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JAL-2137 resolve baseURI for prepending to alignments/PDBs for STRUCTMODEL statement...
[jalview.git]
/
src
/
jalview
/
2016-07-04
Jim Procter
JAL-2137 resolve baseURI for prepending to alignments...
tree
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commitdiff
2016-07-04
Jim Procter
Merge branch 'develop' into spike/JAL-2040_JAL-2137_phyre2
tree
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commitdiff
2016-07-01
tcofoegbu
JAL-2135 bugfix for error preventing processing of...
tree
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commitdiff
2016-06-30
tcofoegbu
JAL-2074 Improvement to StructureChooser and FTS interf...
tree
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commitdiff
2016-06-30
Jim Procter
JAL-2137 basic implementation of STRUCTMODEL annotation...
tree
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commitdiff
2016-06-30
tcofoegbu
JAL-1919 updated PDBSequenceFetcherTest and JMol parser...
tree
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commitdiff
2016-06-29
Jim Procter
JAL-2137 STRUCTMODEL statement added, logic not yet...
tree
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commitdiff
2016-06-29
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-06-29
tcofoegbu
JAL-1479 improved Sifts PID calculation for determining...
tree
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commitdiff
2016-06-29
gmungoc
JAL-1369 fix bug reloading a project with group sequenc...
tree
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commitdiff
2016-06-28
tcofoegbu
JAL-1479 minor refactor and housekeeping
tree
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commitdiff
2016-06-28
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-06-28
tcofoegbu
JAL-1479 improved SiftsClient test coverage and impleme...
tree
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commitdiff
2016-06-27
gmungoc
tidied loop with generic iteration / loop variable
tree
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commitdiff
2016-06-27
gmungoc
JAL-2133 refactored duplicated code to AlignmentViewport
tree
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commitdiff
2016-06-27
gmungoc
JAL-1270 unit tests for HiddenSequences
tree
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commitdiff
2016-06-24
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-06-24
tcofoegbu
JAL-1960 updated unit test to include the test case...
tree
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commitdiff
2016-06-23
gmungoc
JAL-2130 now simply viewer.dispose() to close down...
tree
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commitdiff
2016-06-22
gmungoc
JAL-2015 fixed bug in copy constructor and added tests
tree
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commitdiff
2016-06-22
gmungoc
JAL-1982 defensive checks for null annotations array
tree
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commitdiff
2016-06-22
gmungoc
JAL-1982 defensive test for null array of annotations
tree
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commitdiff
2016-06-21
Jim Procter
Merge branch 'develop' of source.jalview.org/git/jalvie...
tree
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commitdiff
2016-06-21
gmungoc
JAL-2074 suppress prompt to save closed Groovy script...
tree
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commitdiff
2016-06-21
Jim Procter
Merge branch 'features/JAL-1956_featureStyles' into...
tree
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commitdiff
2016-06-21
gmungoc
JAL-2074 reuse Groovy window when reopening; rebind...
tree
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commitdiff
2016-06-21
Jim Procter
JAL-1369 mark reference sequence & view state and resto...
tree
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commitdiff
2016-06-21
Jim Procter
JAL-1369 project XML efficiency TODO
tree
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commitdiff
2016-06-21
Jim Procter
JAL-1369 dead code TODO?
tree
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commitdiff
2016-06-21
Jim Procter
JAL-1369 ensure *real* alignment’s metadata written...
tree
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commitdiff
2016-06-21
Jim Procter
JAL-1369 make sure the fake AlignmentI produced by...
tree
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commitdiff
2016-06-21
Jim Procter
JAL-1369 HUGE WARNING: datamodel.HiddenSequences is...
tree
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commitdiff
2016-06-20
Jim Procter
JAL-1369 updated project schema - flag on JSeq to mark...
tree
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commitdiff
2016-06-20
Jim Procter
JAL-2065 port patch to applet
tree
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commitdiff
2016-06-20
Jim Procter
JAL-1551 tidy
tree
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commitdiff
2016-06-20
Jim Procter
JAL-1551 tidy
tree
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commitdiff
2016-06-20
Jim Procter
JAL-2065 don’t pass stale group reference
tree
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commitdiff
2016-06-20
Jim Procter
JAL-2068 avoid ArrayIndexOutOfBounds when consensus...
tree
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commitdiff
2016-06-20
Jim Procter
JAL-2065 check position lies within group before gettin...
tree
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commitdiff
2016-06-20
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-06-20
tcofoegbu
JAL-1823 Deleted two obsolete methods in PopupMenu...
tree
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commitdiff
2016-06-20
Jim Procter
Merge branch 'develop' into features/JAL-1812_JAL-2083_...
features/JAL-1812_JAL-2083_groovyBinding
tree
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commitdiff
2016-06-20
gmungoc
JAL-2130 call viewer.dispose() on closing Jmol
tree
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commitdiff
2016-06-20
gmungoc
JAL-1667 updated PDB example query to a valid id (witho...
tree
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commitdiff
2016-06-17
tcofoegbu
JAL-1823 Updated tooltip to reflect how a specific...
tree
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commitdiff
2016-06-17
tcofoegbu
JAL-1976 clear message if export is cancelled at 'Rende...
tree
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commitdiff
2016-06-17
tcofoegbu
JAL-1976 improved exception handler.
