raa_db_access *raa_current_db, int num, char *pattern, char **matching);
-int raa_savelist(raa_db_access *raa_current_db, int lrank, FILE *out, int use_acc, char *prefix);
-int raa_modifylist(raa_db_access *raa_current_db, int lrank, char *type /* "length" or "date" */, char *operation /* ">2000" */,
- int *pnewlrank, int (*check_interrupt)(void) , int *p_processed);
-int raa_knowndbs(raa_db_access *raa_current_db, char ***pnames, char ***pdescriptions);
-char *raa_short_descr(raa_db_access *raa_current_db, int seqnum, char *text, int maxlen, raa_long pinf, int div, char *name);
-struct chain_void *raa_get_list_open_dbs(void);
-void *raa_prep_extract(raa_db_access *raa_current_db, char *format, FILE *outstream, char *choix,
- char *feature_name, char *bornes, char *min_bornes, char **message, int lrank);
-int raa_extract_1_seq(void *opaque);
-int raa_extract_interrupt(raa_db_access *raa_current_db, void *opaque);
-void *raa_prep_coordinates(raa_db_access *raa_current_db, int lrank, int seqnum,
- char *operation, /* "simple","fragment","feature","region" */
- char *feature_name, char *bounds, char *min_bounds);
-int *raa_1_coordinate_set(void *);
-int raa_loadtaxonomy(raa_db_access *raa_current_db, char *rootname,
- int (*progress_function)(int, void *), void *progress_arg,
- int (*need_interrupt_f)(void *), void *interrupt_arg);
-char *raa_get_taxon_info(raa_db_access *raa_current_db, char *name, int rank, int tid, int *p_rank,
- int *p_tid, int *p_parent, struct raa_pair **p_desc_list);
-char *raa_getattributes(raa_db_access *raa_current_db, const char *id,
- int *prank, int *plength, int *pframe, int *pgc, char **pacc, char **pdesc, char **pspecies, char **pseq);
-char *raa_seqrank_attributes(raa_db_access *raa_current_db, int rank,
- int *plength, int *pframe, int *pgc, char **pacc, char **pdesc, char **pspecies, char **pseq);
-
-int sock_fputs(raa_db_access *raa_current_db, char *line);
-int sock_flush(raa_db_access *raa_current_db);
-char *read_sock(raa_db_access *raa_current_db);
-
-
-int trim_key(char *name); /* remove trailing spaces */
-void majuscules(char *name);
-int atoi_u(const char *p);
-char *protect_quotes(char *name); /* replace " by \" returns in static memory */
-void compact(char *chaine);
-int strcmptrail(char *s1, int l1, char *s2, int l2);
-
-
-#endif /* RAA_ACNUC_H */
+extern raa_char_void_function raa_error_mess_proc; /*this function sd call raa_acnucclose*/
+
+
+extern int raa_acnucopen (const char* clientid, raa_db_access** psock);
+extern int raa_decode_address(char* url, char** p_ip_name, int* socket, char** p_remote_db);
+extern int raa_acnucopen_alt (const char* serveurName, int port, const char* db_name, const char* clientid, raa_db_access** psock);
+extern int raa_open_socket(const char* serveurName, int port, const char* clientid, raa_db_access** psock);
+extern int raa_opendb(raa_db_access* raa_current_db, const char* db_name);
+int raa_opendb_pw(raa_db_access* raa_current_db, const char* db_name, void* ptr, char*(*getpasswordf)(void*) );
+extern int raa_gfrag(raa_db_access* raa_current_db, int nsub, int first, int lfrag, char* dseq);
+extern void raa_acnucclose(raa_db_access* raa_current_db);
+extern int raa_prep_acnuc_query(raa_db_access* raa_current_db);
+extern int raa_proc_query(raa_db_access* raa_current_db, char* query, char** message, char* nomliste, int* numlist,
+ int* count, int* locus, int* type);
+int raa_nexteltinlist(raa_db_access* raa_current_db, int first, int lrank, char** pname, int* plength);
+int raa_nexteltinlist_annots(raa_db_access* raa_current_db, int first, int lrank, char** pname, int* plength,
+ raa_long* paddr, int* pdiv);
+raa_long scan_raa_long(char* txt);
+int raa_seq_to_annots(raa_db_access* raa_current_db, int numseq, raa_long* faddr, int* div);
+char* print_raa_long(raa_long val, char* buffer);
+char* raa_read_annots(raa_db_access* raa_current_db, raa_long faddr, int div);
+char* raa_next_annots(raa_db_access* raa_current_db, raa_long* faddr);
+char* raa_translate_cds(raa_db_access* raa_current_db, int seqnum);
+char raa_translate_init_codon(raa_db_access* raa_current_db, int numseq);
+int raa_iknum(raa_db_access* raa_current_db, char* name, raa_file cas);
+int raa_isenum(raa_db_access* raa_current_db, char* name);
+int raa_bcount(raa_db_access* raa_current_db, int lrank);
+void raa_bit1(raa_db_access* raa_current_db, int lrank, int num);
+void raa_bit0(raa_db_access* raa_current_db, int lrank, int num);
+int raa_btest(raa_db_access* raa_current_db, int lrank, int num);
+void raa_copylist(raa_db_access* raa_current_db, int from, int to);
+void raa_zerolist(raa_db_access* raa_current_db, int rank);
+void raa_setliststate(raa_db_access* raa_current_db, int lrank, int locus, int type);
+char* raa_getliststate(raa_db_access* raa_current_db, int lrank, int* locus, int* type, int* count);
+char* raa_residuecount(raa_db_access* raa_current_db, int lrank);
+int raa_getemptylist(raa_db_access* raa_current_db, char* name);
+int raa_setlistname(raa_db_access* raa_current_db, int lrank, char* name);
+int raa_getlistrank(raa_db_access* raa_current_db, char* name);
+int raa_releaselist(raa_db_access* raa_current_db, int lrank);
+int raa_countfilles(raa_db_access* raa_current_db, int lrank);
+int raa_alllistranks(raa_db_access* raa_current_db, int** pranks);
+int raa_fcode(raa_db_access* raa_current_db, raa_file cas, char* name);
+int raa_read_first_rec(raa_db_access* raa_current_db, raa_file cas);
+char* raa_readsub(raa_db_access* raa_current_db, int num, int* plength, int* ptype, int* pext, int* plkey, int* plocus,
+ int* pframe, int* pgencode);
+char* raa_readsub_pannots(raa_db_access* raa_current_db, int num, int* plength, int* ptype, int* pext, int* plkey, int* plocus,
+ int* pframe, int* pgencode, raa_long* paddr, int* pdiv);
+char* raa_readloc(raa_db_access* raa_current_db, int num, int* sub, int* pnuc, int* spec, int* host, int* plref,
+ int* molec, int* placc, int* org);
+char* raa_readspec(raa_db_access* raa_current_db, int num, char** plibel, int* plsub, int* desc, int* syno, int* plhost);
+char* raa_readkey(raa_db_access* raa_current_db, int num, char** plibel, int* plsub, int* desc, int* syno);
+char* raa_readsmj(raa_db_access* raa_current_db, int num, char** plibel, int* plong);
+char* raa_readacc(raa_db_access* raa_current_db, int num, int* plsub);
+int raa_readext(raa_db_access* raa_current_db, int num, int* mere, int* deb, int* fin);
+int raa_readlng(raa_db_access* raa_current_db, int num);
+unsigned raa_readshrt(raa_db_access* raa_current_db, unsigned point, int* val);
+unsigned raa_followshrt2(raa_db_access* raa_current_db, int* p_point, int* p_rank, raa_shortl2_kind kind);
+char* raa_ghelp(raa_db_access* raa_current_db, char* fname, char* topic);
+int raa_nextmatchkey(raa_db_access* raa_current_db, int num, char* pattern, char** matching);
+int raa_savelist(raa_db_access* raa_current_db, int lrank, FILE* out, int use_acc, char* prefix);
+int raa_modifylist(raa_db_access* raa_current_db, int lrank, char* type /* "length" or "date" */, char* operation /* ">2000" */,
+ int* pnewlrank, int (* check_interrupt)(void), int* p_processed);
+int raa_knowndbs(raa_db_access* raa_current_db, char*** pnames, char*** pdescriptions);
+char* raa_short_descr(raa_db_access* raa_current_db, int seqnum, char* text, int maxlen, raa_long pinf, int div, char* name);
+void* raa_prep_extract(raa_db_access* raa_current_db, char* format, FILE* outstream, char* choix,
+ char* feature_name, char* bornes, char* min_bornes, char** message, int lrank);
+int raa_extract_1_seq(void* opaque);
+int raa_extract_interrupt(raa_db_access* raa_current_db, void* opaque);
+void* raa_prep_coordinates(raa_db_access* raa_current_db, int lrank, int seqnum,
+ char* operation, /* "simple","fragment","feature","region" */
+ char* feature_name, char* bounds, char* min_bounds);
+int* raa_1_coordinate_set(void*);
+int raa_loadtaxonomy(raa_db_access* raa_current_db, char* rootname,
+ int (* progress_function)(int, void*), void* progress_arg,
+ int (* need_interrupt_f)(void*), void* interrupt_arg);
+char* raa_get_taxon_info(raa_db_access* raa_current_db, char* name, int rank, int tid, int* p_rank,
+ int* p_tid, int* p_parent, struct raa_pair** p_desc_list);
+char* raa_getattributes(raa_db_access* raa_current_db, const char* id,
+ int* prank, int* plength, int* pframe, int* pgc, char** pacc, char** pdesc, char** pspecies, char** pseq);
+char* raa_seqrank_attributes(raa_db_access* raa_current_db, int rank,
+ int* plength, int* pframe, int* pgc, char** pacc, char** pdesc, char** pspecies, char** pseq);
+
+int sock_fputs(raa_db_access* raa_current_db, const char* line);
+int sock_flush(raa_db_access* raa_current_db);
+char* read_sock(raa_db_access* raa_current_db);
+
+
+int trim_key(char* name); /* remove trailing spaces */
+void majuscules(char* name);
+int atoi_u(const char* p);
+void compact(char* chaine);
+int strcmptrail(char* s1, int l1, char* s2, int l2);
+
+
+#endif/* RAA_ACNUC_H */
diff --git a/src/Bpp/Raa/RaaList.cpp b/src/Bpp/Raa/RaaList.cpp
index 4b4658f..a77635f 100644
--- a/src/Bpp/Raa/RaaList.cpp
+++ b/src/Bpp/Raa/RaaList.cpp
@@ -1,4 +1,3 @@
-
#include "RAA.h"
using namespace std;
@@ -6,14 +5,14 @@ using namespace bpp;
RaaList::RaaList()
{
- myraa = NULL;
- from = 1;
+ myraa = NULL;
+ from = 1;
}
int RaaList::getCount(void)
{
- return raa_bcount(myraa->raa_data, rank);
+ return raa_bcount(myraa->raa_data, rank);
}
const string RaaList::LIST_SEQUENCES = "sequence list";
@@ -23,97 +22,103 @@ const string RaaList::LIST_SPECIES = "species list";
int RaaList::firstElement()
{
- from = 1;
- return nextElement();
+ from = 1;
+ return nextElement();
}
int RaaList::nextElement()
{
- char *sname;
- int seqrank = raa_nexteltinlist(myraa->raa_data, from, rank, &sname, &elementlength);
- if(seqrank) {
- elementname = sname;
- from = seqrank;
- }
- return seqrank;
+ char* sname;
+ int seqrank = raa_nexteltinlist(myraa->raa_data, from, rank, &sname, &elementlength);
+ if (seqrank)
+ {
+ elementname = sname;
+ from = seqrank;
+ }
+ return seqrank;
}
void RaaList::setFrom(int element_rank)
{
- from = element_rank;
+ from = element_rank;
}
string RaaList::residueCount()
{
- char *count = raa_residuecount(myraa->raa_data, rank);
- string retval(count);
- return retval;
