jalview

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Commits this week: 18
Total Committers: 72
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Commits this week: 18

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Tuesday 06 Jul
5:42 pm

Jim Procter

5:42 pm

Jim Procter

WIP
WIP
Thursday 25 Feb
3:57 pm

Mungo Carstairs

3:56 pm

Mungo Carstairs

This is likely an improvement on the "roll your own" pattern of setting Runnable handlers for dialog responses as hacked together for JalviewJS (JAL-3048). If so, it would be preferable (but no sma...

This is likely an improvement on the "roll your own" pattern of setting Runnable handlers for dialog responses as hacked together for JalviewJS (JAL-3048). If so, it would be preferable (but no small job) to change all dialogs to this pattern.

There are still numerous dialogs that have not been changed to either pattern (so won't work in SwingJS): see comment at https://issues.jalview.org/browse/?focusedCommentId=20525&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#JAL-3048comment-20525.

2:21 pm

Mungo Carstairs

Class has some compiler warnings which could easily be resolved (typed Hashtable, unused import).

Class has some compiler warnings which could easily be resolved (typed Hashtable, unused import).

2:17 pm

Mungo Carstairs

It would be good to add Javadoc to this method

It would be good to add Javadoc to this method

2:14 pm

Mungo Carstairs

As an aside, I would suggest inlining (removing) the two overloaded constructors that call this one (to reduce code bloat).

As an aside, I would suggest inlining (removing) the two overloaded constructors that call this one (to reduce code bloat).

Wednesday 24 Feb
4:45 pm

Jim Procter

4:43 pm

Jim Procter

JAL-3818 process Jmol callbacks in AWT thread
JAL-3818 process Jmol callbacks in AWT thread
Thursday 11 Feb
5:06 pm

Mungo Carstairs

Or can it be compiled to Java 8 bytecode?

Or can it be compiled to Java 8 bytecode?

3:00 pm

Mungo Carstairs

'var' is since Java 10. We are still supporting Java 8 runtime which will not run this code (sadly). Compile with JDK 8 to find other occurrences (also Preferences, line 596 is not Java 8 compatibl...

'var' is since Java 10. We are still supporting Java 8 runtime which will not run this code (sadly).
Compile with JDK 8 to find other occurrences (also Preferences, line 596 is not Java 8 compatible syntax).

2:27 pm

Mungo Carstairs

Above statement is a duplicate - should only be inside the check for service != null. It fails with NPE if service is null.

Above statement is a duplicate - should only be inside the check for service != null. It fails with NPE if service is null.

2:26 pm

Mungo Carstairs

startjob and canceljob are only referenced in jbinit() so should be local variables in that method.

startjob and canceljob are only referenced in jbinit() so should be local variables in that method.

2:17 pm

Mungo Carstairs

Field startJob used to be the return value of showRunDialog(). As it no longer is, it can be removed.

Field startJob used to be the return value of showRunDialog(). As it no longer is, it can be removed.

12:29 pm

Mungo Carstairs

JAL-3809: Edit web service parameters dialog does not work in jalviewjs
JAL-3809: Edit web service parameters dialog does not work in jalviewjs
Saturday 19 Dec 2020
7:22 am

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

JAL-1713 restore project with no Overview, regardless of Preferences

Options
    • -5
    • +7
    /src/jalview/project/Jalview2XML.java
    • -24
    • +46
    /test/jalview/project/Jalview2xmlTests.java
Thursday 17 Dec 2020
8:44 pm

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

JAL-1713 close and replace auto-opened Overview with restored Overview

Options
    • -0
    • +12
    /src/jalview/gui/AlignmentPanel.java
    • -0
    • +8
    /src/jalview/gui/OverviewPanel.java
    • -153
    • +166
    /src/jalview/project/Jalview2XML.java
    • -1
    • +3
    /test/jalview/project/Jalview2xmlTests.java
Sunday 13 Dec 2020
12:32 pm

