jalview

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Tuesday 20 Aug 2019
10:07 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3364 tweaks to override of FIGURE_FIXEDIDWIDTH for split frame image

Options
    • -17
    • +24
    /src/jalview/gui/AlignmentPanel.java
    • -1
    • +0
    /src/jalview/gui/SeqCanvas.java
Monday 19 Aug 2019
5:30 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3364 align split frame sequence panels with wrapped view scale left

Options
    • -3
    • +7
    /src/jalview/gui/AlignmentPanel.java
    • -5
    • +0
    /src/jalview/gui/FontChooser.java
    • -0
    • +1
    /src/jalview/gui/IdwidthAdjuster.java
    • -2
    • +0
    /src/jalview/gui/SeqPanel.java
    • -13
    • +21
    /src/jalview/gui/SplitFrame.java
Tuesday 30 Jul 2019
2:08 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3364 more careful save/restore of preferences

Options
    • -7
    • +19
    /src/jalview/gui/AlignmentPanel.java
1:41 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3364 use larger of top/bottom 'auto id width' for split frame image

Options
    • -5
    • +36
    /src/jalview/gui/AlignmentPanel.java
12:15 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3364 add SVG option to split frame export

Options
    • -1
    • +1
    /src/jalview/bin/Jalview.java
    • -2
    • +2
    /src/jalview/gui/AlignFrame.java
    • -3
    • +13
    /src/jalview/jbgui/GAlignFrame.java
12:15 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3364 revisions to split frame image export

Options
    • -12
    • +19
    /src/jalview/gui/AlignmentPanel.java
    • -10
    • +7
    /src/jalview/gui/SeqCanvas.java
    • -4
    • +14
    /src/jalview/renderer/AnnotationRenderer.java
    • -9
    • +6
    /src/jalview/util/ImageMaker.java
Monday 29 Jul 2019
3:52 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

Merge branch 'develop' into feature/JAL-3364splitFrameImage

Options
    • -2
    • +5
    /src/jalview/gui/AlignmentPanel.java
    • -27
    • +18
    /src/jalview/gui/SeqCanvas.java
3:48 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3386 correct wrapped width calculation for headless image export

Options
    • -2
    • +3
    /src/jalview/gui/AlignmentPanel.java
3:35 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3377 more reused of SeqCanvas.computeWrappedGeometry

Options
    • -0
    • +2
    /src/jalview/gui/AlignmentPanel.java
    • -20
    • +7
    /src/jalview/gui/IdCanvas.java
    • -27
    • +18
    /src/jalview/gui/SeqCanvas.java
12:16 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3377 fix up failed merge

Options
    • -1
    • +0
    /src/jalview/gui/IdCanvas.java
12:05 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3364 remove debug output

Options
    • -10
    • +5
    /src/jalview/gui/AlignmentPanel.java
11:49 am

gmungoc <g.m.carstairs@dundee.ac.uk>

Merge branch 'develop' into feature/JAL-3364splitFrameImage

Options
    • -0
    • +6
    /src/jalview/gui/AlignmentPanel.java
    • -1
    • +2
    /src/jalview/gui/IdCanvas.java
11:44 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3377 add seq-annotations gap to cheight not to hgap

Options
    • -2
    • +2
    /src/jalview/gui/IdCanvas.java
11:34 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3377 Javadoc added for getWrappedHeight()

Options
    • -0
    • +6
    /src/jalview/gui/AlignmentPanel.java
11:20 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3377 include seq-annotation spacing in getWrappedHeight()

Options
    • -0
    • +1
    /src/jalview/gui/AlignmentPanel.java
11:20 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3377 include seq-annotation spacing in getWrappedHeight()

Options
    • -0
    • +1
    /src/jalview/gui/AlignmentPanel.java
11:18 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3364 export split frame image including annotations and/or wrapped

