File: ChangeLog

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libbpp-seq 2.4.1-3
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19/02/18 -*- Version 2.4.0 -*-

19/02/18 Julien Dutheil
* Increased interface number (new 12)

10/12/17 -*- Version 2.3.2 -*-

08/11/17 Laurent Guéguen
* More efficient codon models.

27/06/17 François Grindaud
* Removed all dynamic exceptions specification

10/05/17 -*- Version 2.3.0 -*-

18/12/16 Julien Dutheil
* Removed exception specifications in Transliterators

17/12/16 Julien Dutheil
* new function SiteTools::isDoubleton
* new function SiteTools::getMinoralleleFrequency
* new function SequenceTools::areSequencesIdentical

19/09/16 Murray Patterson
* Started integration of probabilistic sequences

07/03/16 Julien Dutheil
* Much faster getCompleteSites (does not check for positions)

23/09/14 -*- Version 2.2.0 -*- 

23/09/14 Julien Dutheil
* Fixed bug #73

16/09/14 Julien Dutheil
* Fixed bug #79

24/07/14 Julien Dutheil
* Alphabet code gets a refreshment!

05/03/13 -*- Version 2.1.0 -*- 

07/02/13 Julien Dutheil
* StateProperties => Alphabet index (dir renamed).
* New BppO classes forAlphabet Index 1 and 2, and corresponding methods in SequenceApplicationTools.

19/01/13 Julien Dutheil
* Compiles with -Wconversion.

09/01/13 Julien Dutheil
* Use size_t instead of unsigned int for indexes in containers.

17/09/12 Julien Dutheil
* Reorganized IO classes.

11/09/12 Julien Dutheil
* Added generic container converter function.

30/07/12 Julien Dutheil
* Moved features, fastq and maf to new bpp-seq-omics library.

18/07/12 Julien Dutheil
* Bug fixed in merge maf iterator, in case a sequence is missing in one of the two blocks.

25/06/12 Julien Dutheil
* Extended maf tools and reorganization of the code.
* Extended GFF output.
* New [] operator in SequenceFeatureSet.

18/06/12 Julien Dutheil
* Fixed bug in Maf parser: scores are now parsed correctly.

08/03/12 Julien Dutheil
* Added support for '*' character in proteins (stop codon)

09/02/12 -*- Version 2.0.3 -*-

16/01/12 Julien Dutheil
* Bug #42 solved, new support for extended fasta parser in application tools.
* Added contribution from Benoit Nabholz and Annabelle Haudry on 4-fold degenerated sites.

06/01/12 Julien Dutheil
* Added support for "!" state in nucleic alphabet, which can be either a gap or an unknown character.

24/11/11 Julien Dutheil
* Added SequenceWalker class and test.

22/11/11 Sylvain Gaillard
* Added support for FastQ

21/11/11 Julien Dutheil
* Added support for GFF3.

21/11/11 Sylvain Gaillard
* Bug #35 solved.

18/11/11 Julien Dutheil
* New MafIterators: SequenceStatistics and PairwiseSequenceStatistics.
* Function SequenceTools::getPercentIdentity now allows to exclude gaps.

15/09/11 Julien Dutheil
* Merge function of SequenceWithAnnotation now also merges annotations properly.

17/06/11 Julien Dutheil
* Bug #39 solved.

09/06/11 -*- Version 2.0.2 -*-

08/06/11 Julien Dutheil
* Fixed several Maf iterators.

28/02/11 -*- Version 2.0.1 -*-

* Fixed debian packaging. 

07/02/11 -*- Version 2.0.0 -*-

19/11/10 Julien Dutheil
* Solved bug 0000016 (General comments not copied in containers).
* A few more code cleaning.

01/11/10 Julien Dutheil
* Solved bug 0000005 (Clustal parser).
* Added unit testing for sequence input format.
* Solved bug 0000004 (Remove gap sites in SiteContainer).

12/10/10 Benoît Nabholz
* Added yeast mitochondrial codon alphabet and genetic code.

20/09/10 Julien Dutheil
* Reorganization of the code for version 2.0.

06/09/10 Julien Dutheil
* Added support for masked sequences in SequenceWithAnnotationTools and MafParser.

