tcofoegbu [Fri, 29 Jan 2016 16:52:55 +0000 (16:52 +0000)]
merge from develop
tcofoegbu [Fri, 29 Jan 2016 16:24:29 +0000 (16:24 +0000)]
JAL-1979 refactor out duplicated similar block of code in StructureSelectionManger to a single method
tcofoegbu [Wed, 27 Jan 2016 12:24:27 +0000 (12:24 +0000)]
JAL-1479 fixed off-by-one error in SIFTS mapping output and added the flag 'isGetEntityIdDirectly' to control how an entity to process is determined.
tcofoegbu [Tue, 26 Jan 2016 14:28:31 +0000 (14:28 +0000)]
develop merge
tcofoegbu [Tue, 26 Jan 2016 12:56:22 +0000 (12:56 +0000)]
JAL-1999 JAL-1479 implemented configurable fail-safe mechanism for SIFTS mapping based on a PID threshold. Also added config threshold parameter for auto-computing time-based caching of downloaded SIFTS
tcofoegbu [Mon, 25 Jan 2016 15:06:26 +0000 (15:06 +0000)]
JAL-1998 bugfix for division by zero error for PDB entries with chain(s) consisiting of a single residue
tcofoegbu [Thu, 21 Jan 2016 17:00:16 +0000 (17:00 +0000)]
JAL-1479 JAL-1979 bugfix to check entire annotation property of a resDetail object for NOT_OBSERVED rather than just the topmost value. Intially thought the multiplicity was 0..1 rather than 0..* which it turned out to be following the N2NScan test
tcofoegbu [Thu, 21 Jan 2016 14:59:40 +0000 (14:59 +0000)]
JAL-1479 JAL-1979 updated the modified-aminoacid triplet code dictionary in Jalview using data from SCOP/PDB provided by Fabio
tcofoegbu [Thu, 21 Jan 2016 12:45:30 +0000 (12:45 +0000)]
merge
tcofoegbu [Thu, 21 Jan 2016 12:44:53 +0000 (12:44 +0000)]
JAL-1986 JAL-1996 separated out appletDeploment page from appletParameter page, updated the applet deployment docs, and updated necessary links. Also, having resolved JAL-1994, I've updated the json jars in all applet example pages.
Jim Procter [Thu, 21 Jan 2016 12:07:28 +0000 (12:07 +0000)]
JAL-1995 remove jalviewApplet.jar from tree and added it to .gitignore
tcofoegbu [Thu, 21 Jan 2016 10:05:04 +0000 (10:05 +0000)]
merge
tcofoegbu [Thu, 21 Jan 2016 10:04:29 +0000 (10:04 +0000)]
merge
tcofoegbu [Thu, 21 Jan 2016 10:02:08 +0000 (10:02 +0000)]
JAL-1994 bugfix in build.xml to prevent proguard from obfuscating dynamically accessed classes used in generating json in jalview. Also added some compile-time dependencies
tcofoegbu [Thu, 21 Jan 2016 09:46:43 +0000 (09:46 +0000)]
JAL-1919 basic support for importing and viewing mmCIF files - mapping support not yet available
gmungoc [Mon, 11 Jan 2016 14:58:24 +0000 (14:58 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Mon, 11 Jan 2016 12:37:52 +0000 (12:37 +0000)]
JAL-1989 additional ways to 'mirror' show/hide columns in split frame
tcofoegbu [Mon, 11 Jan 2016 12:37:07 +0000 (12:37 +0000)]
JAL-1990 added a progress indicator for Structure Chooser interface
tcofoegbu [Mon, 11 Jan 2016 11:18:30 +0000 (11:18 +0000)]
merge
tcofoegbu [Mon, 11 Jan 2016 11:16:03 +0000 (11:16 +0000)]
JAL-1991 bug fix for some flat-file printers to check for exact modulus in order to avoid outputing an extra redundant header line with empty sequences
gmungoc [Mon, 11 Jan 2016 11:04:40 +0000 (11:04 +0000)]
JAL-1989 map hidden column ranges
gmungoc [Mon, 11 Jan 2016 11:03:50 +0000 (11:03 +0000)]
JAL-1989 more unit tests and encapsulation for ColumnSelection
gmungoc [Mon, 11 Jan 2016 10:51:36 +0000 (10:51 +0000)]
JAL-1544 "more than" not "more that"
tcofoegbu [Thu, 7 Jan 2016 14:51:48 +0000 (14:51 +0000)]
merge
tcofoegbu [Thu, 7 Jan 2016 14:50:06 +0000 (14:50 +0000)]
JAL-1479 implemented timestamp based caching of SIFTS by providing code which checks if an already downloaded SIFTS file has exceeded a certain threshold upon processing. Also added a method to handle SIFTS entries for cases when an 'entityId' is NOT EQUAL TO 'chainId', this is a heuristic measure achieved using greedy search.