+ char* count = raa_residuecount(myraa->raa_data, rank);
+ string retval(count);
+ return retval;
}
void RaaList::addElement(int elt_rank)
{
- raa_bit1(myraa->raa_data, rank, elt_rank);
+ raa_bit1(myraa->raa_data, rank, elt_rank);
}
bool RaaList::parentsOnly(void)
{
- if(*type == RaaList::LIST_SEQUENCES) return true;
- int isloc;
- raa_getliststate(myraa->raa_data, rank, &isloc, NULL, NULL);
- return (bool)isloc;
+ if (*type == RaaList::LIST_SEQUENCES)
+ return true;
+ int isloc;
+ raa_getliststate(myraa->raa_data, rank, &isloc, NULL, NULL);
+ return (bool)isloc;
}
void RaaList::removeElement(int elt_rank)
{
- raa_bit0(myraa->raa_data, rank, elt_rank);
+ raa_bit0(myraa->raa_data, rank, elt_rank);
}
void RaaList::zeroList(void)
{
- raa_zerolist(myraa->raa_data, rank);
+ raa_zerolist(myraa->raa_data, rank);
}
bool RaaList::isInList(int elt_rank)
{
- return (bool)raa_btest(myraa->raa_data, rank, elt_rank);
+ return (bool)raa_btest(myraa->raa_data, rank, elt_rank);
}
-RaaList *RaaList::modifyByLength(const string &criterion, const string &listname)
+RaaList* RaaList::modifyByLength(const string& criterion, const string& listname)
{
- int err, newlistrank;
- if(getType() != RaaList::LIST_SEQUENCES) return NULL;
- err = raa_modifylist(myraa->raa_data, rank, (char *)"length", (char *)criterion.c_str(), &newlistrank, NULL, NULL);
- if(err) return NULL;
- raa_setlistname(myraa->raa_data, newlistrank, (char *)listname.c_str());
- RaaList *list = new RaaList();
- list->rank = newlistrank;
- list->myraa = myraa;
- list->name = listname;
- list->type = &RaaList::LIST_SEQUENCES;
- return list;
+ int err, newlistrank;
+ if (getType() != RaaList::LIST_SEQUENCES)
+ return NULL;
+ err = raa_modifylist(myraa->raa_data, rank, (char*)"length", (char*)criterion.c_str(), &newlistrank, NULL, NULL);
+ if (err)
+ return NULL;
+ raa_setlistname(myraa->raa_data, newlistrank, (char*)listname.c_str());
+ RaaList* list = new RaaList();
+ list->rank = newlistrank;
+ list->myraa = myraa;
+ list->name = listname;
+ list->type = &RaaList::LIST_SEQUENCES;
+ return list;
}
-RaaList *RaaList::modifyByDate(const string &criterion, const string &listname)
+RaaList* RaaList::modifyByDate(const string& criterion, const string& listname)
{
- int err, newlistrank;
- if(getType() != RaaList::LIST_SEQUENCES) return NULL;
- err = raa_modifylist(myraa->raa_data, rank, (char *)"date", (char *)criterion.c_str(), &newlistrank, NULL, NULL);
- if(err) return NULL;
- raa_setlistname(myraa->raa_data, newlistrank, (char *)listname.c_str());
- RaaList *list = new RaaList();
- list->rank = newlistrank;
- list->myraa = myraa;
- list->name = listname;
- list->type = &RaaList::LIST_SEQUENCES;
- return list;
+ int err, newlistrank;
+ if (getType() != RaaList::LIST_SEQUENCES)
+ return NULL;
+ err = raa_modifylist(myraa->raa_data, rank, (char*)"date", (char*)criterion.c_str(), &newlistrank, NULL, NULL);
+ if (err)
+ return NULL;
+ raa_setlistname(myraa->raa_data, newlistrank, (char*)listname.c_str());
+ RaaList* list = new RaaList();
+ list->rank = newlistrank;
+ list->myraa = myraa;
+ list->name = listname;
+ list->type = &RaaList::LIST_SEQUENCES;
+ return list;
}
diff --git a/src/Bpp/Raa/RaaList.h b/src/Bpp/Raa/RaaList.h
index 950a7ba..1611e74 100644
--- a/src/Bpp/Raa/RaaList.h
+++ b/src/Bpp/Raa/RaaList.h
@@ -2,8 +2,8 @@
#define _RAALIST_H_
#include <string>
-namespace bpp {
-
+namespace bpp
+{
class RAA;
/**
@@ -13,140 +13,140 @@ class RAA;
* one or several elements that are often sequences, but can also be species or keywords.
* Iteration through all elements of the list is possible.
*/
-class RaaList {
- friend class RAA;
- RAA *myraa;
- int rank;
- std::string name;
- const std::string *type;
- int from;
- std::string elementname;
- int elementlength;
+class RaaList
+{
+ friend class RAA;
+ RAA* myraa;
+ int rank;
+ std::string name;
+ const std::string* type;
+ int from;
+ std::string elementname;
+ int elementlength;
+
public:
-
- /**
- * @brief Refers to a sequence list.
- */
- static const std::string LIST_SEQUENCES;
-
- /**
- * @brief Refers to a keyword list.
- */
- static const std::string LIST_KEYWORDS;
-
- /**
- * @brief Refers to a species list.
- */
- static const std::string LIST_SPECIES;
-
- /**
- * @brief Gives the number of elements (often sequences) in the list.
- */
- int getCount();
-
- /**
- * @brief Gives the database rank of the first element of the list.
- */
- int firstElement();
-
- /**
- * @brief Gives the database rank of the list element following the last considered element.
- */
- int nextElement();
-
- /**
- * @brief Sets an element of the list from which nextElement() will start.
- *
- * @param element_rank The database rank of an element of the list, typically returned by
- * a previous nextElement() call.
- */
- void setFrom(int element_rank);
-
- /**
- * @brief Gives the name of the last considered list element.
- */
- std::string elementName() {return elementname; };
-
- /**
- * @brief Gives the length of the last considered list element (meaningful only for sequence lists).
- */
- int elementLength() {return elementlength; };
-
- /**
- * @brief Returns the total # of residues in all sequences of list (meaningful only for sequence lists).
- *
- * Because this count can exceed a long integer, it is returned as a string.
- */
- std::string residueCount();
-
- /**
- * @brief Adds an element identified by its database rank to the list.
- */
- void addElement(int rank);
-
- /**
- * @brief Removes an element identified by its database rank from the list.
- */
- void removeElement(int rank);
-
- /**
- * @brief Tests whether an element identified by its database rank belongs to the list.
- */
- bool isInList(int rank);
-
- /**
- * @brief Removes all elements from the list.
- */
- void zeroList();
-
- /**
- * @brief Gives the rank of the list.
- */
- int getRank() {return rank; };
-
- /**
- * @brief true means that list contains only parent sequences (does not contain any subsequence).
- */
- bool parentsOnly();
-
- /**
- * @brief Indicates whether the list contains sequences, species or keywords.
- *
- * @return can be "sequence list", "species list", or "keyword list"
- */
- std::string getType() {return *type; };
-
- /**
- * @brief Gives the list name.
- */
- std::string getName() {return name; };
-
- /**
- * @brief Modifies a sequence list by a length criterion.
- *
- * @param criterion Length criterion such as "> 1000" or "<5000".
- * @param listname Name to be given to created list of sequences matching the length criterion.
- * @return A new list of sequences matching the length criterion, or NULL if error.
- */
- RaaList *modifyByLength(const std::string &criterion, const std::string &listname);
-
- /**
- * @brief Modifies a sequence list by a database insertion date criterion.
- *
- * The database insertion date of each sequence is that of the last DT record for the embl/swissprot format,
- * or that of the LOCUS record for the GenBank format.
- *
- * @param criterion Date criterion such as "> 1/jun/98" or "<10/DEC/2004". Year can be expressed with 2 or 4 digits.
- * Case is not significant.
- * @param listname Name to be given to the created list of sequences matching the date criterion.
- * @return A new list of sequences matching the date criterion, or NULL if error.
- */
- RaaList *modifyByDate(const std::string &criterion, const std::string &listname);
-private:
- RaaList();
-};
+ /**
+ * @brief Refers to a sequence list.
+ */
+ static const std::string LIST_SEQUENCES;
+
+ /**
+ * @brief Refers to a keyword list.
+ */
+ static const std::string LIST_KEYWORDS;
+
+ /**
+ * @brief Refers to a species list.
+ */
+ static const std::string LIST_SPECIES;
+
+ /**
+ * @brief Gives the number of elements (often sequences) in the list.
+ */
+ int getCount();
+
+ /**
+ * @brief Gives the database rank of the first element of the list.
+ */
+ int firstElement();
+
+ /**
+ * @brief Gives the database rank of the list element following the last considered element.
+ */
+ int nextElement();
+
+ /**
+ * @brief Sets an element of the list from which nextElement() will start.
+ *
+ * @param element_rank The database rank of an element of the list, typically returned by
+ * a previous nextElement() call.
+ */
+ void setFrom(int element_rank);
+
+ /**
+ * @brief Gives the name of the last considered list element.
+ */
+ std::string elementName() {return elementname; }
+
+ /**
+ * @brief Gives the length of the last considered list element (meaningful only for sequence lists).
+ */
+ int elementLength() {return elementlength; }
-} //end of namespace bpp.
+ /**
+ * @brief Returns the total # of residues in all sequences of list (meaningful only for sequence lists).
+ *
+ * Because this count can exceed a long integer, it is returned as a string.
+ */
+ std::string residueCount();
-#endif //_RAALIST_H_
+ /**
+ * @brief Adds an element identified by its database rank to the list.
+ */
+ void addElement(int rank);
+
+ /**
+ * @brief Removes an element identified by its database rank from the list.
+ */
+ void removeElement(int rank);
+
+ /**
+ * @brief Tests whether an element identified by its database rank belongs to the list.
+ */
+ bool isInList(int rank);
+
+ /**
+ * @brief Removes all elements from the list.
+ */
+ void zeroList();
+
+ /**
+ * @brief Gives the rank of the list.
+ */
+ int getRank() {return rank; }
+
+ /**
+ * @brief true means that list contains only parent sequences (does not contain any subsequence).
+ */
+ bool parentsOnly();
+
+ /**
+ * @brief Indicates whether the list contains sequences, species or keywords.
+ *
+ * @return can be "sequence list", "species list", or "keyword list"
+ */
+ std::string getType() {return *type; }
+
+ /**
+ * @brief Gives the list name.
+ */
+ std::string getName() {return name; }
+
+ /**
+ * @brief Modifies a sequence list by a length criterion.
+ *
+ * @param criterion Length criterion such as "> 1000" or "<5000".
+ * @param listname Name to be given to created list of sequences matching the length criterion.
+ * @return A new list of sequences matching the length criterion, or NULL if error.
+ */
+ RaaList* modifyByLength(const std::string& criterion, const std::string& listname);
+
+ /**
+ * @brief Modifies a sequence list by a database insertion date criterion.
