jalview.git
8 years agoJAL-1812 JAL-2068 add Run Groovy Script to AlignFrame Calculate menu
gmungoc [Fri, 22 Apr 2016 15:16:55 +0000 (16:16 +0100)]
JAL-1812 JAL-2068 add Run Groovy Script to AlignFrame Calculate menu

8 years agoJAL-2068 code and test for case of minValue == maxValue
gmungoc [Fri, 22 Apr 2016 15:12:28 +0000 (16:12 +0100)]
JAL-2068 code and test for case of minValue == maxValue

8 years agoJAL-2068 framework and example scripts for pluggable alignment
gmungoc [Fri, 22 Apr 2016 15:03:28 +0000 (16:03 +0100)]
JAL-2068 framework and example scripts for pluggable alignment
annotation workers

8 years agoJAL-2068 Javadoc added
gmungoc [Fri, 22 Apr 2016 14:37:40 +0000 (15:37 +0100)]
JAL-2068 Javadoc added

8 years agoJAL-2068 redundant implements clauses removed
gmungoc [Fri, 22 Apr 2016 14:23:05 +0000 (15:23 +0100)]
JAL-2068 redundant implements clauses removed

8 years agoJAL-2068 convenience helper method for graduated score colour
gmungoc [Fri, 22 Apr 2016 14:20:00 +0000 (15:20 +0100)]
JAL-2068 convenience helper method for graduated score colour

8 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 21 Apr 2016 09:56:53 +0000 (10:56 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

8 years agoMerge branch 'groovy/JAL-2074_upgradeto2.4.4' into develop
Jim Procter [Wed, 20 Apr 2016 16:03:06 +0000 (17:03 +0100)]
Merge branch 'groovy/JAL-2074_upgradeto2.4.4' into develop

8 years agoJAL-2074 updated URLs and removed 'how to get groovy' classpath stuff
Jim Procter [Wed, 20 Apr 2016 16:00:53 +0000 (17:00 +0100)]
JAL-2074 updated URLs and removed 'how to get groovy' classpath stuff

8 years agoJAL-2074 updated groovy-all to 2.4.6-indy
Jim Procter [Wed, 20 Apr 2016 15:59:07 +0000 (16:59 +0100)]
JAL-2074 updated groovy-all to 2.4.6-indy

8 years agofix for JAL-2072
Jim Procter [Wed, 20 Apr 2016 10:56:57 +0000 (11:56 +0100)]
fix for JAL-2072

8 years agoJAL-2067 fixed broken link
gmungoc [Mon, 18 Apr 2016 09:19:06 +0000 (10:19 +0100)]
JAL-2067 fixed broken link

8 years agoJAL-2041 add ID,clinical_significance to feature attributes (for export)
gmungoc [Thu, 14 Apr 2016 13:36:34 +0000 (14:36 +0100)]
JAL-2041 add ID,clinical_significance to feature attributes (for export)

8 years agoJAL-2041 clinical_significance shown on sequence feature tooltip
gmungoc [Thu, 14 Apr 2016 12:32:09 +0000 (13:32 +0100)]
JAL-2041 clinical_significance shown on sequence feature tooltip

8 years agoJAL-1421 typed map / lists, explicit imports, method refactoring
gmungoc [Thu, 14 Apr 2016 12:30:03 +0000 (13:30 +0100)]
JAL-1421 typed map / lists, explicit imports, method refactoring

8 years agoJAL-2049 small refactor of constructors to avoid code duplication
gmungoc [Thu, 14 Apr 2016 11:20:29 +0000 (12:20 +0100)]
JAL-2049 small refactor of constructors to avoid code duplication

8 years agoJAL-1421 type parameter added to some collections
gmungoc [Thu, 14 Apr 2016 11:17:28 +0000 (12:17 +0100)]
JAL-1421 type parameter added to some collections

8 years agoJAL-2049 revised computePeptideVariants to transfer id, clinical_sig
gmungoc [Thu, 14 Apr 2016 11:06:29 +0000 (12:06 +0100)]
JAL-2049 revised computePeptideVariants to transfer id, clinical_sig