Jim Procter [Wed, 9 Dec 2015 16:03:51 +0000 (16:03 +0000)]
JAL-1982 hotfix to prevent NPE with applet launch on Jpred4 site
gmungoc [Thu, 3 Dec 2015 10:05:22 +0000 (10:05 +0000)]
JAL-1827 code and comment tidy up
gmungoc [Wed, 2 Dec 2015 16:52:41 +0000 (16:52 +0000)]
JAL-1827 refactored to handle missing residues better
gmungoc [Wed, 2 Dec 2015 16:43:32 +0000 (16:43 +0000)]
JAL-1827 added overloaded method for convenience
gmungoc [Wed, 2 Dec 2015 16:42:23 +0000 (16:42 +0000)]
JAL-1827 reverted text on generic sequence fetcher to not refer to PDB
tcofoegbu [Wed, 25 Nov 2015 15:29:41 +0000 (15:29 +0000)]
JAL-1479 refactored DBRef fetching code to StructureChooser to enable applet build
tcofoegbu [Wed, 25 Nov 2015 15:13:40 +0000 (15:13 +0000)]
JAL-1479 applet build debug
tcofoegbu [Wed, 25 Nov 2015 14:24:04 +0000 (14:24 +0000)]
JAL-1479 bugfix after decoupling SIFTS preference settings
tcofoegbu [Mon, 23 Nov 2015 18:04:25 +0000 (18:04 +0000)]
JAL-1479 commented out DBRef fetching code from SIFTS to test applet build
tcofoegbu [Tue, 17 Nov 2015 11:10:13 +0000 (11:10 +0000)]
JAL-1479 Refactored Sifts configuration preference in order to rectify applet build
tcofoegbu [Mon, 16 Nov 2015 17:17:27 +0000 (17:17 +0000)]
JAL-1967 JAL-1479 refactored sequence<->structure mapping implementation
tcofoegbu [Fri, 13 Nov 2015 15:22:22 +0000 (15:22 +0000)]
JAL-1479 added transfer of residue annotation for SIFTS mapping, then did some minor house-keeping
tcofoegbu [Wed, 11 Nov 2015 14:21:20 +0000 (14:21 +0000)]
JAL-1479 JAL-1957 Added code to enable simultaneous highlight of multiple atoms positions in all chains
tcofoegbu [Wed, 11 Nov 2015 13:08:02 +0000 (13:08 +0000)]
merge of SIFTs Branch
tcofoegbu [Wed, 11 Nov 2015 13:04:11 +0000 (13:04 +0000)]
merge
tcofoegbu [Wed, 11 Nov 2015 11:49:42 +0000 (11:49 +0000)]
JAL-1957 JAL-1479 Further optimisation of SIFTs Client and addition of support for multi-chain mapping of uniprot <-> pdb residues
tcofoegbu [Tue, 10 Nov 2015 12:00:59 +0000 (12:00 +0000)]
JAL 1960 added code to restrict structure chooser to discover only PDB and Uniprot entries when the references are avaiable
gmungoc [Fri, 6 Nov 2015 09:17:13 +0000 (09:17 +0000)]
JAL-1946 unit tests (and comments) for PID() function
gmungoc [Fri, 6 Nov 2015 09:03:32 +0000 (09:03 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
tcofoegbu [Thu, 5 Nov 2015 12:59:17 +0000 (12:59 +0000)]
JAL-1479 SiftClient house keeping
tcofoegbu [Thu, 5 Nov 2015 12:58:32 +0000 (12:58 +0000)]
JAL-1942 JAL-1479 refactored SequenceI.getDBRef/SequenceI.setDBRef to SequenceI.getDBRefs/SequenceI.setDBRefs
tcofoegbu [Mon, 2 Nov 2015 14:03:46 +0000 (14:03 +0000)]
JAL-1955 Uniprot sequence fetcher refactor
Jim Procter [Fri, 30 Oct 2015 12:31:46 +0000 (12:31 +0000)]
Merge branch 'JAL-1954_pfamformatbroke' into develop
Jim Procter [Fri, 30 Oct 2015 12:27:39 +0000 (12:27 +0000)]
JAL-1954 rejigged PFAMFile to split on ‘\t’ if no space present and optimised for long line searches. Will not cope with mixed space/tab separators.