+ *
+ * The database insertion date of each sequence is that of the last DT record for the embl/swissprot format,
+ * or that of the LOCUS record for the GenBank format.
+ *
+ * @param criterion Date criterion such as "> 1/jun/98" or "<10/DEC/2004". Year can be expressed with 2 or 4 digits.
+ * Case is not significant.
+ * @param listname Name to be given to the created list of sequences matching the date criterion.
+ * @return A new list of sequences matching the date criterion, or NULL if error.
+ */
+ RaaList* modifyByDate(const std::string& criterion, const std::string& listname);
+
+private:
+ RaaList();
+};
+} // end of namespace bpp.
+#endif // _RAALIST_H_
diff --git a/src/Bpp/Raa/RaaSeqAttributes.h b/src/Bpp/Raa/RaaSeqAttributes.h
index a81b0d0..bbedbc8 100644
--- a/src/Bpp/Raa/RaaSeqAttributes.h
+++ b/src/Bpp/Raa/RaaSeqAttributes.h
@@ -5,73 +5,76 @@
namespace bpp
{
-
-
/**
* @brief Contains various attributes of a sequence (length, name, species name, genetic code, etc...).
*
*/
-class RaaSeqAttributes {
- friend class RAA;
+class RaaSeqAttributes
+{
+ friend class RAA;
+
public:
- /**
- * @brief Returns the sequence name.
- */
- std::string getName() {return name; };
-
- /**
- * @brief Returns the sequence length.
- */
- int getLength() {return length; };
-
- /**
- * @brief Returns the sequence database rank.
- */
- int getRank() {return rank; };
-
- /**
- * @brief Returns the sequence's NCBI genetic code number (1 is universal). Meaningful only for CDS sequences.
- */
- int getGeneticCode() {return ncbi_gc; };
-
- /**
- * @brief Returns the sequence reading frame (0, 1, or 2). Meaningful only for CDS sequences.
- */
- int getReadingFrame() {return frame; };
-
- /**
- * @brief Returns the sequence species name.
- */
- std::string getSpeciesName() {return species; };
-
- /**
- * @brief Returns the sequence primary accession number.
- */
- std::string getAccessionNumber() {return accno; };
-
- /**
- * @brief Returns a one-line description of the sequence.
- */
- std::string getDescription() {return description; };
+ /**
+ * @brief Returns the sequence name.
+ */
+ std::string getName() {return name; }
+
+ /**
+ * @brief Returns the sequence length.
+ */
+ int getLength() {return length; }
+
+ /**
+ * @brief Returns the sequence database rank.
+ */
+ int getRank() {return rank; }
+
+ /**
+ * @brief Returns the sequence's NCBI genetic code number (1 is universal).
+
+ Meaningful only for CDS sequences.
+ See <a href=http://doua.prabi.fr/databases/acnuc_data/glossary#GCODE> a description of NCBI-defined genetic codes</a>.
+ */
+ int getGeneticCode() {return ncbi_gc; }
+
+ /**
+ * @brief Returns the sequence reading frame (0, 1, or 2). Meaningful only for CDS sequences.
+ */
+ int getReadingFrame() {return frame; }
+
+ /**
+ * @brief Returns the sequence species name.
+ */
+ std::string getSpeciesName() {return species; }
+
+ /**
+ * @brief Returns the sequence primary accession number.
+ */
+ std::string getAccessionNumber() {return accno; }
+
+ /**
+ * @brief Returns a one-line description of the sequence.
+ */
+ std::string getDescription() {return description; }
+
protected:
-
- /**
- * @brief The database connection of this sequence.
- */
- RAA *raa;
+ /**
+ * @brief The database connection of this sequence.
+ */
+ RAA* raa;
+
private:
- std::string name;
- int rank;
- int length;
- int ncbi_gc;
- int frame;
- std::string species;
- std::string accno;
- std::string description;
- };
-
+ std::string name;
+ int rank;
+ int length;
+ int ncbi_gc;
+ int frame;
+ std::string species;
+ std::string accno;
+ std::string description;
+};
} // namespace bpp
-#endif //_RAASEQATTRIBUTES_H_
+#endif // _RAASEQATTRIBUTES_H_
diff --git a/src/Bpp/Raa/RaaSpeciesTree.cpp b/src/Bpp/Raa/RaaSpeciesTree.cpp
index 99d3333..e38a8e7 100644
--- a/src/Bpp/Raa/RaaSpeciesTree.cpp
+++ b/src/Bpp/Raa/RaaSpeciesTree.cpp
@@ -1,4 +1,3 @@
-
#include "RaaSpeciesTree.h"
#include <string>
using namespace std;
@@ -6,110 +5,136 @@ using namespace bpp;
string RaaSpeciesTree::getName(int rank)
{
- if(rank >= 2 && rank <= max_sp && sp_tree[rank] != NULL) {
- string name(sp_tree[rank]->name);
- return name;
- }
- else {
- string name("");
- return name;
- }
+ if (rank >= 2 && rank <= max_sp && sp_tree[rank] != NULL)
+ {
+ string name(sp_tree[rank]->name);
+ return name;
+ }
+ else
+ {
+ string name("");
+ return name;
+ }
}
int RaaSpeciesTree::parent(int rank)
{
- if(!(rank > 2 && rank <= max_sp && sp_tree[rank] != NULL)) return 0;
- while(sp_tree[rank]->parent == NULL) rank = sp_tree[rank]->syno->rank;
- return sp_tree[rank]->parent->rank;
+ if (!(rank > 2 && rank <= max_sp && sp_tree[rank] != NULL))
+ return 0;
+ while (sp_tree[rank]->parent == NULL)
+ rank = sp_tree[rank]->syno->rank;
+ return sp_tree[rank]->parent->rank;
}
int RaaSpeciesTree::getTid(int rank)
{
- if(rank >= 2 && rank <= max_sp && sp_tree[rank] != NULL) return sp_tree[rank]->parent->tid;
- else return 0;
+ if (rank >= 2 && rank <= max_sp && sp_tree[rank] != NULL)
+ return sp_tree[rank]->parent->tid;
+ else
+ return 0;
}
int RaaSpeciesTree::findNode(int tid)
{
- if(tid >= 0 && tid <= max_tid) return tid_to_rank[tid];
- else return 0;
+ if (tid >= 0 && tid <= max_tid)
+ return tid_to_rank[tid];
+ else
+ return 0;
}
-int RaaSpeciesTree::findNode(const string &taxon, bool allowsynonym)
+int RaaSpeciesTree::findNode(const string& taxon, bool allowsynonym)
{
- if(taxon == string("ROOT")) return 2;
- int num = raa_iknum(raa_data, (char*)taxon.c_str(), raa_spec);
- if(num != 0 && !allowsynonym) while(sp_tree[num]->parent == NULL) num = sp_tree[num]->syno->rank;
- return num;
+ if (taxon == string("ROOT"))
+ return 2;
+ int num = raa_iknum(raa_data, (char*)taxon.c_str(), raa_spec);
+ if (num != 0 && !allowsynonym)
+ while (sp_tree[num]->parent == NULL)
+ num = sp_tree[num]->syno->rank;
+ return num;
}
int RaaSpeciesTree::count(int rank)
{
- if(rank >= 2 && rank <= max_sp && sp_tree[rank] != NULL) return sp_tree[rank]->count;
- else return 0;
+ if (rank >= 2 && rank <= max_sp && sp_tree[rank] != NULL)
+ return sp_tree[rank]->count;
+ else
+ return 0;
}
string RaaSpeciesTree::label(int rank)
{
- char *p;
- if(rank > 2 && rank <= max_sp && sp_tree[rank] != NULL && (p = sp_tree[rank]->libel) != NULL) {
- string retval(p);
- return retval;
- }
- else {
- string retval("");
- return retval;
- }
+ char* p;
+ if (rank > 2 && rank <= max_sp && sp_tree[rank] != NULL && (p = sp_tree[rank]->libel) != NULL)
+ {
+ string retval(p);
+ return retval;
+ }
+ else
+ {
+ string retval("");
+ return retval;
+ }
}
int RaaSpeciesTree::firstChild(int rank)
{
- if(rank >= 2 && rank <= max_sp && sp_tree[rank] != NULL) return sp_tree[rank]->list_desc->value->rank;
- else return 0;
+ if (rank >= 2 && rank <= max_sp && sp_tree[rank] != NULL)
+ return sp_tree[rank]->list_desc->value->rank;
+ else
+ return 0;
}
int RaaSpeciesTree::nextChild(int rank, int child)
{
- if(!(rank >= 2 && rank <= max_sp && child > 2 && child <= max_sp && sp_tree[rank] != NULL &&
- sp_tree[child] != NULL)) return 0;
- struct raa_pair *pair = sp_tree[rank]->list_desc;
- while(pair != NULL && pair->value->rank != child) {
- pair = pair->next;
- }
- return pair == NULL || pair->next == NULL ? 0 : pair->next->value->rank;
+ if (!(rank >= 2 && rank <= max_sp && child > 2 && child <= max_sp && sp_tree[rank] != NULL &&
+ sp_tree[child] != NULL))
+ return 0;
+ struct raa_pair* pair = sp_tree[rank]->list_desc;
+ while (pair != NULL && pair->value->rank != child)
+ {
+ pair = pair->next;
+ }
+ return pair == NULL || pair->next == NULL ? 0 : pair->next->value->rank;
}
bool RaaSpeciesTree::isChild(int parent, int child)
{
- while(child != parent) {
- child = this->parent(child);
- if(child == 0) return false;
- }
- return true;
+ while (child != parent)
+ {
+ child = this->parent(child);
+ if (child == 0)
+ return false;
+ }
+ return true;
}
int RaaSpeciesTree::nextSynonym(int rank)
{
- if(!(rank >= 2 && rank <= max_sp && sp_tree[rank] != NULL)) return 0;
- struct raa_node *mynode = sp_tree[rank]->syno;
- if(mynode == NULL) return 0;
- else return mynode->rank;
+ if (!(rank >= 2 && rank <= max_sp && sp_tree[rank] != NULL))
+ return 0;
+ struct raa_node* mynode = sp_tree[rank]->syno;
+ if (mynode == NULL)
+ return 0;
+ else
+ return mynode->rank;
}
int RaaSpeciesTree::getMajor(int rank)
{
- if(!(rank >= 2 && rank <= max_sp && sp_tree[rank] != NULL)) return 0;
- while(sp_tree[rank]->parent == NULL) rank = sp_tree[rank]->syno->rank;
- return rank;
+ if (!(rank >= 2 && rank <= max_sp && sp_tree[rank] != NULL))
+ return 0;
+ while (sp_tree[rank]->parent == NULL)
+ rank = sp_tree[rank]->syno->rank;
+ return rank;
}
diff --git a/src/Bpp/Raa/RaaSpeciesTree.h b/src/Bpp/Raa/RaaSpeciesTree.h
index a85a2e8..b77ec6b 100644
--- a/src/Bpp/Raa/RaaSpeciesTree.h
+++ b/src/Bpp/Raa/RaaSpeciesTree.h
@@ -7,8 +7,8 @@ extern "C" {
#include <string>
-namespace bpp {
-
+namespace bpp
+{
/**
* @brief To work with the species tree classification of the database.
*
@@ -17,125 +17,124 @@ namespace bpp {
* The root of the tree is named "ROOT" and has database rank 2.