05/09/10 Julien Dutheil
* First draft of CaseMaskedAlphabet, for dealing with repeat-masked sequences for instance.

21/07/10 Julien Dutheil
* Added method hasSequence(name) in SequenceContainer interface.

20/07/10 Julien Dutheil
* New Sequence interface design.
* Maf parser now reads quality scores if there are some.

19/07/10 Julien Dutheil
* New method isInit in CodonAlphabet.
* New method getCDS in SequenceTools.

28/04/10 Julien Dutheil
* New MAF genome alignment parser.

22/04/10 Sylvain Gaillard
* Break SequenceTools interface:
		- renamed invert -> getInvert
		- renamed complement -> getComplement
	now invert and complement methods deals with sequence ref
		- New method invertComplement

16/04/10 Julien Dutheil
* New Stockholm sequence format (output only).
* Refactoring of class ISequence2 => IAlignment + new interface OAlignment.

24/03/10 -*- Version 1.7.0 -*-

11/03/10 Julien Dutheil
* Nexus format now deals with lower case keywords.

17/12/09 Julien Dutheil
* Code cleaning for VectorSiteContainer
* New class CompressedVectorSiteContainer using less memory than
  VectorSiteContainer, but more restricted.

16/11/09 Sylvain Gaillard
* No more "using namespace" in header files.

04/11/09 Julien Dutheil
* Remove SymbolListTools::randomizeContent to a more efficient SymbolList::shuffle
method.

12/10/09 Julien Dutheil
* Now SeqLib compiles with -Weffc++ and -Wshadow without any warning :)

22/09/09 Julien Dutheil
* Finally added 'addSequence' method in SequenceContainer.
* MapSequenceContainer now has a addSequence method that uses the name of the
  sequence as a key by default.
* Several methods in Sequence/SiteContainerTools are not templated anymore and
  have been improved.

09/09/09 Sylvain Gaillard
* Fixed white space skip in Fasta sequence

20/08/09 Julien Dutheil
* Added config files for CMake.

19/08/09 Sylvain Gaillard
* Introduced 3 new interfaces IOSequenceStream, ISequenceStream and
  OSequenceStream. These interfaces are intended to be used by IOFormat
  dealing with Sequence and not SequenceContainers. They are actually
  implemented by the Fasta class.

17/08/09 Adam Smith
* Bug fixed in DefaultAlphabet: unknow state is 37 not 38.

04/08/09 Sylvain Gaillard
* Introduced new classes for Alphabet States

23/07/09 Sylvain Gaillard
* Added SequenceTools::getPutativeHaplotypes

22/07/09 Sylvain Gaillard
* Added SequenceTools::getNumberOfUnresolvedSites
* Updated SequenceTools::getNumberOfSites,
	SequenceTools::getNumberOfCompleteSites and SequenceTools::removeGaps to be
	Alphabet implementation independant.

07/07/07 Julien Dutheil
* Updated GranthamAAChemicalDistance, with a new signed, non-symmetric,
	option.

26/06/09 Sylvain Gaillard
* Added new SequencePositionIterators classes.

23/06/09 Julien Dutheil
* Actualization of the Container classes: now returns references and not
pointer. Several code updates, including copy contructors.

17/06/09 Sylvain Gaillard (Glasgow Workshop)
* Fix DNA/RNA/ProteicAlphabet::getAlias: works now with lower case states.
* Fix SiteTools::isConstant test gap or unknown
* Turning SequenceContainerTools::getFrequencies into void function.

21/07/08 -*- Version 1.6.0 -*-

28/05/09 Julien Dutheil
* Added basic support for the Nexus format.

22/05/09 Julien Dutheil
* Improved Clustal format (solves bug found by Emmanuel M.)
* SequenceApplicationTools uses the keyval syntax for format description.

27/04/09 Julien Dutheil
* Added site randomization method.

28/02/09 Julien Dutheil
* Added mutual information calculation.
* Added pairwise counting methods.
* Frequencies counting methods have been improved (avoid useless copy of maps).

16/01/09 Julien Dutheil
* max_gap_allowed option in SequenceApplicationTools is now a included bound:
  0 or 0% will keep all complete sites, and 'n=number of sequences' or 100%
	will keep all sites.

