jalview

Clone Tools
  • last updated a few seconds ago
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
WIP
WIP
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.

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).

It would be good to add Javadoc to this method

It would be good to add Javadoc to this method

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).

JAL-3818 process Jmol callbacks in AWT thread
JAL-3818 process Jmol callbacks in AWT thread
Or can it be compiled to Java 8 bytecode?

Or can it be compiled to Java 8 bytecode?

'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).

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.

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.

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.

JAL-3809: Edit web service parameters dialog does not work in jalviewjs
JAL-3809: Edit web service parameters dialog does not work in jalviewjs
JAL-3808 handle 1:1 mappings in exonerate gff2 using the ‘similarity’ feature extent to determine direction of mapping generated from alignment

    • -22
    • +138
    /src/jalview/io/gff/ExonerateHelper.java
JAL-3808 example exonerate cdna2genome and coding2genome test data and test

    • -0
    • +74
    /examples/testdata/test_cdna2genome_showquerygff.gff2
    • -0
    • +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
Merge branch 'task/JAL-3796_notarization_no_uninstaller' into develop

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

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

JAL-3521 Updating file opening marker to %u

    • -1
    • +1
    /utils/debian/mime_types_for_debian.pl
JAL-3521 Debian mime-type and desktop helper files, and script to create them

    • binary
    /utils/debian/debian/jalview-file.png
    • binary
    /utils/debian/debian/jalview-icon.png
    • -0
    • +22
    /utils/debian/debian/jalview-mailcap
    • -0
    • +143
    /utils/debian/debian/jalview-mime.xml
    • -0
    • +13
    /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
JAL-3805 Smaller DMG Finder windows for all DS_Store files in utils/channels/... . Removed no longer used DS_Store files from utils/install4j.

    • binary
    /utils/install4j/DS_Store-NON-RELEASE
    • binary
    /utils/install4j/DS_Store-TEST-RELEASE
JAL-3805 New DS_Store for smaller DMG Finder window

JAL-3805 Remove Uninstall Old Jalview.app in Release_2_11_1_Branch

JAL-3038 corrected code that reads editable JComboBox text input

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

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

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

    • -0
    • +1541
    /swingjs/differences.txt
    • -0
    • +10
    /swingjs/ver/3.2.10-j11/DEV_NOTES.txt
    • binary
    /swingjs/ver/3.2.10-j11/SwingJS-site.zip
    • -0
    • +412
    /swingjs/ver/3.2.10-j11/_j2sclasslist.txt
    • -0
    • +1541
    /swingjs/ver/3.2.10-j11/differences.txt
    • binary
    /swingjs/ver/3.2.10-j11/net.sf.j2s.core-j11.jar
    • -0
    • +1
    /swingjs/ver/3.2.10-j11/timestamp
    • -0
    • +10
    /swingjs/ver/3.2.10/DEV_NOTES.txt
    • binary
    /swingjs/ver/3.2.10/SwingJS-site.zip
    • -0
    • +412
    /swingjs/ver/3.2.10/_j2sclasslist.txt
  1. … 32 more files in changeset.
JAL-3280 Fixed the version checking URL formulation (getdown build_properties) for jalviewjs, can also use it for jalviewjs in future