gmungoc [Mon, 5 Jun 2017 13:00:48 +0000 (14:00 +0100)]
JAL-2505 comments updated
gmungoc [Mon, 5 Jun 2017 13:00:08 +0000 (14:00 +0100)]
JAL-2480 remove redundant method, further test coverage
gmungoc [Mon, 5 Jun 2017 08:41:02 +0000 (09:41 +0100)]
JAL-2505 explicit (and final) contactFeature property
gmungoc [Mon, 5 Jun 2017 08:03:10 +0000 (09:03 +0100)]
Merge branch 'features/JAL-2526sequenceCursor' into
features/JAL-2446NCList
Conflicts:
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceI.java
gmungoc [Mon, 5 Jun 2017 07:57:27 +0000 (08:57 +0100)]
Merge branch 'features/JAL-2446NCList' into
features/JAL-2574findFeaturesByColumn
Conflicts:
src/jalview/datamodel/SequenceI.java
gmungoc [Mon, 5 Jun 2017 07:54:11 +0000 (08:54 +0100)]
Merge branch 'features/JAL-2446NCList' into
features/JAL-2526sequenceCursor
Conflicts:
src/jalview/datamodel/SequenceI.java
gmungoc [Mon, 5 Jun 2017 07:52:40 +0000 (08:52 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
Conflicts:
src/jalview/datamodel/SequenceI.java
kiramt [Mon, 5 Jun 2017 06:51:49 +0000 (07:51 +0100)]
JAL-2571 Missed (alwaysRun=true) for @BeforeMethod
Jim Procter [Sun, 4 Jun 2017 15:12:13 +0000 (16:12 +0100)]
JAL-2228 java 1.7 compliance
Jim Procter [Sun, 4 Jun 2017 12:27:45 +0000 (13:27 +0100)]
JAL-2291 updated docs
Jim Procter [Sun, 4 Jun 2017 12:18:38 +0000 (13:18 +0100)]
JAL-2291 only hide/show columns intersecting with currently selected region.
Jim Procter [Sun, 4 Jun 2017 12:18:27 +0000 (13:18 +0100)]
JAL-2291 get bitset representing hidden columns
Jim Procter [Sun, 4 Jun 2017 11:17:31 +0000 (12:17 +0100)]
JAL-2291 use HiddenColumns.hideMarkedBits and take union of selection and sequence under popup
Jim Procter [Sun, 4 Jun 2017 11:05:49 +0000 (12:05 +0100)]
JAL-2291 method taking a BitSet for hiding columns
Jim Procter [Sun, 4 Jun 2017 11:04:31 +0000 (12:04 +0100)]
JAL-2291 bug fix - BitSet.set is [start,end+1)
Jim Procter [Sun, 4 Jun 2017 11:02:16 +0000 (12:02 +0100)]
JAL-2291 fixed broken asserts for SequenceI.getInsertionsAsBits
Jim Procter [Sun, 4 Jun 2017 09:43:01 +0000 (10:43 +0100)]
JAL-2291 ‘Hide Insertions’ now operates on selection or if none available, the sequence that was right-clicked on.
Jim Procter [Sun, 4 Jun 2017 09:41:56 +0000 (10:41 +0100)]
JAL-2291 SequenceI.getInsertionsAsBits for convenient logical operations
Jim Procter [Sun, 4 Jun 2017 09:03:39 +0000 (10:03 +0100)]
JAL-2582 comment about IDs being lost if they resembl ensembl IDs but can’t be resolved to a genomic ID.
Jim Procter [Sun, 4 Jun 2017 09:01:54 +0000 (10:01 +0100)]
JAL-2582 recognise ENS…P peptide IDs and make two getParent requests to get gene ID.
