NCL Free and open source Nexus class library for your Mac
Download

NCL Ranking & Summary

NCL Tags

library C++ library interpret nexus library interpret nexus file nexus

NCL Description

Free and open source Nexus class library for your Mac NCL is a C++ library for interpreting data files created according to the NEXUS file format used in molecular evolution and phylogenetic systematics. What's New in This Release: bug fixes (visible to end-users): · opening files in binary mode (failing to do so cause problems with end-of- line and other special characters). · character index (0-based rather than 1-based number) was being printed in some contexts in error messages · Apple g++-4.2 optimization bug now has a workaround · Characters blocks now reject files in which the datatype is DNA, RNA, or protein if SYMBOLS are added. bug fixes API: · Fixed setting of NXS_HAS_ALL_TAXA_BIT no longer duplicating blocks when the same reader is used to read more than one file · allowing PublicNexusReader::Add to be called · Some Windows-specific modifications to avoid warnings and errors compiling under Visual Studio 2008 (VC9) · characters block now generates an exception if there is no matrix · NxsReader::BlockIsASingeltonReader problem fixed · better cleaning up in the multiformat reader when there is an error in the reading of a file · another accessor added for NxsSimpleTree · PublicNexusReader GetXXXBlock functions changed to return 0L rather than raising an exception if you request a block that is out of range · NCL_CONST_FUNCS macro added API additions: · improvements to phylip reading -- matchchar now accepted (multiformat reader only). · reading a single bare newick tree (as "phyliptree" or "relaxedphyliptree" in multiformat reader stuff). · added cullIdenticalTaxaBlocks() function to nexusreader. You should call this before reading a file if you want all repeated taxa blocks to be destroyed rather than saved · support for genetic codes and translation to amino acids added · GetEscapedDouble and GetEscapedInt added · GetDatatypeMapForMixedType added · added functionality to delete identical taxa blocks even if they are implied blocks. This only will be triggered if the client code has called NxsReader::cullIdenticalTaxaBlocks(true). This corrects an issue DZ was seeing with reading multiple DATA blocks · aliasing of block titles for culled blocks · changed the handling of the + character when a nxstoken instance has been altered by a call to indictate hyphenNotPunctuation is in effecet (this is done via the SetLabileFlagBit function). In almost all case this function is called so that a number (particularly one writtend in scientific notation will be read as a single token, rather than as many as 4 tokens). In rare cases, the + is used before the exponent or even in front of the entire number. So that client code does not have to deal with these cases, the default behavior has been changed to using the hyphenNotPunctuation to indicate that in the reading of the next token neither · nor + should be treated as punctuation. Client code that wishes to use the old behavior can compile NCL with the NCL_VERSION_2_STYLE_HYPHEN macro defined to 1

NCL Related Software