source.jalview.org Git - jalview.git/history

git://source.jalview.org / jalview.git / history

[jalview.git] / src / jalview / analysis /

2008-01-29	jprocter	reinstated proper case insensitive searching for both...	tree \| commitdiff
2007-12-21	jprocter	further bugfix and annotation transfer for dna/protein...	tree \| commitdiff
2007-12-21	jprocter	javadoc and bugfix	tree \| commitdiff
2007-11-16	jprocter	todo for sortbyPID operating on current selection rathe...	tree \| commitdiff
2007-11-16	jprocter	refactor abstract sequence fetching and DBSource machin...	tree \| commitdiff
2007-11-12	jprocter	crossrefs have properly updated pdbId lists	tree \| commitdiff
2007-09-07	jprocter	formatting and ensure that dataset is actually searched...	tree \| commitdiff
2007-08-01	jprocter	null pointer exception bug fix	tree \| commitdiff
2007-07-25	jprocter	fix crossRef retrieval so either protein OR nucleotide	tree \| commitdiff
2007-07-13	jprocter	bugfixes, partially working code for translation using...	tree \| commitdiff
2007-07-13	jprocter	comments for future viz/detection of internal sequence...	tree \| commitdiff
2007-07-13	jprocter	methods for traversing database reference space	tree \| commitdiff
2007-06-17	jprocter	fix aligned DNA codon translation bug(s) and generate...	tree \| commitdiff
2007-06-17	jprocter	javadoc	tree \| commitdiff
2007-05-22	jprocter	fixed jalview 2.3 bug where gapped aligned codons were...	tree \| commitdiff
2007-04-26	jprocter	added 'sort by sequence associated annotation score'	tree \| commitdiff
2007-04-26	jprocter	bug fixed basic score extraction by regex on descriptio...	tree \| commitdiff
2007-04-26	jprocter	basic methods for adding scores extracted from description	tree \| commitdiff
2007-04-25	jprocter	Functions for parsing free text properties on sequences...	tree \| commitdiff
2007-04-25	jprocter	AlignmentAnnotation: added annotation score attribute...	tree \| commitdiff
2007-04-11	jprocter	fixed base lookup bug in dna pairwise alignment and...	tree \| commitdiff
2007-03-19	jprocter	translate aligned cDNA to aligned peptide	tree \| commitdiff
2007-02-07	amwaterhouse	Formatting	tree \| commitdiff
2007-01-30	amwaterhouse	Any character non aa or nucleotide is a space	tree \| commitdiff
2007-01-25	amwaterhouse	1.1 enabled	tree \| commitdiff
2007-01-23	amwaterhouse	Hidden representatives moved from sequence to viewport	tree \| commitdiff
2007-01-23	jprocter	refactoring (added seqIndex/resIndex state for incremen...	tree \| commitdiff
2007-01-23	jprocter	refactored search algorithm from gui classes	tree \| commitdiff
2006-12-14	amwaterhouse	one less cast	tree \| commitdiff
2006-12-06	jprocter	general pairwise substitution score models for pairwise...	tree \| commitdiff
2006-12-05	amwaterhouse	sequence is char []	tree \| commitdiff
2006-11-28	amwaterhouse	off by one group consensus calculation	tree \| commitdiff
2006-11-21	jprocter	fix unselectable tree leaf nodes when node mapping...	tree \| commitdiff
2006-11-15	amwaterhouse	Check if groupWidth is greater than sequence width	tree \| commitdiff
2006-11-09	amwaterhouse	1.1 compatible	tree \| commitdiff
2006-11-07	amwaterhouse	warning note added to consequence	tree \| commitdiff
2006-11-07	amwaterhouse	hidden seqs and setOrder bug fixed	tree \| commitdiff
2006-11-06	amwaterhouse	If start is not zero, we need to put -- at the start	tree \| commitdiff
2006-10-26	amwaterhouse	Error message changed	tree \| commitdiff
2006-10-26	amwaterhouse	Sequences may be hidden, not in this aligment	tree \| commitdiff
2006-10-24	amwaterhouse	setOrder is public	tree \| commitdiff
2006-10-24	jprocter	fixes bug reported by Christopher Tan (help@jalview...	tree \| commitdiff
2006-10-12	amwaterhouse	Comment out debug to compile applet	tree \| commitdiff
2006-10-11	jprocter	fixes exception (array index out of bounds - due to...	tree \| commitdiff
2006-10-10	jprocter	refined id matching to pick the closest match (by lengt...	tree \| commitdiff
2006-10-10	jprocter	debug message bugfix on duplicate tree leaf names.	tree \| commitdiff
