jalview

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Monday 31 Jul 2017
11:01 am

Kira Mourão

JAL-2634 Make overview box full height when alignment is wrapped

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    • -1
    • +1
    /src/jalview/appletgui/AlignmentPanel.java
10:23 am

Kira Mourão

JAL-2634 Added null test for graphics in AnnotationPanel::fastPaint

Options
    • -1
    • +1
    /src/jalview/appletgui/AnnotationPanel.java
Friday 28 Jul 2017
2:17 pm

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

JAL-147 corrected status bar message for wrapped scrolled right view

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    • -2
    • +2
    /src/jalview/appletgui/SeqPanel.java
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    • +2
    /src/jalview/gui/SeqPanel.java
12:12 pm

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

JAL-2622 no vertical scroll of wrapped alignment from trackpad / mouse button

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    • -2
    • +2
    /src/jalview/gui/SeqPanel.java
11:06 am

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

JAL-147 unit test for no vertical move of Overview box in wrapped mode

Options
    • -0
    • +49
    /test/jalview/viewmodel/OverviewDimensionsShowHiddenTest.java
Monday 24 Jul 2017
6:24 am

Jim Procter

Merge branch 'documentation/JAL-2418_release2102' into develop

Options
Saturday 22 Jul 2017
4:38 pm

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

JAL-2624 check feature colour threshold when colouring structure

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    • +7
    /src/jalview/renderer/seqfeatures/FeatureRenderer.java
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    • +9
    /src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
    • -0
    • +65
    /test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
2:48 pm

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

JAL-2623 initialise colour threshold slider correctly

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    • +2
    /src/jalview/appletgui/FeatureColourChooser.java
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    • +2
    /src/jalview/gui/FeatureColourChooser.java
Tuesday 18 Jul 2017
4:24 pm

Jim Procter

JAL-2432 updated documentation for select/hide by annotation to include As Percentage checkbox

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    /help/html/features/AnnotationColumnSelectionWithSM.gif
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    /help/html/features/AnnotationColumnSelectionWithSM.png
    • -2
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    /help/html/features/columnFilterByAnnotation.html
2:44 pm

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

JAL-147 don't scroll up beyond startRes = 0

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    /src/jalview/appletgui/AlignmentPanel.java
    • -2
    • +2
    /src/jalview/gui/AlignmentPanel.java
1:02 pm

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

JAL-147 corrected calculation of vertical scroll position and max

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    • +6
    /src/jalview/appletgui/AlignmentPanel.java
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    • +6
    /src/jalview/gui/AlignmentPanel.java
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    • +29
    /src/jalview/viewmodel/ViewportRanges.java
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    • +31
    /test/jalview/viewmodel/ViewportRangesTest.java
1:01 pm

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

JAL-147 draw up to last position of wrapped alignment!

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    • -2
    • +2
    /src/jalview/appletgui/SeqCanvas.java
    • -2
    • +2
    /src/jalview/gui/SeqCanvas.java
Monday 17 Jul 2017
4:20 pm

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

Merge branch 'develop' into bug/JAL-147scrollWrappedView

Options
12:25 pm

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

JAL-1648 JAL-2447 Spanish translations

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
Thursday 06 Jul 2017
3:59 pm

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

JAL-147 prevent vertical Overview box movement in wrapped mode

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    • -0
    • +5
    /src/jalview/viewmodel/OverviewDimensionsHideHidden.java
    • -0
    • +5
    /src/jalview/viewmodel/OverviewDimensionsShowHidden.java
    • -0
    • +5
    /src/jalview/viewmodel/ViewportRanges.java
3:59 pm

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

JAL-147 unit test for hide/show sequences update ViewportRanges

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    • -1
    • +0
    /src/jalview/viewmodel/AlignmentViewport.java
    • -0
    • +43
    /test/jalview/gui/AlignViewportTest.java
3:03 pm

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

JAL-2605 ensure correct scale width calculation

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    • +3
    /src/jalview/appletgui/SeqCanvas.java
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    • +3
    /src/jalview/gui/SeqCanvas.java
Wednesday 05 Jul 2017
1:43 pm

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

JAL-147 don't update overview for column selection (applet)

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    • -1
    • +1
    /src/jalview/appletgui/ScalePanel.java
1:37 pm

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

JAL-147 additions to unit test, check for negative array index

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    /src/jalview/datamodel/HiddenSequences.java
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    /test/jalview/datamodel/HiddenSequencesTest.java
11:34 am

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

JAL-147 prevent overview box move up over hidden first sequence

Options
    • -1
    • +2
    /src/jalview/datamodel/HiddenSequences.java
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    • +2
    /src/jalview/viewmodel/OverviewDimensionsShowHidden.java
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    • +14
    /test/jalview/datamodel/HiddenSequencesTest.java
Tuesday 04 Jul 2017
4:51 pm

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

JAL-147 revised update of startSeq, endSeq on unhide sequences

Options
    • -2
    • +7
    /src/jalview/viewmodel/AlignmentViewport.java
4:20 pm

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

JAL-147 unit tests added, unused setEndRes removed

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    /src/jalview/viewmodel/ViewportRanges.java
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    • +164
    /test/jalview/viewmodel/ViewportRangesTest.java
11:23 am

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

JAL-147 corrected update of ViewportRanges for show/hide sequences

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    • +13
    /src/jalview/viewmodel/AlignmentViewport.java
11:05 am

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

JAL-147 update ViewportRanges height after show/hide sequences

Options
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    • +3
    /src/jalview/viewmodel/AlignmentViewport.java
10:26 am

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

JAL-147 remove redundant calls to update overview panel

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    • -12
    • +0
    /src/jalview/appletgui/ScalePanel.java
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    • +0
    /src/jalview/gui/AlignFrame.java
    • -12
    • +0
    /src/jalview/gui/ScalePanel.java
9:35 am

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

JAL-2608 tidy up OverviewPanel when closed

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    /src/jalview/appletgui/AlignFrame.java
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    • +25
    /src/jalview/appletgui/OverviewPanel.java
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    /src/jalview/gui/AlignFrame.java
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    • +25
    /src/jalview/gui/OverviewPanel.java
9:12 am

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

JAL-147 call method that sets visible width when drawing wrapped panel

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    /src/jalview/appletgui/SeqCanvas.java
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    /src/jalview/gui/SeqCanvas.java
9:12 am

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

JAL-147 extract local variable for ease of debugging

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    /src/jalview/viewmodel/ViewportRanges.java
Monday 03 Jul 2017
3:39 pm

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

Merge branch 'develop' into bug/JAL-147scrollWrappedView

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    • +41
    /src/jalview/viewmodel/AlignmentViewport.java
3:27 pm

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

JAL-147 correct width out-by-one drawing ids

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    /src/jalview/appletgui/IdCanvas.java
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    /src/jalview/gui/IdCanvas.java