CMakeLists.txt

@@ -35,7 +35,7 @@ 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(${PROJECT_NAME}_VERSION_CURRENT "2")
+SET(${PROJECT_NAME}_VERSION_CURRENT "3")
 SET(${PROJECT_NAME}_VERSION_REVISION "0")
 SET(${PROJECT_NAME}_VERSION_AGE "0")
 
@@ -53,7 +53,7 @@ if (CMAKE_INSTALL_PREFIX)
 endif (CMAKE_INSTALL_PREFIX)
 
 include (GNUInstallDirs)
-find_package (bpp-seq 11.0.0 REQUIRED)
+find_package (bpp-seq 12.0.0 REQUIRED)
 
 # CMake package
 set (cmake-package-location ${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME})
@@ -95,10 +95,10 @@ ENDIF(NO_DEP_CHECK)
 # Packager
 SET(CPACK_PACKAGE_NAME "libbpp-seq-omics")
 SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.3.1")
+SET(CPACK_PACKAGE_VERSION "2.4.0")
 SET(CPACK_PACKAGE_VERSION_MAJOR "2")
-SET(CPACK_PACKAGE_VERSION_MINOR "3")
-SET(CPACK_PACKAGE_VERSION_PATCH "1")
+SET(CPACK_PACKAGE_VERSION_MINOR "4")
+SET(CPACK_PACKAGE_VERSION_PATCH "0")
 SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Sequence-Omics library")
 SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
 SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
@@ -107,6 +107,8 @@ SET(CPACK_SOURCE_GENERATOR "TGZ")
 # /!\ This assumes that an external build is used
 SET(CPACK_SOURCE_IGNORE_FILES 
        "/build/" 
+       "/html/" 
+       "/BppSeqOmics.tag" 
        "/\\\\.git/" 
        "/\\\\.gitignore" 
        ${CPACK_SOURCE_IGNORE_FILES}

ChangeLog

+02/03/18 -*- Version 2.4.0 -*-
+
+02/03/18 Julien Dutheil
+* Removed all dynamic exception specifications
+* Increased interface number to 3
+
+21/01/18 Julien Dutheil
+* Added OrderFilterMafIterator class.
+
+03/01/18 Julien Dutheil
+* Fixed bug in AlnFilter when relative proportions are set. Proportion was relative to block and not to window, which was incorrect.
+
+22/12/17 Julien Dutheil
+* Improved GTF parser, bug fixed when empty token in last column.
+
 10/12/17 -*- Version 2.3.2 -*-
 
 10/05/17 -*- Version 2.3.0 -*-

Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = bpp-seq-omics
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 2.3.0
+PROJECT_NUMBER         = 2.4.0
 
 # 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

bpp-seq-omics.spec

-%define _basename bpp-seq-omics
-%define _version 2.3.1
-%define _release 1
 %define _prefix /usr
 
-URL: http://biopp.univ-montp2.fr/
+URL: https://github.com/BioPP/bpp-seq-omics
 
-Name: %{_basename}
-Version: %{_version}
-Release: %{_release}
+Name: bpp-seq-omics
+Version: 2.4.0
+Release: 1%{?dist}
 License: CECILL-2.0
 Vendor: The Bio++ Project
-Source: http://biopp.univ-montp2.fr/repos/sources/%{_basename}-%{_version}.tar.gz
+Source: %{name}-%{version}.tar.gz
 Summary: Bio++ Sequence library: genomics components
 Group: Development/Libraries/C and C++
-Requires: bpp-core = %{_version}
-Requires: bpp-seq = %{_version}
+Requires: bpp-core = %{version}
+Requires: bpp-seq = %{version}
 
-BuildRoot: %{_builddir}/%{_basename}-root
+BuildRoot: %{_builddir}/%{name}-root
 BuildRequires: cmake >= 2.8.11
 BuildRequires: gcc-c++ >= 4.7.0
-BuildRequires: libbpp-core3 = %{_version}
-BuildRequires: libbpp-core-devel = %{_version}
-BuildRequires: libbpp-seq11 = %{_version}
-BuildRequires: libbpp-seq-devel = %{_version}
+BuildRequires: libbpp-core4 = %{version}
+BuildRequires: libbpp-core-devel = %{version}
+BuildRequires: libbpp-seq12 = %{version}
+BuildRequires: libbpp-seq-devel = %{version}
 
 AutoReq: yes
 AutoProv: yes
@@ -31,26 +28,26 @@ AutoProv: yes
 This library contains the genomics components of the Bio++ sequence library.
 It is part of the Bio++ project.
 
