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JAL-1950 represent duplicate sequences by their representative in the hit alignment
[jalview.git]
/
src
/
jalview
/
2015-11-17
Jim Procter
JAL-1950 represent duplicate sequences by their represe...
tree
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commitdiff
2015-11-16
Jim Procter
JAL-1950 group hits by architecture
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commitdiff
2015-11-16
Jim Procter
JAL-1950 formatting
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commitdiff
2015-11-16
Jim Procter
JAL-1958 modulate per-sequence shading with local score...
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commitdiff
2015-11-16
Jim Procter
JAL-1950 add domain architecture feature
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commitdiff
2015-11-09
Jim Procter
JAL-1950 JAL-1958 bitscore is more effective for shadin...
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commitdiff
2015-11-09
Jim Procter
JAL-1950 - JAL-1958 hardwired hack to explore shading...
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commitdiff
2015-11-09
Jim Procter
JAL-1950 transfer posterior probability onto hit sequences
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commitdiff
2015-11-09
Jim Procter
JAL-1950 magic keys for different parts of the JSON...
tree
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commitdiff
2015-11-09
Jim Procter
JAL-1950 javadoc: clarify AlignmentAnnotation.createSeq...
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commitdiff
2015-11-04
Jim Procter
JAL-1950 hook up JSON result dump parser to hmmerClient
tree
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commitdiff
2015-11-04
Jim Procter
JAL-1950 first stab at Hmmer3 JSON parser and alignment...
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commitdiff
2015-11-04
Jim Procter
JAL-1950 - cache URL as a local file (needs a test...
tree
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commitdiff
2015-11-02
Jim Procter
JAL-1950 keys for hmm search score file parser. not...
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commitdiff
2015-11-02
Jim Procter
JAL-1950 structuring methods and note on parsing flat...
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commitdiff
2015-11-02
Jim Procter
JAL-1934 conditional evaluation structure not needed
tree
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commitdiff
2015-11-02
Jim Procter
JAL-1934 new preference to disable gap character normal...
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commitdiff
2015-10-28
Jim Procter
JAL-1950 JAL-715 fall through for 201 ‘CREATED’ codes...
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commitdiff
2015-10-28
Jim Procter
JAL-1950 extremely rough prototype submission/poll...
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commitdiff
2015-10-28
Jim Procter
JAL-715 tidy up the job poll loop ready to adapt for...
tree
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commitdiff
2015-10-28
Jim Procter
JAL-715 JAL-724 refactored multi harmony definition...
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commitdiff
2015-10-23
gmungoc
JAL-1943 don't try to unmarshal non-xml files in V1...
tree
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commitdiff
2015-10-22
gmungoc
JAL-1932 TrimRegionCommand bug fix, tests and purge...
tree
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commitdiff
2015-10-15
Jim Procter
JAL-1923 formatting
tree
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commitdiff
2015-10-15
Jim Procter
JAL-1923 add groups to codon-complement and notify...
tree
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commitdiff
2015-10-15
Jim Procter
JAL-1923 fix: don’t add group twice
tree
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commitdiff
2015-10-08
Jim Procter
JAL-1894 add licensing
tree
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commitdiff
2015-10-08
Jim Procter
JAL-1894 organise imports
tree
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commitdiff
2015-10-08
tcofoegbu
merge
tree
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commitdiff
2015-10-07
Jim Procter
JAL-1894 source formatting
tree
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commitdiff
2015-10-07
Jim Procter
JAL-1894 organise imports
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commitdiff
2015-10-07
tcofoegbu
JAL-1912 added documentation
features/JAL-1912_biojson-per-sequence-annotation
tree
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commitdiff
2015-10-07
Jim Procter
JAL-1912 formatting
tree
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commitdiff
2015-10-07
Jim Procter
JAL-1912 javadoc for adjustForAlignment stating current...
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commitdiff
2015-10-07
Jim Procter
JAL-1912 efficiency: look up sequenceMapping once per...
tree
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commitdiff
2015-10-07
Jim Procter
Merge branch 'features/JAL-1912_biojson-per-sequence...
tree
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commitdiff
2015-10-05
tcofoegbu
JAL-1912 house keeping
tree
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commitdiff
2015-10-05
tcofoegbu
JAL-1912 added null check for SequenceMapping variable...
tree
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commitdiff
2015-10-05
gmungoc
JAL-1812 set/return currentAlFrame for Groovy in headle...
tree
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commitdiff
2015-10-05
Jim Procter
Merge branch 'develop' into features/JAL-1912_biojson...
tree
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commitdiff
2015-10-05
gmungoc
JAL-1684 JAL-1452 new applet parameters defaultColourNuc
tree
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commitdiff
2015-10-05
tcofoegbu
JAL-1908 bugfix
tree
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commitdiff
2015-10-05
tcofoegbu
JAL-1912 updated AnnotationDisplaySettingPojo
tree
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commitdiff
2015-10-02
gmungoc
JAL-1815 restore split frame geometry including horizon...
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commitdiff
2015-10-02
Jim Procter
JAL-1900 JAL-1625 disable iconify button for internal...
tree
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commitdiff
2015-10-01
tcofoegbu
JAL-1912 Double.NaN breaks JSON serialization - added...
tree
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commitdiff
2015-10-01
tcofoegbu
JAL-1912 refactor annotation refsequence assignemnt...