tree
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commitdiff
2016-06-17
tcofoegbu
JAL-1976 added an intermediate message between a user...
tree
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commitdiff
2016-06-16
gmungoc
JAL-1993 close sequence fetcher when opening database...
tree
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commitdiff
2016-06-16
gmungoc
JAL-2112 optimisation of EMBL CDS parsing
tree
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commitdiff
2016-06-16
gmungoc
JAL-1993 hide sequence fetcher dialogue until database...
tree
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commitdiff
2016-06-15
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-06-15
tcofoegbu
JAL-2002 disabled 'Best Uniport Coverage' filter. JAL...
tree
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commitdiff
2016-06-15
gmungoc
JAL-2025 unit tests added
tree
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commitdiff
2016-06-14
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-06-14
tcofoegbu
JAL-2102 right justify 'Mass' in uniprot FTS, and ...
tree
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commitdiff
2016-06-14
gmungoc
JAL-2114 more helpful reporting of parse failures
tree
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commitdiff
2016-06-14
gmungoc
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-06-14
tcofoegbu
JAL-2047 trapped block that could likely cause ClassCas...
tree
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commitdiff
2016-06-14
tcofoegbu
JAL-2047 resolved structure chooser's displayed column...
tree
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commitdiff
2016-06-10
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-06-10
tcofoegbu
JAL-1479 updated SIFTS FTP download URL, added improvem...
tree
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commitdiff
2016-06-10
Jim Procter
JAL-1941 added test URL and notes about PyRNA restclient
tree
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commitdiff
2016-06-09
gmungoc
JAL-2114 corrected Javadoc
tree
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commitdiff
2016-06-08
tcofoegbu
JAL-1479 JAL- Fix to eradicate duplicate mapping output...
tree
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commitdiff
2016-06-06
tcofoegbu
JAL-1919, JAL-1960 fix to disable refetching dbrefs...
tree
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commitdiff
2016-06-06
tcofoegbu
JAL-1944 bugfix for wrong alignment numbering when...
tree
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commitdiff
2016-06-02
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-06-02
tcofoegbu
JAL-2020 fix for Jmol choking jalview while loading...
tree
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commitdiff
2016-06-02
gmungoc
JAL-1424 corrected typos in message text keys
tree
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commitdiff
2016-06-02
tcofoegbu
JAL-1944 java doc update and minor house keeping
tree
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commitdiff
2016-06-01
Jim Procter
JAL-2038 ensure bare Strings are lowercased before...
tree
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commitdiff
2016-06-01
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-06-01
tcofoegbu
JAL-1944 updated bugfix implementation
tree
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commitdiff
2016-06-01
gmungoc
JAL-1424 utility to check resource bundle labels used...
tree
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commitdiff
2016-06-01
Jim Procter
fix build
tree
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commitdiff
2016-05-31
Jim Procter
JAL-1551 JAL-2106 javadoc
tree
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commitdiff
2016-05-31
Jim Procter
JAL-2110 abstract methods should never reference their...
tree
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commitdiff
2016-05-31
tcofoegbu
merge
tree
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commitdiff
2016-05-31
tcofoegbu
JAL-1944 fix for visible seqs sometimes been replaced...
tree
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commitdiff
2016-05-31
gmungoc
JAL-2023 adjustments to mappings added for split frame...
tree
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commitdiff
2016-05-31
gmungoc
JAL-2110 refactor + tests to allow a dbref version...
tree
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commitdiff
2016-05-31
Jim Procter
Merge branch 'develop' into features/JAL-2113_emblXml1.2
tree
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commitdiff
2016-05-31
Jim Procter
Merge branch 'jims/291patches' into develop
tree
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commitdiff
2016-05-31
gmungoc
JAL-1011 JAL-1989 don't mirror column-only selections...
tree
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commitdiff
2016-05-31
gmungoc
JAL-2123 use "rlabel" command to highlight with label...
tree
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commitdiff
2016-05-30
tcofoegbu
JAL-2038 fix to enable case-insensitive file name ...
tree
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commitdiff
2016-05-30
Jim Procter
JAL-553 JAL-1557 always send selections after triggerin...
tree
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commitdiff
2016-05-30
Jim Procter
JAL-1557 allow group associated rows to be used to...
tree
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commitdiff
2016-05-30
Jim Procter
JAL-2077 fix: convenience method and checks for CMD...
tree
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commitdiff
2016-05-30
Jim Procter
JAL-1551 formatting
tree
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commitdiff
2016-05-30
gmungoc
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-05-30
gmungoc
JAL-1989 equals method strengthened to fully match...
tree
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commitdiff
2016-05-30
Jim Procter
JAL-1552 fix JAL-2122 resolve File->string before addin...
tree
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commitdiff
2016-05-27
gmungoc
JAL-1989 tightened up use of flag for 'column selection...
tree
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commitdiff
2016-05-27
gmungoc
JAL-1989 added hashCode and equals, renamed field to...
tree
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commitdiff
2016-05-27
gmungoc
JAL-1911 use existing object when setting 'Prompt each...
tree
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commitdiff
2016-05-27
tcofoegbu
merge
tree
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commitdiff
2016-05-27
tcofoegbu
JAL-1823 improvement to all chain code specification...
tree
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commitdiff
2016-05-27
tcofoegbu
JAL-1911 further improvement to bugfix - do not save...
tree
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commitdiff
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