-%package -n libbpp-seq-omics2
+%package -n libbpp-seq-omics3
 Summary: Bio++ Sequence library: genomics components
 Group: Development/Libraries/C and C++
 
-%description -n libbpp-seq-omics2
+%description -n libbpp-seq-omics3
 This library contains the genomics components of the Bio++ sequence library.
 It is part of the Bio++ project.
 
 %package -n libbpp-seq-omics-devel
 Summary: Bio++ Sequence library: genomics components
 Group: Development/Libraries/C and C++
-Requires: libbpp-seq-omics2 = %{_version}
-Requires: libbpp-seq11 = %{_version}
-Requires: libbpp-seq-devel = %{_version}
-Requires: libbpp-core3 = %{_version}
-Requires: libbpp-core-devel = %{_version}
+Requires: libbpp-seq-omics3 = %{version}
+Requires: libbpp-seq12 = %{version}
+Requires: libbpp-seq-devel = %{version}
+Requires: libbpp-core4 = %{version}
+Requires: libbpp-core-devel = %{version}
 
 %description -n libbpp-seq-omics-devel
 The libbpp-seq-omics-devel package contains the header files and static libraries for
-building applications which use %{_basename}.
+building applications which use %{name}.
 
 %prep
 %setup -q
@@ -67,11 +64,11 @@ make DESTDIR=$RPM_BUILD_ROOT install
 %clean
 rm -rf $RPM_BUILD_ROOT
 
-%post -n libbpp-seq-omics2 -p /sbin/ldconfig
+%post -n libbpp-seq-omics3 -p /sbin/ldconfig
 
-%postun -n libbpp-seq-omics2 -p /sbin/ldconfig
+%postun -n libbpp-seq-omics3 -p /sbin/ldconfig
 
-%files -n libbpp-seq-omics2
+%files -n libbpp-seq-omics3
 %defattr(-,root,root)
 %doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog
 %{_prefix}/%{_lib}/lib*.so.*
@@ -87,6 +84,9 @@ rm -rf $RPM_BUILD_ROOT
 %{_prefix}/include/*
 
 %changelog
+* Fri Mar 03 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.0-1
+- Increased interface number
+- Removed dynamic exceptions declarations.
 * Tue Jun 06 2017 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.3.1-1
 - Increased interface number
 * Wed May 10 2017 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.3.0-1

debian/changelog

+libbpp-seq-omics (2.4.0-1) UNRELEASED; urgency=medium
+
+  * New upstream version.
+
+ -- Julien Dutheil <julien.dutheil@univ-montp2.fr>  Wed, 28 Mar 2018 10:00:23 +0200
+
 libbpp-seq-omics (2.3.2-1) unstable; urgency=medium
 
   [ Julien Dutheil ]

debian/control

@@ -7,7 +7,7 @@ Priority: optional
 Build-Depends: debhelper (>= 11~),
                cmake,
                d-shlibs (>= 0.80),
-               libbpp-seq-dev (>= 2.3.2)
+               libbpp-seq-dev (>= 2.4.0)
 Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libbpp-seq-omics.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/libbpp-seq-omics.git
@@ -16,9 +16,9 @@ Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
 Package: libbpp-seq-omics-dev
 Architecture: any
 Section: libdevel
-Depends: libbpp-seq-omics2 (= ${binary:Version}),
+Depends: libbpp-seq-omics3 (= ${binary:Version}),
          ${misc:Depends},
-         libbpp-seq-dev (>= 2.3.2)
+         libbpp-seq-dev (>= 2.4.0)
 Description: Bio++ Sequence library: genomics components (development files)
  Bio++ is a set of C++ libraries for Bioinformatics, including sequence
  analysis, phylogenetics, molecular evolution and population genetics.
@@ -29,7 +29,7 @@ Description: Bio++ Sequence library: genomics components (development files)
  This package contains the static library and the header files of the
  Bio++ classes dedicated to genomic sequencing.
 
