format adapter should return AlignmentI
[jalview.git] / src / jalview / analysis /
2012-11-17 jproctermethod to construct sequence mapping for matching posit...
2012-11-17 jprocterconvenience method for performing pairwise alignment
2012-11-17 jprocterformatting and javadoc
2012-11-15 jproctersource formatting
2012-11-15 jprocterMerge branch 'develop' into menard
2012-11-08 jproctertidy imports
2012-10-22 jprocterJalview 2.8 Source Header
2012-10-03 jprocterformatting
2012-09-06 jprocterJAL-1013 - employ index parameter rather than hardcode...
2012-09-02 jprocterJAL-1007 refactored code and patched calculation bug
2012-08-17 jprocterMerge branch 'develop' into menard
2012-08-14 Anne Menardlast version stay many bugs ..
2012-08-03 jprocterJAL-1115 reference to List<SequenceI> passed in 'alignm...
2012-07-05 Anne MenardAdd support RNAML format
2012-06-15 jprocterformatting
2012-06-15 jprocterJAL-1125 option to switch between Jalview and SeqSpace...
2012-06-15 jprocterMerge branch 'JAL-1013_pca_rna_dna' into develop
2012-06-13 jprocterjavatidy
2012-06-12 jprocterJAL-1115 refactor base collection for Alignment from...
2012-06-07 jprocterJAL-967, JAL-1114, JAL-1115 more concurrent access...
2012-06-07 jprocterjavatidy
2012-06-07 jprocterJAL-967, JAL-1114, JAL-1115 - modified render and calcu...
2012-05-31 jprocterformatting
2012-05-30 jprocterJAL-1114 - refactor methods handling Vectors and Hashta...
2012-04-20 jprocter(JAL-1071) hacked the square matrix that stores the...
2011-12-08 jprocter(JAL-1013) allow sequence type to be specified enabling...
2011-10-28 jprocterJAL-885 more efficient calculation and robust for misma...
2011-10-28 jprocteruse stack rather than vector and throw parse exceptions
2011-10-28 jprocterJAL-580 ensure WUSS annotation is reparsed if necessary...
2011-10-21 jprocterstatic convenience methods for constructing and calcula...
2011-10-21 jprocteruse List rather than Vector
2011-10-11 jprocternormalised logo rendering (JAL-958)
2011-10-10 jprocterupdate author list in license for (JAL-826)
2011-10-04 jprocterMerge remote-tracking branch 'remotes/origin/2_5_1_rna_...
2011-09-27 jprocterapply version 2.7 copyright
2011-09-16 jprocterpatch for JAL-935 - warning messages raised when alignm...
2011-08-30 jprocterfix for JAL-917 - ensure all sequence strings are made...
2011-08-30 jprocterfix for JAL-917 - ensure all sequence strings are made...
2011-08-15 janengelhardtJAL-891; Tooltips for Structure logos implemented;
2011-08-15 janengelhardtJAL-891; Labeling of structure conservation is improved...
2011-08-15 janengelhardtJAL-891; Sorting of Structure logo implemented; bug...
2011-08-10 janengelhardtJAL-885; Structure conservation row is just added if...
2011-08-09 janengelhardtJAL-891; base-pair logos can now be activated for structure
2011-08-08 janengelhardtJAL-891; structure logo is adapted to two char's; Missi...
2011-08-08 janengelhardtJAL-891; sequence logos are available on structure...
2011-08-03 janengelhardtJAL-885; Multi-helix bug is solved; One should think...
2011-07-31 janengelhardtJAL-885; StructureConservation row is displayed at...
2011-07-29 janengelhardtJAL-885; Implementation of StructureFrequency.java...
2011-07-25 janengelhardtStart merging of Laurens Code
2011-07-21 jprocterretrieve all sequences matching a particular name ...
2011-07-09 jproctertodo re JAL-732
2011-05-30 jprocterbug for clients using NJTree directly - pwtype should...
2011-04-07 jprocterresolves JAL-804
2011-02-27 jprocterpatch for JAL-780
2011-02-18 jprocterfix for occasional race conditions
2011-01-17 jproctereliminate utf8 compilation errors
2011-01-07 jprocterrefactored to use SequenceI
2010-11-14 jprocternode rename for deuniquifying trees from web service...
2010-09-23 jprocterNPE race condition alert - see JAL-661
2010-09-23 jprocterapply jalview code style
2010-09-23 jprocterJalview 2.6 source licence
2010-09-02 jprocterfix occasional arrayIndexOutOfBounds when sequences...
2010-08-18 jprocteroutput the eigenvector matrix in full: JAL-616
2010-06-29 jprocterpatch for npe that occurs for importing Jalview project...
2010-05-12 jprocterfix for JAL-527
2010-04-30 jprocterjalview 2.5 release banner
2010-04-28 jprocterfind incrementally searches ID then subsequence matches.
2010-04-14 jprocterfix order/reverse order issue for sortByFeature
2009-11-02 jproctergracefully cope with non-standard nucleotide or amino...
2009-08-21 jprocter1.1 compatibility
2009-08-21 jprocternew sortbyPID for specific start/end region
2009-08-21 jproctercommented debug lines indicating calculation progress
2009-08-21 jprocterstart/stop for per-group consensus calculation
2009-08-21 jprocterstore symbol profile and extract it for display
2009-08-21 jprocterroutines for creating groups over an alignment
2009-07-24 jproctercomplete alignment annotation row procedure
2009-06-24 jproctertake the average of the three consecutive codon sites...
2009-06-19 jprocterdebug
2009-06-08 jprocterapply gpl development license
2009-06-01 jprocterlook in database references for more ID strings to...
2009-06-01 jprocterapply method for a NodeTransform to nodes in a tree
2009-02-06 jprocterfix occasional nullpointer ref when seq ID retrieval...
2008-12-19 jproctersort by length
2008-12-15 jproctertemporary fix and note about null feature group mucking...
2008-12-08 jprocteroutput average score to stdout
2008-12-08 jprocternew sort functions for ordering sequence by annotated...
2008-12-01 jproctermatch case switch should work for both sequence ID...
2008-11-12 jprocterminor translation bug
2008-11-12 jprocteravoid exception if search returns valid object but...
2008-09-04 jproctermerge from 2_4_Release branch
2008-08-26 jprocterensure successive matches to a regex have distinct...
2008-08-19 jprocterbetter check for molecule type when identifying interna...
2008-08-06 jprocterextra checks for datasetsequence for when getDbRefs...
2008-06-30 jprocterjava 1.1 compatibility
2008-04-17 jprocterjavadoc and quiet flag
2008-04-10 jprocterquick fix for conservation calculation when residue...
2008-01-29 jprocterreinstated proper case insensitive searching for both...
2007-12-21 jprocterfurther bugfix and annotation transfer for dna/protein...
2007-12-21 jprocterjavadoc and bugfix
2007-11-16 jproctertodo for sortbyPID operating on current selection rathe...
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