Jim Procter [Fri, 30 Oct 2015 12:08:01 +0000 (12:08 +0000)]
JAL-1954 formatting
tcofoegbu [Thu, 29 Oct 2015 13:59:29 +0000 (13:59 +0000)]
JAL-1926 JAL-1479 updated PDBfile fetcher to add sourceDBRef on importing sequences
Jim Procter [Wed, 28 Oct 2015 14:19:02 +0000 (14:19 +0000)]
JAL-1954 test PFAM import results in AlignmentI.hasValidSequences()==true with/out limits.
tcofoegbu [Wed, 28 Oct 2015 11:48:20 +0000 (11:48 +0000)]
JAL-1479 added support for SIFTs mapping output viewing and implemented exception handling
tcofoegbu [Wed, 28 Oct 2015 11:45:20 +0000 (11:45 +0000)]
JAL-1952 bugfix
tcofoegbu [Wed, 28 Oct 2015 11:34:34 +0000 (11:34 +0000)]
JAL-1887 JAL-1479 bugfix for incorrect start/end for aligned sequence mapping, and a bit of StructureSelectionManager refactoring for SIFTs
gmungoc [Wed, 28 Oct 2015 10:40:00 +0000 (10:40 +0000)]
JAL-1946 additional unit test cases for PID calculation
gmungoc [Fri, 23 Oct 2015 09:30:56 +0000 (10:30 +0100)]
JAL-1943 don't try to unmarshal non-xml files in V1 project
tcofoegbu [Thu, 22 Oct 2015 17:08:14 +0000 (18:08 +0100)]
JAL-1479 added basic support for SIFTs mapping - more work to follow
tcofoegbu [Thu, 22 Oct 2015 15:14:58 +0000 (16:14 +0100)]
JAL-1479 implemented preferences for SIFTs / Needleman & Wunsch selection in structures preference tab
tcofoegbu [Thu, 22 Oct 2015 15:10:56 +0000 (16:10 +0100)]
JAL-1942 JAL-1479 DBRefFetcher refactor
gmungoc [Thu, 22 Oct 2015 10:10:49 +0000 (11:10 +0100)]
JAL-1932 TrimRegionCommand bug fix, tests and purge of unused code
Jim Procter [Fri, 16 Oct 2015 06:47:16 +0000 (07:47 +0100)]
JAL-1925 version change
Jim Procter [Fri, 16 Oct 2015 06:46:50 +0000 (07:46 +0100)]
JAL-1925 update what's new and release notes
Jim Procter [Thu, 15 Oct 2015 16:35:18 +0000 (17:35 +0100)]
JAL-1791 remove blanket sign of examples/*.jar
Jim Procter [Thu, 15 Oct 2015 16:27:30 +0000 (17:27 +0100)]
JAL-1791 id rather than name attrib
Jim Procter [Thu, 15 Oct 2015 15:59:31 +0000 (16:59 +0100)]
JAL-1791 sign the applet with/out timestamps
Jim Procter [Thu, 15 Oct 2015 15:28:58 +0000 (16:28 +0100)]
JAL-1791 add explicit proxy for benefit of jalview's build server when timestamping signed jars
Jim Procter [Thu, 15 Oct 2015 13:52:24 +0000 (14:52 +0100)]
JAL-1791 fix ant target dependencies
Jim Procter [Thu, 15 Oct 2015 13:45:06 +0000 (14:45 +0100)]
JAL-1791 make timestamping optional using -Dtimestamp
Jim Procter [Thu, 15 Oct 2015 13:20:38 +0000 (14:20 +0100)]
JAL-1791 add jalview.tsaurl for specifying timestamp server when signing jars
tcofoegbu [Thu, 15 Oct 2015 14:16:37 +0000 (15:16 +0100)]
JAL-1479 refactored SequenceI interface - changed getDBRef() to getDBRefs() since it returns an array of DBRefEntry
Jim Procter [Thu, 15 Oct 2015 13:20:38 +0000 (14:20 +0100)]
JAL-1791 add jalview.tsaurl for specifying timestamp server when signing jars
Jim Procter [Thu, 15 Oct 2015 13:00:15 +0000 (14:00 +0100)]