*/
-
-class RaaSpeciesTree {
- friend class RAA;
+
+class RaaSpeciesTree
+{
+ friend class RAA;
+
public:
-
- /**
- * @brief Returns the database rank of a taxon identified by its name.
- *
- * @param taxon A taxon name. Case is not significant.
- * @param allowsynonym If true, the return value will give the synonym's rank rather than the rank of its
- * major taxon.
- * @return The database rank of this taxon, or 0 if no such taxon exists in tree.
- */
- int findNode(const std::string &taxon, bool allowsynonym = false);
-
- /**
- * @brief Returns the database rank of a taxon identified by a TID.
- *
- * @param tid A TID value.
- * @return The database rank of this taxon, or 0 if no such taxon exists in tree.
- */
- int findNode(int tid);
-
- /**
- * @brief Returns the name of a taxon identified by its database rank.
- *
- * @param rank The database rank of a taxon.
- * @return The name of this taxon.
- */
- std::string getName(int rank);
-
- /**
- * @brief Returns the database rank of the parent of a taxon in the tree.
- *
- * @param rank The database rank of a taxon.
- * @return The database rank of the parent of this taxon in the tree, or 0 if no such taxon exists in tree.
- */
- int parent(int rank);
-
- /**
- * @brief Returns the TID of a taxon.
- *
- * @param rank The database rank of a taxon.
- * @return The TID of this taxon, or 0 if no such taxon exists in tree.
- */
- int getTid(int rank);
-
- /**
- * @brief Returns the number of sequences attached to a taxon or to taxa below it in the species tree.
- *
- * @param rank The database rank of a taxon.
- * @return The number of sequences attached to this taxon or to taxa below it, or 0 if no such taxon exists in tree.
- */
- int count(int rank);
-
- /**
- * @brief Returns the label of a taxon of given rank.
- *
- * Labels may contain taxon common names, genetic code information, TID values, and taxonomic
- * level information (e.g., genus, order).
- * @param rank The database rank of a taxon.
- * @return The label of this taxon, or "" if no such taxon or label exists in tree.
- */
- std::string label(int rank);
-
- /**
- * @brief Returns the rank of the first child taxon of a given taxon.
- *
- * @param rank The database rank of a taxon.
- * @return The rank of its first child taxon, or 0 if no child taxon exists in tree.
- */
- int firstChild(int rank);
-
- /**
- * @brief Allows to loop around all child taxa of a given taxon.
- *
- * @param parent The database rank of a taxon.
- * @param child The database rank of a child of taxon of rank parent.
- * @return The rank of the next child taxon of parent after taxon child, or 0 if no more child taxon exists in tree.
- */
- int nextChild(int parent, int child);
-
- /**
- * @brief Tells whether there is a downward path from taxon parent to taxon child in the species tree.
- *
- * @param parent The database rank of a taxon.
- * @param child The database rank of another taxon.
- * @return true iff child is below parent (possibly with intermediate nodes) in the species tree.
- */
- bool isChild(int parent, int child);
-
- /**
- * @brief Allows to loop around all synonymous taxa of a given taxon.
- *
- * Synonymous taxa of a taxon are chained in a closed loop, among which only one, the major taxon,
- * has a parent taxon.
- *
- * @param rank The database rank of a taxon.
- * @return The rank of the next synonymous taxon, or 0 if taxon rank has no synonymous taxon.
- */
- int nextSynonym(int rank);
-
- /**
- * @brief Gives the major taxon among all synonyms of a given taxon.
- *
- * @param rank The database rank of a taxon.
- * @return The rank of the major taxon of taxon rank (can be itself).
- */
- int getMajor(int rank);
-
+ /**
+ * @brief Returns the database rank of a taxon identified by its name.
+ *
+ * @param taxon A taxon name. Case is not significant.
+ * @param allowsynonym If true, the return value will give the synonym's rank rather than the rank of its
+ * major taxon.
+ * @return The database rank of this taxon, or 0 if no such taxon exists in tree.
+ */
+ int findNode(const std::string& taxon, bool allowsynonym = false);
+
+ /**
+ * @brief Returns the database rank of a taxon identified by a TID.
+ *
+ * @param tid A TID value.
+ * @return The database rank of this taxon, or 0 if no such taxon exists in tree.
+ */
+ int findNode(int tid);
+
+ /**
+ * @brief Returns the name of a taxon identified by its database rank.
+ *
+ * @param rank The database rank of a taxon.
+ * @return The name of this taxon.
+ */
+ std::string getName(int rank);
+
+ /**
+ * @brief Returns the database rank of the parent of a taxon in the tree.
+ *
+ * @param rank The database rank of a taxon.
+ * @return The database rank of the parent of this taxon in the tree, or 0 if no such taxon exists in tree.
+ */
+ int parent(int rank);
+
+ /**
+ * @brief Returns the TID of a taxon.
+ *
+ * @param rank The database rank of a taxon.
+ * @return The TID of this taxon, or 0 if no such taxon exists in tree.
+ */
+ int getTid(int rank);
+
+ /**
+ * @brief Returns the number of sequences attached to a taxon or to taxa below it in the species tree.
+ *
+ * @param rank The database rank of a taxon.
+ * @return The number of sequences attached to this taxon or to taxa below it, or 0 if no such taxon exists in tree.
+ */
+ int count(int rank);
+
+ /**
+ * @brief Returns the label of a taxon of given rank.
+ *
+ * Labels may contain taxon common names, genetic code information, TID values, and taxonomic
+ * level information (e.g., genus, order).
+ * @param rank The database rank of a taxon.
+ * @return The label of this taxon, or "" if no such taxon or label exists in tree.
+ */
+ std::string label(int rank);
+
+ /**
+ * @brief Returns the rank of the first child taxon of a given taxon.
+ *
+ * @param rank The database rank of a taxon.
+ * @return The rank of its first child taxon, or 0 if no child taxon exists in tree.
+ */
+ int firstChild(int rank);
+
+ /**
+ * @brief Allows to loop around all child taxa of a given taxon.
+ *
+ * @param parent The database rank of a taxon.
+ * @param child The database rank of a child of taxon of rank parent.
+ * @return The rank of the next child taxon of parent after taxon child, or 0 if no more child taxon exists in tree.
+ */
+ int nextChild(int parent, int child);
+
+ /**
+ * @brief Tells whether there is a downward path from taxon parent to taxon child in the species tree.
+ *
+ * @param parent The database rank of a taxon.
+ * @param child The database rank of another taxon.
+ * @return true iff child is below parent (possibly with intermediate nodes) in the species tree.
+ */
+ bool isChild(int parent, int child);
+
+ /**
+ * @brief Allows to loop around all synonymous taxa of a given taxon.
+ *
+ * Synonymous taxa of a taxon are chained in a closed loop, among which only one, the major taxon,
+ * has a parent taxon.
+ *
+ * @param rank The database rank of a taxon.
+ * @return The rank of the next synonymous taxon, or 0 if taxon rank has no synonymous taxon.
+ */
+ int nextSynonym(int rank);
+
+ /**
+ * @brief Gives the major taxon among all synonyms of a given taxon.
+ *
+ * @param rank The database rank of a taxon.
+ * @return The rank of the major taxon of taxon rank (can be itself).
+ */
+ int getMajor(int rank);
+
private:
- raa_db_access *raa_data;
- raa_node **sp_tree;
- int *tid_to_rank;
- int max_tid;
- int max_sp;
+ raa_db_access* raa_data;
+ raa_node** sp_tree;
+ int* tid_to_rank;
+ int max_tid;
+ int max_sp;
};
-
-} //namespace bpp.
+} // namespace bpp.
#endif // _RAASPECIESTREE_H_
-
diff --git a/src/Bpp/Raa/md5.c b/src/Bpp/Raa/md5.c
index f98774c..eddd16f 100644
--- a/src/Bpp/Raa/md5.c
+++ b/src/Bpp/Raa/md5.c
@@ -16,7 +16,7 @@
* needed on buffers full of bytes, and then call MD5_Final, which
* will fill a supplied 16-byte array with the digest.
*
- * Modified 12 June 2003 Jeremy Katz <katzj at redhat.com> to handle
+ * Modified 12 June 2003 Jeremy Katz <katzj at redhat.com> to handle
* endianness better
*
*/
@@ -37,30 +37,33 @@
typedef unsigned int uint32;
-struct MD5Context {
- uint32 buf[4];
- uint32 bits[2];
- unsigned char in[64];
- int doByteReverse;
+struct MD5Context
+{
+ uint32 buf[4];
+ uint32 bits[2];
+ unsigned char in[64];
+ int doByteReverse;
};
-static void MD5_Transform(uint32 *buf, uint32 const *in);
+static void MD5_Transform(uint32* buf, uint32 const* in);
-static void byteReverse(unsigned char *buf, unsigned longs);
+static void byteReverse(unsigned char* buf, unsigned longs);
#ifndef ASM_MD5
/*
* Note: this code is harmless on little-endian machines.
*/
-static void byteReverse(unsigned char *buf, unsigned longs)
+static void byteReverse(unsigned char* buf, unsigned longs)
{
- uint32 t;
- do {
- t = (uint32) ((unsigned) buf[3] << 8 | buf[2]) << 16 |
- ((unsigned) buf[1] << 8 | buf[0]);
- *(uint32 *) buf = t;
- buf += 4;
- } while (--longs);
+ uint32 t;
+ do
+ {
+ t = (uint32) ((unsigned) buf[3] << 8 | buf[2]) << 16 |
+ ((unsigned) buf[1] << 8 | buf[0]);
+ *(uint32*) buf = t;
+ buf += 4;
+ }
+ while (--longs);
}
#endif
@@ -68,114 +71,125 @@ static void byteReverse(unsigned char *buf, unsigned longs)
* Start MD5 accumulation. Set bit count to 0 and buffer to mysterious
* initialization constants.
*/
-static void MD5_Init(struct MD5Context *ctx)
+static void MD5_Init(struct MD5Context* ctx)
{
- ctx->buf[0] = 0x67452301U;
- ctx->buf[1] = 0xefcdab89U;
- ctx->buf[2] = 0x98badcfeU;
- ctx->buf[3] = 0x10325476U;
+ ctx->buf[0] = 0x67452301U;
+ ctx->buf[1] = 0xefcdab89U;
+ ctx->buf[2] = 0x98badcfeU;
+ ctx->buf[3] = 0x10325476U;
- ctx->bits[0] = 0;
- ctx->bits[1] = 0;
+ ctx->bits[0] = 0;
+ ctx->bits[1] = 0;
- if (IS_BIG_ENDIAN)
- ctx->doByteReverse = 1;
- else
- ctx->doByteReverse = 0;
+ if (IS_BIG_ENDIAN)
+ ctx->doByteReverse = 1;
+ else
+ ctx->doByteReverse = 0;
}
/*
* Update context to reflect the concatenation of another buffer full
* of bytes.
