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jalview.git
2015-12-22
gmungoc
JAL-1191 stub class for a SequenceOntology wrapper
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2015-12-22
gmungoc
JAL-1551 don't autoformat /* comments */
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2015-12-22
gmungoc
JAL-1421 parameterised map constructor used
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2015-12-22
gmungoc
JAL-653 encapsulate Strand, Attributes, Status of Seque...
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2015-12-22
gmungoc
JAL-653 realise virtual mappings and align when adding...
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2015-12-22
gmungoc
JAL-391 new Calculate options to Reverse, Reverse Compl...
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2015-12-22
gmungoc
JAL-653 AlignedCodonFrame collections changed from...
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2015-12-22
gmungoc
JAL-653 set showSequenceFeatures=true on loading a...
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2015-12-22
gmungoc
JAL-653 GFF new/refactored helper classes
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2015-12-22
gmungoc
JAL-653 AlignedCodonFrame internal refactor, merge...
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2015-12-22
gmungoc
JAL-653 hold AlignedCodonFrame collections as list...
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2015-12-09
Jim Procter
JAL-1982 hotfix to prevent NPE with applet launch on...
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2015-12-03
gmungoc
JAL-653 code tidy / tests for 'realise gff mappings'
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2015-12-03
gmungoc
JAL-653 handle reverse strand mapping in SearchResults...
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2015-12-03
gmungoc
JAL-653 mappings always reside on the dataset alignment...
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2015-12-03
gmungoc
JAL-653 handle reverse strand mappings also
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2015-12-03
gmungoc
JAL-1827 code and comment tidy up
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2015-12-02
gmungoc
JAL-1827 refactored to handle missing residues better
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2015-12-02
gmungoc
JAL-1827 added overloaded method for convenience
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2015-12-02
gmungoc
JAL-1827 reverted text on generic sequence fetcher...
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2015-11-30
gmungoc
JAL-1421 generics loop syntax; 'bug?' comment added
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2015-11-30
gmungoc
JAL-653 test for 'resolving GFF mappings to sequences...
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2015-11-30
gmungoc
JAL-653 small comment change only
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2015-11-30
gmungoc
JAL-652 refactored to remove one method
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2015-11-30
gmungoc
JAL-653 (experimental) 'realise' dummy sequences in...
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2015-11-30
gmungoc
JAL-1980 check for null alignment; JAL-1551 @Override...
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2015-11-30
gmungoc
JAL-653 (experimental) methods to resolve dummy to...
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2015-11-30
gmungoc
JAL-1270 constructor test added
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2015-11-30
gmungoc
JAL-653 getStrand javadoc/refactor/test
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2015-11-30
gmungoc
JAL-1421 use generics JAL-1551 @Override annotations...
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2015-11-30
gmungoc
JAL-1270 constructor tests added, compiler warnings...
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2015-11-30
gmungoc
JAL-652 further refactoring / tests
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2015-11-30
gmungoc
JAL-652 correct case for test file name
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2015-11-30
gmungoc
JAL-653 MapList constructor merges any contiguous ranges
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2015-11-25
tcofoegbu
JAL-1479 refactored DBRef fetching code to StructureCho...
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2015-11-25
tcofoegbu
JAL-1479 applet build debug
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2015-11-25
tcofoegbu
JAL-1479 bugfix after decoupling SIFTS preference settings
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2015-11-23
tcofoegbu
JAL-1479 commented out DBRef fetching code from SIFTS...
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2015-11-23
gmungoc
JAL-653 Gff tests moved back in to FeaturesFileTest
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2015-11-22
gmungoc
JAL-653 test for 'groups file' and mixed Jalview/GFF
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2015-11-21
gmungoc
JAL-1968 remove feature links
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2015-11-21
gmungoc
JAL-653 JAL-1968 FeaturesFile now handles Jalview or...
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2015-11-17
tcofoegbu
JAL-1479 Refactored Sifts configuration preference...
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2015-11-17
gmungoc
JAL-1961 update link to GFF2 spec
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2015-11-16
tcofoegbu
JAL-1967 JAL-1479 refactored sequence<->structure mappi...
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2015-11-13
tcofoegbu
JAL-1479 added transfer of residue annotation for SIFTS...
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2015-11-11
tcofoegbu
JAL-1479 JAL-1957 Added code to enable simultaneous...
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2015-11-11
tcofoegbu
merge of SIFTs Branch
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2015-11-11
tcofoegbu
merge
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2015-11-11
tcofoegbu
JAL-1957 JAL-1479 Further optimisation of SIFTs Client...
features/JAL-1479_SIFTS-mapping
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2015-11-10
Jim Procter
JAL-653 added missing pragma string to processing filter
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2015-11-10
Jim Procter
Merge branch 'features/JAL-1705_ensembl' of source...
features/JAL-1705_ensembl
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2015-11-10
tcofoegbu
JAL 1960 added code to restrict structure chooser to...
