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JAL-3878 Move array index search to ArrayUtils
[jalview.git]
/
src
/
jalview
/
datamodel
/
2018-09-10
gmungoc
JAL-3099 new method AlignmentI.getVisibleWidth()
tree
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commitdiff
2018-08-27
Ben Soares
JAL-3061 / JAL-3053
tree
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commitdiff
2018-08-16
gmungoc
Merge branch 'bug/JAL-3082selectRegex' into Jalview...
tree
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commitdiff
2018-08-16
gmungoc
JAL-3082 handle regex error, exclusive threshold, unit...
tree
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commitdiff
2018-08-10
gmungoc
JAL-3076 refactor for more efficient scan of 'gene...
tree
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commitdiff
2018-08-02
Ben Soares
JAL-3053
tree
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commitdiff
2018-07-30
bsoares
Fixed bug ignoring "alpha" extended braces in RNA SS...
tree
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commitdiff
2018-07-26
gmungoc
Merge remote-tracking branch 'origin/bug/JAL-3072scroll...
tree
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commitdiff
2018-07-25
gmungoc
JAL-3074 don't scroll up/down on drag out of scale...
tree
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commitdiff
2018-07-20
gmungoc
JAL-3048 revised AlignExportSettings dialog with respon...
tree
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commitdiff
2018-07-18
Jim Procter
Merge branch 'features/mchmmer' into features/mchmmer_m...
features/mchmmer_merge_JAL-1950
tree
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commitdiff
2018-07-11
Jim Procter
JAL-3048 refactored export settings to bean+dialog...
Jalview-BH/JAL-3048_exportSettingsrefactor
tree
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commitdiff
2018-07-06
gmungoc
JAL-3032 use Math.min/max not Float.min/max
tree
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commitdiff
2018-07-02
hansonr
JAL-3026 GD#75 Stockholm file load fails
tree
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commitdiff
2018-06-22
gmungoc
JAL-3032 avoid assignments on the same line as synchronized
tree
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commitdiff
2018-06-05
gmungoc
Merge branch 'develop' into features/mchmmer
tree
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commitdiff
2018-06-04
Jim Procter
JAL-3017 parse multiple variant elements for uniprot...
tree
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commitdiff
2018-06-02
Jim Procter
JAL-3017 parse multiple variant elements for uniprot...
tree
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commitdiff
2018-06-01
Jim Procter
JAL-1950 JAL-2937 allow individual groups to be remater...
tree
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commitdiff
2018-06-01
Jim Procter
JAL-1551 formatting
tree
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commitdiff
2018-06-01
Jim Procter
JAL-1950 JAL-2937 allow copy of group without sequences...
tree
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commitdiff
2018-06-01
Jim Procter
JAL-1950 JAL-2937 allow copy of sequences from group...
tree
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commitdiff
2018-05-31
gmungoc
JAL-2808 don't capture or report min-max for mixed...
tree
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commitdiff
2018-05-31
Jim Procter
Merge branch 'spike/JAL-1950_hmmer3client' into feature...
tree
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commitdiff
2018-05-31
Jim Procter
Merge branch 'develop' into spike/JAL-1950_hmmer3client
tree
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commitdiff
2018-05-28
gmungoc
Merge branch 'develop' into features/mchmmer
tree
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commitdiff
2018-05-28
gmungoc
Merge remote-tracking branch 'origin/releases/Release_2...
tree
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commitdiff
2018-05-21
gmungoc
JAL-2920 use HGVS notation for protein variant feature
tree
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commitdiff
2018-05-11
gmungoc
Merge branch 'develop' into features/mchmmer
tree
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commitdiff
2018-05-11
gmungoc
JAL-2986 corrected findIndex for out of range residue...
tree
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commitdiff
2018-05-10
Jim Procter
Merge branch 'bug/JAL-2920_uniprotvariantfeature' into...
tree
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commitdiff
2018-05-10
Jim Procter
JAL-2920 simplified logic and added corner cases for...