Options
    • -15
    • +25
    /src/jalview/gui/AlignmentPanel.java
    • -9
    • +24
    /src/jalview/gui/SeqCanvas.java
    • -2
    • +1
    /src/jalview/io/HtmlSvgOutput.java
    • -1
    • +4
    /src/jalview/renderer/AnnotationRenderer.java
Sunday 28 Jul 2019
11:05 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3377 corrected wrapped widths height for IdCanvas

Options
    • -7
    • +8
    /src/jalview/gui/IdCanvas.java
11:05 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3377 corrected wrapped widths height for IdCanvas

Options
    • -7
    • +8
    /src/jalview/gui/IdCanvas.java
Thursday 25 Jul 2019
11:48 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3375 ignore '.' values for VCF data

Options
    • -0
    • +23
    /src/jalview/datamodel/features/FeatureAttributes.java
    • -1
    • +3
    /src/jalview/io/vcf/VCFLoader.java
    • -55
    • +95
    /test/jalview/io/vcf/VCFLoaderTest.java
Sunday 21 Jul 2019
6:28 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3364 tidy and i18n makeAlignmentImage

Options
    • -0
    • +3
    /resources/lang/Messages.properties
    • -20
    • +23
    /src/jalview/gui/AlignmentPanel.java
    • -21
    • +8
    /src/jalview/gui/AppJmol.java
    • -19
    • +7
    /src/jalview/gui/PCAPanel.java
Tuesday 16 Jul 2019
11:23 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-2987 tolerate null double values when formatting JTable

Options
    • -6
    • +5
    /src/jalview/fts/core/DecimalFormatTableCellRenderer.java
Monday 15 Jul 2019
9:54 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3364 tooltip for nucleotide/protein above in exported image

Options
    • -0
    • +1
    /resources/lang/Messages.properties
    • -0
    • +1
    /resources/lang/Messages_es.properties
    • -1
    • +0
    /src/jalview/gui/AlignmentPanel.java
    • -2
    • +2
    /src/jalview/gui/SplitFrame.java
    • -3
    • +8
    /src/jalview/jbgui/GAlignFrame.java
9:24 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3364 submenu for Export Split Frame Image

Options
    • -0
    • +1
    /resources/lang/Messages.properties
    • -0
    • +1
    /resources/lang/Messages_es.properties
    • -2
    • +2
    /src/jalview/bin/Jalview.java
    • -11
    • +13
    /src/jalview/gui/AlignFrame.java
    • -22
    • +50
    /src/jalview/gui/AlignmentPanel.java
    • -10
    • +40
    /src/jalview/jbgui/GAlignFrame.java
    • -0
    • +18
    /src/jalview/util/ImageMaker.java
Sunday 14 Jul 2019
8:52 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3364 white fill before writing

Options
    • -2
    • +3
    /src/jalview/gui/AlignmentPanel.java
8:37 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3364 image export handle wrapped and/or unwrapped in split frame

Options
    • -105
    • +73
    /src/jalview/gui/AlignmentPanel.java
    • -1
    • +1
    /src/jalview/io/HtmlSvgOutput.java
3:14 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3364 initial version of export split frame

Options
    • -18
    • +86
    /src/jalview/gui/AlignmentPanel.java
    • -5
    • +5
    /src/jalview/io/HtmlSvgOutput.java
    • -23
    • +2
    /src/jalview/math/AlignmentDimension.java
Wednesday 10 Jul 2019
2:09 pm

Jim Procter

JAL-3289 bamboo properties for ‘BUILD’ getdown channel - fix

Options
    • -1
    • +1
    /build.gradle
1:55 pm

Jim Procter

JAL-3289 bamboo properties for ‘BUILD’ getdown channel

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    • -0
    • +3
    /build.gradle
    • -0
    • +5
    /gradle.properties
Friday 05 Jul 2019
10:43 am

Ben Soares

JAL-1544 fixed a html encoding of '<' (%lt; -> &lt;) in commandline.html

Options
    • -1
    • +1
    /help/help/html/features/commandline.html