*/
-static void MD5_Update(struct MD5Context *ctx, unsigned const char *buf, unsigned len)
+static void MD5_Update(struct MD5Context* ctx, unsigned const char* buf, unsigned len)
{
- uint32 t;
-
- /* Update bitcount */
-
- t = ctx->bits[0];
- if ((ctx->bits[0] = t + ((uint32) len << 3)) < t)
- ctx->bits[1]++; /* Carry from low to high */
- ctx->bits[1] += len >> 29;
-
- t = (t >> 3) & 0x3f; /* Bytes already in shsInfo->data */
-
- /* Handle any leading odd-sized chunks */
-
- if (t) {
- unsigned char *p = (unsigned char *) ctx->in + t;
-
- t = 64 - t;
- if (len < t) {
- memcpy(p, buf, len);
- return;
- }
- memcpy(p, buf, t);
- if (ctx->doByteReverse) byteReverse(ctx->in, 16);
- MD5_Transform(ctx->buf, (uint32 *) ctx->in);
- buf += t;
- len -= t;
- }
- /* Process data in 64-byte chunks */
-
- while (len >= 64) {
- memcpy(ctx->in, buf, 64);
- if (ctx->doByteReverse) byteReverse(ctx->in, 16);
- MD5_Transform(ctx->buf, (uint32 *) ctx->in);
- buf += 64;
- len -= 64;
- }
-
- /* Handle any remaining bytes of data. */
-
- memcpy(ctx->in, buf, len);
+ uint32 t;
+
+ /* Update bitcount */
+
+ t = ctx->bits[0];
+ if ((ctx->bits[0] = t + ((uint32) len << 3)) < t)
+ ctx->bits[1]++; /* Carry from low to high */
+ ctx->bits[1] += len >> 29;
+
+ t = (t >> 3) & 0x3f; /* Bytes already in shsInfo->data */
+
+ /* Handle any leading odd-sized chunks */
+
+ if (t)
+ {
+ unsigned char* p = (unsigned char*) ctx->in + t;
+
+ t = 64 - t;
+ if (len < t)
+ {
+ memcpy(p, buf, len);
+ return;
+ }
+ memcpy(p, buf, t);
+ if (ctx->doByteReverse)
+ byteReverse(ctx->in, 16);
+ MD5_Transform(ctx->buf, (uint32*) ctx->in);
+ buf += t;
+ len -= t;
+ }
+ /* Process data in 64-byte chunks */
+
+ while (len >= 64)
+ {
+ memcpy(ctx->in, buf, 64);
+ if (ctx->doByteReverse)
+ byteReverse(ctx->in, 16);
+ MD5_Transform(ctx->buf, (uint32*) ctx->in);
+ buf += 64;
+ len -= 64;
+ }
+
+ /* Handle any remaining bytes of data. */
+
+ memcpy(ctx->in, buf, len);
}
/*
- * Final wrapup - pad to 64-byte boundary with the bit pattern
+ * Final wrapup - pad to 64-byte boundary with the bit pattern
* 1 0* (64-bit count of bits processed, MSB-first)
*/
-static void MD5_Final(unsigned char digest[16], struct MD5Context *ctx)
+static void MD5_Final(unsigned char digest[16], struct MD5Context* ctx)
{
- unsigned count;
- unsigned char *p;
-
- /* Compute number of bytes mod 64 */
- count = (ctx->bits[0] >> 3) & 0x3F;
-
- /* Set the first char of padding to 0x80. This is safe since there is
- always at least one byte free */
- p = ctx->in + count;
- *p++ = 0x80;
-
- /* Bytes of padding needed to make 64 bytes */
- count = 64 - 1 - count;
-
- /* Pad out to 56 mod 64 */
- if (count < 8) {
- /* Two lots of padding: Pad the first block to 64 bytes */
- memset(p, 0, count);
- if (ctx->doByteReverse) byteReverse(ctx->in, 16);
- MD5_Transform(ctx->buf, (uint32 *) ctx->in);
-
- /* Now fill the next block with 56 bytes */
- memset(ctx->in, 0, 56);
- } else {
- /* Pad block to 56 bytes */
- memset(p, 0, count - 8);
- }
- if (ctx->doByteReverse) byteReverse(ctx->in, 14);
-
- /* Append length in bits and transform */
- ((uint32 *) ctx->in)[14] = ctx->bits[0];
- ((uint32 *) ctx->in)[15] = ctx->bits[1];
-
- MD5_Transform(ctx->buf, (uint32 *) ctx->in);
- if (ctx->doByteReverse) byteReverse((unsigned char *) ctx->buf, 4);
- memcpy(digest, ctx->buf, 16);
- memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */
+ unsigned count;
+ unsigned char* p;
+
+ /* Compute number of bytes mod 64 */
+ count = (ctx->bits[0] >> 3) & 0x3F;
+
+ /* Set the first char of padding to 0x80. This is safe since there is
+ always at least one byte free */
+ p = ctx->in + count;
+ *p++ = 0x80;
+
+ /* Bytes of padding needed to make 64 bytes */
+ count = 64 - 1 - count;
+
+ /* Pad out to 56 mod 64 */
+ if (count < 8)
+ {
+ /* Two lots of padding: Pad the first block to 64 bytes */
+ memset(p, 0, count);
+ if (ctx->doByteReverse)
+ byteReverse(ctx->in, 16);
+ MD5_Transform(ctx->buf, (uint32*) ctx->in);
+
+ /* Now fill the next block with 56 bytes */
+ memset(ctx->in, 0, 56);
+ }
+ else
+ {
+ /* Pad block to 56 bytes */
+ memset(p, 0, count - 8);
+ }
+ if (ctx->doByteReverse)
+ byteReverse(ctx->in, 14);
+
+ /* Append length in bits and transform */
+ ((uint32*) ctx->in)[14] = ctx->bits[0];
+ ((uint32*) ctx->in)[15] = ctx->bits[1];
+
+ MD5_Transform(ctx->buf, (uint32*) ctx->in);
+ if (ctx->doByteReverse)
+ byteReverse((unsigned char*) ctx->buf, 4);
+ memcpy(digest, ctx->buf, 16);
+ memset(ctx, 0, sizeof(struct MD5Context)); /* In case it's sensitive */
}
#ifndef ASM_MD5
@@ -190,7 +204,7 @@ static void MD5_Final(unsigned char digest[16], struct MD5Context *ctx)
/* This is the central step in the MD5 algorithm. */
#define MD5STEP(f, w, x, y, z, data, s) \
- ( w += f(x, y, z) + data, w = w<<s | w>>(32-s), w += x )
+ ( w += f(x, y, z) + data, w = w << s | w >> (32 - s), w += x )
/*
* The core of the MD5 algorithm, this alters an existing MD5 hash to
@@ -199,112 +213,113 @@ static void MD5_Final(unsigned char digest[16], struct MD5Context *ctx)
*/
static void MD5_Transform(uint32 buf[4], uint32 const in[16])
{
- register uint32 a, b, c, d;
-
- a = buf[0];
- b = buf[1];
- c = buf[2];
- d = buf[3];
-
- MD5STEP(F1, a, b, c, d, in[0] + 0xd76aa478U, 7);
- MD5STEP(F1, d, a, b, c, in[1] + 0xe8c7b756U, 12);
- MD5STEP(F1, c, d, a, b, in[2] + 0x242070dbU, 17);
- MD5STEP(F1, b, c, d, a, in[3] + 0xc1bdceeeU, 22);
- MD5STEP(F1, a, b, c, d, in[4] + 0xf57c0fafU, 7);
- MD5STEP(F1, d, a, b, c, in[5] + 0x4787c62aU, 12);
- MD5STEP(F1, c, d, a, b, in[6] + 0xa8304613U, 17);
- MD5STEP(F1, b, c, d, a, in[7] + 0xfd469501U, 22);
- MD5STEP(F1, a, b, c, d, in[8] + 0x698098d8U, 7);
- MD5STEP(F1, d, a, b, c, in[9] + 0x8b44f7afU, 12);
- MD5STEP(F1, c, d, a, b, in[10] + 0xffff5bb1U, 17);
- MD5STEP(F1, b, c, d, a, in[11] + 0x895cd7beU, 22);
- MD5STEP(F1, a, b, c, d, in[12] + 0x6b901122U, 7);
- MD5STEP(F1, d, a, b, c, in[13] + 0xfd987193U, 12);
- MD5STEP(F1, c, d, a, b, in[14] + 0xa679438eU, 17);
- MD5STEP(F1, b, c, d, a, in[15] + 0x49b40821U, 22);
-
- MD5STEP(F2, a, b, c, d, in[1] + 0xf61e2562U, 5);
- MD5STEP(F2, d, a, b, c, in[6] + 0xc040b340U, 9);
- MD5STEP(F2, c, d, a, b, in[11] + 0x265e5a51U, 14);
- MD5STEP(F2, b, c, d, a, in[0] + 0xe9b6c7aaU, 20);
- MD5STEP(F2, a, b, c, d, in[5] + 0xd62f105dU, 5);
- MD5STEP(F2, d, a, b, c, in[10] + 0x02441453U, 9);
- MD5STEP(F2, c, d, a, b, in[15] + 0xd8a1e681U, 14);
- MD5STEP(F2, b, c, d, a, in[4] + 0xe7d3fbc8U, 20);
- MD5STEP(F2, a, b, c, d, in[9] + 0x21e1cde6U, 5);
- MD5STEP(F2, d, a, b, c, in[14] + 0xc33707d6U, 9);
- MD5STEP(F2, c, d, a, b, in[3] + 0xf4d50d87U, 14);
- MD5STEP(F2, b, c, d, a, in[8] + 0x455a14edU, 20);
- MD5STEP(F2, a, b, c, d, in[13] + 0xa9e3e905U, 5);
- MD5STEP(F2, d, a, b, c, in[2] + 0xfcefa3f8U, 9);
- MD5STEP(F2, c, d, a, b, in[7] + 0x676f02d9U, 14);
- MD5STEP(F2, b, c, d, a, in[12] + 0x8d2a4c8aU, 20);
-
- MD5STEP(F3, a, b, c, d, in[5] + 0xfffa3942U, 4);
- MD5STEP(F3, d, a, b, c, in[8] + 0x8771f681U, 11);
- MD5STEP(F3, c, d, a, b, in[11] + 0x6d9d6122U, 16);
- MD5STEP(F3, b, c, d, a, in[14] + 0xfde5380cU, 23);
- MD5STEP(F3, a, b, c, d, in[1] + 0xa4beea44U, 4);
- MD5STEP(F3, d, a, b, c, in[4] + 0x4bdecfa9U, 11);
- MD5STEP(F3, c, d, a, b, in[7] + 0xf6bb4b60U, 16);
- MD5STEP(F3, b, c, d, a, in[10] + 0xbebfbc70U, 23);
- MD5STEP(F3, a, b, c, d, in[13] + 0x289b7ec6U, 4);
- MD5STEP(F3, d, a, b, c, in[0] + 0xeaa127faU, 11);
- MD5STEP(F3, c, d, a, b, in[3] + 0xd4ef3085U, 16);
- MD5STEP(F3, b, c, d, a, in[6] + 0x04881d05U, 23);
- MD5STEP(F3, a, b, c, d, in[9] + 0xd9d4d039U, 4);
- MD5STEP(F3, d, a, b, c, in[12] + 0xe6db99e5U, 11);
- MD5STEP(F3, c, d, a, b, in[15] + 0x1fa27cf8U, 16);
- MD5STEP(F3, b, c, d, a, in[2] + 0xc4ac5665U, 23);
-
- MD5STEP(F4, a, b, c, d, in[0] + 0xf4292244U, 6);
- MD5STEP(F4, d, a, b, c, in[7] + 0x432aff97U, 10);
- MD5STEP(F4, c, d, a, b, in[14] + 0xab9423a7U, 15);
- MD5STEP(F4, b, c, d, a, in[5] + 0xfc93a039U, 21);
