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JAL-2465 missed commit for refactore renaming of getPdbFile() method to getStructureF...
[jalview.git]
/
src
/
jalview
/
2017-03-28
tcofoegbu
JAL-2465 missed commit for refactore renaming of getPdb...
tree
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commitdiff
2017-03-28
tcofoegbu
JAL-2465 bugfix and rerefactor renamed getPdbFile(...
tree
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commitdiff
2017-03-23
tcofoegbu
JAL-2463 bugfix
tree
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commitdiff
2017-03-20
tcofoegbu
Merge JAL-2136_phyre2_integration to develop
tree
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commitdiff
2017-03-17
tcofoegbu
JAL-2136 JAL-2137 Improvements: enable STRUCTMODEL...
merge/JAL-2136_phyre2_integration
tree
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commitdiff
2017-03-16
Jim Procter
Merge branch 'merges/develop_JAL2295setChimeraAttribute...
tree
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commitdiff
2017-03-16
Jim Procter
JAL-1933 refactor parameter for code clarity
tree
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commitdiff
2017-03-14
tcofoegbu
JAL-2136 JAL-2137 Improved STRUCTMODEL annotation synta...
tree
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commitdiff
2017-03-10
tcofoegbu
JAL-2136 JAL-2137 Modified STRUCTMODEL annotation forma...
tree
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commitdiff
2017-03-09
kiramt
JAL-2426 Checks on conservation thread in case we are...
tree
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commitdiff
2017-03-09
kiramt
JAL-2426 Removal of NPE in conservation thread when...
tree
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commitdiff
2017-03-08
gmungoc
JAL-2430 colour columns hidden in alignment gray on...
tree
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commitdiff
2017-03-08
gmungoc
JAL-2295 avoid quotes breaking attribute value parsing
tree
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commitdiff
2017-03-07
gmungoc
JAL-2295 status messages for Chimera attributes set...
tree
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commitdiff
2017-03-02
gmungoc
JAL-2295 tweak order and wording of Superpose menu...
tree
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commitdiff
2017-03-02
gmungoc
JAL-2295 make 'Jmol' menu appear; enable/disable Superp...
tree
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commitdiff
2017-03-01
gmungoc
Merge branch 'features/JAL-2295setChimeraAttributes...
tree
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commitdiff
2017-02-28
tcofoegbu
JAL-2136 added improvement to parse crudelist file...
tree
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commitdiff
2017-02-20
tcofoegbu
JAL-2136 merged and resolved conflicts with 80edaa84d6d...
tree
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commitdiff
2017-02-20
Jim Procter
Merge branch 'features/JAL-2379pcaMemory' into develop
tree
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commitdiff
2017-02-15
Jim Procter
JAL-2374 JAL-2419 - TODO suspiciously redundant nested...
bug/JAL-2374_JAL-2419_overlappinggroups_currentselection_popupmenu
tree
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commitdiff
2017-02-15
Jim Procter
fix for JAL-2419 - don’t trash the current selection
tree
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commitdiff
2017-02-15
Jim Procter
JAL-2374 don’t search twice for containing group to...
tree
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commitdiff
2017-02-15
Jim Procter
JAL-2374 new contains methods for seq and seq,apos
tree
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commitdiff
2017-02-15
Jim Procter
JAL-2374 javadoc - qualify that sequence argument to...
tree
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commitdiff
2017-02-10
gmungoc
JAL-2371 small move of code, typo correction
tree
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commitdiff
2017-02-09
Jim Procter
Merge branch 'develop' into features/JAL-2316
features/JAL-2316
tree
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commitdiff
2017-02-09
gmungoc
JAL-2401 change 'Lower Case Colour' to checkbox with...
tree
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commitdiff
2017-02-09
gmungoc
JAL-2371 ensure some colour scheme (may be None) is...
tree
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commitdiff
2017-02-09
gmungoc
Merge branch 'develop' into features/JAL-2379pcaMemory
features/JAL-2379pcaMemory
tree
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commitdiff
2017-02-09
gmungoc
JAL-2371 skip upper-casing consensus as it already is
tree
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commitdiff
2017-02-09
gmungoc
JAL-2405 check for circular reference in SequenceGroup...