2006-10-10	jprocter	bugfix for dodgy trees which contain the same leafname...	tree \| commitdiff
2006-10-10	amwaterhouse	MaxResidue must be at least 2	tree \| commitdiff
2006-10-10	amwaterhouse	Optimized	tree \| commitdiff
2006-10-10	amwaterhouse	aaIndex replaces aaHash	tree \| commitdiff
2006-10-10	amwaterhouse	static final strings for consensus keys	tree \| commitdiff
2006-10-09	jprocter	imported Vamsas bindings and alpha vamsas client code...	tree \| commitdiff
2006-10-06	amwaterhouse	AAFrequency optimized	tree \| commitdiff
2006-08-21	amwaterhouse	header updated	tree \| commitdiff
2006-08-04	jprocter	recover original data for tree and pca as alignment...	tree \| commitdiff
2006-07-27	amwaterhouse	Sends gapChar to seqData	tree \| commitdiff
2006-07-26	jprocter	Ignore list created	tree \| commitdiff
2006-07-26	jprocter	Implemented CIGAR representation of an Alignment view...	tree \| commitdiff
2006-07-21	amwaterhouse	this.seqs = seqs	tree \| commitdiff
2006-07-21	amwaterhouse	Load tree from file constructor fixed	tree \| commitdiff
2006-07-19	amwaterhouse	Original tree data output in PFAM format	tree \| commitdiff
2006-07-19	amwaterhouse	Check for all gapped seqs	tree \| commitdiff
2006-07-18	amwaterhouse	Works on strings, not seqs	tree \| commitdiff
2006-07-18	amwaterhouse	Takes string[] instead of seq[]	tree \| commitdiff
2006-07-12	amwaterhouse	sequences are private in SequenceGroup	tree \| commitdiff
2006-07-07	amwaterhouse	Sequence numbering maintained	tree \| commitdiff
2006-04-10	amwaterhouse	dont need to set - to -	tree \| commitdiff
2006-04-07	amwaterhouse	Set all gaps to - symbol	tree \| commitdiff
2006-03-01	jprocter	fixed after refactoring of SequenceFeature[] seq.getSeq...	tree \| commitdiff
2006-02-24	amwaterhouse	Features now array	tree \| commitdiff
2005-12-15	amwaterhouse	Prevents confusing extra line being output in Java...	tree \| commitdiff
2005-12-08	jprocter	exception checks for (de)uniquify	tree \| commitdiff
2005-12-08	amwaterhouse	After merge	tree \| commitdiff
2005-12-06	amwaterhouse	hasDistances added	tree \| commitdiff
2005-12-06	amwaterhouse	after merge	tree \| commitdiff
2005-11-18	jprocter	Fixed bug dragonfly.compbio.dundee.ac.uk/mantis/view...	tree \| commitdiff
2005-10-03	amwaterhouse	Remove redundancy from eclipse	tree \| commitdiff
2005-09-30	amwaterhouse	Restore file before eclipse changes	tree \| commitdiff
2005-09-30	amwaterhouse	Remove redundancy in Eclipse	tree \| commitdiff
2005-09-23	amwaterhouse	Capture output as details	tree \| commitdiff
2005-09-08	amwaterhouse	REmove unnecessary imports	tree \| commitdiff
2005-08-23	amwaterhouse	Finalize calculate method	tree \| commitdiff
2005-08-22	jprocter	fixed uniquify seq[]	tree \| commitdiff
2005-08-22	jprocter	comment on WORD_SEP values	tree \| commitdiff
2005-08-18	amwaterhouse	Character methods don't exist in java 1.1	tree \| commitdiff
2005-08-18	jprocter	various case sensitivity bugs fixed in residue comparis...	tree \| commitdiff
2005-08-17	jprocter	Fixed basic name to sequence ID matching (bug dragonfly...	tree \| commitdiff
2005-08-15	amwaterhouse	Declare variables outside loops	tree \| commitdiff
2005-08-15	amwaterhouse	Calculate gap and nogap ratio here	tree \| commitdiff
2005-08-12	jprocter	fixed leafMapping bug for Id's like SequenceX (where...	tree \| commitdiff
2005-06-30	amwaterhouse	Formatting changes	tree \| commitdiff
2005-06-30	amwaterhouse	Not used in Jalview	tree \| commitdiff
2005-06-16	amwaterhouse	Sort Groups modified	tree \| commitdiff
2005-06-10	amwaterhouse	Remove imports	tree \| commitdiff
2005-06-08	amwaterhouse	Formatted source	tree \| commitdiff
2005-06-08	amwaterhouse	GPL license added	tree \| commitdiff
2005-06-03	jprocter	Reinstated 'create tree from selected region only'...	tree \| commitdiff
2005-06-02	jprocter	minor changes to try and make jalopy happy	tree \| commitdiff
2005-05-30	jprocter	Changed sortByPID to use the gapped PID function.	tree \| commitdiff
2005-05-25	jprocter	tidied up system.out messages and moved many to stderr.	tree \| commitdiff
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