- MD5STEP(F4, a, b, c, d, in[12] + 0x655b59c3U, 6);
- MD5STEP(F4, d, a, b, c, in[3] + 0x8f0ccc92U, 10);
- MD5STEP(F4, c, d, a, b, in[10] + 0xffeff47dU, 15);
- MD5STEP(F4, b, c, d, a, in[1] + 0x85845dd1U, 21);
- MD5STEP(F4, a, b, c, d, in[8] + 0x6fa87e4fU, 6);
- MD5STEP(F4, d, a, b, c, in[15] + 0xfe2ce6e0U, 10);
- MD5STEP(F4, c, d, a, b, in[6] + 0xa3014314U, 15);
- MD5STEP(F4, b, c, d, a, in[13] + 0x4e0811a1U, 21);
- MD5STEP(F4, a, b, c, d, in[4] + 0xf7537e82U, 6);
- MD5STEP(F4, d, a, b, c, in[11] + 0xbd3af235U, 10);
- MD5STEP(F4, c, d, a, b, in[2] + 0x2ad7d2bbU, 15);
- MD5STEP(F4, b, c, d, a, in[9] + 0xeb86d391U, 21);
-
- buf[0] += a;
- buf[1] += b;
- buf[2] += c;
- buf[3] += d;
+ register uint32 a, b, c, d;
+
+ a = buf[0];
+ b = buf[1];
+ c = buf[2];
+ d = buf[3];
+
+ MD5STEP(F1, a, b, c, d, in[0] + 0xd76aa478U, 7);
+ MD5STEP(F1, d, a, b, c, in[1] + 0xe8c7b756U, 12);
+ MD5STEP(F1, c, d, a, b, in[2] + 0x242070dbU, 17);
+ MD5STEP(F1, b, c, d, a, in[3] + 0xc1bdceeeU, 22);
+ MD5STEP(F1, a, b, c, d, in[4] + 0xf57c0fafU, 7);
+ MD5STEP(F1, d, a, b, c, in[5] + 0x4787c62aU, 12);
+ MD5STEP(F1, c, d, a, b, in[6] + 0xa8304613U, 17);
+ MD5STEP(F1, b, c, d, a, in[7] + 0xfd469501U, 22);
+ MD5STEP(F1, a, b, c, d, in[8] + 0x698098d8U, 7);
+ MD5STEP(F1, d, a, b, c, in[9] + 0x8b44f7afU, 12);
+ MD5STEP(F1, c, d, a, b, in[10] + 0xffff5bb1U, 17);
+ MD5STEP(F1, b, c, d, a, in[11] + 0x895cd7beU, 22);
+ MD5STEP(F1, a, b, c, d, in[12] + 0x6b901122U, 7);
+ MD5STEP(F1, d, a, b, c, in[13] + 0xfd987193U, 12);
+ MD5STEP(F1, c, d, a, b, in[14] + 0xa679438eU, 17);
+ MD5STEP(F1, b, c, d, a, in[15] + 0x49b40821U, 22);
+
+ MD5STEP(F2, a, b, c, d, in[1] + 0xf61e2562U, 5);
+ MD5STEP(F2, d, a, b, c, in[6] + 0xc040b340U, 9);
+ MD5STEP(F2, c, d, a, b, in[11] + 0x265e5a51U, 14);
+ MD5STEP(F2, b, c, d, a, in[0] + 0xe9b6c7aaU, 20);
+ MD5STEP(F2, a, b, c, d, in[5] + 0xd62f105dU, 5);
+ MD5STEP(F2, d, a, b, c, in[10] + 0x02441453U, 9);
+ MD5STEP(F2, c, d, a, b, in[15] + 0xd8a1e681U, 14);
+ MD5STEP(F2, b, c, d, a, in[4] + 0xe7d3fbc8U, 20);
+ MD5STEP(F2, a, b, c, d, in[9] + 0x21e1cde6U, 5);
+ MD5STEP(F2, d, a, b, c, in[14] + 0xc33707d6U, 9);
+ MD5STEP(F2, c, d, a, b, in[3] + 0xf4d50d87U, 14);
+ MD5STEP(F2, b, c, d, a, in[8] + 0x455a14edU, 20);
+ MD5STEP(F2, a, b, c, d, in[13] + 0xa9e3e905U, 5);
+ MD5STEP(F2, d, a, b, c, in[2] + 0xfcefa3f8U, 9);
+ MD5STEP(F2, c, d, a, b, in[7] + 0x676f02d9U, 14);
+ MD5STEP(F2, b, c, d, a, in[12] + 0x8d2a4c8aU, 20);
+
+ MD5STEP(F3, a, b, c, d, in[5] + 0xfffa3942U, 4);
+ MD5STEP(F3, d, a, b, c, in[8] + 0x8771f681U, 11);
+ MD5STEP(F3, c, d, a, b, in[11] + 0x6d9d6122U, 16);
+ MD5STEP(F3, b, c, d, a, in[14] + 0xfde5380cU, 23);
+ MD5STEP(F3, a, b, c, d, in[1] + 0xa4beea44U, 4);
+ MD5STEP(F3, d, a, b, c, in[4] + 0x4bdecfa9U, 11);
+ MD5STEP(F3, c, d, a, b, in[7] + 0xf6bb4b60U, 16);
+ MD5STEP(F3, b, c, d, a, in[10] + 0xbebfbc70U, 23);
+ MD5STEP(F3, a, b, c, d, in[13] + 0x289b7ec6U, 4);
+ MD5STEP(F3, d, a, b, c, in[0] + 0xeaa127faU, 11);
+ MD5STEP(F3, c, d, a, b, in[3] + 0xd4ef3085U, 16);
+ MD5STEP(F3, b, c, d, a, in[6] + 0x04881d05U, 23);
+ MD5STEP(F3, a, b, c, d, in[9] + 0xd9d4d039U, 4);
+ MD5STEP(F3, d, a, b, c, in[12] + 0xe6db99e5U, 11);
+ MD5STEP(F3, c, d, a, b, in[15] + 0x1fa27cf8U, 16);
+ MD5STEP(F3, b, c, d, a, in[2] + 0xc4ac5665U, 23);
+
+ MD5STEP(F4, a, b, c, d, in[0] + 0xf4292244U, 6);
+ MD5STEP(F4, d, a, b, c, in[7] + 0x432aff97U, 10);
+ MD5STEP(F4, c, d, a, b, in[14] + 0xab9423a7U, 15);
+ MD5STEP(F4, b, c, d, a, in[5] + 0xfc93a039U, 21);
+ MD5STEP(F4, a, b, c, d, in[12] + 0x655b59c3U, 6);
+ MD5STEP(F4, d, a, b, c, in[3] + 0x8f0ccc92U, 10);
+ MD5STEP(F4, c, d, a, b, in[10] + 0xffeff47dU, 15);
+ MD5STEP(F4, b, c, d, a, in[1] + 0x85845dd1U, 21);
+ MD5STEP(F4, a, b, c, d, in[8] + 0x6fa87e4fU, 6);
+ MD5STEP(F4, d, a, b, c, in[15] + 0xfe2ce6e0U, 10);
+ MD5STEP(F4, c, d, a, b, in[6] + 0xa3014314U, 15);
+ MD5STEP(F4, b, c, d, a, in[13] + 0x4e0811a1U, 21);
+ MD5STEP(F4, a, b, c, d, in[4] + 0xf7537e82U, 6);
+ MD5STEP(F4, d, a, b, c, in[11] + 0xbd3af235U, 10);
+ MD5STEP(F4, c, d, a, b, in[2] + 0x2ad7d2bbU, 15);
+ MD5STEP(F4, b, c, d, a, in[9] + 0xeb86d391U, 21);
+
+ buf[0] += a;
+ buf[1] += b;
+ buf[2] += c;
+ buf[3] += d;
}
#endif
/* function for very simple interface */
-void raa_MD5String (char *in_string, char out_digest[33])
+void raa_MD5String (char* in_string, char out_digest[33])
/*
-in_string: string to be MD5-digested
-out_digest: resulting digest as 32 hexadecimal digits plus final NULL
-*/
+ in_string: string to be MD5-digested
+ out_digest: resulting digest as 32 hexadecimal digits plus final NULL
+ */
{
struct MD5Context context;
unsigned int len = strlen (in_string);
- char *p;
+ char* p;
int i;
unsigned char digest[16];
MD5_Init (&context);
- MD5_Update (&context, (unsigned const char *)in_string, len);
+ MD5_Update (&context, (unsigned const char*)in_string, len);
MD5_Final (digest, &context);
p = out_digest;
- for (i = 0; i < 16; i++) {
- sprintf (p, "%02x", digest[i]);
- p += 2;
- }
+ for (i = 0; i < 16; i++)
+ {
+ sprintf (p, "%02x", digest[i]);
+ p += 2;
+ }
memset(&context, 0, sizeof(struct MD5Context));
}
diff --git a/src/Bpp/Raa/misc_acnuc.c b/src/Bpp/Raa/misc_acnuc.c
index 0c1d802..be2e887 100644
--- a/src/Bpp/Raa/misc_acnuc.c
+++ b/src/Bpp/Raa/misc_acnuc.c
@@ -18,9 +18,10 @@ int calc_codon_number(char* codon);
char codaa(char* codon, int code);
int get_ncbi_gc_number(int gc);
int get_acnuc_gc_number(int ncbi_gc);
-int strcmptrail(char *s1, int l1, char *s2, int l2);
-void majuscules(char *name);
-void compact(char *chaine);
+int strcmptrail(char* s1, int l1, char* s2, int l2);
+void majuscules(char* name);
+void compact(char* chaine);
+void* mycalloc(int nbr, size_t taille);
char complementer_base(char nucl);
void complementer_seq(char* deb_ch, int l);
char init_codon_to_aa(char* codon, int gc);
@@ -34,11 +35,11 @@ void gets_no_echo(char* password, size_t lpw);
int trim_key(char* name) /* remove trailing spaces */
{
char* p;
- int l = strlen(name);
+ int l = (int)strlen(name);
p = name + l - 1;
while (p >= name && *p == ' ')
*(p--) = 0;
- return (p + 1) - name;
+ return (int)((p + 1) - name);
}
@@ -47,14 +48,14 @@ void padtosize(char* pname, char* name, int length)
int i;
strncpy(pname, name, length);
pname[length] = 0;
- for (i = strlen(pname); i < length; i++)
+ for (i = (int)strlen(pname); i < length; i++)
{
pname[i] = ' ';
}
}
-#define TOTCODES 18 /* nbre total de codes definis, 0 inclus */
+#define TOTCODES 19 /* nbre total de codes definis, 0 inclus */
int totcodes = TOTCODES;
char aminoacids[] = "RLSTPAGVKNQHEDYCFIMW*X";
@@ -303,6 +304,19 @@ struct genetic_code_libel genetic_code[TOTCODES] =
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0} /* UUG */
}
+ ,
+ { /* 18: Candidate Division SR1 and Gracilibacteria */
+ {"UGA=G"},
+ /*ANN*/ {9, 10, 9, 10, 4, 4, 4, 4, 1, 3, 1, 3, 18, 18, 19, 18,
+ /*CNN*/ 11, 12, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2,
+ /*GNN*/ 13, 14, 13, 14, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8,
+ /*TNN*/ 21, 15, 21, 15, 3, 3, 3, 3, 7, 16, 20, 16, 2, 17, 2, 17, 22},
+ /*ncbi*/ 25,
+ /*init*/ {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* AUG */
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0, /* CUG */
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0} /* UUG */
+ }
/* 1 2
@@ -342,7 +356,7 @@ int calc_codon_number(char* codon)
break;
}
else
- base = (p - nucleotides) / 2;
+ base = (int)(p - nucleotides) / 2;
num = num * 4 + nucnum[base];
codon++;
}
@@ -400,12 +414,12 @@ int strcmptrail(char* s1, int l1, char* s2, int l2)
if (l1 > 0)
{
if ( (fin = (char*)memchr(s1, 0, l1) ) != NULL)
- l1 = fin - s1;
+ l1 = (int)(fin - s1);
}
if (l2 > 0)
{
if ( (fin = (char*)memchr(s2, 0, l2) ) != NULL)
- l2 = fin - s2;
+ l2 = (int)(fin - s2);
}
if (l2 > l1)
@@ -446,7 +460,7 @@ void compact(char* chaine)
int l;
char* p, * q;
- l = strlen(chaine); p = chaine + l;