-Package: libbpp-seq-omics2
+Package: libbpp-seq-omics3
 Architecture: any
 Multi-Arch: same
 Section: libs

debian/copyright

 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: B++-Seq-Omics
+Upstream-Name: Bpp-Seq-Omics
 Upstream-Contact: Julien Yann Dutheil <julien.dutheil@univ-montp2.fr>
-Source: http://biopp.univ-montp2.fr/Repositories/sources/
+Source: https://github.com/BioPP/bpp-seq-omics/
 
 Files: *
 Copyright: 2010-2016 Julien Yann Dutheil <julien.dutheil@univ-montp2.fr>

debian/patches/fix_test_cmakelist.patch

-Author: Julien Y. Dutheil <dutheil@evolbio.mpg.de>
-Last-Update: Mon Jul 17 22:57:56 2017 +0200
-Description: Fixed unit tests for more portability.
-
---- a/test/CMakeLists.txt
-+++ b/test/CMakeLists.txt
-@@ -16,9 +16,11 @@ foreach (test_cpp_file ${test_cpp_files}
-   get_filename_component (test_name ${test_cpp_file} NAME_WE)
-   add_executable (${test_name} ${test_cpp_file})
-   target_link_libraries (${test_name} ${PROJECT_NAME}-shared)
-+  set_target_properties (${test_name} PROPERTIES POSITION_INDEPENDENT_CODE TRUE) 
-   add_test (
-     NAME ${test_name}
-     WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-     COMMAND ${test_name}
-     )
-+  set_tests_properties (${test_name} PROPERTIES TIMEOUT 60000)
- endforeach (test_cpp_file)

debian/patches/series

 unforce-cxxflags.patch
-fix_test_cmakelist.patch

debian/patches/unforce-cxxflags.patch

@@ -11,7 +11,7 @@ Comment: Upstream version 2.3.0 now has additional -std=c++11 which might
  
  # Compile options
 -set (CMAKE_CXX_FLAGS "-std=c++11 -Wall -Weffc++ -Wshadow -Wconversion")
-+set (CMAKE_CXX_FLAGS "-std=c++11 -Wno-deprecated -g")
++#set (CMAKE_CXX_FLAGS "-std=c++11 -g")
  
  IF(NOT CMAKE_BUILD_TYPE)
    SET(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING

src/Bpp/Seq/Feature/Bed/BedGraphFeatureReader.cpp

@@ -66,7 +66,7 @@ void BedGraphFeatureReader::getNextLine_() {
   }
 }
 
-const BasicSequenceFeature BedGraphFeatureReader::nextFeature() throw (Exception)
+const BasicSequenceFeature BedGraphFeatureReader::nextFeature()
 {
   if (!hasMoreFeature())
     throw Exception("BedGraphFeatureReader::nextFeature(). No more feature in file.");

src/Bpp/Seq/Feature/Bed/BedGraphFeatureReader.h

@@ -92,7 +92,7 @@ class BedGraphFeatureReader:
 
   public:
     bool hasMoreFeature() const { return nextLine_ != ""; }
-    const BasicSequenceFeature nextFeature() throw (Exception);
+    const BasicSequenceFeature nextFeature();
 
     void getAllFeatures(SequenceFeatureSet& features) {
       while (hasMoreFeature()) {

src/Bpp/Seq/Feature/FeatureReader.h

@@ -64,7 +64,7 @@ class FeatureReader
 
   public:
     virtual bool hasMoreFeature() const = 0;
-    virtual const BasicSequenceFeature nextFeature() throw (Exception) = 0;
+    virtual const BasicSequenceFeature nextFeature() = 0;
     virtual void getAllFeatures(SequenceFeatureSet& features) = 0;
     virtual void getFeaturesOfType(const std::string& type, SequenceFeatureSet& features) = 0;
     virtual void getFeaturesOfSequence(const std::string& seqId, SequenceFeatureSet& features) = 0;