8 years agoJAL-1705 refactored/utility methods to detect e.g. 'PhenCode_variation'
gmungoc [Thu, 14 Apr 2016 11:04:15 +0000 (12:04 +0100)]
JAL-1705 refactored/utility methods to detect e.g. 'PhenCode_variation'

8 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 14 Apr 2016 11:00:38 +0000 (12:00 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

8 years agoJAL-653 test updated for 'use ID for description'
gmungoc [Thu, 14 Apr 2016 10:17:05 +0000 (11:17 +0100)]
JAL-653 test updated for 'use ID for description'

8 years agoJAL-1270 JAL-653 use 'parse immediately' FeaturesFile constructor
gmungoc [Thu, 14 Apr 2016 10:14:48 +0000 (11:14 +0100)]
JAL-1270 JAL-653 use 'parse immediately' FeaturesFile constructor

8 years agomerge
tcofoegbu [Thu, 14 Apr 2016 10:09:51 +0000 (11:09 +0100)]
merge

8 years agoJAL-1994 Removed redistributed plugin.jar from applet build path
tcofoegbu [Thu, 14 Apr 2016 10:09:18 +0000 (11:09 +0100)]
JAL-1994 Removed redistributed plugin.jar from applet build path

8 years agoJAL-2046 fix: patched SeqsetUtils so sequence features aren’t duplicated when reinsta...
Jim Procter [Wed, 13 Apr 2016 20:31:42 +0000 (21:31 +0100)]
JAL-2046 fix: patched SeqsetUtils so sequence features aren’t duplicated when reinstating sequence details

8 years agoJAL-2046 test to demonstrate feature duplication bug
Jim Procter [Wed, 13 Apr 2016 20:27:10 +0000 (21:27 +0100)]
JAL-2046 test to demonstrate feature duplication bug

8 years agoMerge branch 'bug/JAL-2046_ds_sharing_features_broken' into develop
Jim Procter [Wed, 13 Apr 2016 15:46:52 +0000 (16:46 +0100)]
Merge branch 'bug/JAL-2046_ds_sharing_features_broken' into develop

8 years agoJAL-1270 more fix for failing Functional test
tcofoegbu [Wed, 13 Apr 2016 14:39:19 +0000 (15:39 +0100)]
JAL-1270 more fix for failing Functional test

8 years agomerge
tcofoegbu [Wed, 13 Apr 2016 09:46:55 +0000 (10:46 +0100)]
merge

8 years agoJAL-1270 Fixed failing tests due to race conditions in PDBSearchPanelTest and PDBSequ...
tcofoegbu [Wed, 13 Apr 2016 09:44:22 +0000 (10:44 +0100)]
JAL-1270 Fixed failing tests due to race conditions in PDBSearchPanelTest and PDBSequenceFetcherTest classes

8 years agoJAL-2047 delay to allow table model initilisation to complete
tcofoegbu [Wed, 13 Apr 2016 09:41:13 +0000 (10:41 +0100)]
JAL-2047 delay to allow table model initilisation to complete

8 years agoJAL-2050 only hide introns if exons are present! Removed 'hide introns'
gmungoc [Tue, 12 Apr 2016 13:01:42 +0000 (14:01 +0100)]
JAL-2050 only hide introns if exons are present! Removed 'hide introns'
checkbox from Preferences gui

8 years agoJAL-2049 separate protein variant per dna variant (combinations tbd)
gmungoc [Tue, 12 Apr 2016 09:36:51 +0000 (10:36 +0100)]
JAL-2049 separate protein variant per dna variant (combinations tbd)

8 years agoJAL-1705 code/comment tidy only
gmungoc [Mon, 11 Apr 2016 15:42:20 +0000 (16:42 +0100)]
JAL-1705 code/comment tidy only

8 years agoJAL-2051 fetch Ensembl Gene accessions one at a time
gmungoc [Mon, 11 Apr 2016 15:37:04 +0000 (16:37 +0100)]
JAL-2051 fetch Ensembl Gene accessions one at a time

