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
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 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
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
Jim Procter [Fri, 26 May 2017 16:37:57 +0000 (17:37 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Fri, 26 May 2017 16:37:31 +0000 (17:37 +0100)]
JAL-2418 updated JPred documentation and screenshot for JPred4
Jim Procter [Fri, 26 May 2017 16:37:07 +0000 (17:37 +0100)]
JAL-2418 JAL-2549 JABAWS 2.2 release notes
Jim Procter [Fri, 26 May 2017 15:29:20 +0000 (16:29 +0100)]
Merge branch 'features/JAL-2549_updateJABAWSto220' into develop
tcofoegbu [Fri, 26 May 2017 14:27:16 +0000 (15:27 +0100)]
JAL-2465 Improvement to re-instate storing recently opened URLs for alignments loaded from a structure format via URL
tcofoegbu [Fri, 26 May 2017 13:48:44 +0000 (14:48 +0100)]
JAL-2465 fix to prevent files loaded from the system's temporary directory from being included in recently opend files store
gmungoc [Fri, 26 May 2017 11:05:38 +0000 (12:05 +0100)]
JAL-2290 no update if no change of residue JAL-2547 no features on
tooltip over gap
gmungoc [Fri, 26 May 2017 07:33:28 +0000 (08:33 +0100)]
JAL-2480 move ContiguousI and Range to jalview.datamodel
gmungoc [Thu, 25 May 2017 16:52:12 +0000 (17:52 +0100)]
JAL-2557 removal of Sequence.sequenceFeatures
kiramt [Thu, 25 May 2017 13:31:51 +0000 (14:31 +0100)]
JAl-2034 Ported to applet
kiramt [Thu, 25 May 2017 13:06:38 +0000 (14:06 +0100)]
JAL-2034 don't update overview after click without drag on group
gmungoc [Thu, 25 May 2017 10:54:39 +0000 (11:54 +0100)]
JAL-2050 make SequenceFeature.score final, adjust constructor calls
gmungoc [Thu, 25 May 2017 09:35:08 +0000 (10:35 +0100)]
JAL-2505 simplifying number of SequenceFeature constructors JAL-2060
constant for NO_SCORE defined in SequenceFeature
gmungoc [Thu, 25 May 2017 09:16:49 +0000 (10:16 +0100)]
JAL-2505 removed SequenceFeature constructor JAL-1641 include
description, otherDetails in feature roundtrip verification
gmungoc [Thu, 25 May 2017 08:30:53 +0000 (09:30 +0100)]
JAL-2490 test coverage of empty and null feature group in Jalview format
export
kiramt [Thu, 25 May 2017 07:49:08 +0000 (08:49 +0100)]
Merge branch 'bug/JAL-2551' into bug/JAL-2034contextchange
gmungoc [Wed, 24 May 2017 15:42:50 +0000 (16:42 +0100)]
JAL-2505 make SequenceFeature type, begin, end, featureGroup final
gmungoc [Wed, 24 May 2017 15:42:06 +0000 (16:42 +0100)]
JAL-2506 relocate Uniprot binding classes, bind to UniprotFeature not
SequenceFeature
gmungoc [Wed, 24 May 2017 14:55:19 +0000 (15:55 +0100)]
JAL-2505 remove setters for SequenceFeature.begin,end,type,featureGroup
gmungoc [Wed, 24 May 2017 14:45:16 +0000 (15:45 +0100)]
JAL-2529 add object_type=cdna to EnsemblCdna parameters
gmungoc [Wed, 24 May 2017 14:21:43 +0000 (15:21 +0100)]
Merge branch 'bug/JAL-2541cutWithFeatures' into features/JAL-2446NCList
gmungoc [Wed, 24 May 2017 13:47:36 +0000 (14:47 +0100)]
JAL-2505 JAL-2542 SequenceFeatures.shift() to shift all positional
features
kiramt [Wed, 24 May 2017 12:47:58 +0000 (13:47 +0100)]
JAL-2551 Fix to group colouring when group extent is reduced
gmungoc [Wed, 24 May 2017 10:26:11 +0000 (11:26 +0100)]
JAL-2542 correct adjustment of sequence features for flanking sequence
kiramt [Wed, 24 May 2017 09:44:47 +0000 (10:44 +0100)]
JAL-2034 Added isDefined flag to SequenceGroup
gmungoc [Wed, 24 May 2017 08:17:07 +0000 (09:17 +0100)]
JAL-2505 delete and readd modified feature after Cut or Paste
Jim Procter [Tue, 23 May 2017 19:39:17 +0000 (20:39 +0100)]
JAL-2549 RNAAliFold result to annotation file roundtrip test fails test due to JAL-2550 - Upper/lower case alphabet recognised as WUSS RNA annotation
Jim Procter [Tue, 23 May 2017 19:35:59 +0000 (20:35 +0100)]
JAL-2549 skip ‘Unrecognised Service’ which resolves to a null entry in the get supported services list
Jim Procter [Tue, 23 May 2017 19:35:23 +0000 (20:35 +0100)]
JAL-2549 replace JABAWS 2.1 with 2.2 client and remove JPredWS client and tests
gmungoc [Tue, 23 May 2017 16:10:23 +0000 (17:10 +0100)]
JAL-2490 find features for export as GFF, JAL-2548 respect group
visibility
gmungoc [Tue, 23 May 2017 13:50:28 +0000 (14:50 +0100)]
JAL-2490 test coverage for printGffFormat before refactoring
gmungoc [Tue, 23 May 2017 12:52:39 +0000 (13:52 +0100)]
JAL-2490 unit tests for getFeaturesForGroup
gmungoc [Tue, 23 May 2017 11:55:08 +0000 (12:55 +0100)]
