gmungoc [Thu, 3 Aug 2017 12:13:24 +0000 (14:13 +0200)]
Merge branch 'develop' into features/JAL-2446NCList
gmungoc [Thu, 3 Aug 2017 12:13:00 +0000 (14:13 +0200)]
JAL-2500 JAL-2365 feature colour "gray" _not_ "lightgray" for backwards
compatibility!!
gmungoc [Thu, 3 Aug 2017 11:47:18 +0000 (13:47 +0200)]
JAL-2500 JAL-2365 lightGray changed to lightgray for backwards
compatibility!
gmungoc [Thu, 3 Aug 2017 11:45:25 +0000 (13:45 +0200)]
JAL-2500 JAL-2365 lightGray changed to gray in example file for
backwards compatibility
gmungoc [Thu, 3 Aug 2017 11:18:03 +0000 (13:18 +0200)]
JAL-2435 test for 'mirror font' option visible (not enabled) (safer)
Jim Procter [Wed, 2 Aug 2017 16:02:06 +0000 (17:02 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 2 Aug 2017 16:01:50 +0000 (17:01 +0100)]
Merge branch 'develop' into documentation/JAL-2418_release2102
Jim Procter [Wed, 2 Aug 2017 16:01:02 +0000 (17:01 +0100)]
Merge branch 'bug/JAL-2321_merged' into develop
Jim Procter [Wed, 2 Aug 2017 14:31:01 +0000 (15:31 +0100)]
Merge branch 'bug/JAL-2321' into bug/JAL-2321_merged
Jim Procter [Wed, 2 Aug 2017 14:28:12 +0000 (15:28 +0100)]
JAL-2418 release notes for JAL-2582
gmungoc [Wed, 2 Aug 2017 14:23:29 +0000 (16:23 +0200)]
Merge branch 'develop' into features/JAL-2446NCList
gmungoc [Wed, 2 Aug 2017 14:02:14 +0000 (16:02 +0200)]
JAL-2418 corrected link url for "overview" target
Jim Procter [Tue, 1 Aug 2017 16:12:05 +0000 (17:12 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Tue, 1 Aug 2017 16:11:32 +0000 (17:11 +0100)]
JAL-2418 known defect for eggnog tree import (JAL-2590)
Jim Procter [Tue, 1 Aug 2017 15:42:52 +0000 (16:42 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Tue, 1 Aug 2017 15:42:43 +0000 (16:42 +0100)]
Merge branch 'develop' into documentation/JAL-2418_release2102
Jim Procter [Tue, 1 Aug 2017 15:42:28 +0000 (16:42 +0100)]
Merge branch 'bug/JAL-2632' into develop
Jim Procter [Tue, 1 Aug 2017 15:39:23 +0000 (16:39 +0100)]
JAL-2418 documentation
Jim Procter [Tue, 1 Aug 2017 15:16:05 +0000 (16:16 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Tue, 1 Aug 2017 15:15:46 +0000 (16:15 +0100)]
JAL-2631 JAL-2623 JAL-2624 JAL-2630 JAL-147 JAL-2034 release notes and signoff
Jim Procter [Tue, 1 Aug 2017 15:14:53 +0000 (16:14 +0100)]
JAL-2418 update 2.10.2 release date
gmungoc [Tue, 1 Aug 2017 10:09:37 +0000 (12:09 +0200)]
Merge branch 'develop' into features/JAL-2446NCList
gmungoc [Tue, 1 Aug 2017 10:08:34 +0000 (12:08 +0200)]
JAL-2611 reinstate missed merge - again!