8 years agomerge
tcofoegbu [Mon, 11 Apr 2016 15:29:00 +0000 (16:29 +0100)]
merge

8 years agoJAL-2054 Renamed getStartEnd in AlignFrame to getVisibleStartAndEndIndex, and refacto...
tcofoegbu [Mon, 11 Apr 2016 15:28:12 +0000 (16:28 +0100)]
JAL-2054 Renamed getStartEnd in AlignFrame to getVisibleStartAndEndIndex, and refactored method to Alignment class, and created a test for it accordingly

8 years agoJAL-391 help for reverse / complement options
gmungoc [Mon, 11 Apr 2016 14:57:56 +0000 (15:57 +0100)]
JAL-391 help for reverse / complement options

8 years agoJAL-1705 (new preference option to) hide introns when fetching genomic
gmungoc [Mon, 11 Apr 2016 14:51:46 +0000 (15:51 +0100)]
JAL-1705 (new preference option to) hide introns when fetching genomic
sequences

8 years agomerge
tcofoegbu [Mon, 11 Apr 2016 10:49:08 +0000 (11:49 +0100)]
merge

8 years agoRestored auto-deleted file from commit: ad54c1ae5bc1b931a6a0cd0b914c19cbc27fe12d
tcofoegbu [Mon, 11 Apr 2016 10:48:40 +0000 (11:48 +0100)]
Restored auto-deleted file from commit: ad54c1ae5bc1b931a6a0cd0b914c19cbc27fe12d

8 years agoMerge branch 'feature/JAL-2050_intronhidden' into develop
Jim Procter [Fri, 8 Apr 2016 15:37:22 +0000 (16:37 +0100)]
Merge branch 'feature/JAL-2050_intronhidden' into develop

8 years agoJAL-2050 JAL-1722 new getSelectedRange() method to quickly hide selected columns
Jim Procter [Fri, 8 Apr 2016 15:18:15 +0000 (16:18 +0100)]
JAL-2050 JAL-1722 new getSelectedRange() method to quickly hide selected columns

8 years agoJAL-2053 fix erratic hidden column marker display
Jim Procter [Fri, 8 Apr 2016 14:43:58 +0000 (15:43 +0100)]
JAL-2053 fix erratic hidden column marker display

8 years agoJAL-2053 JAL-1551 javadoc and simpler code
Jim Procter [Fri, 8 Apr 2016 14:43:31 +0000 (15:43 +0100)]
JAL-2053 JAL-1551 javadoc and simpler code

8 years agoJAL-1722 fix: don’t draw visible regions outside viewport view
Jim Procter [Thu, 7 Apr 2016 16:58:45 +0000 (17:58 +0100)]
JAL-1722 fix: don’t draw visible regions outside viewport view

8 years agomerge
tcofoegbu [Wed, 6 Apr 2016 14:04:26 +0000 (15:04 +0100)]
merge

8 years agoJAL-2047 JAL-1919 fixed empty tooltip text when a cell in PDB Search and Structure...
tcofoegbu [Wed, 6 Apr 2016 14:02:54 +0000 (15:02 +0100)]
JAL-2047 JAL-1919 fixed empty tooltip text when a cell in PDB Search and Structure Chooser interface has empty text and trapped other minor exceptions

8 years agoJAL-1960 updated test to capture new behaviour improvement
tcofoegbu [Wed, 6 Apr 2016 13:56:37 +0000 (14:56 +0100)]
JAL-1960 updated test to capture new behaviour improvement

8 years agoJAL-2046 RFC about cyclic dataset sequence references - should be disallowed ?
Jim Procter [Tue, 5 Apr 2016 17:36:33 +0000 (18:36 +0100)]
JAL-2046 RFC about cyclic dataset sequence references - should be disallowed ?