Jim Procter [Fri, 2 Jun 2017 16:11:15 +0000 (17:11 +0100)]
Merge branch 'bug/JAL-2578' into develop
Jim Procter [Fri, 2 Jun 2017 16:04:38 +0000 (17:04 +0100)]
Merge branch 'bug/JAL-2577' into develop
Jim Procter [Fri, 2 Jun 2017 15:58:12 +0000 (16:58 +0100)]
Merge branch 'features/JAL-2228_featureSetCounts_minRangeTweak' into develop
gmungoc [Fri, 2 Jun 2017 15:37:06 +0000 (16:37 +0100)]
Merge branch 'features/JAL-2446NCList' into features/JAL-2526sequenceCursor
gmungoc [Fri, 2 Jun 2017 15:36:22 +0000 (16:36 +0100)]
Merge branch 'features/JAL-2446NCList' into features/JAL-2574findFeaturesByColumn
gmungoc [Fri, 2 Jun 2017 15:35:33 +0000 (16:35 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
gmungoc [Fri, 2 Jun 2017 15:33:44 +0000 (16:33 +0100)]
JAL-2526 additional tests for findPosition with/without cursor/edit
tcofoegbu [Fri, 2 Jun 2017 14:29:25 +0000 (15:29 +0100)]
JAL-2473 revised default minimum dimension for Alignment Frame windows
Jim Procter [Fri, 2 Jun 2017 13:12:21 +0000 (14:12 +0100)]
JAL-2228 always create zero score annotations, since select/hide annotation filter ignores null positions in rows
Jim Procter [Fri, 2 Jun 2017 13:11:30 +0000 (14:11 +0100)]
JAL-2228 always set minimum for count to zero for annotation row
kiramt [Fri, 2 Jun 2017 13:00:13 +0000 (14:00 +0100)]
JAL-2577 Don't allow viewport ranges below 0. Unit tests updated.
kiramt [Fri, 2 Jun 2017 08:59:22 +0000 (09:59 +0100)]
JAL-2578 Moved hidden columns reveal to before selection adjustment
gmungoc [Fri, 2 Jun 2017 08:15:29 +0000 (09:15 +0100)]
Merge branch 'features/JAL-2446NCList' into features/JAL-2574findFeaturesByColumn
gmungoc [Thu, 1 Jun 2017 15:43:22 +0000 (16:43 +0100)]
JAL-2526 additional calls to sequenceChanged() after edits
gmungoc [Thu, 1 Jun 2017 15:11:45 +0000 (16:11 +0100)]
JAL-2526 zapCursor() renamed sequenceChanged()
gmungoc [Thu, 1 Jun 2017 15:06:39 +0000 (16:06 +0100)]
Merge branch 'features/JAL-2446NCList' into features/JAL-2526sequenceCursor
gmungoc [Thu, 1 Jun 2017 14:36:41 +0000 (15:36 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
Conflicts:
test/jalview/ext/jmol/JmolParserTest.java
gmungoc [Thu, 1 Jun 2017 13:35:10 +0000 (14:35 +0100)]
JAL-2754 Sequence.findFeatures(fromCol, toCol)
Jim Procter [Thu, 1 Jun 2017 13:17:05 +0000 (14:17 +0100)]
Merge branch 'features/JAL-1648_cache_user_inputs' into develop
gmungoc [Thu, 1 Jun 2017 12:33:26 +0000 (13:33 +0100)]
JAL-2563 JAL-2547 amended unit tests for amended setStatusMessage
Jim Procter [Wed, 31 May 2017 21:02:55 +0000 (22:02 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 31 May 2017 21:02:41 +0000 (22:02 +0100)]
JAL-2418 release notes for JAL-2547, JAL-2563, JAL-1256
Jim Procter [Wed, 31 May 2017 20:23:52 +0000 (21:23 +0100)]
Merge branch 'JAL-2571' into develop
Jim Procter [Wed, 31 May 2017 20:21:59 +0000 (21:21 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 31 May 2017 20:10:33 +0000 (21:10 +0100)]
JAL-2398 - updated groovy script for direct field modification
Jim Procter [Wed, 31 May 2017 20:07:04 +0000 (21:07 +0100)]
JAL-2418 JAL-2563 release notes
Jim Procter [Wed, 31 May 2017 20:06:31 +0000 (21:06 +0100)]
JAL-2418 typo
Jim Procter [Wed, 31 May 2017 20:05:39 +0000 (21:05 +0100)]
Merge branch 'develop' into documentation/JAL-2418_release2102
