jalview.git
8 years agoJAL-1705 return Ensembl genes for model species for a gene name
gmungoc [Fri, 19 Feb 2016 16:49:46 +0000 (16:49 +0000)]
JAL-1705 return Ensembl genes for model species for a gene name

8 years agoJAL-1705 JAL-1191 more terms added to hard-coded version
gmungoc [Fri, 19 Feb 2016 16:46:01 +0000 (16:46 +0000)]
JAL-1705 JAL-1191 more terms added to hard-coded version

8 years agoJAL-1706 reverted setting start position as too confusing for -ve strand
gmungoc [Fri, 19 Feb 2016 16:45:10 +0000 (16:45 +0000)]
JAL-1706 reverted setting start position as too confusing for -ve strand

8 years agoJAL-1705 lenient DBRef matcher added (accession id only)
gmungoc [Fri, 19 Feb 2016 16:42:34 +0000 (16:42 +0000)]
JAL-1705 lenient DBRef matcher added (accession id only)

8 years agoJAL-1705 helper method for mapping excluding stop codon
gmungoc [Fri, 19 Feb 2016 16:37:02 +0000 (16:37 +0000)]
JAL-1705 helper method for mapping excluding stop codon

8 years agoJAL-1270 remove trailing space + test
gmungoc [Fri, 12 Feb 2016 16:58:15 +0000 (16:58 +0000)]
JAL-1270 remove trailing space + test

8 years agoJAL-1705 various refactoring towards Uniprot-to-Ensembl fetching
gmungoc [Fri, 12 Feb 2016 16:55:19 +0000 (16:55 +0000)]
JAL-1705 various refactoring towards Uniprot-to-Ensembl fetching

8 years agoJAL-1191 additions to SOLite, tweak to test
gmungoc [Fri, 12 Feb 2016 16:53:14 +0000 (16:53 +0000)]
JAL-1191 additions to SOLite, tweak to test

8 years agoJAL-1705 take feature ID for description if nothing better found
gmungoc [Fri, 12 Feb 2016 16:51:14 +0000 (16:51 +0000)]
JAL-1705 take feature ID for description if nothing better found

8 years agoJAL-282 wrap very long id in tooltip
gmungoc [Fri, 12 Feb 2016 16:47:48 +0000 (16:47 +0000)]
JAL-282 wrap very long id in tooltip

8 years agoJAL-1705 JAL-1686 stronger SequenceFeature.equals() test
gmungoc [Fri, 12 Feb 2016 16:42:34 +0000 (16:42 +0000)]
JAL-1705 JAL-1686 stronger SequenceFeature.equals() test

8 years agoJAL-2010 simple prototype of 'Highlight Selection' onto Chimera view
gmungoc [Fri, 12 Feb 2016 15:03:51 +0000 (15:03 +0000)]
JAL-2010 simple prototype of 'Highlight Selection' onto Chimera view

8 years agoJAL-2008 updates for String[] to List<String> change
gmungoc [Fri, 12 Feb 2016 14:53:02 +0000 (14:53 +0000)]
JAL-2008 updates for String[] to List<String> change

8 years agoJAL-2008 avoid unnecessary repaints; signatures changed from String[] to
gmungoc [Fri, 12 Feb 2016 14:51:28 +0000 (14:51 +0000)]
JAL-2008 avoid unnecessary repaints; signatures changed from String[] to
List<String>

8 years agoJAL-265 updated help text
gmungoc [Fri, 12 Feb 2016 14:37:11 +0000 (14:37 +0000)]
JAL-265 updated help text

8 years agoMerge branch 'develop' into
gmungoc [Fri, 12 Feb 2016 14:11:34 +0000 (14:11 +0000)]
Merge branch 'develop' into
features/JAL-653_JAL-1766_htslib_refseqsupport

Conflicts:
resources/lang/Messages.properties
src/jalview/gui/FeatureColourChooser.java

8 years agoJAL-1976 catch and handle OOM Error
tcofoegbu [Tue, 9 Feb 2016 13:11:08 +0000 (13:11 +0000)]
JAL-1976 catch and handle OOM Error

8 years agoJAL-1976 Added progress indicators for HTML_SVG and BioJS export operations
tcofoegbu [Tue, 9 Feb 2016 13:05:31 +0000 (13:05 +0000)]
JAL-1976 Added progress indicators for HTML_SVG and BioJS export operations

8 years agoJAL-1975 updated image export pipeline to produce more informative messages.
tcofoegbu [Tue, 9 Feb 2016 11:56:17 +0000 (11:56 +0000)]
JAL-1975 updated image export pipeline to produce more informative messages.