8 years agoJAL-2046 revise test for ambiguous case
Jim Procter [Tue, 5 Apr 2016 17:35:56 +0000 (18:35 +0100)]
JAL-2046 revise test for ambiguous case

8 years agoJAL-2046 ambiguous test for addSequenceFeature when dataset ref is present or absent
Jim Procter [Tue, 5 Apr 2016 17:35:25 +0000 (18:35 +0100)]
JAL-2046 ambiguous test for addSequenceFeature when dataset ref is present or absent

8 years agoJAL-2046 RFC on addSequenceFeature behaviour after deriveSequence
Jim Procter [Tue, 5 Apr 2016 17:34:26 +0000 (18:34 +0100)]
JAL-2046 RFC on addSequenceFeature behaviour after deriveSequence

8 years agoJAL-2046 test behaviour of copy constructor in different contexts
Jim Procter [Tue, 5 Apr 2016 17:33:13 +0000 (18:33 +0100)]
JAL-2046 test behaviour of copy constructor in different contexts

8 years agoJAL-2046 add/delete SequenceFeature operate on dataset if one is defined
Jim Procter [Tue, 5 Apr 2016 17:32:07 +0000 (18:32 +0100)]
JAL-2046 add/delete SequenceFeature operate on dataset if one is defined

8 years agoJAL-2046 setSequenceFeature contract implementation and warning message
Jim Procter [Tue, 5 Apr 2016 17:31:32 +0000 (18:31 +0100)]
JAL-2046 setSequenceFeature contract implementation and warning message

8 years agoJAL-2046 explicit contract for get/set SequenceFeatures on SequenceI
Jim Procter [Tue, 5 Apr 2016 17:30:57 +0000 (18:30 +0100)]
JAL-2046 explicit contract for get/set SequenceFeatures on SequenceI

8 years agoJAL-2046 remove javadoc
Jim Procter [Tue, 5 Apr 2016 17:26:23 +0000 (18:26 +0100)]
JAL-2046 remove javadoc

8 years agoJAL-2046 simpler deriveSequence - promote to dataset and initSeqFrom or defer to...
Jim Procter [Tue, 5 Apr 2016 17:25:27 +0000 (18:25 +0100)]
JAL-2046 simpler deriveSequence - promote to dataset and initSeqFrom or defer to copy constructor

8 years agoJAL-2046 clarify contract for copy constructor and initSeqFrom implementation
Jim Procter [Tue, 5 Apr 2016 17:17:03 +0000 (18:17 +0100)]
JAL-2046 clarify contract for copy constructor and initSeqFrom implementation
- with existing dataset sequence reference, no sequence features are cloned

8 years agoJAL-2046 explicitly copy char[] when cloning sequence data for copy-constructor/deriv...
Jim Procter [Tue, 5 Apr 2016 17:14:42 +0000 (18:14 +0100)]
JAL-2046 explicitly copy char[] when cloning sequence data for copy-constructor/deriveSequence


8 years agoJAL-2046 safer createDatasetSequence manipulates private fields and moves sequenceFea...
Jim Procter [Tue, 5 Apr 2016 17:12:59 +0000 (18:12 +0100)]
JAL-2046 safer createDatasetSequence manipulates private fields and moves sequenceFeatures to dataset

8 years agoJAL-2046 basic test to make sure any derived sequence has a null sequence feature...
Jim Procter [Mon, 4 Apr 2016 16:02:43 +0000 (17:02 +0100)]
JAL-2046 basic test to make sure any derived sequence has a null sequence feature array

8 years agoMerge branch 'optimisation/JAL-2001' into develop
Jim Procter [Mon, 4 Apr 2016 15:15:07 +0000 (16:15 +0100)]
Merge branch 'optimisation/JAL-2001' into develop

8 years agoJAL-2001 drop isSelected(int) in favour of original ‘contains(int)’ method
Jim Procter [Mon, 4 Apr 2016 15:13:21 +0000 (16:13 +0100)]
JAL-2001 drop isSelected(int) in favour of original ‘contains(int)’ method

8 years agoJAL-2001 catch -ve column values
Jim Procter [Mon, 4 Apr 2016 15:12:48 +0000 (16:12 +0100)]
JAL-2001 catch -ve column values
(fixes failing test jalview.util.MappingUtilsTest.testMapColumnSelection)

8 years agoJAL-2001 TODO for new ColumnSelection API
Jim Procter [Mon, 4 Apr 2016 14:49:37 +0000 (15:49 +0100)]
JAL-2001 TODO for new ColumnSelection API

