| 2017-02-07 |
gmungoc | JAL-2397 scripts to toggle 2.10.1 / 2.10.2 PCA calculation...
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| 2017-02-07 |
gmungoc | JAL-2397 PCA gap cost uses last column of score matrix
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| 2017-02-07 |
gmungoc | JAL-2398 corrected entry for C->R in Blosum62 matrix
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| 2017-02-06 |
gmungoc | JAL-2379 computePairwiseScores() moved to ScoreMatrix
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| 2017-02-03 |
gmungoc | JAL-2379 'direct' pairwise score calculation for PCA...
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| 2017-01-27 |
gmungoc | JAL-2379 commented out code removed
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| 2017-01-26 |
gmungoc | Merge branch 'develop' into features/JAL-2379pcaMemory
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commit | commitdiff | tree |
| 2017-01-26 |
gmungoc | JAL-2344 test fix and code tidy for review comments
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commit | commitdiff | tree |
| 2017-01-26 |
gmungoc | JAL-2380 code tidy after review
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| 2017-01-25 |
gmungoc | JAL-2344 push Cache.getProperty("LAST_DIRECTORY") inside...
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| 2017-01-23 |
gmungoc | JAL-2379 made SparseMatrix.divide() so as to exactly...
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| 2017-01-20 |
gmungoc | JAL-2385 tweak to applet 'switch colour slider context'
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| 2017-01-20 |
gmungoc | JAL-2385 update slider settings when switching slider...
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| 2017-01-20 |
gmungoc | JAL-2383 check for null, spelling
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commit | commitdiff | tree |
| 2017-01-20 |
gmungoc | JAL-2383 make popup colour menu order and wording consistent
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| 2017-01-20 |
gmungoc | JAL-2383 restore group conservation slider setting...
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| 2017-01-19 |
gmungoc | JAL-2383 restore PID colour threshold from project...
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| 2017-01-19 |
gmungoc | JAL-2370 unit tests for extracted ColumnSelection.stretchGroup()
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| 2017-01-19 |
gmungoc | JAL-2370 corrected applet mouse drag, refactored into...
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| 2017-01-18 |
gmungoc | JAL-2379 more realistic matrices for unit tests
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| 2017-01-17 |
gmungoc | JAL-2370 fix bug when hiding a range including two...
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| 2017-01-17 |
gmungoc | JAL-2379 use SparseMatrix for encoded sequences, tidy...
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| 2017-01-17 |
gmungoc | JAL-2379 SparseMatrix alternative to Matrix, both MatrixI
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| 2017-01-17 |
gmungoc | JAL-2379 SparseDoubleArray added (for use by SparseMatrix)
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commit | commitdiff | tree |
| 2017-01-16 |
gmungoc | JAL-1270 class renamed
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commit | commitdiff | tree |
| 2017-01-16 |
gmungoc | JAL-2380 fix Matrix.postMultiply()
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| 2017-01-16 |
gmungoc | JAL-1270 tweaks to AlignmentGenerator / client class
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commit | commitdiff | tree |
| 2017-01-12 |
gmungoc | JAL-1270 renamed AlignmentGenerator, and added peptide...
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| 2017-01-12 |
gmungoc | JAL-2379 null references to PCA model when panel is...
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| 2017-01-12 |
gmungoc | JAL-2344 now flagging formats as 'identifiable' instead...
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commit | commitdiff | tree |
| 2017-01-11 |
gmungoc | JAL-2344 separated AlignmentFileI into AlignmentFileReaderI,
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| 2017-01-11 |
gmungoc | JAL-2344 groovy script that registers a new file format
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| 2017-01-11 |
gmungoc | JAL-2344 FileFormats singleton for formats, FileFormatI...
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| 2017-01-11 |
gmungoc | JAL-2344 addSequence() method added to support Groovy...
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| 2017-01-10 |
gmungoc | JAL-2377 avoid infinite loop formatting 1.0E-310
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commit | commitdiff | tree |
| 2017-01-05 |
gmungoc | JAL-2374 unit test for (modified) Alignment.findGroup()
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commit | commitdiff | tree |
| 2017-01-05 |
gmungoc | JAL-2374 fix popup out by one and multiple groups bugs
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commit | commitdiff | tree |
| 2017-01-05 |
gmungoc | JAL-2373 set state of Above PID, By Conservation in...