13/01/09 Sylvain Gaillard
* Little optimization in Fasta::write() method.

12/01/09 Sylvain Gaillard
* Added support for comments (HUPO-PSI like) in Fasta.

08/01/09 Julien Dutheil
* SequenceTools::reverse method has been deprecated in favor of the
  SequenceTools::inverse method, of witch it is now an alias.

07/01/09 Julien Dutheil
* Code improvement in Vector containers.

21/12/08 Julien Dutheil
* Return type for clone() methods corrected (Sequence, Site, SiteContainer and derivated classes).
* Bug fixed in SequenceApplicationTools::get[Sequence/Site]Container, phylip format.

21/07/08 -*- Version 1.5.0 -*-

05/12/08 Julien Dutheil
* VectorSiteContainer::getSite() faster (more than 10 times faster on a ~500
	sequences data set!)

04/12/08 Julien Dutheil
* Fixed missing redefinition of translate and reverse methods in class DNAToRNA.
* Made inheritance virtual.

01/12/08 Julien Dutheil
* New methods getSupportedInts and getSupportedChars in Alphabet classes.

18/11/08 Julien Dutheil
* biopp-help-forum 91 (by Stephen Smith): Fasta, Mase, Clustal and Phylip now
  have an option to turn off the name checking and decrease loading time.
* biopp-help-forum 93 (by Stephen Smith): Phylip format now supports any
 delimiter when reading/writing files in extended format.

14/11/08 Sylvain Gaillard
* New method SequenceTools::subtractHaplotype(Sequence, Sequence, string,
  unsigned int).

07/11/08 Julien Dutheil
* New contructor in VectorSiteContainer now as a tag to disable position
  checking, which can turn to be quite slow.

06/11/08 Sylvain Gaillard
* New class PhredPhd to read sequence from phd files produced by the phred
  program
* Removed an unused method in PhredPoly

05/11/08 Sylvain Gaillard
* New methods Alphabet::getGeneric(states) implemented in AbstractAlphabet,
  DefaultAlphabet, DNA, RNA and ProteicAlphabet.
* New alphabet exception CharStateNotSupportedException.
* New class PhredPoly to read sequence from poly files produced by the phred
  program.
* Fixed heterozygous site read in PhredPoly.

09/10/08 Julien Dutheil
* New method SequenceTools::invert(Sequence).

24/09/08 Bastien Boussau & Julien Dutheil
* Memory leak fixed in Fasta and Mase readers.

21/07/08 -*- Version 1.4.1 -*-

26/06/08 Julien Dutheil
* Bug fixed in Clustal format.

20/04/08 Julien Dutheil
* New interface ISequence2 for reading alignments.

18/03/08 Julien Dutheil and Bastien Boussau
* Bowker's test for homogeneity implemented in SequenceTools.

08/02/08 Julien Dutheil
* Bug fixed in VectorSequenceContainer: method addSequence is now virtual!
  (thanks to Laurent Gueguen for pointing out this bug)!.

07/02/08 Julien Dutheil
* Added function isDNAAlphabet and isRNAAlphabet in AlphabetTools.
* Bug fixed in getAlphabetFromSequence method.
* Method getContent in Sequence and Site now outputs a reference.

18/01/08 -*- Version 1.4.0 -*-

09/01/08 Julien Dutheil
* All classes included in the new 'bpp' namespace.

06/11/07 Julien Dutheil
* New function SequenceContainerTools::merge.

02/10/07 Julien Dutheil
* New class GenBank, enabling GenBank sequence format support for input.
* Added new copy constructors from SequenceContainer in
  Vector[Site/Sequence]Container.
* New methods changeUnresolvedCharacterToGaps and changeGapsToUnknownCharacters in SymbolListTools.
* Bug fixed in changeUnresolvedCharacterToGaps in SiteContainerTools.

06/07/07 -*- Version 1.3.0 -*-

12/06/07 Julien Dutheil
* More tools in class alphabet (isGap, isUnresolved, etc.)
* New class DistanceMatrix, previously in phyllib.
* New similarity measures in SiteContainerTools.