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commitdiff
2015-09-30
tcofoegbu
house keeping
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commitdiff
2015-09-30
tcofoegbu
JAL-1860 house keeping
tree
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commitdiff
2015-09-30
tcofoegbu
JAL-1852 made disabling querying of unpublished PDB...
tree
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commitdiff
2015-09-30
tcofoegbu
JAL-1912 added support of tcoffee annotation and other...
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commitdiff
2015-09-30
tcofoegbu
JAL-1852 disable querying of unpublished PDB entries...
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commitdiff
2015-09-29
tcofoegbu
JAL-1896 fixed NPE for RNA Helice without equivalent...
tree
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commitdiff
2015-09-28
tcofoegbu
merge
tree
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commitdiff
2015-09-28
tcofoegbu
JAL-1896 revised implementation to construct a ColourSc...
tree
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commitdiff
2015-09-28
gmungoc
JAL-1909 repaint complementary alignment panel after...
tree
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commitdiff
2015-09-25
gmungoc
JAL-1859 try hoverDelay of 0.1s in Jmol for more respon...
tree
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commitdiff
2015-09-25
tcofoegbu
merge
tree
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commitdiff
2015-09-25
tcofoegbu
JAL-1907 bugfix for NPE while parsing a features file
tree
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commitdiff
2015-09-25
gmungoc
JAL-1815 restore split frame geometry correctly includi...
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commitdiff
2015-09-25
tcofoegbu
merge
tree
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commitdiff
2015-09-25
tcofoegbu
JAL-1860 disabled default enter behaviour on pdb search...
tree
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commitdiff
2015-09-24
gmungoc
JAL-1905 parse url including & correctly
tree
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commitdiff
2015-09-24
gmungoc
JAL-1904 parse feature file colours on to alignment...
tree
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commitdiff
2015-09-24
tcofoegbu
JAL-1860 only allow enter key when valid selection...
tree
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commitdiff
2015-09-24
tcofoegbu
JAL-1860 keyboard operation of pdb sequence fetcher...
tree
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commitdiff
2015-09-24
tcofoegbu
JAL-1896 bugfix to enabled Jalview restore clustal...
tree
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commitdiff
2015-09-22
tcofoegbu
JAL-1774 house keeping
tree
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commitdiff
2015-09-21
tcofoegbu
merge
tree
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commitdiff
2015-09-21
tcofoegbu
JAL-1774 modifed warning dialog to use JVDialog rather...
tree
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commitdiff
2015-09-21
gmungoc
JAL-1799 update height of annotation labels to match...
tree
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commitdiff
2015-09-21
gmungoc
JAL-1152 set initial state of show alignment/sequence...
tree
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commitdiff
2015-09-18
gmungoc
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2015-09-18
Jim Procter
JAL-1889 remove non-UTF8 characters so we can build...
tree
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commitdiff
2015-09-18
tcofoegbu
JAL-1774 JAL-1506 revised implementaion for clear highl...
tree
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commitdiff
2015-09-18
tcofoegbu
JAL-1506 revised implementation to clear only selected...
tree
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commitdiff
2015-09-18
gmungoc
JAL-1859 reinstated full path to file option (for local...
tree
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commitdiff
2015-09-17
tcofoegbu
JAL-1774 bugfix for misleading message after trying...
tree
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commitdiff
2015-09-16
tcofoegbu
merge
tree
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commitdiff
2015-09-16
tcofoegbu
JAL-1486 off-by-one error bugfix
tree
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commitdiff
2015-09-16
gmungoc
JAL-1882 variable renamed to avoid confusion with membe...
tree
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commitdiff
2015-09-16
gmungoc
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2015-09-16
gmungoc
JAL-1885 small fix to isVersionStringLaterThan plus...
tree
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commitdiff
2015-09-16
tcofoegbu
merge
tree
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commitdiff
2015-09-16
tcofoegbu
JAL-1881 Bugfix for annotation import from BioJS
tree
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commitdiff
2015-09-16
gmungoc
JAL-1859 refactor duplicated code to new HttpUtils...
tree
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commitdiff
2015-09-16
gmungoc
JAL-1859 code tidy, remove 'absolute URL' option
tree
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commitdiff
2015-09-16
gmungoc
JAL-1859 debug logging removed
tree
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commitdiff
2015-09-16
gmungoc
JAL-1859 revert to resolving full path to PDB file
tree
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commitdiff
2015-09-16
gmungoc
JAL-1859 refactor addProtocol, setProtocolState as...
tree
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commitdiff
2015-09-16
gmungoc
JAL-1859 temporary debug output
tree
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commitdiff
2015-09-15
gmungoc
JAL-1859 use unresolved PDB filename
tree
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commitdiff
2015-09-15
gmungoc
JAL-1859 strip file name from applet documentbase
tree
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commitdiff
2015-09-15
gmungoc
JAL-1859 refactoring / debugging added
tree
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commitdiff
2015-09-14
gmungoc
JAL-1865 fixed so initial state of annotation sort...
tree
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commitdiff
2015-09-14
gmungoc
JAL-1851 add retrieved sequence's start (-1) to match...
tree
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commitdiff
2015-09-14
gmungoc
JAL-1880 handle sequence offsets properly when mapping...
tree
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commitdiff
2015-09-14
gmungoc
JAL-1684 align added alignment to match original in...
tree
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commitdiff
2015-09-14
gmungoc
JAL-1684 align added alignment to match original in...
tree
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commitdiff
2015-09-14
gmungoc
JAL-1684 ensure cDNA placed above protein in SplitFrame
tree
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commitdiff
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