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commit | commitdiff | tree |
| 2016-12-16 |
gmungoc | JAL-2356 enhanced unit test to verify reuse (or not...
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commit | commitdiff | tree |
| 2016-12-09 |
gmungoc | JAL-2105 updated for reviewed REST version 4.8
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commit | commitdiff | tree |
| 2016-12-09 |
gmungoc | JAL-1895 suppress RNA interaction colour option
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commit | commitdiff | tree |
| 2016-12-08 |
gmungoc | JAL-2359 add Window menu entry only after all danger...
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commit | commitdiff | tree |
| 2016-12-07 |
gmungoc | JAL-2356 use cached Sifts file if not expired
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commit | commitdiff | tree |
| 2016-12-07 |
gmungoc | JAL-2354 handle error response when fetching features
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commit | commitdiff | tree |
| 2016-12-07 |
gmungoc | JAL-2344 handle null format, simplify JalviewFileChooser...
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commit | commitdiff | tree |
| 2016-11-30 |
gmungoc | JAL-2344 use ".cif" for saved mmCIF file (and refactor...
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commit | commitdiff | tree |
| 2016-11-29 |
gmungoc | JAL-2329 tests to confirm behaviour of Java extended...
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| 2016-11-29 |
gmungoc | Merge branch 'develop' of https://source.jalview.org...
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commit | commitdiff | tree |
| 2016-11-29 |
gmungoc | JAL-2344 corrected conversion of Type enum to FileFormat
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commit | commitdiff | tree |
| 2016-11-29 |
gmungoc | JAL-2344 FileFormat.isStructureFile replaces
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commit | commitdiff | tree |
| 2016-11-28 |
gmungoc | Merge branch 'develop' into trialMerge
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commit | commitdiff | tree |
| 2016-11-28 |
gmungoc | JAL-2344 added FileFormatI.isStructureFile()
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commit | commitdiff | tree |
| 2016-11-28 |
gmungoc | JAL-2345 cache generated ImageIcon per file path
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commit | commitdiff | tree |
| 2016-11-25 |
gmungoc | JAL-2344 dynamically determine recognised extensions...
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commit | commitdiff | tree |
| 2016-11-25 |
gmungoc | Merge branch 'develop' into trialMerge
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commit | commitdiff | tree |
| 2016-11-25 |
gmungoc | JAL-2344 override to ignore (obsolete?) JalviewFileView
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commit | commitdiff | tree |
| 2016-11-25 |
gmungoc | JAL-2344 use .equals() to compare FileFormatI objects
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commit | commitdiff | tree |
| 2016-11-25 |
gmungoc | JAL-2344 correct roundtrip test to exclude Jalview...
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commit | commitdiff | tree |
| 2016-11-24 |
gmungoc | Distinguish text-only output formats and others (.jar...
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commit | commitdiff | tree |
| 2016-11-24 |
gmungoc | Further tweaks to get tests passing
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commit | commitdiff | tree |
| 2016-11-24 |
gmungoc | FileFormatI further tweaks, clean compile
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commit | commitdiff | tree |
| 2016-11-23 |
gmungoc | JAL-1738 Spanish versions added
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commit | commitdiff | tree |
| 2016-11-22 |
gmungoc | JAL-2337 fix: only adjust once for scroll offset
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commit | commitdiff | tree |
| 2016-11-22 |
gmungoc | JAL-1919 JAL-2177 handle empty pdbentries list correctly
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commit | commitdiff | tree |
| 2016-11-22 |
gmungoc | JAL-2277 refactored AlignmentPanel.printUnwrapped to...
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commit | commitdiff | tree |
| 2016-11-21 |
gmungoc | JAL-2333 test beefed up with gaps
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commit | commitdiff | tree |
| 2016-11-21 |
gmungoc | JAL-2333 corrected select columns with 'contact' feature
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commit | commitdiff | tree |
| 2016-11-21 |
gmungoc | Merge branch 'develop' into bug/JAL-2323disulfideOverview
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commit | commitdiff | tree |
| 2016-11-18 |
gmungoc | JAL-98 with the two types missing from last commit...
