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
Wednesday 03 Feb
4:34 pm

Jim Procter

JAL-3808 handle 1:1 mappings in exonerate gff2 using the ‘similarity’ feature extent to determine direction of mapping generated from alignment

Options
    • -22
    • +138
    /src/jalview/io/gff/ExonerateHelper.java
4:33 pm

Jim Procter

JAL-3808 example exonerate cdna2genome and coding2genome test data and test

Options
    • -0
    • +74
    /examples/testdata/test_cdna2genome_showquerygff.gff2
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    • +81
    /examples/testdata/test_cdna2genome_showtargetgff.gff2
    • -0
    • +76
    /examples/testdata/test_coding2genome_showquerygff.gff2
    • -0
    • +82
    /examples/testdata/test_coding2genome_showtargetgff.gff2
    • -0
    • +42
    /test/jalview/io/FeaturesFileTest.java
Thursday 28 Jan
2:02 pm

Jalview Development Admin <jalview-dev-owner@jalview.org>

Merge branch 'task/JAL-3796_notarization_no_uninstaller' into develop

Options
1:50 pm

Jalview Development Admin <jalview-dev-owner@jalview.org>

Merge branch 'task/JAL-3805_Remove_Uninstall_Old_Jalview_application_for_develop_branch' into task/JAL-3796_notarization_no_uninstaller

Options
    • -6
    • +0
    /build.gradle
    • -15
    • +1
    /utils/install4j/install4j8_template.install4j
12:46 pm

Jalview Development Admin <jalview-dev-owner@jalview.org>

Merge branch 'develop' into task/JAL-3796_notarization_no_uninstaller

Options
    • -4
    • +37
    /build.gradle
    • -1
    • +13
    /gradle.properties
Tuesday 26 Jan
3:27 pm

Ben Soares

JAL-3521 Updating file opening marker to %u

Options
    • -1
    • +1
    /utils/debian/debian/jalview.desktop
    • -1
    • +1
    /utils/debian/mime_types_for_debian.pl
1:59 pm

Ben Soares

JAL-3521 Debian mime-type and desktop helper files, and script to create them

Options
    • binary
    /utils/debian/debian/jalview-file.png
    • binary
    /utils/debian/debian/jalview-icon.png
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    /utils/debian/debian/jalview-mailcap
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    • +143
    /utils/debian/debian/jalview-mime.xml
    • -0
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    /utils/debian/debian/jalview.desktop
    • -0
    • +1
    /utils/debian/file_associations_template-mailcap.txt
    • -0
    • +6
    /utils/debian/file_associations_template-shared-mime-info.xml
    • -0
    • +249
    /utils/debian/mime_types_for_debian.pl
Friday 22 Jan
1:54 pm

Ben Soares

JAL-3805 Smaller DMG Finder windows for all DS_Store files in utils/channels/... . Removed no longer used DS_Store files from utils/install4j.

Options
    • binary
    /utils/channels/release/images/jalview_dmg_DS_Store
    • binary
    /utils/channels/test-release/images/jalview_test-release_dmg_DS_Store
    • binary
    /utils/install4j/DS_Store
    • binary
    /utils/install4j/DS_Store-DEVELOP
    • binary
    /utils/install4j/DS_Store-NON-RELEASE
    • binary
    /utils/install4j/DS_Store-TEST-RELEASE
    • binary
    /utils/install4j/DS_Store_no_link
    • -1
    • +1
    /utils/install4j/install4j8_template.install4j
11:42 am

Ben Soares

JAL-3805 New DS_Store for smaller DMG Finder window

Options
    • binary
    /utils/install4j/DS_Store
Thursday 21 Jan
11:42 pm

Ben Soares

JAL-3805 Remove Uninstall Old Jalview.app in Release_2_11_1_Branch

Options
    • -7
    • +1
    /build.gradle
    • -74
    • +0
    /utils/install4j/Uninstall Old Jalview.app/Contents/Info.plist
    • binary
    /utils/install4j/Uninstall Old Jalview.app/Contents/MacOS/applet
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    • +0
    /utils/install4j/Uninstall Old Jalview.app/Contents/PkgInfo
    • binary
    /utils/install4j/Uninstall Old Jalview.app/Contents/Resources/Scripts/main.scpt
    • binary
    /utils/install4j/Uninstall Old Jalview.app/Contents/Resources/applet.icns
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    /utils/install4j/Uninstall Old Jalview.app/Contents/Resources/applet.rsrc
    • -5
    • +0
    /utils/install4j/Uninstall Old Jalview.app/Contents/Resources/description.rtfd/TXT.rtf
    • -177
    • +0
    /utils/install4j/Uninstall Old Jalview.app/Contents/_CodeSignature/CodeResources
    • binary
    /utils/install4j/Uninstall Old Jalview.scpt
    • -15
    • +1
    /utils/install4j/install4j8_template.install4j
5:18 pm

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

JAL-3038 corrected code that reads editable JComboBox text input

Options
    • -3
    • +3
    /src/jalview/gui/Desktop.java
Thursday 14 Jan
3:34 pm

Jalview Development Admin <jalview-dev-owner@jalview.org>

JAL-3796 update to Install4j 8.0.10 and add config for code notarization

Options
    • -1
    • +13
    /build.gradle
    • -0
    • +2
    /gradle.properties
    • -2
    • +23
    /utils/install4j/install4j8_template.install4j
Monday 11 Jan
9:30 pm

Ben Soares

JAL-3789 Use j2s.config.altfileproperty in .j2s for alternative temporary build/jalviewjs/config/j2s settings file when running a headless build in gradle

Options
    • -4
    • +37
    /build.gradle
    • -1
    • +13
    /gradle.properties
9:28 pm

Ben Soares

JAL-3789 New swingjs for Java2Script 3.2.10 with j2s.config.altfileproperty

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    • -8
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    /swingjs/README.txt
    • binary
    /swingjs/SwingJS-site.zip
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    /swingjs/differences.txt
    • binary
    /swingjs/net.sf.j2s.core-j11.jar
    • binary
    /swingjs/net.sf.j2s.core.jar
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    /swingjs/timestamp
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    /swingjs/ver/3.2.10-j11/DEV_NOTES.txt
    • binary
    /swingjs/ver/3.2.10-j11/SwingJS-site.zip
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    /swingjs/ver/3.2.10-j11/_j2sclasslist.txt
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    /swingjs/ver/3.2.10-j11/differences.txt
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    /swingjs/ver/3.2.10-j11/net.sf.j2s.core-j11.jar
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    /swingjs/ver/3.2.10-j11/timestamp
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    /swingjs/ver/3.2.10/DEV_NOTES.txt
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    /swingjs/ver/3.2.10/SwingJS-site.zip
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    /swingjs/ver/3.2.10/_j2sclasslist.txt
  16. … 32 more files in changeset.
Monday 14 Dec 2020
11:18 pm

Ben Soares

JAL-3280 Fixed the version checking URL formulation (getdown build_properties) for jalviewjs, can also use it for jalviewjs in future

Options
    • -13
    • +35
    /src/jalview/bin/Cache.java