tree
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commitdiff
2017-02-09
gmungoc
JAL-2405 set initial selection group alignment context
tree
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commitdiff
2017-02-09
gmungoc
JAL-2405 enable nucleotide/peptide colour schemes in...
tree
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commitdiff
2017-02-08
gmungoc
JAL-2405 set context on selection group for tailored...
tree
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commitdiff
2017-02-08
Jim Procter
JAL-2136 update merged code for JAL-2040 for new FileFo...
reviews/features/JAL-2136_phyre2_integration_withJims
tree
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commitdiff
2017-02-08
gmungoc
JAL-2401 fix for NPE on selectedButtons, tweak for...
tree
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commitdiff
2017-02-08
kiramt
Merge remote-tracking branch 'origin/develop' into...
tree
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commitdiff
2017-02-08
Jim Procter
JAL-2366 updated default URL to jalview.org/services...
tree
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commitdiff
2017-02-07
Jim Procter
Merge branch 'features/JAL-2371collectionColourScheme...
tree
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commitdiff
2017-02-07
gmungoc
JAL-2401 Lower Case Colour toggleable, help text added
tree
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commitdiff
2017-02-07
gmungoc
JAL-2379 removed unused commented code
tree
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commitdiff
2017-02-07
gmungoc
JAL-2397 flag provided for 2.10.1 PCA gap calculation...
tree
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commitdiff
2017-02-07
gmungoc
JAL-2397 PCA gap cost uses last column of score matrix
tree
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commitdiff
2017-02-07
gmungoc
JAL-2398 corrected entry for C->R in Blosum62 matrix
tree
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commitdiff
2017-02-06
gmungoc
JAL-2379 computePairwiseScores() moved to ScoreMatrix
tree
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commitdiff
2017-02-03
gmungoc
JAL-2379 'direct' pairwise score calculation for PCA...
tree
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commitdiff
2017-02-01
gmungoc
JAL-2371 (slight!) simplification of isApplicableTo()
tree
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commitdiff
2017-01-31
gmungoc
JAL-2371 commented code removed only
tree
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commitdiff
2017-01-31
gmungoc
JAL-2371 rename global/viewportColourScheme to residueS...
tree
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commitdiff
2017-01-31
gmungoc
JAL-2385 more tests/bug fixes mostly for gui.SliderPane...
tree
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commitdiff
2017-01-27
gmungoc
JAL-2379 commented out code removed
tree
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commitdiff
2017-01-27
gmungoc
JAL-2371 CollectionColourScheme renamed ResidueShader...
tree
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commitdiff
2017-01-27
gmungoc
JAL-2360 JAL-2371 updates from review CR-JAL-1
tree
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commitdiff
2017-01-27
kiramt
JAL-2366 Removed unneeded setEnabled calls
tree
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commitdiff
2017-01-26
gmungoc
JAL-2360 corrected comment
tree
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commitdiff
2017-01-26
kiramt
Merge remote-tracking branch 'origin/develop' into...
tree
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commitdiff
2017-01-26
gmungoc
Merge branch 'features/JAL-2360colourSchemeApplicabilit...
tree
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commitdiff
2017-01-26
gmungoc
Merge branch 'develop' into features/JAL-2360colourSche...
tree
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commitdiff
2017-01-26
kiramt
JAL-2316 Updated to use identifiers jalview service
tree
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commitdiff
2017-01-26
gmungoc
Merge branch 'develop' into features/JAL-2379pcaMemory
tree
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commitdiff
2017-01-26
gmungoc
JAL-2344 test fix and code tidy for review comments
tree
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commitdiff
2017-01-26
gmungoc
JAL-2380 code tidy after review
tree
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commitdiff
2017-01-25
gmungoc
JAL-2344 push Cache.getProperty("LAST_DIRECTORY") insid...
tree
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commitdiff
2017-01-23
gmungoc
JAL-2379 made SparseMatrix.divide() so as to exactly...
tree
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commitdiff
2017-01-23
Jim Procter
Merge branch 'features/JAL-2040_JAL-2137_phyre2' into...