8 years agoJAL-1551 formatting
Jim Procter [Mon, 4 Apr 2016 14:49:02 +0000 (15:49 +0100)]
JAL-1551 formatting

8 years agoJAL-2001 - note about possible side effect on JalviewLite.selectIn due to refactored...
Jim Procter [Mon, 4 Apr 2016 14:48:42 +0000 (15:48 +0100)]
JAL-2001 - note about possible side effect on JalviewLite.selectIn due to refactored columnSelection - maybe need a test here

8 years agoJAL-2010 refactoring todo
Jim Procter [Mon, 4 Apr 2016 14:45:09 +0000 (15:45 +0100)]
JAL-2010 refactoring todo

8 years agoJAL-2001 use fast column selection test
Jim Procter [Mon, 4 Apr 2016 14:23:52 +0000 (15:23 +0100)]
JAL-2001 use fast column selection test

8 years agoJAL-969 refactor columnselection operation (during JAL-2001)
Jim Procter [Mon, 4 Apr 2016 14:22:56 +0000 (15:22 +0100)]
JAL-969 refactor columnselection operation (during JAL-2001)

8 years agoJAL-2001 faster check for a column being selected
Jim Procter [Mon, 4 Apr 2016 14:21:04 +0000 (15:21 +0100)]
JAL-2001 faster check for a column being selected
TODO: consider deprecate Integer variant ?

8 years agoJAL-2001 javadoc
Jim Procter [Mon, 4 Apr 2016 14:19:52 +0000 (15:19 +0100)]
JAL-2001 javadoc

8 years agoJAL-2001 faster getMax/getMin selected column, with tests
Jim Procter [Mon, 4 Apr 2016 14:19:27 +0000 (15:19 +0100)]
JAL-2001 faster getMax/getMin selected column, with tests

8 years agoJAL-2001 JAL-1722 - store selection as ArrayList and BitSet for fast addition of...
Jim Procter [Mon, 4 Apr 2016 13:13:08 +0000 (14:13 +0100)]
JAL-2001 JAL-1722 - store selection as ArrayList and BitSet for fast addition of very large numbers of columns - all tests pass but needs verification

8 years agoMerge branch 'features/JAL-653_JAL-1766_htslib_refseqsupport' into develop
gmungoc [Fri, 1 Apr 2016 20:02:08 +0000 (21:02 +0100)]
Merge branch 'features/JAL-653_JAL-1766_htslib_refseqsupport' into develop

8 years agoJAL-1705 ensure the right mapping is used to align CDS to cDNA
gmungoc [Fri, 1 Apr 2016 20:00:26 +0000 (21:00 +0100)]
JAL-1705 ensure the right mapping is used to align CDS to cDNA

8 years agoJAL-2048 Update to structureviz2 package from cytoscape
tcofoegbu [Fri, 1 Apr 2016 16:03:12 +0000 (17:03 +0100)]
JAL-2048 Update to structureviz2 package from cytoscape

8 years agoMerge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport
gmungoc [Fri, 1 Apr 2016 15:52:19 +0000 (16:52 +0100)]
Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport

8 years agoJAL-2046 fix for broken test for deriveSequence
gmungoc [Fri, 1 Apr 2016 15:46:53 +0000 (16:46 +0100)]
JAL-2046 fix for broken test for deriveSequence

8 years agoJAL-1705 reworked AlignmentUtils.makeCdsAlignment and associated code
gmungoc [Fri, 1 Apr 2016 15:46:20 +0000 (16:46 +0100)]
JAL-1705 reworked AlignmentUtils.makeCdsAlignment and associated code

8 years agoJAL-653 updated test to match parsing of multi-valued GFF attribute
gmungoc [Fri, 1 Apr 2016 10:57:02 +0000 (11:57 +0100)]
JAL-653 updated test to match parsing of multi-valued GFF attribute

8 years agoJAL-1705 tweak to MapList.toString for debugging
gmungoc [Fri, 1 Apr 2016 10:51:02 +0000 (11:51 +0100)]
JAL-1705 tweak to MapList.toString for debugging

8 years agoJAL-1705 generalised getLength() to handle [start1, end1, start2,
gmungoc [Fri, 1 Apr 2016 10:44:04 +0000 (11:44 +0100)]
JAL-1705 generalised getLength() to handle [start1, end1, start2,
end2..]