8 years agoJAL-1957 deleted stale comment
tcofoegbu [Tue, 9 Feb 2016 10:28:59 +0000 (10:28 +0000)]
JAL-1957 deleted stale comment

8 years agomerge
tcofoegbu [Tue, 9 Feb 2016 10:25:37 +0000 (10:25 +0000)]
merge

8 years agoJAL-1957 enabled multi-chain mapping and highlight for Chimera viewer
tcofoegbu [Tue, 9 Feb 2016 10:25:14 +0000 (10:25 +0000)]
JAL-1957 enabled multi-chain mapping and highlight for Chimera viewer

8 years agoJAL-2006 scale even very small score ranges to a usable threshold slider
gmungoc [Fri, 5 Feb 2016 14:56:13 +0000 (14:56 +0000)]
JAL-2006 scale even very small score ranges to a usable threshold slider

8 years agoJAL-1544 spelling fix
gmungoc [Thu, 4 Feb 2016 15:26:24 +0000 (15:26 +0000)]
JAL-1544 spelling fix

8 years agoMerge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport
gmungoc [Thu, 4 Feb 2016 14:49:17 +0000 (14:49 +0000)]
Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport

8 years agoJAL-2005 added (stable) sort methods parameterised by
gmungoc [Thu, 4 Feb 2016 14:41:35 +0000 (14:41 +0000)]
JAL-2005 added (stable) sort methods parameterised by
ascending/descending

8 years agoJAL-599 bug fixed so array of visible types is populated
gmungoc [Thu, 4 Feb 2016 14:02:16 +0000 (14:02 +0000)]
JAL-599 bug fixed so array of visible types is populated

8 years agoJAL-1705 temporary variable to aid inspection in debugger
gmungoc [Thu, 4 Feb 2016 10:29:42 +0000 (10:29 +0000)]
JAL-1705 temporary variable to aid inspection in debugger

8 years agoJAL-1705 additional tests, validation regexp tweaks, javadoc
gmungoc [Thu, 4 Feb 2016 10:29:09 +0000 (10:29 +0000)]
JAL-1705 additional tests, validation regexp tweaks, javadoc

8 years agoJAL-2003 export features on alignment, not alignment dataset
gmungoc [Thu, 4 Feb 2016 10:28:29 +0000 (10:28 +0000)]
JAL-2003 export features on alignment, not alignment dataset

8 years agoJAL-1705 further unit tests
gmungoc [Mon, 1 Feb 2016 16:44:17 +0000 (16:44 +0000)]
JAL-1705 further unit tests

8 years agoJAL-1705 set Uniprot xref as 'source dbref' (for SIFTS mapping)
gmungoc [Mon, 1 Feb 2016 12:54:13 +0000 (12:54 +0000)]
JAL-1705 set Uniprot xref as 'source dbref' (for SIFTS mapping)

8 years agoJAL-1191 more terms added to SequenceOntologyLite
gmungoc [Mon, 1 Feb 2016 12:53:46 +0000 (12:53 +0000)]
JAL-1191 more terms added to SequenceOntologyLite

8 years agoMerge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport
gmungoc [Mon, 1 Feb 2016 10:23:29 +0000 (10:23 +0000)]
Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport

8 years agoJAL-1705 tests added
gmungoc [Mon, 1 Feb 2016 10:18:03 +0000 (10:18 +0000)]
JAL-1705 tests added

8 years agoJAL-1705 JAL-1191 SequenceOntologyLite added as hard-coded alternative
gmungoc [Mon, 1 Feb 2016 10:17:49 +0000 (10:17 +0000)]
JAL-1705 JAL-1191 SequenceOntologyLite added as hard-coded alternative

8 years agoJAL-1705 refactored cross-reference fetching (CCDS, Uniprot, PDB)
gmungoc [Sat, 30 Jan 2016 06:33:01 +0000 (06:33 +0000)]
JAL-1705 refactored cross-reference fetching (CCDS, Uniprot, PDB)

8 years agoJAL-1979 refactor out duplicated similar block of code in StructureSelectionManger...
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

