StatCVS - Directory src/jalview/analysis/

Lines of Code

src/jalview/analysis/ Lines of Code

Developers

Author	Changes	Lines of Code	Lines per Change
Totals	278 (100.0%)	20774 (100.0%)	74.7
andrew	133 (47.8%)	11574 (55.7%)	87.0
jprocter	92 (33.1%)	4628 (22.3%)	50.3
jimp	48 (17.3%)	4287 (20.6%)	89.3
amwaterhouse	5 (1.8%)	285 (1.4%)	57.0

Most Recent Commits

jprocter 2010-09-02 16:59

fix occasional arrayIndexOutOfBounds when sequences in subgroup are shorter than alignment width

6 lines of code changed in:

src/jalview/analysis: AAFrequency.java (+6 -1)

jprocter 2010-08-18 17:51

output the eigenvector matrix in full: JAL-616

11 lines of code changed in:

src/jalview/analysis: PCA.java (+11 -4)

jprocter 2010-06-29 16:21

patch for npe that occurs for importing Jalview projects where group conservation is displayed but no conservation for alignment is displayed - (observed during Jmol patching)

6 lines of code changed in:

src/jalview/analysis: AAFrequency.java (+6 -1)

jprocter 2010-05-12 09:38

fix for JAL-527

16 lines of code changed in:

src/jalview/analysis: AlignSeq.java (+16 -5)

jprocter 2010-04-30 10:29

jalview 2.5 release banner

665 lines of code changed in:

src/jalview/analysis: AAFrequency.java (+17 -18), AlignSeq.java (+48 -48), AlignmentSorter.java (+207 -162), Conservation.java (+49 -41), CrossRef.java (changed), Dna.java (changed), Finder.java (+32 -34), Grouping.java (+141 -207), NJTree.java (+81 -78), PCA.java (+24 -24), ParseProperties.java (+19 -20), SeqsetUtils.java (+26 -27), SequenceIdMatcher.java (+21 -22)

jprocter 2010-04-28 15:03

find incrementally searches ID then subsequence matches.

28 lines of code changed in:

src/jalview/analysis: Finder.java (+28 -6)

jprocter 2010-04-14 15:35

fix order/reverse order issue for sortByFeature

21 lines of code changed in:

src/jalview/analysis: AlignmentSorter.java (+21 -11)

jprocter 2009-11-02 13:25

gracefully cope with non-standard nucleotide or amino acid symbols in pairwise alignment.

11 lines of code changed in:

src/jalview/analysis: AlignSeq.java (+11 -25)

jprocter 2009-08-21 15:33

1.1 compatibility

2 lines of code changed in:

src/jalview/analysis: Conservation.java (+2 -2)

jprocter 2009-08-21 12:12

new sortbyPID for specific start/end region

17 lines of code changed in:

src/jalview/analysis: AlignmentSorter.java (+17)

jprocter 2009-08-21 12:09

commented debug lines indicating calculation progress

18 lines of code changed in:

src/jalview/analysis: NJTree.java (+18 -6)

jprocter 2009-08-21 12:08

start/stop for per-group consensus calculation

12 lines of code changed in:

src/jalview/analysis: Conservation.java (+12 -6)

jprocter 2009-08-21 12:04

store symbol profile and extract it for display

129 lines of code changed in:

src/jalview/analysis: AAFrequency.java (+129 -13)

jprocter 2009-08-21 11:57

routines for creating groups over an alignment

273 lines of code changed in:

src/jalview/analysis: Grouping.java (new 273)

jprocter 2009-07-24 15:42

complete alignment annotation row procedure

127 lines of code changed in:

src/jalview/analysis: AAFrequency.java (+44 -1), Conservation.java (+83 -1)

jprocter 2009-06-24 09:22

take the average of the three consecutive codon sites when translating annotation row scores from cDNA to protein.

0 lines of code changed in:

src/jalview/analysis: Dna.java (changed)

jprocter 2009-06-19 10:48

debug

0 lines of code changed in:

src/jalview/analysis: CrossRef.java (changed)

jprocter 2009-06-08 11:34

apply gpl development license

26 lines of code changed in:

src/jalview/analysis: AAFrequency.java (+3 -3), AlignSeq.java (+3 -3), AlignmentSorter.java (+2 -2), Conservation.java (+3 -3), CrossRef.java (changed), Dna.java (changed), Finder.java (+2 -2), NJTree.java (+4 -4), PCA.java (+3 -3), ParseProperties.java (+2 -2), SeqsetUtils.java (+2 -2), SequenceIdMatcher.java (+2 -2)

jprocter 2009-06-01 16:45

look in database references for more ID strings to match against node labels

14 lines of code changed in:

src/jalview/analysis: SequenceIdMatcher.java (+14)

jprocter 2009-06-01 16:45

apply method for a NodeTransform to nodes in a tree

12 lines of code changed in:

src/jalview/analysis: NJTree.java (+12 -3)

(154 more)