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JAL-1486 JAL-535 refactor code for trimming alignment annotation according to selecti...
[jalview.git] / src / jalview / analysis /
2014-06-06 Jim ProcterJAL-1517 source formatting tree | commitdiff
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2 tree | commitdiff
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2 tree | commitdiff
2014-06-05 Jim ProcterMerge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch tree | commitdiff
2014-05-22 Jim ProcterJAL-1503 update version in GPL header tree | commitdiff
2014-05-02 Jim ProcterMerge branch 'JAL-1397' into develop tree | commitdiff
2014-05-01 Jim Proctermake sure valid value for non-gapped calculation with... tree | commitdiff
2014-04-21 Jim ProcterMerge branch 'jims_marckhacks' into develop tree | commitdiff
2014-04-21 Jim ProcterJAL-1466 don't include empty columns if no upstream... tree | commitdiff
2014-04-21 Jim ProcterJAL-1466 improved test and patched off by one that... tree | commitdiff
2014-04-21 Jim ProcterJAL-1466 new calculation menu option to recover the... tree | commitdiff
2014-04-21 Jim ProcterJAL-1473 refactor score matrices and tree score calcula... tree | commitdiff
2014-02-25 Jim ProcterMerge branch 'JAL-1454_patch' into develop tree | commitdiff
2014-02-25 Jim ProcterJAL-1454 catch exceptions during calculation and report... tree | commitdiff
2014-02-18 Jim ProcterMerge branch 'JAL-1445' into develop tree | commitdiff
2014-02-03 Jim ProcterMerge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge tree | commitdiff
2014-01-29 Jim ProcterJAL-1432 updated copyright notices tree | commitdiff
2013-10-16 Jim ProcterMerge branch 'JAL-1395' into develop tree | commitdiff
2013-10-16 Jim ProcterJAL-1395 do not calculate non-gap consensus when no... tree | commitdiff
2013-10-15 Jim ProcterJAL-1159 Merging 2.8.1 patches and Anne Menards work... tree | commitdiff
2013-10-14 Jim ProcterMerge branch 'develop' into dev_from_2_8_1 tree | commitdiff
2013-09-03 Jim ProcterJAL-1373 tweak precision calculation so alignments... tree | commitdiff
2013-09-03 Jim ProcterJAL-920 compute a consensus for single sequence tree | commitdiff
2013-09-02 Jim ProcterMerge branch 'JAL-1373_precision' into develop tree | commitdiff
2013-09-02 Jim ProcterJAL-1373 generate percentages with appropriate precision tree | commitdiff
2013-09-02 Jim ProcterJAL-1373 pass size of sequence set to consensus renderi... tree | commitdiff
2013-06-18 Jim ProcterJAL-674 fix the mapping generation algorithm tree | commitdiff
2013-06-18 Jim ProcterMerge branch 'develop' into develop_m2_8_1_2 tree | commitdiff
2013-06-17 Jim ProcterMerge branch 'JAL-1312_ambiguity_na' into develop tree | commitdiff
2013-06-17 Jim ProcterJAL-1035 option to allow 'STOP' codon to translate... tree | commitdiff
2013-06-17 Jim ProcterJAL-1312 rewrite of code for first reported exception... tree | commitdiff
2013-06-17 Jim ProcterJAL-1318 - route warnings to stderr (need to find a... tree | commitdiff
2013-06-17 Jim ProcterJAL-1318 avoid failure if SequenceI objects don't have... tree | commitdiff
2013-06-17 Jim ProcterJAL-966 avoid using java.util.Vector tree | commitdiff
2012-12-07 jprocterconsensus secondary structure algorithm (possibly came... tree | commitdiff
2012-12-07 jprocterrevised RNA stem/loop processing code that copes with... tree | commitdiff
2012-12-07 jprocterupdate authors for RNA processing routines tree | commitdiff
2012-12-07 jprocterformatting tree | commitdiff
2012-11-17 jproctermethod to construct sequence mapping for matching posit... tree | commitdiff
2012-11-17 jprocterconvenience method for performing pairwise alignment tree | commitdiff
2012-11-17 jprocterformatting and javadoc tree | commitdiff
2012-11-15 jproctersource formatting tree | commitdiff
2012-11-15 jprocterMerge branch 'develop' into menard tree | commitdiff
2012-11-08 jproctertidy imports tree | commitdiff
2012-10-22 jprocterJalview 2.8 Source Header tree | commitdiff
2012-10-03 jprocterformatting tree | commitdiff
2012-09-06 jprocterJAL-1013 - employ index parameter rather than hardcode... tree | commitdiff
2012-09-02 jprocterJAL-1007 refactored code and patched calculation bug tree | commitdiff
2012-08-17 jprocterMerge branch 'develop' into menard tree | commitdiff