src/Bpp/Seq/Feature/Gff/GffFeatureReader.cpp

@@ -76,7 +76,7 @@ void GffFeatureReader::getNextLine_() {
   }
 }
 
-const BasicSequenceFeature GffFeatureReader::nextFeature() throw (Exception)
+const BasicSequenceFeature GffFeatureReader::nextFeature()
 {
   if (!hasMoreFeature())
     throw Exception("GffFeatureReader::nextFeature(). No more feature in file.");

src/Bpp/Seq/Feature/Gff/GffFeatureReader.h

@@ -93,7 +93,7 @@ class GffFeatureReader:
 
   public:
     bool hasMoreFeature() const { return nextLine_ != ""; }
-    const BasicSequenceFeature nextFeature() throw (Exception);
+    const BasicSequenceFeature nextFeature();
 
     void getAllFeatures(SequenceFeatureSet& features) {
       while (hasMoreFeature()) {

src/Bpp/Seq/Feature/Gtf/GtfFeatureReader.cpp

@@ -51,9 +51,9 @@ knowledge of the CeCILL license and that you accept its terms.
 using namespace bpp;
 using namespace std;
 
-const std::string GtfFeatureReader::GTF_PHASE = "GTF_PHASE";
-const std::string GtfFeatureReader::GTF_GENE_ID = "gene_id";
-const std::string GtfFeatureReader::GTF_TRANSCRIPT_ID = "transcript_id";
+const string GtfFeatureReader::GTF_PHASE = "GTF_PHASE";
+const string GtfFeatureReader::GTF_GENE_ID = "gene_id";
+const string GtfFeatureReader::GTF_TRANSCRIPT_ID = "transcript_id";
 
 void GtfFeatureReader::getNextLine_() {
   nextLine_ = "";
@@ -70,7 +70,7 @@ void GtfFeatureReader::getNextLine_() {
   }
 }
 
-const BasicSequenceFeature GtfFeatureReader::nextFeature() throw (Exception)
+const BasicSequenceFeature GtfFeatureReader::nextFeature()
 {
   if (!hasMoreFeature())
     throw Exception("GtfFeatureReader::nextFeature(). No more feature in file.");
@@ -81,28 +81,30 @@ const BasicSequenceFeature GtfFeatureReader::nextFeature() throw (Exception)
     throw Exception("GtfFeatureReader::nextFeature(). Wrong GTF file format: should have 9 tab delimited columns.");
   
   //if ok, we can parse each column:
-  std::string seqId       = st.nextToken();
-  std::string source      = st.nextToken();
-  std::string type        = st.nextToken();
+  string seqId       = st.nextToken();
+  string source      = st.nextToken();
+  string type        = st.nextToken();
   unsigned int start = TextTools::to<unsigned int>(st.nextToken()) - 1;
   unsigned int end   = TextTools::to<unsigned int>(st.nextToken());
   double score       = TextTools::to<double>(st.nextToken());
-  std::string strand      = st.nextToken();
-  std::string phase       = st.nextToken();
-  std::string attrDesc    = st.nextToken();
-  std::map<string, string> attributes;
-  bpp::StringTokenizer st1(attrDesc, ";");
+  string strand      = st.nextToken();
+  string phase       = st.nextToken();
+  string attrDesc    = st.nextToken();
+  map<string, string> attributes;
+  StringTokenizer st1(attrDesc, ";");
   while (st1.hasMoreToken()) {
-    std::string item(bpp::TextTools::removeSurroundingWhiteSpaces(st1.nextToken()));
-    std::string::size_type idx = item.find_first_of(' ');
-    std::string key(item.substr(0, idx));
-    std::string value(item.substr(idx));
+    string item(st1.nextToken());
+    if (TextTools::isEmpty(item)) continue;
+    item = TextTools::removeSurroundingWhiteSpaces(item);
+    string::size_type idx = item.find_first_of(' ');
+    string key(item.substr(0, idx));
+    string value(item.substr(idx));
     // remove first "
     while (
         value.size() > 0 
         && (
           value[0] == '"' 
-          || bpp::TextTools::isWhiteSpaceCharacter(value[0])
+          || TextTools::isWhiteSpaceCharacter(value[0])
           )
         ) {
       value.erase(value.begin());
@@ -112,7 +114,7 @@ const BasicSequenceFeature GtfFeatureReader::nextFeature() throw (Exception)
         value.size() > 0 
         && (
           value[value.size() - 1] == '"' 
-          || bpp::TextTools::isWhiteSpaceCharacter(value[value.size() - 1])
+          || TextTools::isWhiteSpaceCharacter(value[value.size() - 1])
           )
         ) {
       value.erase(value.end() - 1);
@@ -122,15 +124,15 @@ const BasicSequenceFeature GtfFeatureReader::nextFeature() throw (Exception)
   }
   //KeyvalTools::multipleKeyvals(attrDesc, attributes, ";", false);
   //std::string id = attributes["ID"];
-  std::string id = "";
+  string id = "";
   BasicSequenceFeature feature(id, seqId, source, type, start, end, strand[0], score);
   