tree
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commitdiff
2018-05-08
gmungoc
Merge branch 'develop' into features/mchmmer
tree
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commitdiff
2018-05-07
gmungoc
Merge branch 'releases/Release_2_10_4_Branch' into...
tree
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commitdiff
2018-05-07
gmungoc
JAL-1767 unit test for save and restore PCA
features/JAL-1767pcaInProject
tree
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commitdiff
2018-05-07
Jim Procter
JAL-2906 apply GPLv3 license source
tree
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commitdiff
2018-05-04
gmungoc
JAL-1767 refactorings to enable faithful restore of...
tree
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commitdiff
2018-04-27
gmungoc
JAL-1767 refactoring and tidying of RotatableCanvas...
tree
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commitdiff
2018-04-26
gmungoc
JAL-2962 code tidying/documentation (non-functional...
tree
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commitdiff
2018-04-23
gmungoc
JAL-2956 save/restore HMMER profile to/from Jalview...
tree
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commitdiff
2018-04-23
gmungoc
JAL-2954 more efficient SearchResults.markColumns
tree
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commitdiff
2018-04-17
gmungoc
JAL-2629 choice of hmm profile now a parameter not...
tree
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commitdiff
2018-04-16
gmungoc
JAL-2629 JAL-2937 remove redundant is/setHMMConsensusSe...
tree
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commitdiff
2018-04-09
Mungo Carstairs
JAL-2629 more error checking
tree
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commitdiff
2018-03-30
gmungoc
JAL-2599 MapList from HMM nodes to consensus dataset...
tree
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commitdiff
2018-03-30
gmungoc
JAL-2939 field/method naming more consistent
tree
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commitdiff
2018-03-30
gmungoc
JAL-2941 'map hmm to RF' removed pending clarifications
tree
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commitdiff
2018-03-26
gmungoc
JAL-2939 always store Information profile
tree
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commitdiff
2018-03-20
gmungoc
JAL-2629 InformationThread.findOrCreateAnnotation and...
tree
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commitdiff
2018-03-20
gmungoc
Merge branch 'develop' into features/mchmmer
tree
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commitdiff
2018-03-16
gmungoc
Merge remote-tracking branch 'origin/releases/Release_2...
tree
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commitdiff
2018-03-16
gmungoc
Merge branch 'develop' into trialMerge
tree
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commitdiff
2018-03-14
gmungoc
JAL-2893 include ENSEMBLGENOMES as a 'roundtrip db...
tree
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commitdiff
2018-03-13
gmungoc
JAL-2839 addResult ignores duplicates
tree
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commitdiff
2018-03-09
gmungoc
JAL-2839 Finder refactoring prior to fixing the defect
tree
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commitdiff
2018-03-07
Jim Procter
Merge branch 'releases/Release_2_10_4_Branch' into...
tree
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commitdiff
2018-03-07
gmungoc
JAL-2925 handle empty annotation when copying group...
tree
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commitdiff
2018-03-07
gmungoc
JAL-2629 storage and lifecycle of alignment/group HMM...
tree
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commitdiff
2018-03-01
gmungoc
JAL-2629 revising hmmer annotation updating (wip)
tree
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commitdiff
2018-02-28
gmungoc
JAL-2629 some tidying of Hmmer commands (wip)
tree
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commitdiff
2018-02-27
gmungoc
JAL-2668 method name change for clarity
tree
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commitdiff
2018-02-27
gmungoc
JAL-2717 JAL-2668 fixes to HMMER colour scheme display...
tree
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commitdiff
2018-02-27
Jim Procter
Merge branch 'feature/JAL-2759' into merge/JAL-2759_2104
tree
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commitdiff
2018-02-26
Jim Procter
JAL-2920 parse variation and original elements of the...
tree
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commitdiff
2018-02-26
gmungoc
JAL-2599 test coverage and bug fixes for 'minimal file...
