jalview

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Commits this week: 2
Total Committers: 56
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Commits this week: 2

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Tuesday 02 Mar
8:50 pm

Ben Soares

JAL-3826 Simple configuration with CodeStyle implemented in .editorconfig file

Options
    • -0
    • +618
    ./.editorconfig
  2. … 2 more files in changeset.
3:24 pm

Arnaud Gucciardi

First commit of 3DB FTS Panel & Restclient

Options
    • -0
    • +213
    ./jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
    • -0
    • +240
    ./jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
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
Monday 22 Feb
6:26 pm

Mateusz Warowny

Merge branch 'bug/JAL-3807_jpred-with-slivka' into alpha/JAL-3066_Jalview_212_slivka-integration

Options
    • -12
    • +28
    ./jalview/ws/slivkaws/SlivkaWSInstance.java
Thursday 18 Feb
6:42 pm

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

JAL-3822 pass panel height and width to wrapped geometry calculations

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    • -1
    • +1
    ./jalview/gui/SeqCanvas.java
    • -0
    • +6
    ./jalview/gui/SeqPanel.java
  3. … 1 more file in changeset.
11:43 am

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

JAL-2422 remove temporary patch (requires ChimeraX Daily or 1.2 build)

Options
    • -2
    • +2
    ./jalview/gui/JalviewChimeraXBindingModel.java
Wednesday 17 Feb
5:16 pm

Jim Procter

JAL-3821 patch for 2.11.2 to retrieve RNA ENA records as RNA

Options
    • -1
    • +65
    ./jalview/io/EmblFlatFile.java
4:08 pm

Jim Procter

JAL-3821 rough and ready patch translates t/T to u/U when mol_type includes rna

Options
    • -2
    • +62
    ./jalview/io/EmblFlatFile.java
Friday 12 Feb
4:19 pm

Mateusz Warowny

JAL-3807 - Add single sequence capabilities to jws2.JPredClient

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    • -16
    • +0
    ./jalview/ws/api/JPredMutlipleAlignmentServiceI.java
    • -0
    • +16
    ./jalview/ws/api/JPredServiceI.java
    • -16
    • +16
    ./jalview/ws/jws2/JPredClient.java
    • -52
    • +131
    ./jalview/ws/jws2/JPredThread.java
    • -4
    • +33
    ./jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
4:19 pm

Mateusz Warowny

JAL-3807 - Add single sequence capabilities to jws2.JPredClient

Options
    • -16
    • +0
    ./jalview/ws/api/JPredMutlipleAlignmentServiceI.java
    • -0
    • +16
    ./jalview/ws/api/JPredServiceI.java
    • -16
    • +16
    ./jalview/ws/jws2/JPredClient.java
    • -52
    • +131
    ./jalview/ws/jws2/JPredThread.java
    • -4
    • +33
    ./jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
11:26 am

Mateusz Warowny

JAL-3807 - Move new JPred client to the jws2 package.

Options
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    • +0
    ./jalview/ws/JPredClient.java
    • -323
    • +0
    ./jalview/ws/JPredThread.java
    • -1
    • +1
    ./jalview/ws/api/ServiceWithParameters.java
    • -0
    • +69
    ./jalview/ws/jws2/JPredClient.java
    • -0
    • +327
    ./jalview/ws/jws2/JPredThread.java
11:26 am

Mateusz Warowny

JAL-3807 - Move new JPred client to the jws2 package.

Options
    • -67
    • +0
    ./jalview/ws/JPredClient.java
    • -323
    • +0
    ./jalview/ws/JPredThread.java
    • -1
    • +1
    ./jalview/ws/api/ServiceWithParameters.java
    • -0
    • +69
    ./jalview/ws/jws2/JPredClient.java
    • -0
    • +327
    ./jalview/ws/jws2/JPredThread.java
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?

4:15 pm

Mateusz Warowny

JAL-3807 - Re-implement results processing.

Options
    • -13
    • +114
    ./jalview/ws/JPredThread.java
    • -2
    • +5
    ./jalview/ws/api/JPredMutlipleAlignmentServiceI.java
    • -3
    • +23
    ./jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
4:15 pm

Mateusz Warowny

JAL-3807 - Re-implement results processing.

Options
    • -13
    • +114
    ./jalview/ws/JPredThread.java
    • -2
    • +5
    ./jalview/ws/api/JPredMutlipleAlignmentServiceI.java
    • -3
    • +23
    ./jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
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
11:30 am

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

JAL-3818 process Jmol callbacks in AWT thread

Options
    • -23
    • +47
    ./jalview/ext/jmol/JalviewJmolBinding.java
Wednesday 10 Feb
5:19 pm

Ben Soares

JAL-3251 On linux set (sun.awt.X11.XToolkit.)awtAppClassName to set the grouped application name in the taskbar

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    • +49
    ./jalview/gui/Desktop.java
12:19 am

Ben Soares

JAL-3521 Change grouped Jalview windows on linux taskbar to have name Jalview

Options
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    • +65
    ./jalview/gui/Desktop.java
Friday 05 Feb
5:07 pm

Jim Procter

JAL-3814 don’t automatically launch the news browser when the desktop is first opened

Options
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    • +8
    ./jalview/gui/BlogReader.java