JAL-2547 don't show features in tooltip over a gap
gmungoc [Tue, 23 May 2017 11:37:10 +0000 (12:37 +0100)]
JAL-2490 tidy code and tests for feature export in Jalview format
gmungoc [Tue, 23 May 2017 09:54:57 +0000 (10:54 +0100)]
JAL-2490 improved lookup of features for Export Features (Jalview
format)
gmungoc [Tue, 23 May 2017 09:54:15 +0000 (10:54 +0100)]
JAL-2480 methods to get features for group
gmungoc [Mon, 22 May 2017 15:40:48 +0000 (16:40 +0100)]
JAL-2505 use setter not direct access to sf.description
gmungoc [Mon, 22 May 2017 15:40:14 +0000 (16:40 +0100)]
JAL-2505 updates after conflicting merge of JAL-2504
gmungoc [Mon, 22 May 2017 14:55:53 +0000 (15:55 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
Conflicts:
src/jalview/gui/FeatureRenderer.java
gmungoc [Mon, 22 May 2017 14:37:32 +0000 (15:37 +0100)]
JAL-2504 update the right feature colour when creating a new feature
gmungoc [Mon, 22 May 2017 14:16:40 +0000 (15:16 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
Conflicts:
src/jalview/analysis/AlignmentSorter.java
src/jalview/appletgui/FeatureSettings.java
src/jalview/appletgui/SeqPanel.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/FeatureSettings.java
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
test/jalview/analysis/AlignmentSorterTest.java
gmungoc [Mon, 22 May 2017 13:39:57 +0000 (14:39 +0100)]
JAL-2544 unit tests for sort by feature score
gmungoc [Mon, 22 May 2017 13:33:07 +0000 (14:33 +0100)]
JAL-2544 check feature overlaps selection region
gmungoc [Mon, 22 May 2017 13:13:23 +0000 (14:13 +0100)]
JAL-2543 identify as JSON before HTML
gmungoc [Mon, 22 May 2017 13:06:19 +0000 (14:06 +0100)]
JAL-2546 JAL-2490 efficient lookup of features, correct handling of
non-positional features
gmungoc [Mon, 22 May 2017 12:02:47 +0000 (13:02 +0100)]
JAL-2490 add non-positional feature case to test prior to refactoring
gmungoc [Mon, 22 May 2017 11:24:56 +0000 (12:24 +0100)]
JAL-2480 always include all non-positional features in getAllFeatures()
kiramt [Mon, 22 May 2017 10:57:47 +0000 (11:57 +0100)]
Merge remote-tracking branch 'origin/bug/JAL-2256' into develop
Jim Procter [Mon, 22 May 2017 10:34:46 +0000 (11:34 +0100)]
JAL-2418 patch build - broken htsjdk import
gmungoc [Fri, 19 May 2017 15:59:48 +0000 (16:59 +0100)]
JAL-2526 removed redundant call to Sequence.findPosition()
gmungoc [Fri, 19 May 2017 15:46:41 +0000 (16:46 +0100)]
JAL-2490 refactored test for 'hasFeatures'
gmungoc [Fri, 19 May 2017 10:48:11 +0000 (11:48 +0100)]
JAL-2544 only include features in selected columns for sort
gmungoc [Fri, 19 May 2017 10:47:16 +0000 (11:47 +0100)]
JAL-2490 performant lookup of features for sorting
gmungoc [Fri, 19 May 2017 07:38:35 +0000 (08:38 +0100)]
JAL-2490 only count sequences where feature overlap is confirmed
gmungoc [Fri, 19 May 2017 07:21:54 +0000 (08:21 +0100)]
JAL-2505 unit test for sort by feature density, Javadoc
gmungoc [Thu, 18 May 2017 16:01:44 +0000 (17:01 +0100)]
JAL-2490 initial unit tests prior to refactoring
Jim Procter [Thu, 18 May 2017 15:33:00 +0000 (16:33 +0100)]
Merge branch 'bug/JAL-2388_typeCheckAlignView.getUpdatedView' into develop
Jim Procter [Thu, 18 May 2017 15:31:27 +0000 (16:31 +0100)]
JAL-2388 return empty hidden columns for fully visible alignment view
gmungoc [Thu, 18 May 2017 14:56:25 +0000 (15:56 +0100)]
JAL-2490 lookup sequence features for "labelClass"
gmungoc [Thu, 18 May 2017 14:51:10 +0000 (15:51 +0100)]
JAL-2490 lookup features at each column position
gmungoc [Thu, 18 May 2017 14:28:54 +0000 (15:28 +0100)]
JAL-2543 html-encode quote characters in feature description
gmungoc [Thu, 18 May 2017 13:57:37 +0000 (14:57 +0100)]
JAL-2490 retrieve visible features only
gmungoc [Thu, 18 May 2017 13:28:18 +0000 (14:28 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
gmungoc [Thu, 18 May 2017 13:15:32 +0000 (14:15 +0100)]
JAL-2541 initial unit tests for edit cut relocate features
gmungoc [Thu, 18 May 2017 13:15:04 +0000 (14:15 +0100)]
JAL-2541 fix to initSeqFrom (and minor code tidy); more tests for
deleteChars
kiramt [Thu, 18 May 2017 13:09:21 +0000 (14:09 +0100)]
JAL-2256 Corrected AllCols/Rows iterator behaviour for single element
Jim Procter [Thu, 18 May 2017 11:18:14 +0000 (12:18 +0100)]
JAL-2418 remove explicit test suite stats
Jim Procter [Wed, 17 May 2017 15:26:52 +0000 (16:26 +0100)]
Merge branch 'develop' into documentation/JAL-2418_release2102
git://source.jalview.org / jalview.git / log