   //Set phase attributes:
-  phase = bpp::TextTools::removeSurroundingWhiteSpaces(phase);
+  phase = TextTools::removeSurroundingWhiteSpaces(phase);
   if (phase != ".") feature.setAttribute(GTF_PHASE, phase);
 
   //now check additional attributes:
-  for (std::map<std::string, std::string>::iterator it = attributes.begin(); it != attributes.end(); ++it) {
+  for (map<std::string, std::string>::iterator it = attributes.begin(); it != attributes.end(); ++it) {
     feature.setAttribute(it->first, it->second); //We accept all attributes, even if they are not standard.
     //std::cout << "[" << it->first << "] = [" << it->second << "]" << std::endl;
     //std::cout << "phase: " << phase << std::endl;

src/Bpp/Seq/Feature/Gtf/GtfFeatureReader.h

@@ -84,7 +84,7 @@ class GtfFeatureReader:
 
   public:
     bool hasMoreFeature() const { return nextLine_ != ""; }
-    const BasicSequenceFeature nextFeature() throw (Exception);
+    const BasicSequenceFeature nextFeature();
 
     void getAllFeatures(SequenceFeatureSet& features) {
       while (hasMoreFeature()) {

src/Bpp/Seq/Io/Fastq.cpp

@@ -44,7 +44,7 @@ knowledge of the CeCILL license and that you accept its terms.
 
 using namespace bpp;
 
-bool Fastq::nextSequence(std::istream& input, Sequence& seq) const throw (Exception) {
+bool Fastq::nextSequence(std::istream& input, Sequence& seq) const {
   if (input && ! input.eof()) {
     //SequenceWithQuality& sq;
     std::string buffer;
@@ -85,7 +85,7 @@ bool Fastq::nextSequence(std::istream& input, Sequence& seq) const throw (Except
 
 /******************************************************************************/
 
-void Fastq::writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception)
+void Fastq::writeSequence(std::ostream& output, const Sequence& seq) const
 {
   std::string qual(seq.size(), static_cast<char>(33));
   try {

src/Bpp/Seq/Io/Fastq.h

@@ -118,7 +118,7 @@ namespace bpp
        * in.close();
        * @endcode
        */
-      bool nextSequence(std::istream& input, Sequence& seq) const throw (Exception);
+      bool nextSequence(std::istream& input, Sequence& seq) const;
       /** @} */
 
       /**
@@ -130,7 +130,7 @@ namespace bpp
        * @copydoc OSequenceStream::writeSequence()
        * @author Sylvain Gaillard
        */
-      void writeSequence(std::ostream& output, const Sequence& seq) const throw (Exception);
+      void writeSequence(std::ostream& output, const Sequence& seq) const;
       /** @} */
   };
 }