8 years agoJAL-1705 fetch Uniprot and PDB xrefs for Ensembl protein products
gmungoc [Fri, 29 Jan 2016 16:11:36 +0000 (16:11 +0000)]
JAL-1705 fetch Uniprot and PDB xrefs for Ensembl protein products

8 years agoJAL-1705 copy feature settings when opening a split frame for show
gmungoc [Fri, 29 Jan 2016 16:10:56 +0000 (16:10 +0000)]
JAL-1705 copy feature settings when opening a split frame for show
product

8 years agoJAL-1705 more correct title (CDS not cDNA) on split frame
gmungoc [Thu, 28 Jan 2016 16:44:10 +0000 (16:44 +0000)]
JAL-1705 more correct title (CDS not cDNA) on split frame

8 years agoJAL-1705 refine feature copying to including 5' and 3' overlaps
gmungoc [Thu, 28 Jan 2016 16:43:51 +0000 (16:43 +0000)]
JAL-1705 refine feature copying to including 5' and 3' overlaps

8 years agoJAL-1705 tests added, minor bugfix and refactoring
gmungoc [Thu, 28 Jan 2016 15:00:17 +0000 (15:00 +0000)]
JAL-1705 tests added, minor bugfix and refactoring

8 years agoMerge branch 'develop' into JAL-1705_trialMerge
gmungoc [Thu, 28 Jan 2016 12:07:40 +0000 (12:07 +0000)]
Merge branch 'develop' into JAL-1705_trialMerge

Conflicts:
src/jalview/analysis/AlignmentUtils.java
src/jalview/analysis/CrossRef.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/ws/dbsources/Uniprot.java
test/jalview/analysis/AlignmentUtilsTests.java
test/jalview/util/MappingUtilsTest.java
test/jalview/ws/seqfetcher/DbRefFetcherTest.java

8 years agoJAL-1551 wrap enum declarations
gmungoc [Thu, 28 Jan 2016 10:17:03 +0000 (10:17 +0000)]
JAL-1551 wrap enum declarations

8 years agoJAL-1705 merge contiguous ranges when constructing a MapList (e.g. for
gmungoc [Thu, 28 Jan 2016 09:39:21 +0000 (09:39 +0000)]
JAL-1705 merge contiguous ranges when constructing a MapList (e.g. for
exons in cDNA)

8 years agoJAL-1705 add exon name to features and render on peptide (to show
gmungoc [Wed, 27 Jan 2016 16:57:11 +0000 (16:57 +0000)]
JAL-1705 add exon name to features and render on peptide (to show
boundaries)

8 years agoJAL-1479 fixed off-by-one error in SIFTS mapping output and added the flag 'isGetEnti...
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.

8 years agoJAL-1705 use GET for single queries; set gene name as description on
gmungoc [Wed, 27 Jan 2016 11:59:35 +0000 (11:59 +0000)]
JAL-1705 use GET for single queries; set gene name as description on
transcript

8 years agoJAL-1705 derive transcript sequences from gene sequence/GFF; handle CDS
gmungoc [Tue, 26 Jan 2016 16:36:03 +0000 (16:36 +0000)]
JAL-1705 derive transcript sequences from gene sequence/GFF; handle CDS
phase != 0

8 years agoJAL-1999 JAL-1479 implemented configurable fail-safe mechanism for SIFTS mapping...
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

8 years agoJAL-1998 bugfix for division by zero error for PDB entries with chain(s) consisiting...
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

8 years agoJAL-1705 EnsemblGene added, and related refactoring
gmungoc [Mon, 25 Jan 2016 10:45:02 +0000 (10:45 +0000)]
JAL-1705 EnsemblGene added, and related refactoring

8 years agoJAL-1997 database browser support tooltip if available
gmungoc [Mon, 25 Jan 2016 10:43:06 +0000 (10:43 +0000)]
JAL-1997 database browser support tooltip if available

8 years agoJAL-1355 get dialog title from message bundle
gmungoc [Sat, 23 Jan 2016 06:15:20 +0000 (06:15 +0000)]
JAL-1355 get dialog title from message bundle

8 years agoJAL-1705 copy 'show sequence features' setting in 'show products'
gmungoc [Sat, 23 Jan 2016 06:13:18 +0000 (06:13 +0000)]
JAL-1705 copy 'show sequence features' setting in 'show products'