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

JAL-1713 unit test for save/restore Overview in project

Options
    • -0
    • +92
    /test/jalview/project/Jalview2xmlTests.java
11:47 am

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

JAL-1713 renamed method to OverviewPanel.get/setFrameBounds()

Options
    • -6
    • +4
    /src/jalview/gui/OverviewPanel.java
    • -2
    • +2
    /src/jalview/project/Jalview2XML.java
Saturday 12 Dec 2020
2:39 pm

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

JAL-1713 JAL-3119 JAL-3785 refactored get/set Overview bounds and title

Options
    • -35
    • +15
    /src/jalview/gui/AlignFrame.java
    • -39
    • +65
    /src/jalview/gui/AlignmentPanel.java
    • -38
    • +91
    /src/jalview/gui/OverviewPanel.java
    • -15
    • +5
    /src/jalview/io/FileLoader.java
    • -8
    • +4
    /src/jalview/project/Jalview2XML.java
    • -1
    • +41
    /test/jalview/gui/AlignmentPanelTest.java
Friday 11 Dec 2020
9:04 pm

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

JAL-3785 set full title on automatically opened Overview windows

Options
    • -8
    • +34
    /src/jalview/gui/AlignFrame.java
    • -0
    • +16
    /src/jalview/io/FileLoader.java
7:51 am

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

JAL-1713 fix typo; overview in project with open overview in preferences

Options
    • -5
    • +4
    /src/jalview/gui/AlignFrame.java
    • -1
    • +1
    /src/jalview/renderer/OverviewResColourFinder.java
Thursday 10 Dec 2020
4:08 pm

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

JAL-3784 null the right overview reference when it is closed

Options
    • -1
    • +2
    /src/jalview/gui/AlignFrame.java
4:01 pm

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

JAL-1713 read/set OverviewPanel geometry on parent JInternalFrame

Options
    • -11
    • +8
    /src/jalview/project/Jalview2XML.java
3:53 pm

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

JAL-1713 save Overview title in project, don't save Overview on New View

Options
    • -0
    • +1
    /schemas/jalview.xsd
    • -15
    • +34
    /src/jalview/project/Jalview2XML.java
    • -75
    • +104
    /src/jalview/xml/binding/jalview/JalviewModel.java
    • -1
    • +1
    /src/jalview/xml/binding/jalview/package-info.java
2:56 pm

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

JAL-3119 include view name (if any) in Overview title

Options
    • -2
    • +8
    /src/jalview/gui/AlignFrame.java
1:05 pm

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

JAL-1713 save/restore Overview in project (todo: restore geometry)

Options
    • -0
    • +32
    /src/jalview/project/Jalview2XML.java
1:04 pm

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

JAL-1713 refactorings to allow save/restore Overview to/from project

Options
    • -3
    • +11
    /src/jalview/gui/AlignFrame.java
    • -16
    • +54
    /src/jalview/gui/OverviewCanvas.java
    • -12
    • +21
    /src/jalview/gui/OverviewPanel.java
    • -30
    • +23
    /src/jalview/gui/Preferences.java
    • -1
    • +1
    /src/jalview/renderer/OverviewRenderer.java
    • -45
    • +59
    /src/jalview/renderer/OverviewResColourFinder.java
    • -6
    • +7
    /test/jalview/renderer/OverviewRendererTest.java
    • -49
    • +36
    /test/jalview/renderer/OverviewResColourFinderTest.java
1:02 pm

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

JAL-1713 schema and JAXB changes to save Overview in project file

Options
    • -0
    • +9
    /schemas/jalview.xsd
    • -2
    • +292
    /src/jalview/xml/binding/jalview/JalviewModel.java
    • -1
    • +9
    /src/jalview/xml/binding/jalview/ObjectFactory.java
    • -1
    • +1
    /src/jalview/xml/binding/jalview/package-info.java
Monday 07 Dec 2020
1:29 pm

Ben Soares

JAL-3754 Fixed jar task creating strange dir because of outputs.file()

Options
    • -2
    • +3
    /build.gradle