8 years agoJAL-1705 test updated for canonicalised UNIPROT sequence name
gmungoc [Fri, 1 Apr 2016 10:42:08 +0000 (11:42 +0100)]
JAL-1705 test updated for canonicalised UNIPROT sequence name

8 years agoJAL-1705 include stop codon in mapped CDS range so it is included in the
gmungoc [Fri, 1 Apr 2016 10:34:58 +0000 (11:34 +0100)]
JAL-1705 include stop codon in mapped CDS range so it is included in the
generated CDS sequence

8 years agoJAL-2037 set DBRefEntry.version to "0" not "" in EMBL xrefs
gmungoc [Fri, 1 Apr 2016 10:33:33 +0000 (11:33 +0100)]
JAL-2037 set DBRefEntry.version to "0" not "" in EMBL xrefs

8 years agoJAL-1705 fetch all Ensembl xrefs (except GO terms)
gmungoc [Fri, 1 Apr 2016 10:26:16 +0000 (11:26 +0100)]
JAL-1705 fetch all Ensembl xrefs (except GO terms)

8 years agoJAL-2045 JAL-2047 improvement for sorting PDB quality measure numerically, and improv...
tcofoegbu [Fri, 1 Apr 2016 10:07:14 +0000 (11:07 +0100)]
JAL-2045 JAL-2047 improvement for sorting PDB quality measure numerically, and improvment to make PDB Search and Structure Chooser table column rendering smarter

8 years agoJAL-2035 improvement to add binding to multiple model
tcofoegbu [Thu, 31 Mar 2016 11:36:25 +0000 (12:36 +0100)]
JAL-2035 improvement to add binding to multiple model

8 years agoJAL-1668 further clean-up of popup menu and NPE check while transfering ResNum featur...
tcofoegbu [Wed, 30 Mar 2016 15:47:44 +0000 (16:47 +0100)]
JAL-1668 further clean-up of popup menu and NPE check while transfering ResNum features in PDBChain

8 years agoJAL-2038 bug fix for NPE while setting progress message during d'n'd PDB files associ...
tcofoegbu [Wed, 30 Mar 2016 10:14:06 +0000 (11:14 +0100)]
JAL-2038 bug fix for NPE while setting progress message during d'n'd PDB files association

8 years agomerge
tcofoegbu [Mon, 28 Mar 2016 14:37:00 +0000 (15:37 +0100)]
merge

8 years agoJAL-1919 Fixed broken test in DBRefUtilsTest
tcofoegbu [Mon, 28 Mar 2016 13:16:17 +0000 (14:16 +0100)]
JAL-1919 Fixed broken test in DBRefUtilsTest

8 years agoJAL-1668 removed redundant UI elements in PopupMenu class associated with the old...
tcofoegbu [Mon, 28 Mar 2016 13:13:25 +0000 (14:13 +0100)]
JAL-1668 removed redundant UI elements in PopupMenu class associated with the old structure selection mechanism

8 years agoJAL-1705 Javadoc / debug output tweaks
gmungoc [Mon, 28 Mar 2016 09:12:36 +0000 (10:12 +0100)]
JAL-1705 Javadoc / debug output tweaks

8 years agoJAL-2016 push getFeatureColourScheme(source) into SequenceFetcher
gmungoc [Mon, 28 Mar 2016 09:02:46 +0000 (10:02 +0100)]
JAL-2016 push getFeatureColourScheme(source) into SequenceFetcher

8 years agoJAL-2036 update AlignFrame menus when dbreffetcher is complete
gmungoc [Mon, 28 Mar 2016 08:47:54 +0000 (09:47 +0100)]
JAL-2036 update AlignFrame menus when dbreffetcher is complete

8 years agoJAL-2035 improvement to bind Jalview to Chimera model when opening an mmCIF file
tcofoegbu [Fri, 25 Mar 2016 16:12:42 +0000 (16:12 +0000)]
JAL-2035 improvement to bind Jalview to Chimera model when opening an mmCIF file