04/06/07 Julien Dutheil
* New constructor from sequence names in VectorSiteContainer.

01/06/07 Julien Dutheil
* New method SiteContainerTools::boostrapSites to bootstrap an alignment.

21/05/07 Julien Dutheil
* New method SequenceContainerTools::getSequenceContainer to read non-aligned
  sequences.

04/05/07 Julien Dutheil
* Bug fixed in global alignment with gap opening and extending penalties.
* New generic score scheme.
* Compatibility update (NumCalc)

24/04/07 Benoît Nabholz & Julien Dutheil
* GeneticCode classes can now translate unknow codons to unknown amino acids.

02/04/07 Julien Dutheil
* VIRTUAL_COV variable changed to NO_VIRTUAL_COV. configure.ac file updated.
  => Default behaviour is now /really/ to use covariant return type with
	virtual inheritence, even when importing the files in an IDE. To use the old
	compilers behaviour, one must set the NO_VIRTUAL_COV preproc variable.
* this modification also solves a problem with the old configure.ac which
  was not correctly updated in version 1.2.0 :(
* Bug fixed in SymbolListTools::getCounts.

02/04/07 Julien Dutheil
* New method getAlphabetIndex1() in class SimpleIndexDistance.

24/02/07 Julien Dutheil
* New pairwise alignment algorithm: gap opening and extending penalties.
	
22/02/07 Julien Dutheil
* GeneticCode derivated classes now properly redefine the translate(Sequence&)
	method.

19/01/07 -*- Version 1.2.0 -*-

19/01/07 Julien Dutheil
* Functions AlphabetTools::getType() and StringSequenceTools::getAlphabetFromSequence() rewritten.
* New DefaultNucleotideScore matrix.
* New AAIndex1Entry and AAIndex2Entry classes which create AlphabetIndex1 and
AlphabetIndex2 objects from AAIndex1 and AAIndex2 entries, respectively.

18/12/06 Julien Dutheil
* New alignment tools in SiteContainerTools, including the Needleman and
Wunsch alogrithm.
* BLOSUM50 matrix available.
* Bug fixed in Sequence.h: method setContent is now properly redefined.
* Bug fixed in ProteicAlphabet->getAbbr(int). The returned result is now
correct!!!

06/12/06 Julien Dutheil
* DefaultAlphabet now accepts "." characters.
* New AlphabetTools::isDefaultAlphabet(const Alphabet *) method.
* New SiteContainerTools::resolveDottedAlignment(const Sitecontainer &, const Alphabet *) method.

30/08/06 Julien Dutheil
* Bug fixed in phylip sequential reader, + duplicated sequence in container
now throws sequence name. (included in 1.1.1 release).

28/08/06 -*- Version 1.1.1 -*-

08/08/06 Julien Dutheil
* Bug fixed in Phylip sequential read method.

15/06/06 Julien Dutheil
* Method changeGapsToUnknownCharacters() moved from SequenceContainerTools to
SiteContainerTools, and is really faster!
* New removeGapOnlySites() method in SiteContainerTools.
* New method SiteTools::isGapOnly().
* new 'sequence.max_gap_allowed' option in SequenceApplicationTools::getSitesToAnalyse().

13/06/06 Julien Dutheil
* Phylip sequential format improved, no more empty line between sequences
needed.

12/06/06 Julien Dutheil
* SiteTools::isConstant() method now has a 'ignoreUnknown' option.

01/01/06 Julien Dutheil
* VectorSiteContainer and AlignedSequenceContainer now number sites from 1 (and not 0). 

17/05/06 Benoît Nabholz, Sylvain Glémin & Julien Dutheil
* Bug fixed in SiteContainerTools::getConsensus(), + SymbolListTools::getFrequencies() and getCounts() improved.

15/05/06 Julien Dutheil
* Bug fixed: Added getUnknownCharacterCode() method in DefaultAlphabet.

09/05/06 Julien Dutheil
* New AAChargeIndex class.
* Bug fixed in SiteTools::hasUnknown(Site).

18/04/06 -*- Version 1.1.0 -*-

18/04/06 Julien Dutheil
* New IOSequenceFactory class.

06/04/06 Julien Dutheil
* New () function operators defined on SequenceContainers.