+ l = (int)strlen(chaine); p = chaine + l;
while (*(--p) == ' ' && p >= chaine)
*p = 0;
while ((p = strchr(chaine, ' ')) != NULL)
@@ -454,7 +468,7 @@ void compact(char* chaine)
q = p + 1;
while (*q == ' ')
q++;
- l = q - p;
+ l = (int)(q - p);
while (*q != 0)
{
*(q - l) = *q; q++;
@@ -464,6 +478,20 @@ void compact(char* chaine)
}
+void* mycalloc(int nbre, size_t size)
+{
+ void* point;
+
+ point = calloc(nbre, size);
+ if (point == NULL)
+ {
+ fprintf(stderr, "Error: problem allocating memory.\n");
+ exit(1);
+ }
+ return point;
+}
+
+
char complementer_base(char nucl)
{
switch (nucl)
@@ -602,7 +630,7 @@ int compch(char* cible, int lcible, char** posmot, int nbrmots)
pos = cible + lcible - 1;
while (pos >= cible && *pos == ' ')
pos--;
- lcible = pos - cible + 1;
+ lcible = (int)(pos - cible + 1);
memcpy(vcible, cible, lcible);
vcible[lcible] = 0;
cible = vcible;
@@ -613,7 +641,7 @@ int compch(char* cible, int lcible, char** posmot, int nbrmots)
if (posmot[0] != NULL) /* comparaison avec mot initial */
{
- l = strlen(posmot[0]);
+ l = (int)strlen(posmot[0]);
if (strncmp(cible, posmot[0], l) != 0)
return 0;
cible += l;
@@ -625,14 +653,14 @@ int compch(char* cible, int lcible, char** posmot, int nbrmots)
pos = strstr(cible, posmot[num]);
if (pos == NULL)
return 0;
- l = strlen(posmot[num]);
+ l = (int)strlen(posmot[num]);
cible = pos + l;
num++;
}
if (total == nbrmots - 1)
return 1; /* template se termine par @ */
/* test si cible se termine par dernier mot du template */
- l = strlen(posmot[nbrmots - 1]);
+ l = (int)strlen(posmot[nbrmots - 1]);
if (strcmp(vcible + lcible - l, posmot[nbrmots - 1]) == 0)
return 1;
return 0;
@@ -750,5 +778,3 @@ void gets_no_echo(char* password, size_t lpw)
#endif
return;
}
-
-
diff --git a/src/Bpp/Raa/parser.c b/src/Bpp/Raa/parser.c
index 39376be..6a1b581 100644
--- a/src/Bpp/Raa/parser.c
+++ b/src/Bpp/Raa/parser.c
@@ -1,114 +1,128 @@
#include "parser.h"
-char *unprotect_quotes(char *name);
-
+char* unprotect_quotes(char* name);
/** initialisation d'une r�ponse **/
-Reponse * initreponse(void) {
- Reponse *rep;
- rep = (Reponse *) malloc (sizeof(Reponse));
+Reponse* initreponse(void)
+{
+ Reponse* rep;
+ rep = (Reponse*) malloc (sizeof(Reponse));
rep->nbarguments = 0;
rep->arg = NULL;
return rep;
}
-void clear_reponse(Reponse * rep) {
+void clear_reponse(Reponse* rep)
+{
int pti;
-
- for(pti=0; pti < rep->nbarguments; pti++) {
+
+ for (pti = 0; pti < rep->nbarguments; pti++)
+ {
free(rep->arg[pti]);
}
- if(rep->arg != NULL) free(rep->arg);
+ if (rep->arg != NULL)
+ free(rep->arg);
free(rep);
}
-void ajout_reponse(Reponse *rep, char *pile, int len) {
+void ajout_reponse(Reponse* rep, char* pile, int len)
+{
int pti;
- if (rep->nbarguments==0)
- rep->arg = (char **)malloc(1 * sizeof(char *));
- else
- rep->arg= (char**) realloc(rep->arg,(rep->nbarguments+1)* sizeof(char *)) ; /* ici j'ai deja alloue donc realloc (plus de ligne) */
-
- rep->arg[rep->nbarguments]=(char *) malloc(len + 1); /* j'alloue l'espace pour l'argument */
-
- pti=rep->nbarguments;
- memcpy(rep->arg[pti], pile, len); /* je stocke l'argument */
- rep->arg[pti][len] = 0;
-
- rep->nbarguments++;
-
- }
+ if (rep->nbarguments == 0)
+ rep->arg = (char**)malloc(1 * sizeof(char*));
+ else
+ rep->arg = (char**) realloc(rep->arg, (rep->nbarguments + 1) * sizeof(char*)); /* ici j'ai deja alloue donc realloc (plus de ligne) */
+
+ rep->arg[rep->nbarguments] = (char*) malloc(len + 1); /* j'alloue l'espace pour l'argument */
+ pti = rep->nbarguments;
+ memcpy(rep->arg[pti], pile, len); /* je stocke l'argument */
+ rep->arg[pti][len] = 0;
+ rep->nbarguments++;
+}
/** le parseur qui rempli la structure Reponse **/
-void parse(char *chaine, Reponse *rep) {
-char *ori;
-
-ori=chaine;
-while(*chaine != 0) {
- if (*chaine == '"' ) {
- do { /* chercher le prochain " en ignorant les \" sauf si en fin de partie entre " " */
- chaine++;
- if(*chaine == 0) break;
- }
- while(*chaine != '"' || ( *(chaine-1) == '\\' && *(chaine+1) != '&' && *(chaine+1) != 0) );
- if(*chaine == 0) break;
- chaine++;
- }
- if(*chaine == '&') {
- ajout_reponse(rep, ori, chaine-ori);
- ori=chaine+1;
- }
- chaine++;
+void parse(char* chaine, Reponse* rep)
+{
+ char* ori;
+
+ ori = chaine;
+ while (*chaine != 0)
+ {
+ if (*chaine == '"')
+ {
+ do /* chercher le prochain " en ignorant les \" sauf si en fin de partie entre " " */
+ {
+ chaine++;
+ if (*chaine == 0)
+ break;
+ }
+ while (*chaine != '"' || ( *(chaine - 1) == '\\' && *(chaine + 1) != '&' && *(chaine + 1) != 0) );
+ if (*chaine == 0)
+ break;
+ chaine++;
}
-ajout_reponse(rep, ori, chaine-ori);
+ if (*chaine == '&')
+ {
+ ajout_reponse(rep, ori, chaine - ori);
+ ori = chaine + 1;
+ }
+ chaine++;
+ }
+ ajout_reponse(rep, ori, chaine - ori);
}
-
/** pour rechercher la valeur d'un argument dans la structure **/
-char *val(Reponse *Mono, char *argument)
+char* val(Reponse* Mono, char* argument)
{
-int count, num, l, larg;
-char *retval = NULL, *debut, *p;
-
-count = Mono->nbarguments;
-larg = strlen(argument);
-for(num=0; num < count; num++) {
- debut = Mono->arg[num];
- p = strchr(debut, '=');
- if(p == NULL || larg != p - debut) continue;
- p++;
- if(strncmp(argument, debut, larg) != 0) continue;
- l = strlen(p);
- retval = (char *)malloc(l+1);
- strcpy(retval, p);
- unprotect_quotes(retval);
- break;
- }
-return retval;
+ int count, num, l, larg;
+ char* retval = NULL, * debut, * p;
+
+ count = Mono->nbarguments;
+ larg = strlen(argument);
+ for (num = 0; num < count; num++)
+ {
+ debut = Mono->arg[num];
+ p = strchr(debut, '=');
+ if (p == NULL || larg != p - debut)
+ continue;
+ p++;
+ if (strncmp(argument, debut, larg) != 0)
+ continue;
+ l = strlen(p);
+ retval = (char*)malloc(l + 1);
+ strcpy(retval, p);
+ unprotect_quotes(retval);
+ break;
+ }
+ return retval;
}
-char *unprotect_quotes(char *name)
+char* unprotect_quotes(char* name)
/* enlever les " " encadrantes et decoder les \" internes en " */
{
-char *p;
-int l;
-
-l = strlen(name);
-if(*name == '"') {
- memmove(name, name+1, l--); /* enlever la " initiale */
- if( *(name+l-1) == '"') *(name + --l) = 0; /* enlever la " terminale */
- }
+ char* p;
+ int l;
+
+ l = strlen(name);
+ if (*name == '"')
+ {
+ memmove(name, name + 1, l--); /* enlever la " initiale */
+ if (*(name + l - 1) == '"')
+ *(name + --l) = 0; /* enlever la " terminale */
+ }
-while ((p = strstr(name, "\\\"" /* la chaine \" */ )) != NULL) { memmove(p, p+1, name + l - p); l--; }
-return name;
+ while ((p = strstr(name, "\\\"" /* la chaine \" */ )) != NULL)
+ {
+ memmove(p, p + 1, name + l - p); l--;
+ }
+ return name;
}
-
diff --git a/src/Bpp/Raa/parser.h b/src/Bpp/Raa/parser.h
index ad738ef..e38dbca 100644
--- a/src/Bpp/Raa/parser.h
+++ b/src/Bpp/Raa/parser.h
@@ -1,15 +1,14 @@
#include <stdlib.h>
#include <string.h>
-typedef struct ThisReponse{
-
- char **arg; /* je stocke les arguments */
+typedef struct ThisReponse
+{
+ char** arg; /* je stocke les arguments */
int nbarguments; /* je stocke le nombre d'arguments */
-
-} Reponse ;
+} Reponse;
-extern Reponse * initreponse(void) ;
-extern void clear_reponse(Reponse * rep) ;
-void ajout_reponse(Reponse *rep, char *pile, int len) ;
-extern void parse(char *chaine, Reponse *rep) ;
-extern char *val(Reponse *Mono, char *argument) ;
+extern Reponse* initreponse(void);
+extern void clear_reponse(Reponse* rep);
+void ajout_reponse(Reponse* rep, char* pile, int len);
+extern void parse(char* chaine, Reponse* rep);
+extern char* val(Reponse* Mono, char* argument);
diff --git a/src/Bpp/Raa/zsockr.c b/src/Bpp/Raa/zsockr.c
index 1778818..d8813f7 100644
--- a/src/Bpp/Raa/zsockr.c
+++ b/src/Bpp/Raa/zsockr.c
@@ -1,5 +1,5 @@
/* functions to handle zlib-compressed data read from socket
-*/
+ */
#include <zlib.h>
#include <unistd.h>
#include <stdlib.h>
@@ -11,135 +11,147 @@
/* included functions */
-void *prepare_sock_gz_r(FILE *sockr);
-int z_getc(void *v);