8 years agoJAL-1705 todo comment re writing DBRefEntry/SequenceFeature to dataset
gmungoc [Sat, 23 Jan 2016 06:12:13 +0000 (06:12 +0000)]
JAL-1705 todo comment re writing DBRefEntry/SequenceFeature to dataset

8 years agoJAL-1705 compute peptide variants from dna; add "consequence" feature on
gmungoc [Sat, 23 Jan 2016 06:11:30 +0000 (06:11 +0000)]
JAL-1705 compute peptide variants from dna; add "consequence" feature on
CDS

8 years agoJAL-1479 JAL-1979 bugfix to check entire annotation property of a resDetail object...
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

8 years agoJAL-1705 transfer features to the dataset sequence if there is one
gmungoc [Thu, 21 Jan 2016 16:25:55 +0000 (16:25 +0000)]
JAL-1705 transfer features to the dataset sequence if there is one

8 years agoJAL-1705 reworked Ensembl clients now fetching and mapping features &
gmungoc [Thu, 21 Jan 2016 16:01:19 +0000 (16:01 +0000)]
JAL-1705 reworked Ensembl clients now fetching and mapping features &
peptide

8 years agoJAL-653 refactor / tidy
gmungoc [Thu, 21 Jan 2016 15:58:15 +0000 (15:58 +0000)]
JAL-653 refactor / tidy

8 years agoJAL-653 JAL-1705 set strand for GFF sequence feature
gmungoc [Thu, 21 Jan 2016 15:57:43 +0000 (15:57 +0000)]
JAL-653 JAL-1705 set strand for GFF sequence feature

8 years agoJAL-1705 removed (only) usage of otherwise unused constant
gmungoc [Thu, 21 Jan 2016 15:56:06 +0000 (15:56 +0000)]
JAL-1705 removed (only) usage of otherwise unused constant

8 years agoJAL-653 comments/javadoc tidy only
gmungoc [Thu, 21 Jan 2016 15:55:20 +0000 (15:55 +0000)]
JAL-653 comments/javadoc tidy only

8 years agoJAL-1796 parse ensembl genomic coordinates to set start position
gmungoc [Thu, 21 Jan 2016 15:49:08 +0000 (15:49 +0000)]
JAL-1796 parse ensembl genomic coordinates to set start position

8 years agoJAL-1705 AlignmentUtils method renamed
gmungoc [Thu, 21 Jan 2016 15:33:18 +0000 (15:33 +0000)]
JAL-1705 AlignmentUtils method renamed

8 years agoJAL-1705 ENSEMBL added, unused constants removed
gmungoc [Thu, 21 Jan 2016 15:31:11 +0000 (15:31 +0000)]
JAL-1705 ENSEMBL added, unused constants removed

8 years agoJAL-1705 features transferred to CDS sequence; makeExon renamed makeCds
gmungoc [Thu, 21 Jan 2016 15:23:20 +0000 (15:23 +0000)]
JAL-1705 features transferred to CDS sequence; makeExon renamed makeCds

8 years agoJAL-1705 redundant comment removed
gmungoc [Thu, 21 Jan 2016 15:20:43 +0000 (15:20 +0000)]
JAL-1705 redundant comment removed

8 years agoJAL-1705 suppress jvsuffix (for sequence id matching to work)
gmungoc [Thu, 21 Jan 2016 15:18:59 +0000 (15:18 +0000)]
JAL-1705 suppress jvsuffix (for sequence id matching to work)

8 years agoJAL-1705 unused import removed
gmungoc [Thu, 21 Jan 2016 15:18:13 +0000 (15:18 +0000)]
JAL-1705 unused import removed

8 years agoJAL-1705 include dummy sequences in returned alignment
gmungoc [Thu, 21 Jan 2016 15:17:12 +0000 (15:17 +0000)]
JAL-1705 include dummy sequences in returned alignment

8 years agoJAL-1479 JAL-1979 updated the modified-aminoacid triplet code dictionary in Jalview...
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

8 years agoJAL-1705 tidy and todo comment, no functional change
gmungoc [Thu, 21 Jan 2016 14:56:27 +0000 (14:56 +0000)]
JAL-1705 tidy and todo comment, no functional change

8 years agoJAL-1705 tests for amended toString
gmungoc [Thu, 21 Jan 2016 14:54:41 +0000 (14:54 +0000)]
JAL-1705 tests for amended toString