gmungoc [Tue, 1 Aug 2017 09:57:49 +0000 (11:57 +0200)]
Merge branch 'develop' into features/JAL-2446NCList
gmungoc [Tue, 1 Aug 2017 09:55:35 +0000 (11:55 +0200)]
Merge branch 'feature/JAL-2611' into develop
gmungoc [Tue, 1 Aug 2017 09:39:24 +0000 (11:39 +0200)]
Merge branch 'bug/JAL-2630gradColourUpdateOverview' into develop
gmungoc [Mon, 31 Jul 2017 09:28:09 +0000 (11:28 +0200)]
JAL-2623 updated Overview/structure on input of threshold value
gmungoc [Mon, 31 Jul 2017 09:20:15 +0000 (11:20 +0200)]
JAL-2622 don't vertical scroll wrapped alignment id panel from trackpad
gmungoc [Mon, 31 Jul 2017 08:36:34 +0000 (10:36 +0200)]
JAL-2631 test updated for added kd graduated feature colour
gmungoc [Mon, 31 Jul 2017 08:32:11 +0000 (10:32 +0200)]
JAL-2623 JAL-2015 set Below Threshold on FeatureColour when selected!
gmungoc [Mon, 31 Jul 2017 08:10:24 +0000 (10:10 +0200)]
JAL-2630 applet update overview on release of threshold slider
kiramt [Fri, 28 Jul 2017 15:35:32 +0000 (17:35 +0200)]
JAL-2632 Added paintAlignment(true) to show cols code
gmungoc [Fri, 28 Jul 2017 13:18:58 +0000 (15:18 +0200)]
Merge branch 'develop' into features/JAL-2446NCList
gmungoc [Fri, 28 Jul 2017 13:17:08 +0000 (15:17 +0200)]
JAL-147 corrected status bar message for wrapped scrolled right view
gmungoc [Fri, 28 Jul 2017 11:48:28 +0000 (13:48 +0200)]
Merge branch 'develop' into features/JAL-2446NCList
gmungoc [Fri, 28 Jul 2017 11:12:50 +0000 (13:12 +0200)]
JAL-2622 no vertical scroll of wrapped alignment from trackpad / mouse
button
gmungoc [Fri, 28 Jul 2017 10:20:37 +0000 (12:20 +0200)]
Merge branch 'develop' into features/JAL-2446NCList
gmungoc [Fri, 28 Jul 2017 10:06:39 +0000 (12:06 +0200)]
JAL-147 unit test for no vertical move of Overview box in wrapped mode
gmungoc [Fri, 28 Jul 2017 08:45:57 +0000 (10:45 +0200)]
JAL-2006 squash rounding errors at min/max threshold slider positions
gmungoc [Fri, 28 Jul 2017 08:12:44 +0000 (10:12 +0200)]
JAL-2631 make minimum colour not white
gmungoc [Fri, 28 Jul 2017 08:04:10 +0000 (10:04 +0200)]
JAL-2630 update Overview/structure from graduated colour options dialog
gmungoc [Fri, 28 Jul 2017 08:02:38 +0000 (10:02 +0200)]
JAL-2631 add graduated colour kdH features to example
gmungoc [Mon, 24 Jul 2017 16:24:05 +0000 (18:24 +0200)]
JAL-1858 updated unit test asserts
gmungoc [Mon, 24 Jul 2017 08:24:48 +0000 (09:24 +0100)]
JAL-2624 additional tests for FeatureColour.getColour(),
filterFeaturesForDisplay
gmungoc [Mon, 24 Jul 2017 05:48:34 +0000 (06:48 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
Jim Procter [Mon, 24 Jul 2017 05:24:15 +0000 (07:24 +0200)]
Merge branch 'documentation/JAL-2418_release2102' into develop
gmungoc [Sun, 23 Jul 2017 08:37:51 +0000 (09:37 +0100)]