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| 2016-11-17 |
gmungoc | JAL-2323 revert to thread-safe iteration over array...
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commit | commitdiff | tree |
| 2016-11-17 |
gmungoc | JAL-98 ProfilesI container for profiles for columns
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commit | commitdiff | tree |
| 2016-11-17 |
gmungoc | JAL-98 javadoc, third party acknowledgements (and very...
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commit | commitdiff | tree |
| 2016-11-17 |
gmungoc | JAL-2327 disulfide bond abstracted to SequenceFeature...
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commit | commitdiff | tree |
| 2016-11-17 |
gmungoc | JAL-2327 add isContactFeature
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commit | commitdiff | tree |
| 2016-11-16 |
gmungoc | JAL-2323 render disulfide bond correctly on overview...
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commit | commitdiff | tree |
| 2016-11-16 |
gmungoc | JAL-2324 fix and tests for comparison of Float.NaN...
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commit | commitdiff | tree |
| 2016-11-16 |
gmungoc | JAL-2319 corrected reporting of SIFTS mapping
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commit | commitdiff | tree |
| 2016-11-10 |
gmungoc | JAL-2320 thread to close Chimera viewer panel if Chimera...
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commit | commitdiff | tree |
| 2016-11-10 |
gmungoc | JAL-2320 added getViewer() method to return Chimera...
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commit | commitdiff | tree |
| 2016-11-08 |
gmungoc | JAL-2301 corrected search example to match AA properties...
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commit | commitdiff | tree |
| 2016-11-08 |
gmungoc | JAL-2301 made T hydrophobic as per the cited conservation...
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commit | commitdiff | tree |
| 2016-11-08 |
gmungoc | JAL-1961 added link to GFF3 format as well as GFF2
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commit | commitdiff | tree |
| 2016-11-07 |
gmungoc | JAL-1270 renamed helper method so it is not run as...
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commit | commitdiff | tree |
| 2016-11-07 |
gmungoc | JAL-2272 another test case
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commit | commitdiff | tree |
| 2016-11-07 |
gmungoc | JAL-1805 groups=Functional added where missing
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commit | commitdiff | tree |
| 2016-11-07 |
gmungoc | JAL-2272 unit tests added for Platform.isControlDown
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commit | commitdiff | tree |
| 2016-11-07 |
gmungoc | JAL-2318 updated help text
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commit | commitdiff | tree |
| 2016-11-07 |
gmungoc | JAL-2282 show url links that need checked; remove ...
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commit | commitdiff | tree |
| 2016-11-04 |
gmungoc | JAL-2272 right mouse button on Mac is not Cmd equivalent!
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commit | commitdiff | tree |
| 2016-11-04 |
gmungoc | JAL-966 JAL-1854 removed redundant methods / modifiers...
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commit | commitdiff | tree |
| 2016-11-04 |
gmungoc | JAL-2302 unit tests added for Finder
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commit | commitdiff | tree |
| 2016-11-03 |
gmungoc | JAL-2310 don't double-count sequence matches; code...
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commit | commitdiff | tree |
| 2016-11-03 |
gmungoc | JAL-2281 test added to show searchRefs is now not case...
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commit | commitdiff | tree |
| 2016-11-02 |
gmungoc | JAL-2301 table formatted, and corrected to match the...
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commit | commitdiff | tree |
| 2016-11-02 |
gmungoc | JAL-98 JAL-1854 encapsulate 'magic number' threshold...
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commit | commitdiff | tree |
| 2016-11-02 |
gmungoc | JAL-98 ProfileI interface for Profile
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commit | commitdiff | tree |
| 2016-11-02 |
gmungoc | JAL-98 test updated for percentage rounded
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commit | commitdiff | tree |
| 2016-11-02 |
gmungoc | JAL-98 Profile and ResidueCount moved from analysis...
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commit | commitdiff | tree |
| 2016-11-02 |
gmungoc | JAL-98 wording "negatively conserved" now "absence...
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commit | commitdiff | tree |
| 2016-11-01 |
gmungoc | Conservation now using ResidueCount; tests added
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commit | commitdiff | tree |
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