gmungoc [Wed, 31 May 2017 15:15:52 +0000 (16:15 +0100)]
Merge branch 'features/JAL-2446NCList' into features/JAL-2526sequenceCursor
gmungoc [Wed, 31 May 2017 15:12:17 +0000 (16:12 +0100)]
JAL-2483 JAL-2575 don't sort newly discovered features
tcofoegbu [Wed, 31 May 2017 10:46:22 +0000 (11:46 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 31 May 2017 10:46:08 +0000 (11:46 +0100)]
JAL-2375 fix unit test to reflect improvement
tcofoegbu [Wed, 31 May 2017 10:08:24 +0000 (11:08 +0100)]
Fixed failing tests
gmungoc [Wed, 31 May 2017 10:00:53 +0000 (11:00 +0100)]
Merge branch 'features/JAL-2446NCList' into features/JAL-2526sequenceCursor
gmungoc [Wed, 31 May 2017 09:59:58 +0000 (10:59 +0100)]
JAL-2574 preparation for Sequence.findFeatures(col1, col2)
tcofoegbu [Wed, 31 May 2017 09:59:45 +0000 (10:59 +0100)]
JAL-2533 updated unit test to reflect improvement
gmungoc [Wed, 31 May 2017 08:04:56 +0000 (09:04 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
gmungoc [Wed, 31 May 2017 08:00:46 +0000 (09:00 +0100)]
JAL-2547 handle contact features 'around' a gap correctly
kiramt [Tue, 30 May 2017 18:28:42 +0000 (19:28 +0100)]
JAL-2573 Fixes for alignment < viewport width, and similarly height
gmungoc [Tue, 30 May 2017 15:34:46 +0000 (16:34 +0100)]
Merge branch 'features/JAL-2446NCList' into features/JAL-2526sequenceCursor
gmungoc [Tue, 30 May 2017 15:32:36 +0000 (16:32 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
Conflicts:
src/jalview/appletgui/APopupMenu.java
src/jalview/appletgui/FeatureRenderer.java
src/jalview/appletgui/Finder.java
src/jalview/appletgui/SeqPanel.java
src/jalview/gui/SeqPanel.java
gmungoc [Tue, 30 May 2017 15:01:44 +0000 (16:01 +0100)]
JAL-2547 tooltip/AmendFeatures on gap straddled by feature, not for
adjacent feature
kiramt [Tue, 30 May 2017 09:36:34 +0000 (10:36 +0100)]
JAL-2571 Corrected alignment width/height checks to visible only
gmungoc [Tue, 30 May 2017 09:34:09 +0000 (10:34 +0100)]
Merge branch 'features/JAL-2446NCList' into features/JAL-2526sequenceCursor
gmungoc [Tue, 30 May 2017 09:33:32 +0000 (10:33 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
Conflicts:
src/jalview/appletgui/SeqPanel.java
gmungoc [Tue, 30 May 2017 09:26:46 +0000 (10:26 +0100)]
JAL-2570 don't zap group colour scheme when mapping over split frame
gmungoc [Tue, 30 May 2017 07:54:59 +0000 (08:54 +0100)]
JAL-2526 first draft of findIndex/findPosition with SequenceCursor
Jim Procter [Mon, 29 May 2017 16:38:34 +0000 (17:38 +0100)]
Merge branch 'bug/JAL-2034contextchange' into develop
Jim Procter [Mon, 29 May 2017 16:35:35 +0000 (17:35 +0100)]
JAL-2388 release notes
tcofoegbu [Mon, 29 May 2017 14:12:17 +0000 (15:12 +0100)]
JAL-1648 improvement on finder searchbox keyboard control - Enter to update search box if popup is displayed otherwise perform find next action
Jim Procter [Mon, 29 May 2017 14:00:18 +0000 (15:00 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Mon, 29 May 2017 13:58:33 +0000 (14:58 +0100)]
JAL-2520 properly documented as a fixed bug in release notes
Jim Procter [Mon, 29 May 2017 13:26:21 +0000 (14:26 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Mon, 29 May 2017 13:25:40 +0000 (14:25 +0100)]
JAL-2465,JAL-2520,JAL-2533 release notes
Jim Procter [Mon, 29 May 2017 13:19:41 +0000 (14:19 +0100)]