Merge branch 'bug/JAL-1923_290b2_group_annots' into develop
Jim Procter [Thu, 15 Oct 2015 12:59:34 +0000 (13:59 +0100)]
JAL-1923 formatting
Jim Procter [Thu, 15 Oct 2015 12:59:22 +0000 (13:59 +0100)]
JAL-1923 add groups to codon-complement and notify annotation update for all linked views
Jim Procter [Thu, 15 Oct 2015 12:58:22 +0000 (13:58 +0100)]
JAL-1923 fix: don’t add group twice
tcofoegbu [Wed, 14 Oct 2015 11:27:33 +0000 (12:27 +0100)]
JAL-1926 created interface for DBRefEntry
tcofoegbu [Wed, 14 Oct 2015 11:24:40 +0000 (12:24 +0100)]
JAL-1926 added supporting model changes to enable saving sourceDBRef data for sequences
tcofoegbu [Tue, 13 Oct 2015 15:08:29 +0000 (16:08 +0100)]
JAL-1479 added SIFTS XSD and generated JAXB bindings from it
Jim Procter [Thu, 8 Oct 2015 14:47:39 +0000 (15:47 +0100)]
JAL-1684 updated fragment alignment for example and added aligned protein and cDNA
Jim Procter [Thu, 8 Oct 2015 11:11:51 +0000 (12:11 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Thu, 8 Oct 2015 11:05:01 +0000 (12:05 +0100)]
JAL-1894 add licensing
tcofoegbu [Thu, 8 Oct 2015 11:02:04 +0000 (12:02 +0100)]
JAL-1912 JAL-1896 release notes updated
Jim Procter [Thu, 8 Oct 2015 10:58:43 +0000 (11:58 +0100)]
JAL-1894 update what's new
Jim Procter [Thu, 8 Oct 2015 10:52:15 +0000 (11:52 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
tcofoegbu [Thu, 8 Oct 2015 10:45:07 +0000 (11:45 +0100)]
JAL-1912 JAL-1896 release notes updated
gmungoc [Thu, 8 Oct 2015 10:40:08 +0000 (11:40 +0100)]
JAL-1544 typo fix
Jim Procter [Thu, 8 Oct 2015 10:33:48 +0000 (11:33 +0100)]
JAL-1894 formatting
Jim Procter [Thu, 8 Oct 2015 10:31:24 +0000 (11:31 +0100)]
JAL-1894 organise imports
tcofoegbu [Thu, 8 Oct 2015 10:09:41 +0000 (11:09 +0100)]
merge
Jim Procter [Wed, 7 Oct 2015 21:35:09 +0000 (22:35 +0100)]
JAL-1894 source formatting
Jim Procter [Wed, 7 Oct 2015 21:29:55 +0000 (22:29 +0100)]
JAL-1894 organise imports
Jim Procter [Wed, 7 Oct 2015 21:21:52 +0000 (22:21 +0100)]
JAL-1894 update release date
tcofoegbu [Wed, 7 Oct 2015 16:39:59 +0000 (17:39 +0100)]
JAL-1912 added documentation
Jim Procter [Wed, 7 Oct 2015 11:52:23 +0000 (12:52 +0100)]
JAL-1912 formatting
Jim Procter [Wed, 7 Oct 2015 11:51:59 +0000 (12:51 +0100)]
JAL-1912 javadoc for adjustForAlignment stating current behaviour
Jim Procter [Wed, 7 Oct 2015 11:51:27 +0000 (12:51 +0100)]
JAL-1912 efficiency: look up sequenceMapping once per position and only when sequenceMapping!=null
Jim Procter [Wed, 7 Oct 2015 10:57:37 +0000 (11:57 +0100)]
Merge branch 'features/JAL-1912_biojson-per-sequence-annotation' of source.jalview.org/git/jalview into features/JAL-1912_biojson-per-sequence-annotation
tcofoegbu [Mon, 5 Oct 2015 17:08:09 +0000 (18:08 +0100)]
JAL-1912 house keeping
tcofoegbu [Mon, 5 Oct 2015 16:33:01 +0000 (17:33 +0100)]
JAL-1912 added null check for SequenceMapping variable at the point of reference
git://source.jalview.org / jalview.git / log