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| Revision history for Perl extension HMM. | ||
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| 0.01 Thd Jul 17 17:54:00 2003 | ||
| - Initial alpha release; Just one test up to now, very basic Font-DIR setting | ||
| - Methods for reading out Profile HMMs and producing HMM-Logos | ||
| 0.02 Fri Jul 25 15:42:00 2003 | ||
| - Fix: Better positioning of characters in draw_logo() | ||
| 0.03 Fri Aug 1 19:31:00 2003 | ||
| - Change: Threshold for character display set to 1 instead of 3 for accuracy | ||
| - Added option to display parts of a profile through -startpos -endpos | ||
| 0.04 Mon, Aug 4 16:40:00 2003 | ||
| - Modified character positioning again - Now it should finally be as good as it gets | ||
| - Fixed errors in partial display | ||
| 0.1 Fri, Aug 15 13:33:00 2003 | ||
| - We think it is time for a first release! | ||
| - The parse and simple read functionality has been passed to HMM rather than HMM::Profile | ||
| - Thus, HMM::Profile now inherits from HMM | ||
| - Thus, HMM is not an exporter class any more, so HMM::Profile has to be included explicitly | ||
| 0.2 Thd, Aug 21 11:23:00 2003 | ||
| - Added PFAM direct download support. Thus, libbwww-perl is required now | ||
| - Tried to reduce startup-time by usinf PDL::LiteF rather than PDL | ||
| - Changed the parser to work with strings instead of globs | ||
| 0.2.1 Tue, Aug 26 14:16:00 2003 | ||
| - Added experimental retention-time calculation for insert states | ||
| 0.3 Fri, Aug 29 12:47:00 2003 | ||
| - Modified retention-time calculation. HP is now a sub-column of Insert-States where width is determined by HP*Est.Ret.Time | ||
| - ATTENTION: toWidth is now toHPM and returns a Matrix of all Hitting Probabilities rather than a vector for M and I | ||
| 0.31 Thd Okt 30 15:24:00 2003 | ||
| - Fixed a bug concerning Windows line-breaks | ||
| 0.32 Thd Nov 20 19:29:00 2003 | ||
| - Workaround fixing a bug in the getter for pfam entries | ||
| 0.4 Thd Nov 20 22:50:00 2003 | ||
| - Added option to create greyscaled logos | ||
| 0.5 Tue, Jan 20 15:20:00 2004 | ||
| - Added more methods to access scores instead of probabilites in HMM | ||
| 0.5.1 Fri, May 14 11:43:00 2004 | ||
| - Modified package to work with Imager-0.4.3. Note that 0.5 and 0.5.1 are incompatible! | ||
| - Fixed a bug concerning ignoration of small characters | ||
| - Removed lot's of annoying warnings | ||
| 0.6 Thd Jan 27 13:56:00 2005 | ||
| - Added the Alignment.pm class. This is a major amendment, so beware of problems! | ||
| - Changed the methods in HMM.pm to be lvaluable. Now HMMs can be modified | ||
| - Added a method toHMMer that allows writing a HMMer file representing an HMM object | ||
| - Minor changes to the Makefile | ||
| 0.6.1 Thd Feb 3 13:59:00 2005 | ||
| - Fixed a bug that resulted in faulty glyph width | ||
| 0.6.2 Mon Feb 7 16:53:00 2005 | ||
| - Added some warning during file-parsing | ||
| - Enabled greyscaling | ||
| - Changed execution of prc from 'exec' to open("... |") because of reported problems | ||
| - Changed greyscale letter colouring to show hydrophobicity/acidity only | ||
| 0.6.3 Thd Mar 3 14:25:00 2005 | ||
| - Fixed bug that caused crash when last aligned char was D | ||
| 0.7 Mon Mar 7 16:11:00 2005 | ||
| - Changed the alignment style to solid blocks instead of centred lines | ||
| 0.7.1 Wed Mar 9 11:15:00 2005 | ||
| - Added the possibility to pass IO::File objects instead of Filehandles or GLOBs | ||
| 0.7.2 Fri Jan 6 13:53:00 2006 | ||
| - Fixed several parsing errors with different build settings for HMMer | ||
| 0.7.3 Mon Jan 9 13:14:00 2006 | ||
| - Changed Alignment.pm to remove trailing gaps from prc alignments | ||
| 0.7.4 Wed Nov 9 11:07:00 2006 | ||
| - Now takes custom font path, size and colouring | ||
| - Removed font path check from Makefile | ||
| - Bug fixed: Exporter not working | ||
| 0.7.5 Mon Nov 20 13:21:00 2006 | ||
| - Emission and transition matrices can now be passed manually at creation time | ||
| 0.7.6 Fri Aug 24 14:07:00 2007 | ||
| - Added methods to parse and retrieve the state-to-column mapping provided in the HMMer files | ||
| 0.7.7 Fri Oct 25 14:03:00 2007 | ||
| - Fixed several errors in Alignment.pm which accidentally slipped through | ||
| - Synchronised Alignment.pm with the version on the Pfam servers | ||
| 0.7.8 Thu Aug 21 11:18:00 2008 | ||
| - Changed the URL in HMM.pm to connect to the new Pfam website correctly | ||
| 0.8 Fri Apr 24 11:40:00 2009 | ||
| - Now also parses HMMER3 format files and creates logos from them. There are some | ||
| issues related to changes in the Profile structure in HMMER3 which have not yet been resolved | ||
| - Added tests for the parsers; More tests should be made | ||
| - Cleaned up the code a little bit | ||
| 0.81 Tue Sep 20 16:26:00 2011 | ||
| - added method to dump raw perl arrays for logo data, in preparation for a JSON version |
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