Merge branch 'features/JAL-2465_No-mapping_Jmol-structures-loaded-via-url' into develop
Jim Procter [Mon, 29 May 2017 13:07:47 +0000 (14:07 +0100)]
JAL-2533 update javadoc
Jim Procter [Mon, 29 May 2017 12:51:59 +0000 (13:51 +0100)]
JAL-2465 fixed groups for JmolViewerTest.testStructureLoadingViaURL
gmungoc [Mon, 29 May 2017 12:45:57 +0000 (13:45 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
tcofoegbu [Mon, 29 May 2017 12:05:05 +0000 (13:05 +0100)]
JAL-1648 code fix - enter key should pick selected item on finder searchbox
Jim Procter [Mon, 29 May 2017 11:18:53 +0000 (12:18 +0100)]
Merge branch 'bug/JAL-2536' into develop
Jim Procter [Mon, 29 May 2017 11:18:09 +0000 (12:18 +0100)]
JAL-2536 tweak javadoc wording
Jim Procter [Mon, 29 May 2017 11:10:54 +0000 (12:10 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Mon, 29 May 2017 11:10:33 +0000 (12:10 +0100)]
JAL-2517 release notes
gmungoc [Mon, 29 May 2017 11:08:24 +0000 (12:08 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
Conflicts:
src/jalview/appletgui/SeqPanel.java
gmungoc [Mon, 29 May 2017 10:54:47 +0000 (11:54 +0100)]
JAL-2526 Sequence.findPositions to get residue positions for column
range
Jim Procter [Mon, 29 May 2017 10:52:46 +0000 (11:52 +0100)]
Merge branch 'bug/JAL-2517cancelAppletColour' into develop
Jim Procter [Mon, 29 May 2017 10:50:01 +0000 (11:50 +0100)]
release notes
JAL-2550 known defect
JAL-2535 stockholm->PP annotation
Jim Procter [Mon, 29 May 2017 10:01:19 +0000 (11:01 +0100)]
JAL-2418 updated JABAWS server in what’s new
Jim Procter [Mon, 29 May 2017 10:00:56 +0000 (11:00 +0100)]
JAL-2491 JAL-2526 JAL-2566 JAL-2563 JAL-2547 release notes
Jim Procter [Sat, 27 May 2017 13:16:18 +0000 (14:16 +0100)]
Merge branch 'bug/JAL-2491' into develop
Jim Procter [Sat, 27 May 2017 13:02:54 +0000 (14:02 +0100)]
Merge branch 'bug/JAL-2547tooltipOnGap' into develop
Jim Procter [Sat, 27 May 2017 13:01:59 +0000 (14:01 +0100)]
Merge branch 'task/JAL-2562_SequenceI.findPosition' into develop
Jim Procter [Sat, 27 May 2017 13:01:41 +0000 (14:01 +0100)]
JAL-2563 failing test to verify SetStatus returns position and message includes the position for ambiguous peptide ‘B’.
Jim Procter [Sat, 27 May 2017 13:00:49 +0000 (14:00 +0100)]
JAL-2563 test to verify SetStatus returns -1 so mouseOver events are raised via StructureSelectionManager (JAL-2491, expected fixed by JAL-2547)
Jim Procter [Sat, 27 May 2017 11:58:30 +0000 (12:58 +0100)]
Merge branch 'task/JAL-2562_SequenceI.findPosition' into develop
Jim Procter [Sat, 27 May 2017 11:57:37 +0000 (12:57 +0100)]
JAL-2547 JAL-2562 rejig SetStatusMessage return value test for legibility and maximum assert coverage before JAL-2526 causes failure
Jim Procter [Sat, 27 May 2017 11:41:43 +0000 (12:41 +0100)]
Merge branch 'task/JAL-2562_SequenceI.findPosition' into develop
Jim Procter [Sat, 27 May 2017 11:32:09 +0000 (12:32 +0100)]
JAL-2526 test and documentation for SeqPanel.setStatus behaviour needed to fix bug noted on JAL-2491 where mouseover at gap highlights position for sequence to right of gap in complementary view.
Jim Procter [Sat, 27 May 2017 10:25:02 +0000 (11:25 +0100)]
JAL-2562 javadoc TODO
kiramt [Fri, 26 May 2017 21:11:00 +0000 (22:11 +0100)]
JAL-2491 Missed port to applet from JAL-1691
git://source.jalview.org / jalview.git / log