2012-08-14 Anne Menardlast version stay many bugs .. tree | commitdiff
2012-08-03 jprocterJAL-1115 reference to List<SequenceI> passed in 'alignm... tree | commitdiff
2012-07-05 Anne MenardAdd support RNAML format tree | commitdiff
2012-06-15 jprocterformatting tree | commitdiff
2012-06-15 jprocterJAL-1125 option to switch between Jalview and SeqSpace... tree | commitdiff
2012-06-15 jprocterMerge branch 'JAL-1013_pca_rna_dna' into develop tree | commitdiff
2012-06-13 jprocterjavatidy tree | commitdiff
2012-06-12 jprocterJAL-1115 refactor base collection for Alignment from... tree | commitdiff
2012-06-07 jprocterJAL-967, JAL-1114, JAL-1115 more concurrent access... tree | commitdiff
2012-06-07 jprocterjavatidy tree | commitdiff
2012-06-07 jprocterJAL-967, JAL-1114, JAL-1115 - modified render and calcu... tree | commitdiff
2012-05-31 jprocterformatting tree | commitdiff
2012-05-30 jprocterJAL-1114 - refactor methods handling Vectors and Hashta... tree | commitdiff
2012-04-20 jprocter(JAL-1071) hacked the square matrix that stores the... tree | commitdiff
2011-12-08 jprocter(JAL-1013) allow sequence type to be specified enabling... tree | commitdiff
2011-10-28 jprocterJAL-885 more efficient calculation and robust for misma... tree | commitdiff
2011-10-28 jprocteruse stack rather than vector and throw parse exceptions tree | commitdiff
2011-10-28 jprocterJAL-580 ensure WUSS annotation is reparsed if necessary... tree | commitdiff
2011-10-21 jprocterstatic convenience methods for constructing and calcula... tree | commitdiff
2011-10-21 jprocteruse List rather than Vector tree | commitdiff
2011-10-11 jprocternormalised logo rendering (JAL-958) tree | commitdiff
2011-10-10 jprocterupdate author list in license for (JAL-826) tree | commitdiff
2011-10-04 jprocterMerge remote-tracking branch 'remotes/origin/2_5_1_rna_... tree | commitdiff
2011-09-27 jprocterapply version 2.7 copyright tree | commitdiff
2011-09-16 jprocterpatch for JAL-935 - warning messages raised when alignm... tree | commitdiff
2011-08-30 jprocterfix for JAL-917 - ensure all sequence strings are made... tree | commitdiff
2011-08-30 jprocterfix for JAL-917 - ensure all sequence strings are made... tree | commitdiff
2011-08-15 janengelhardtJAL-891; Tooltips for Structure logos implemented; tree | commitdiff
2011-08-15 janengelhardtJAL-891; Labeling of structure conservation is improved... tree | commitdiff
2011-08-15 janengelhardtJAL-891; Sorting of Structure logo implemented; bug... tree | commitdiff
2011-08-10 janengelhardtJAL-885; Structure conservation row is just added if... tree | commitdiff
2011-08-09 janengelhardtJAL-891; base-pair logos can now be activated for structure tree | commitdiff
2011-08-08 janengelhardtJAL-891; structure logo is adapted to two char's; Missi... tree | commitdiff
2011-08-08 janengelhardtJAL-891; sequence logos are available on structure... tree | commitdiff
2011-08-03 janengelhardtJAL-885; Multi-helix bug is solved; One should think... tree | commitdiff
2011-07-31 janengelhardtJAL-885; StructureConservation row is displayed at... tree | commitdiff
2011-07-29 janengelhardtJAL-885; Implementation of StructureFrequency.java... tree | commitdiff
2011-07-25 janengelhardtStart merging of Laurens Code tree | commitdiff
2011-07-21 jprocterretrieve all sequences matching a particular name ... tree | commitdiff
2011-07-09 jproctertodo re JAL-732 tree | commitdiff
2011-05-30 jprocterbug for clients using NJTree directly - pwtype should... tree | commitdiff
2011-04-07 jprocterresolves JAL-804 tree | commitdiff
2011-02-27 jprocterpatch for JAL-780 tree | commitdiff
2011-02-18 jprocterfix for occasional race conditions tree | commitdiff
2011-01-17 jproctereliminate utf8 compilation errors tree | commitdiff
2011-01-07 jprocterrefactored to use SequenceI tree | commitdiff
2010-11-14 jprocternode rename for deuniquifying trees from web service... tree | commitdiff
2010-09-23 jprocterNPE race condition alert - see JAL-661 tree | commitdiff
2010-09-23 jprocterapply jalview code style tree | commitdiff
2010-09-23 jprocterJalview 2.6 source licence tree | commitdiff
2010-09-02 jprocterfix occasional arrayIndexOutOfBounds when sequences... tree | commitdiff
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