-char *z_gets(void *v, char *line, size_t len);
-char *z_read_sock(void *v);
-int close_sock_gz_r(void *v);
-
+void* prepare_sock_gz_r(FILE* sockr);
+int z_getc(void* v);
+char* z_gets(void* v, char* line, size_t len);
+char* z_read_sock(void* v);
+int close_sock_gz_r(void* v);
#define ZBSIZE 100000
-typedef struct {
- z_stream stream;
- char z_buffer[ZBSIZE]; /* compressed input buffer */
- char text_buffer[4 * ZBSIZE]; /* decompressed buffer */
- char *pos, *endbuf;
+typedef struct
+{
+ z_stream stream;
+ char z_buffer[ZBSIZE]; /* compressed input buffer */
+ char text_buffer[4 * ZBSIZE]; /* decompressed buffer */
+ char* pos, * endbuf;
#ifdef WIN32
- SOCKET fd;
+ SOCKET fd;
#else
- int fd;
+ int fd;
#endif
- } sock_gz_r;
+} sock_gz_r;
-
-void *prepare_sock_gz_r(FILE *sockr)
+void* prepare_sock_gz_r(FILE* sockr)
{
-int err;
-sock_gz_r *big;
-
-big = (sock_gz_r *)malloc(sizeof(sock_gz_r));
-if(big == NULL) return NULL;
-big->stream.next_in = Z_NULL;
-big->stream.avail_in = 0;
-big->stream.avail_out = 0;
-big->stream.zalloc = Z_NULL;
-big->stream.zfree = Z_NULL;
-big->stream.opaque = NULL;
-big->pos = big->text_buffer;
-big->endbuf = big->pos;
+ int err;
+ sock_gz_r* big;
+
+ big = (sock_gz_r*)malloc(sizeof(sock_gz_r));
+ if (big == NULL)
+ return NULL;
+ big->stream.next_in = Z_NULL;
+ big->stream.avail_in = 0;
+ big->stream.avail_out = 0;
+ big->stream.zalloc = Z_NULL;
+ big->stream.zfree = Z_NULL;
+ big->stream.opaque = NULL;
+ big->pos = big->text_buffer;
+ big->endbuf = big->pos;
#ifdef WIN32
-big->fd = (SOCKET)sockr;
+ big->fd = (SOCKET)sockr;
#else
-big->fd = fileno(sockr);
+ big->fd = fileno(sockr);
#endif
-err = inflateInit(&big->stream);
-return err == Z_OK ? (void *)big : NULL;
+ err = inflateInit(&big->stream);
+ return err == Z_OK ? (void*)big : NULL;
}
-int z_getc(void *v)
+int z_getc(void* v)
{
-int q;
-sock_gz_r *big = (sock_gz_r *)v;
-z_streamp zs;
-
-if(big->pos < big->endbuf) {
- return *(big->pos++);
- }
-zs = &(big->stream);
-zs->next_out = (Bytef *)big->text_buffer;
-zs->avail_out = sizeof(big->text_buffer);
-big->pos = (char *)zs->next_out;
-do {
- if(zs->avail_in == 0) {
- int lu;
+ int q;
+ sock_gz_r* big = (sock_gz_r*)v;
+ z_streamp zs;
+
+ if (big->pos < big->endbuf)
+ {
+ return *(big->pos++);
+ }
+ zs = &(big->stream);
+ zs->next_out = (Bytef*)big->text_buffer;
+ zs->avail_out = sizeof(big->text_buffer);
+ big->pos = (char*)zs->next_out;
+ do
+ {
+ if (zs->avail_in == 0)
+ {
+ int lu;
#ifdef WIN32
- lu = recv( big->fd , big->z_buffer, ZBSIZE, 0 );
+ lu = recv( big->fd, big->z_buffer, ZBSIZE, 0 );
#else
- lu = read( big->fd , big->z_buffer, ZBSIZE );
+ lu = read( big->fd, big->z_buffer, ZBSIZE );
#endif
- if(lu == -1) return EOF;
- zs->next_in = (Bytef *)big->z_buffer;
- zs->avail_in = lu;
- }
- q = inflate(zs, Z_NO_FLUSH);
- if(q == Z_STREAM_END) break;
- if(q != Z_OK) {
- break;
- }
- }
-while ( (char *)zs->next_out == big->pos);
-big->endbuf = (char *)zs->next_out;
-if(big->pos < big->endbuf) return *(big->pos++);
-else
- return EOF;
+ if (lu == -1)
+ return EOF;
+ zs->next_in = (Bytef*)big->z_buffer;
+ zs->avail_in = lu;
+ }
+ q = inflate(zs, Z_NO_FLUSH);
+ if (q == Z_STREAM_END)
+ break;
+ if (q != Z_OK)
+ {
+ break;
+ }
+ }
+ while ( (char*)zs->next_out == big->pos);
+ big->endbuf = (char*)zs->next_out;
+ if (big->pos < big->endbuf)
+ return *(big->pos++);
+ else
+ return EOF;
}
-char *z_gets(void *v, char *line, size_t len)
+char* z_gets(void* v, char* line, size_t len)
{
-int c;
-char *p;
-
-p = line;
-while(len > 1) {
- c = z_getc( v );
- if(c == EOF) {
- if(p == line) return NULL;
- break;
- }
- *(p++) = c;
- if(c == '\n') break;
- len--;
- }
-*p = 0;
-return line;
+ int c;
+ char* p;
+
+ p = line;
+ while (len > 1)
+ {
+ c = z_getc( v );
+ if (c == EOF)
+ {
+ if (p == line)
+ return NULL;
+ break;
+ }
+ *(p++) = c;
+ if (c == '\n')
+ break;
+ len--;
+ }
+ *p = 0;
+ return line;
}
-char *z_read_sock(void *v)
+char* z_read_sock(void* v)
{
-static char line[500];
-char *p;
-int l;
-
-p = z_gets(v, line, sizeof(line));
-if(p == NULL) return NULL;
-l = strlen(line);
-if(l > 0 && line[l-1] == '\n') line[l-1] = 0;
-return line;
+ static char line[500];
+ char* p;
+ int l;
+
+ p = z_gets(v, line, sizeof(line));
+ if (p == NULL)
+ return NULL;
+ l = strlen(line);
+ if (l > 0 && line[l - 1] == '\n')
+ line[l - 1] = 0;
+ return line;
}
-int close_sock_gz_r(void *v)
+int close_sock_gz_r(void* v)
{
-sock_gz_r *big = (sock_gz_r *)v;
-int val;
+ sock_gz_r* big = (sock_gz_r*)v;
+ int val;
-val = inflateEnd(&(big->stream));
-free(big);
-return val;
+ val = inflateEnd(&(big->stream));
+ free(big);
+ return val;
}
-
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 29d8c29..d3b565f 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,54 +1,59 @@
# CMake script for Bio++ Remote Acnuc Access
-# Author: Sylvain Gaillard and Julien Dutheil
+# Authors:
+# Sylvain Gaillard
+# Julien Dutheil
+# Francois Gindraud (2017)
# Created: 11/09/2009
-# File list
-set(C_FILES
- Bpp/Raa/md5.c
- Bpp/Raa/parser.c
- Bpp/Raa/zsockr.c
- Bpp/Raa/misc_acnuc.c
- Bpp/Raa/RAA_acnuc.c
-)
-
-set(CPP_FILES
- Bpp/Raa/RAA.cpp
- Bpp/Raa/RaaList.cpp
- Bpp/Raa/RaaSpeciesTree.cpp
-)
+set (C_FILES
+ Bpp/Raa/RAA_acnuc.c
+ Bpp/Raa/md5.c
+ Bpp/Raa/misc_acnuc.c
+ Bpp/Raa/parser.c
+ Bpp/Raa/zsockr.c
+ )
-set(H_FILES
- Bpp/Raa/parser.h
- Bpp/Raa/RAA.h
- Bpp/Raa/RaaSeqAttributes.h
- Bpp/Raa/RAA_acnuc.h
- Bpp/Raa/RaaList.h
- Bpp/Raa/RaaSpeciesTree.h
-)
+set (CPP_FILES
+ Bpp/Raa/RAA.cpp
+ Bpp/Raa/RaaList.cpp
+ Bpp/Raa/RaaSpeciesTree.cpp
+ )
# Build the static lib
-add_library(bppraa-static STATIC ${CPP_FILES} ${C_FILES})
-set_target_properties(bppraa-static
- PROPERTIES OUTPUT_NAME bpp-raa
- CLEAN_DIRECT_OUTPUT 1
+add_library (${PROJECT_NAME}-static STATIC ${CPP_FILES} ${C_FILES})
+target_include_directories (${PROJECT_NAME}-static PUBLIC
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
+ $<INSTALL_INTERFACE:$<INSTALL_PREFIX>/${CMAKE_INSTALL_INCLUDEDIR}>
)
-target_link_libraries(bppraa-static ${LIBS})
+set_target_properties (${PROJECT_NAME}-static PROPERTIES OUTPUT_NAME ${PROJECT_NAME})
+target_link_libraries (${PROJECT_NAME}-static ${BPP_LIBS_STATIC} zlib)
# Build the shared lib
-add_library(bppraa-shared SHARED ${CPP_FILES} ${C_FILES})
-set_target_properties(bppraa-shared
- PROPERTIES OUTPUT_NAME bpp-raa
- CLEAN_DIRECT_OUTPUT 1
- VERSION ${BPPRAA_VERSION}
- SOVERSION ${BPPRAA_VERSION_MAJOR}
+add_library (${PROJECT_NAME}-shared SHARED ${CPP_FILES} ${C_FILES})
+target_include_directories (${PROJECT_NAME}-shared PUBLIC
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
+ $<INSTALL_INTERFACE:$<INSTALL_PREFIX>/${CMAKE_INSTALL_INCLUDEDIR}>
)
-target_link_libraries(bppraa-shared ${LIBS})
-
-# Install libs
-install(TARGETS bppraa-static bppraa-shared DESTINATION lib${LIB_SUFFIX})
-
-# Install headers
-install(DIRECTORY Bpp/ DESTINATION include/Bpp FILES_MATCHING PATTERN "*.h")
-
-# Generate generic include files (.all)
-INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${CMAKE_SOURCE_DIR}/genIncludes.sh ${CMAKE_PREFIX_PATH}/include/Bpp)")
+set_target_properties (${PROJECT_NAME}-shared
+ PROPERTIES OUTPUT_NAME ${PROJECT_NAME}
+ MACOSX_RPATH 1
+ VERSION ${${PROJECT_NAME}_VERSION}
+ SOVERSION ${${PROJECT_NAME}_VERSION_MAJOR}
+ )
+target_link_libraries (${PROJECT_NAME}-shared ${BPP_LIBS_SHARED} zlib)
+
+# Install libs and headers
+install (
+ TARGETS ${PROJECT_NAME}-static ${PROJECT_NAME}-shared
+ EXPORT ${PROJECT_NAME}-targets
+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+ RUNTIME DESTINATION ${CMAKE_INSTALL_LIBDIR}
+ )
+install (
+ DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/Bpp
+ DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+ FILES_MATCHING PATTERN "*.h"
+ )
+# Install cmake file representing targets
+install (EXPORT ${PROJECT_NAME}-targets DESTINATION ${cmake-package-location})
--
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