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JAL-2397 scripts to toggle 2.10.1 / 2.10.2 PCA calculation mode
[jalview.git]
/
src
/
jalview
/
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
2017-01-27
gmungoc
JAL-2379 commented out code removed
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
2017-01-20
gmungoc
JAL-2385 tweak to applet 'switch colour slider context'
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
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
2017-01-19
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-2370 fix bug when hiding a range including two...
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
2017-01-05
gmungoc
JAL-2374 fix popup out by one and multiple groups bugs
tree
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commitdiff
2017-01-05
gmungoc
JAL-2373 set state of Above PID, By Conservation in...
tree
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commitdiff
2016-12-16
gmungoc
JAL-2356 enhanced unit test to verify reuse (or not...
tree
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commitdiff
2016-12-14
Jim Procter
Merge branch 'patch/JAL-2197_jpredforjnets' into develop
tree
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commitdiff
2016-12-09
gmungoc
JAL-2105 updated for reviewed REST version 4.8
tree
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commitdiff
2016-12-09
gmungoc
JAL-1895 suppress RNA interaction colour option
tree
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commitdiff
2016-12-08
gmungoc
JAL-2359 add Window menu entry only after all danger...
tree
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commitdiff
2016-12-07
gmungoc
JAL-2356 use cached Sifts file if not expired
tree
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commitdiff
2016-12-07
gmungoc
JAL-2354 handle error response when fetching features
tree
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commitdiff
2016-12-07
gmungoc
JAL-2344 handle null format, simplify JalviewFileChoose...
tree
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commitdiff
2016-11-30
Jim Procter
Merge branch 'features/JAL-2320_closeChimeraAction...
tree
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commitdiff
2016-11-30
gmungoc
JAL-2344 use ".cif" for saved mmCIF file (and refactor...
tree
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commitdiff
2016-11-29
gmungoc
JAL-2344 corrected conversion of Type enum to FileFormat
features/JAL-2344FileFormatI
tree
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commitdiff
2016-11-29
gmungoc
JAL-2344 FileFormat.isStructureFile replaces
tree
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commitdiff
2016-11-28
gmungoc
Merge branch 'develop' into trialMerge
tree
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commitdiff
2016-11-28
tcofoegbu
Merge branch 'features/JAL-2326_JOptionPane-refactoring...
tree
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commitdiff
2016-11-28
gmungoc
JAL-2344 added FileFormatI.isStructureFile()
tree
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commitdiff
2016-11-28
gmungoc
JAL-2345 cache generated ImageIcon per file path
tree
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commitdiff
2016-11-25
gmungoc
JAL-2344 dynamically determine recognised extensions...
tree
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commitdiff
2016-11-25
gmungoc
Merge branch 'develop' into trialMerge
tree
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commitdiff
2016-11-25
gmungoc
JAL-2344 override to ignore (obsolete?) JalviewFileView
tree
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commitdiff
2016-11-25
gmungoc
JAL-2344 use .equals() to compare FileFormatI objects
tree
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commitdiff
2016-11-24
gmungoc
Distinguish text-only output formats and others (.jar...
tree
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commitdiff
2016-11-24
tcofoegbu
JAL-2326 updated references of JOptionPane to JvOptionPane
tree
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commitdiff
2016-11-24
gmungoc
Further tweaks to get tests passing
tree
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commitdiff
2016-11-24
tcofoegbu
JAL-2326 added layer of abstraction between Jalview...
tree
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commitdiff
2016-11-24
Jim Procter
JAL-2325 apply license to new source files
tree
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commitdiff
2016-11-24
gmungoc
FileFormatI further tweaks, clean compile
tree
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commitdiff
2016-11-23
Jim Procter
Merge branch 'bug/JAL-2323disulfideOverview' into develop
tree
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commitdiff
2016-11-23
Jim Procter
Merge branch 'documentation/JAL-2325_release2101' into...
tree
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commitdiff
2016-11-23
Jim Procter
Merge branch 'develop' of source.jalview.org/git/jalvie...
tree
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commitdiff
2016-11-22
Jim Procter
JAL-2197 changed tooltip for Jnet annotation rows to...
tree
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commitdiff
2016-11-22
tcofoegbu
Merge branch 'bug/JAL-2277_refactorPrintUnwrapped'...
tree
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commitdiff
2016-11-22
Jim Procter
Merge branch 'features/JAL-2177_update_jmol_to_14.6...