JAL-2481 JAL-2624 test for render feature below score feature outwith
threshold
gmungoc [Sun, 23 Jul 2017 07:59:37 +0000 (08:59 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
Conflicts:
src/jalview/renderer/seqfeatures/FeatureRenderer.java
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
gmungoc [Sat, 22 Jul 2017 15:38:54 +0000 (16:38 +0100)]
JAL-2624 check feature colour threshold when colouring structure
gmungoc [Sat, 22 Jul 2017 13:48:22 +0000 (14:48 +0100)]
JAL-2623 initialise colour threshold slider correctly
kiramt [Sat, 22 Jul 2017 09:18:41 +0000 (11:18 +0200)]
Merge branch 'develop' into feature/JAL-2611
Conflicts:
src/jalview/gui/OverviewPanel.java
src/jalview/viewmodel/OverviewDimensionsHideHidden.java
src/jalview/viewmodel/OverviewDimensionsShowHidden.java
gmungoc [Wed, 19 Jul 2017 15:39:11 +0000 (16:39 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
Conflicts:
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/SeqCanvas.java
src/jalview/gui/SeqPanel.java
Jim Procter [Tue, 18 Jul 2017 15:24:26 +0000 (16:24 +0100)]
JAL-2432 updated documentation for select/hide by annotation to include As Percentage checkbox
kiramt [Tue, 18 Jul 2017 14:44:30 +0000 (15:44 +0100)]
JAL-2611 unit tests
kiramt [Tue, 18 Jul 2017 13:45:38 +0000 (14:45 +0100)]
JAL-2611 Tidies, initial unit tests
gmungoc [Tue, 18 Jul 2017 13:44:27 +0000 (14:44 +0100)]
JAL-147 don't scroll up beyond startRes = 0
gmungoc [Tue, 18 Jul 2017 12:02:15 +0000 (13:02 +0100)]
JAL-147 corrected calculation of vertical scroll position and max
gmungoc [Tue, 18 Jul 2017 12:01:46 +0000 (13:01 +0100)]
JAL-147 draw up to last position of wrapped alignment!
kiramt [Tue, 18 Jul 2017 11:12:23 +0000 (12:12 +0100)]
JAL-2611 Better
gmungoc [Mon, 17 Jul 2017 15:20:37 +0000 (16:20 +0100)]
Merge branch 'develop' into bug/JAL-147scrollWrappedView
kiramt [Mon, 17 Jul 2017 15:02:03 +0000 (16:02 +0100)]
JAL-2611 Still not happy with behaviour
gmungoc [Mon, 17 Jul 2017 11:25:04 +0000 (12:25 +0100)]
JAL-1648 JAL-2447 Spanish translations
kiramt [Fri, 14 Jul 2017 13:31:51 +0000 (14:31 +0100)]
JAL-2611 First pass, not thrilled with hidden column behaviour
kiramt [Fri, 14 Jul 2017 09:01:25 +0000 (10:01 +0100)]
Merge branch 'feature/JAL-2613' into feature/JAL-2611
Conflicts:
src/jalview/viewmodel/OverviewDimensions.java
kiramt [Fri, 14 Jul 2017 08:59:38 +0000 (09:59 +0100)]
JAL-2611 Pre-merge checkin
kiramt [Fri, 14 Jul 2017 06:59:45 +0000 (07:59 +0100)]
JAL-2611 More unit tests
kiramt [Fri, 14 Jul 2017 06:41:09 +0000 (07:41 +0100)]
JAL-2613 Missed unit test
kiramt [Thu, 13 Jul 2017 15:54:22 +0000 (16:54 +0100)]
JAL-2611 Added overview dimensions test for position in box
kiramt [Thu, 13 Jul 2017 14:52:20 +0000 (15:52 +0100)]
JAL-2613 Unit tests and a fix. Phew.