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2015-11-09
gmungoc
JAL-1705 type enum can encapsulate the corresponding...
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2015-11-06
gmungoc
JAL-1946 unit tests (and comments) for PID() function
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2015-11-06
gmungoc
Merge branch 'develop' of https://source.jalview.org...
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2015-11-05
tcofoegbu
JAL-1479 SiftClient house keeping
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2015-11-05
tcofoegbu
JAL-1942 JAL-1479 refactored SequenceI.getDBRef/Sequenc...
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2015-11-02
tcofoegbu
JAL-1955 Uniprot sequence fetcher refactor
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2015-10-30
Jim Procter
Merge branch 'JAL-1954_pfamformatbroke' into develop
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2015-10-30
Jim Procter
JAL-1954 rejigged PFAMFile to split on ‘\t’ if no space...
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2015-10-30
Jim Procter
JAL-1954 formatting
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2015-10-29
tcofoegbu
JAL-1926 JAL-1479 updated PDBfile fetcher to add source...
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2015-10-28
Jim Procter
JAL-1954 test PFAM import results in AlignmentI.hasVali...
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2015-10-28
tcofoegbu
JAL-1479 added support for SIFTs mapping output viewing...
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2015-10-28
tcofoegbu
JAL-1952 bugfix
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2015-10-28
tcofoegbu
JAL-1887 JAL-1479 bugfix for incorrect start/end for...
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2015-10-28
gmungoc
JAL-1946 additional unit test cases for PID calculation
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2015-10-23
gmungoc
JAL-1943 don't try to unmarshal non-xml files in V1...
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2015-10-22
tcofoegbu
JAL-1479 added basic support for SIFTs mapping - more...
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2015-10-22
tcofoegbu
JAL-1479 implemented preferences for SIFTs / Needleman...
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2015-10-22
tcofoegbu
JAL-1942 JAL-1479 DBRefFetcher refactor
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2015-10-22
gmungoc
JAL-1932 TrimRegionCommand bug fix, tests and purge...
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2015-10-16
Jim Procter
JAL-1925 version change
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2015-10-16
Jim Procter
JAL-1925 update what's new and release notes
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2015-10-15
Jim Procter
JAL-653 JAL-1766 merge 290b1 - fix erroneous conflicts...
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2015-10-15
Jim Procter
Merge branch 'develop' into features/JAL-653_JAL-1766_h...
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2015-10-15
Jim Procter
Merge branch 'develop' into features/JAL-1705_ensembl
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2015-10-15
Jim Procter
JAL-1791 remove blanket sign of examples/*.jar
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2015-10-15
Jim Procter
JAL-1791 id rather than name attrib
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2015-10-15
Jim Procter
JAL-1791 sign the applet with/out timestamps
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2015-10-15
Jim Procter
JAL-1791 add explicit proxy for benefit of jalview...
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2015-10-15
Jim Procter
JAL-1791 fix ant target dependencies
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2015-10-15
Jim Procter
JAL-1791 make timestamping optional using -Dtimestamp
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2015-10-15
Jim Procter
JAL-1791 add jalview.tsaurl for specifying timestamp...
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2015-10-15
tcofoegbu
JAL-1479 refactored SequenceI interface - changed getDB...
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2015-10-15
Jim Procter
JAL-1791 add jalview.tsaurl for specifying timestamp...
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2015-10-15
Jim Procter
Merge branch 'bug/JAL-1923_290b2_group_annots' into...
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2015-10-15
Jim Procter
JAL-1923 formatting
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2015-10-15
Jim Procter
JAL-1923 add groups to codon-complement and notify...
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2015-10-15
Jim Procter
JAL-1923 fix: don’t add group twice
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2015-10-14
tcofoegbu
JAL-1926 created interface for DBRefEntry
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2015-10-14
tcofoegbu
JAL-1926 added supporting model changes to enable savin...
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2015-10-13
tcofoegbu
JAL-1479 added SIFTS XSD and generated JAXB bindings...
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2015-10-08
Jim Procter
JAL-1684 updated fragment alignment for example and...
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2015-10-08
Jim Procter
Merge branch 'develop' of source.jalview.org/git/jalvie...
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2015-10-08
Jim Procter
JAL-1894 add licensing
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2015-10-08
tcofoegbu
JAL-1912 JAL-1896 release notes updated
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2015-10-08
Jim Procter
JAL-1894 update what's new
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2015-10-08
Jim Procter
Merge branch 'develop' of source.jalview.org/git/jalvie...
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