8 years agoJAL-1705 added isSequenceVariant(), commonly used SO terms as constants
gmungoc [Thu, 21 Jan 2016 14:44:15 +0000 (14:44 +0000)]
JAL-1705 added isSequenceVariant(), commonly used SO terms as constants

8 years agoJAL-1705 isFromForwardStrand added; toString (for debug) tweaked
gmungoc [Thu, 21 Jan 2016 14:40:17 +0000 (14:40 +0000)]
JAL-1705 isFromForwardStrand added; toString (for debug) tweaked

8 years agoJAL-1705 canonicalise ENSEMBL name; code tidy
gmungoc [Thu, 21 Jan 2016 14:38:21 +0000 (14:38 +0000)]
JAL-1705 canonicalise ENSEMBL name; code tidy

8 years agoJAL-1705 get xrefs only for dna/peptide; code tidy
gmungoc [Thu, 21 Jan 2016 14:34:54 +0000 (14:34 +0000)]
JAL-1705 get xrefs only for dna/peptide; code tidy

8 years agoJAL-1705 toString() added (for debugging)
gmungoc [Thu, 21 Jan 2016 14:30:31 +0000 (14:30 +0000)]
JAL-1705 toString() added (for debugging)

8 years agoJAL-1705 isEmpty() and (debug) toString() methods added
gmungoc [Thu, 21 Jan 2016 14:29:42 +0000 (14:29 +0000)]
JAL-1705 isEmpty() and (debug) toString() methods added

8 years agomerge
tcofoegbu [Thu, 21 Jan 2016 12:45:30 +0000 (12:45 +0000)]
merge

8 years agoJAL-1986 JAL-1996 separated out appletDeploment page from appletParameter page, updat...
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.

8 years agoJAL-1995 remove jalviewApplet.jar from tree and added it to .gitignore
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

8 years agomerge
tcofoegbu [Thu, 21 Jan 2016 10:05:04 +0000 (10:05 +0000)]
merge

8 years agomerge
tcofoegbu [Thu, 21 Jan 2016 10:04:29 +0000 (10:04 +0000)]
merge

8 years agoJAL-1994 bugfix in build.xml to prevent proguard from obfuscating dynamically accesse... bug/JAL-1994_Jalviewlite-json-parser-in-browsers
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

8 years agoJAL-1191 cache isA (great-)grandparents as well for fast isA testing
gmungoc [Tue, 12 Jan 2016 08:58:01 +0000 (08:58 +0000)]
JAL-1191 cache isA (great-)grandparents as well for fast isA testing

8 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
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

8 years agoJAL-1989 additional ways to 'mirror' show/hide columns in split frame
gmungoc [Mon, 11 Jan 2016 12:37:52 +0000 (12:37 +0000)]
JAL-1989 additional ways to 'mirror' show/hide columns in split frame

8 years agoJAL-1990 added a progress indicator for Structure Chooser interface
tcofoegbu [Mon, 11 Jan 2016 12:37:07 +0000 (12:37 +0000)]
JAL-1990 added a progress indicator for Structure Chooser interface

8 years agomerge
tcofoegbu [Mon, 11 Jan 2016 11:18:30 +0000 (11:18 +0000)]
merge

8 years agoJAL-1991 bug fix for some flat-file printers to check for exact modulus in order...
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

8 years agoJAL-1989 map hidden column ranges
gmungoc [Mon, 11 Jan 2016 11:04:40 +0000 (11:04 +0000)]
JAL-1989 map hidden column ranges

8 years agoJAL-1989 more unit tests and encapsulation for ColumnSelection
gmungoc [Mon, 11 Jan 2016 11:03:50 +0000 (11:03 +0000)]
JAL-1989 more unit tests and encapsulation for ColumnSelection

8 years agoJAL-1544 "more than" not "more that"
gmungoc [Mon, 11 Jan 2016 10:51:36 +0000 (10:51 +0000)]
JAL-1544 "more than" not "more that"

8 years agoJAL-1705 DbSourceProxy properties converted to methods, tidy/format code
gmungoc [Fri, 8 Jan 2016 10:03:40 +0000 (10:03 +0000)]
JAL-1705 DbSourceProxy properties converted to methods, tidy/format code

8 years agomerge
tcofoegbu [Thu, 7 Jan 2016 14:51:48 +0000 (14:51 +0000)]
merge

8 years agoJAL-1479 implemented timestamp based caching of SIFTS by providing code which checks...
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.