tree
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commitdiff
2016-11-22
gmungoc
JAL-2337 fix: only adjust once for scroll offset
bug/JAL-2277_refactorPrintUnwrapped
tree
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commitdiff
2016-11-22
gmungoc
JAL-1919 JAL-2177 handle empty pdbentries list correctly
features/JAL-2177_update_jmol_to_14.6.4_2016.10.26
tree
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commitdiff
2016-11-22
Jim Procter
Merge branch 'develop' of source.jalview.org/git/jalvie...
tree
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commitdiff
2016-11-22
tcofoegbu
JAL-2322 added runnable interface to HTMLOutput class...
tree
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commitdiff
2016-11-22
Jim Procter
Merge branch 'features/JAL-1738_JAL-345_selectionfromhi...
tree
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commitdiff
2016-11-22
Jim Procter
JAL-1738 JAL-345 changed keystroke to ‘B’ (with modifie...
tree
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commitdiff
2016-11-22
gmungoc
JAL-2277 refactored AlignmentPanel.printUnwrapped to...
tree
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commitdiff
2016-11-21
tcofoegbu
JAL-2277 bug fix for mis-alligned graphics output for...
tree
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commitdiff
2016-11-21
Jim Procter
JAL-2335 patched FeatureRendererModel.findFeaturesAtRes...
bug/JAL-2323disulfideOverview
tree
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commitdiff
2016-11-21
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-11-21
tcofoegbu
JAL-2332 bugfix to enable structure chooser opening...
tree
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commitdiff
2016-11-21
gmungoc
JAL-2333 corrected select columns with 'contact' feature
tree
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commitdiff
2016-11-21
gmungoc
Merge branch 'develop' into bug/JAL-2323disulfideOverview
tree
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commitdiff
2016-11-18
gmungoc
JAL-98 with the two types missing from last commit...
bug/JAL-98consensusMemory
tree
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commitdiff
2016-11-17
gmungoc
JAL-2323 revert to thread-safe iteration over array...
tree
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commitdiff
2016-11-17
gmungoc
JAL-98 ProfilesI container for profiles for columns
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commitdiff
2016-11-17
gmungoc
JAL-98 javadoc, third party acknowledgements (and very...
tree
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commitdiff
2016-11-17
gmungoc
JAL-2327 disulfide bond abstracted to SequenceFeature...
tree
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commitdiff
2016-11-17
gmungoc
JAL-2327 add isContactFeature
tree
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commitdiff
2016-11-16
Jim Procter
Merge branch 'features/JAL-1723_sequenceReport' into...
tree
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commitdiff
2016-11-16
gmungoc
JAL-2323 render disulfide bond correctly on overview...
tree
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commitdiff
2016-11-16
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-11-16
tcofoegbu
JAL-2322 JAL-2309 replaced references to isheadless...
tree
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commitdiff
2016-11-16
gmungoc
JAL-2324 fix and tests for comparison of Float.NaN...
tree
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commitdiff
2016-11-16
gmungoc
JAL-2319 corrected reporting of SIFTS mapping
tree
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commitdiff
2016-11-14
tcofoegbu
JAL-2322 Refactored unified architecture for data ...
tree
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commitdiff
2016-11-11
tcofoegbu
JAL-2277 Refactored out duplicated method - printUnwrap...
tree
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commitdiff
2016-11-10
tcofoegbu
Merge branch 'develop' into bug/JAL-2317_jmol_chimera...
tree
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commitdiff
2016-11-10
tcofoegbu
JAL-2317 Fixed Chimera command for hiding/showing disti...
bug/JAL-2317_jmol_chimera-chain-factorisation
tree
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commitdiff
2016-11-10
tcofoegbu
Bugfix to enable accurate chain extraction/association...
tree
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commitdiff
2016-11-10
gmungoc
JAL-2320 thread to close Chimera viewer panel if Chimer...
features/JAL-2320_closeChimeraAction
tree
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commitdiff
2016-11-10
gmungoc
JAL-2320 added getViewer() method to return Chimera...
tree
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commitdiff
2016-11-08
gmungoc
JAL-2301 made T hydrophobic as per the cited conservati...
tree
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commitdiff
2016-11-08
tcofoegbu
JAL-2292 updated method calls
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commitdiff
2016-11-08
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-11-08
tcofoegbu
JAL-2292 renamed method and improved implementation...
tree
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commitdiff
2016-11-07
gmungoc
JAL-2272 unit tests added for Platform.isControlDown
tree
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commitdiff
2016-11-07
gmungoc
JAL-2282 show url links that need checked; remove ...
tree
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commitdiff
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