tree
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commitdiff
2017-01-23
gmungoc
JAL-2386 unit tests for change colour (and minor refact...
tree
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commitdiff
2017-01-23
gmungoc
JAL-2386 simplify changeColour (doesn't change colour...
tree
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commitdiff
2017-01-20
tcofoegbu
JAL-2375 JAL-2376 First commit of implementation for...
tree
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commitdiff
2017-01-20
gmungoc
Merge branch 'features/JAL-2360colourSchemeApplicabilit...
tree
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commitdiff
2017-01-20
gmungoc
Merge branch 'develop' into features/JAL-2360colourSche...
tree
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commitdiff
2017-01-20
gmungoc
JAL-2385 tweak to applet 'switch colour slider context'
tree
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commitdiff
2017-01-20
gmungoc
Merge branch 'features/JAL-2360colourSchemeApplicabilit...
tree
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commitdiff
2017-01-20
gmungoc
Merge branch 'develop' into features/JAL-2360colourSche...
tree
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commitdiff
2017-01-20
gmungoc
JAL-2385 update slider settings when switching slider...
tree
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commitdiff
2017-01-20
gmungoc
Merge branch 'features/JAL-2360colourSchemeApplicabilit...
tree
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commitdiff
2017-01-20
gmungoc
JAL-2383 fixup from last merge
tree
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commitdiff
2017-01-20
gmungoc
Merge branch 'develop' into features/JAL-2360colourSche...
tree
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commitdiff
2017-01-20
gmungoc
JAL-2383 check for null, spelling
tree
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commitdiff
2017-01-20
gmungoc
JAL-2383 make popup colour menu order and wording consi...
tree
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commitdiff
2017-01-20
gmungoc
JAL-2383 restore group conservation slider setting...
tree
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commitdiff
2017-01-20
gmungoc
Merge branch 'develop' into features/JAL-2360colourSche...
tree
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commitdiff
2017-01-19
Jim Procter
Merge branch 'spike/JAL-2040_JAL-2137_phyre2' into...
features/JAL-2040_JAL-2137_phyre2
tree
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commitdiff
2017-01-19
gmungoc
JAL-2383 restore PID colour threshold from project...
tree
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commitdiff
2017-01-19
gmungoc
JAL-2370 corrected applet mouse drag, refactored into...
tree
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commitdiff
2017-01-17
gmungoc
JAL-1933 update threshold on focus lost in text field
features/JAL-2295setChimeraAttributes
tree
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commitdiff
2017-01-17
gmungoc
Merge branch 'develop' into features/JAL-2295setChimera...
tree
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commitdiff
2017-01-17
gmungoc
JAL-2370 fix bug when hiding a range including two...
tree
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commitdiff
2017-01-17
gmungoc
Merge branch 'features/JAL-2360colourSchemeApplicabilit...
tree
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commitdiff
2017-01-17
gmungoc
Merge branch 'develop' into features/JAL-2360colourSche...
tree
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commitdiff
2017-01-17
gmungoc
JAL-2379 use SparseMatrix for encoded sequences, tidy...
tree
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commitdiff
2017-01-17
gmungoc
JAL-2379 SparseMatrix alternative to Matrix, both MatrixI
tree
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commitdiff
2017-01-17
gmungoc
JAL-2379 SparseDoubleArray added (for use by SparseMatrix)
tree
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commitdiff
2017-01-16
gmungoc
JAL-2380 fix Matrix.postMultiply()
tree
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commitdiff
2017-01-12
gmungoc
JAL-2379 null references to PCA model when panel is...
tree
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commitdiff
2017-01-12
gmungoc
JAL-2344 now flagging formats as 'identifiable' instead...
tree
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commitdiff
2017-01-11
gmungoc
JAL-2344 separated AlignmentFileI into AlignmentFileRea...
tree
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commitdiff
2017-01-11
gmungoc
JAL-2344 FileFormats singleton for formats, FileFormatI...
tree
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commitdiff
2017-01-11
gmungoc
JAL-2344 addSequence() method added to support Groovy...
tree
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commitdiff
2017-01-10
gmungoc
JAL-2377 avoid infinite loop formatting 1.0E-310
tree
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commitdiff
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