kiramt [Wed, 12 Jul 2017 13:58:03 +0000 (14:58 +0100)]
JAL-2613 Centre alignment at click point
gmungoc [Thu, 6 Jul 2017 16:39:37 +0000 (17:39 +0100)]
JAL-1858 fast paint wrapped highlights unless view was scrolled
gmungoc [Thu, 6 Jul 2017 16:38:18 +0000 (17:38 +0100)]
JAL-1858 scrollToWrappedVisible preserve any horizontal offset of view
gmungoc [Thu, 6 Jul 2017 14:59:43 +0000 (15:59 +0100)]
JAL-147 prevent vertical Overview box movement in wrapped mode
gmungoc [Thu, 6 Jul 2017 14:59:09 +0000 (15:59 +0100)]
JAL-147 unit test for hide/show sequences update ViewportRanges
gmungoc [Thu, 6 Jul 2017 14:03:24 +0000 (15:03 +0100)]
JAL-2605 ensure correct scale width calculation
gmungoc [Wed, 5 Jul 2017 14:43:28 +0000 (15:43 +0100)]
JAL-1858 fastpaint highlights on wrapped alignment
gmungoc [Wed, 5 Jul 2017 12:43:48 +0000 (13:43 +0100)]
JAL-147 don't update overview for column selection (applet)
gmungoc [Wed, 5 Jul 2017 12:37:26 +0000 (13:37 +0100)]
JAL-147 additions to unit test, check for negative array index
gmungoc [Wed, 5 Jul 2017 10:34:50 +0000 (11:34 +0100)]
JAL-147 prevent overview box move up over hidden first sequence
gmungoc [Tue, 4 Jul 2017 15:51:34 +0000 (16:51 +0100)]
JAL-147 revised update of startSeq, endSeq on unhide sequences
gmungoc [Tue, 4 Jul 2017 15:20:03 +0000 (16:20 +0100)]
JAL-147 unit tests added, unused setEndRes removed
gmungoc [Tue, 4 Jul 2017 10:23:32 +0000 (11:23 +0100)]
JAL-147 corrected update of ViewportRanges for show/hide sequences
gmungoc [Tue, 4 Jul 2017 10:05:15 +0000 (11:05 +0100)]
JAL-147 update ViewportRanges height after show/hide sequences
gmungoc [Tue, 4 Jul 2017 09:26:43 +0000 (10:26 +0100)]
JAL-147 remove redundant calls to update overview panel
gmungoc [Tue, 4 Jul 2017 08:35:01 +0000 (09:35 +0100)]
JAL-2608 tidy up OverviewPanel when closed
gmungoc [Tue, 4 Jul 2017 08:12:49 +0000 (09:12 +0100)]
JAL-147 call method that sets visible width when drawing wrapped panel
gmungoc [Tue, 4 Jul 2017 08:12:13 +0000 (09:12 +0100)]
JAL-147 extract local variable for ease of debugging
gmungoc [Mon, 3 Jul 2017 14:39:09 +0000 (15:39 +0100)]
Merge branch 'develop' into bug/JAL-147scrollWrappedView
gmungoc [Mon, 3 Jul 2017 14:27:01 +0000 (15:27 +0100)]
JAL-147 correct width out-by-one drawing ids
gmungoc [Mon, 3 Jul 2017 14:26:33 +0000 (15:26 +0100)]
JAL-147 don't scroll Overview box outside panel dimensions
gmungoc [Mon, 3 Jul 2017 14:25:48 +0000 (15:25 +0100)]
JAL-147 ViewportRanges calculate wrapped vertical scroll position
gmungoc [Mon, 3 Jul 2017 14:17:27 +0000 (15:17 +0100)]
JAL-147 don't draw ScalePanel when in wrapped mode
gmungoc [Mon, 3 Jul 2017 13:54:11 +0000 (14:54 +0100)]
JAL-2034 don't refresh Overview for selection in id panel
gmungoc [Fri, 30 Jun 2017 15:17:47 +0000 (16:17 +0100)]
JAL-2505 correct handling of change of feature type
gmungoc [Fri, 30 Jun 2017 15:16:13 +0000 (16:16 +0100)]
JAL-2483 corrected finding feature groups
gmungoc [Fri, 30 Jun 2017 14:30:05 +0000 (15:30 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
gmungoc [Fri, 30 Jun 2017 14:06:50 +0000 (15:06 +0100)]
JAL-2602 unit test added
gmungoc [Fri, 30 Jun 2017 13:49:13 +0000 (14:49 +0100)]
JAL-147 don't page up above origin, repaint ids for scroll in wrapped
mode
gmungoc [Fri, 30 Jun 2017 12:00:56 +0000 (13:00 +0100)]
Merge branch 'bug/JAL-2597' into develop
gmungoc [Fri, 30 Jun 2017 10:48:15 +0000 (11:48 +0100)]
JAL-2602 pulled up identical methods to base class
git://source.jalview.org / jalview.git / log