tree
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commitdiff
2018-02-23
gmungoc
JAL-2599 corrected case-insensitive symbol indexing
tree
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commitdiff
2018-02-23
gmungoc
JAL-2599 parser and datamodel use primitive double...
tree
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commitdiff
2018-02-22
gmungoc
JAL-2629 tidy tests, refactor hmmer node mapping slightly
tree
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commitdiff
2018-02-22
gmungoc
JAL-2629 tidy unit tests, constants etc
tree
|
commitdiff
2018-02-21
Jim Procter
Merge branch 'bug/JAL-2778again' into releases/Release_...
tree
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commitdiff
2018-02-21
kiramt
JAL-2778 Revert back to old synchronisation
tree
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commitdiff
2018-02-20
gmungoc
JAL-2629 removed SequenceI.get/setLastPosition and...
tree
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commitdiff
2018-02-20
gmungoc
Merge branch 'develop' into features/mchmmer
tree
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commitdiff
2018-02-20
Jim Procter
Merge branch 'releases/Release_2_10_4_Branch' into...
tree
|
commitdiff
2018-02-06
kiramt
Merge branch 'develop' into feature/JAL-2759
feature/JAL-2759
tree
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commitdiff
2018-02-05
Jim Procter
JAL-2780 JAL-2781 - patch and first test for AlignmentI...
tree
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commitdiff
2018-02-05
kiramt
JAL-2759 Fix errant RangeElementsIterator (unit tests...
tree
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commitdiff
2018-02-05
kiramt
JAL-2759 Rename getBoundedStartIterator
tree
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commitdiff
2018-02-05
kiramt
JAL-2759 Changes to StartRegionIterator after review
tree
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commitdiff
2018-02-05
kiramt
JAL-2788 possible adjustments to sequence accesses
tree
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commitdiff
2018-02-01
kiramt
JAL-2759 use right iterator for getVisibleColsIterator
tree
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commitdiff
2018-01-31
kiramt
JAL-2759 Rationalise VisibleColsIterator and HiddenCols...
tree
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commitdiff
2018-01-31
kiramt
JAL-2759 Generalised HiddenColsIterator naming
tree
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commitdiff
2018-01-31
kiramt
JAL-2759 minor refactor to hiding bitsets
tree
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commitdiff
2018-01-30
kiramt
JAL-2759 Add missing hiddenColumns empty check
tree
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commitdiff
2018-01-30
kiramt
JAL-2759 updateForDeletedRegion no longer needed
tree
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commitdiff
2018-01-30
kiramt
JAL-2759 Rationalising hidden cols cursor, and sorting...
tree
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commitdiff
2018-01-30
kiramt
JAL-2759 comment
tree
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commitdiff
2018-01-30
kiramt
JAL-2759 Additional tests and tweaks to numColumns...
tree
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commitdiff
2018-01-30
kiramt
JAL-2759 Keep numColumns up to date
tree
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commitdiff
2018-01-29
kiramt
JAL-2759 Combine findRegionForColumn code in HiddenColu...
tree
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commitdiff
2018-01-29
kiramt
JAL-2759 numColumns reset
tree
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commitdiff
2018-01-29
kiramt
JAL-2759 remove redundant hiddenColumns.clear()
tree
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commitdiff
2018-01-29
kiramt
JAL-2759 Tidy
tree
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commitdiff
2018-01-29
kiramt
JAL-2759 make a new cursor instead of resetting, update...
tree
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commitdiff
2018-01-29
kiramt
JAL-2759 Fix unintended type change
tree
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commitdiff
2018-01-26
kiramt
JAL-2778 try another way to draw sequences with reduced...
tree
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commitdiff
2018-01-22
kiramt
JAL-2579 Moved locateVisibleStartOfSequence to Sequence...
tree
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commitdiff
2018-01-22
kiramt
JAL-2759 Various minor HiddenColumns updates after...
tree
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commitdiff
2018-01-19
kiramt
JAL-2759 Changes to getVisibleSequenceStrings after...
tree
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commitdiff
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