Ben Soares <b.soares@dundee.ac.uk>: Author Summary
| Build | Completed | Code commits | Tests |
|---|---|---|---|
| JB › GDBI › #21 | 2 years ago |
JAL-4186 fixed a test
JAL-4186 fix dialog. broken in JalviewJS
JAL-4186 attempts to work in jalviewjs, still not working
JAL-4186 Turn JvOptionPane Callable<Void> handlers back into Runnable for jalviewjs (now working)
|
Testless build |
| JB › GTC › #19 | 2 months ago |
JAL-4581 Switched to using https://github.com/meyfa/java-sha256 which has MIT license
JAL-4603 adjustments to the test
JAL-4581. Added an MD5 hash for jalview.ext.htsjdk.HtsContigDb. Made jalview.util.DigestUtils for MD5 and SHA256 digest. Adapted net.meyfa.sha256.Sha256 to not use java.nio.IntBuffer and java.nio.ByteBuffer (not supported by SwingJS).
JAL-4581 Updated commons-codec jar and switched SHA256 hash to use it
JAL-4607 minor changes required for install4j 11.0.5 gradle plugin
JAL-4607 Fix background colour of install4j wizard in dark mode, with update to 11.0.5
Merge branch 'development/Release_2_11_5_Branch' into bug/JAL-4594_ss_consensus_overlap_other_annot
JAL-4603 Nail down the number of wrappedWidths being rendered for an image export
Merge branch 'bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection' into development/Release_2_11_5_Branch
JAL-4603 Use the disableInput() and enableInput() methods for the AlignFrame while exporting SVG/EPS
JAL-4581 added MIT license listed for https://github.com/meyfa/java-sha256
JAL-4603 An example file needed for ImageExporterTest.java
JAL-4603 prevent other ways of resizing the AlignFrame
JAL-4604 Fixed Console logger being initiated too early and log level in props file not being set. This was causing jalview.util.Log4jTest.testLog4j to fail. Neatened the args in that test to use '--' to prevent mixed argstyle warning.
JAL-4604 Changes to getdown/LaunchUtils to fix the arguments bug, and also detect being launched with the spurious arguments and remove them
JAL-4604 getdown upgrade bug avert in GetdownApp.java
JAL-4601 Enable Secondary Structure Consensus to appear immediately after annotation file load
Merge branch 'development/Release_2_11_5_Branch' into bug/JAL-4594_ss_consensus_overlap_other_annot
JAL-4581 Include com.dyspersja.Sha256MessageDigest to use a builtin hashing algorithm that j2s can transpile. No change in colours generated.
JAL-4604 Bug in LaunchUtils not removing previous 'appbase' 'appid' arguments
JAL-4603 Removed the not-working-test for release patch
JAL-4604 Ensure getdownappdir is now set and passed through. Some indentation fixes in getdown...Application.java
JAL-4603 Add glass pane methods to AlignFrame to disable/re-enable user input
JAL-4604 This needed for some old installations. Normally set in getdown separately
JAL-4604 Allow getdown to use its own version in jar comparison
JAL-4603 grey panel on the glasspane now changes with size of AlignFrame
JAL-4604 Now ensure non-buggy arguments are passed as-is
JAL-4603 Optionally don't grey out the status bar when calling AlignFrame.disableInput()
JAL-4604 Check for old install4j set property for appdir to swap in new getdown-launcher.jar
Modernised CLI arguments in jvlfiles.html help file.
JAL-4604 removed a line marked REMOVE THIS LINE
|
Testless build |
| JB › GDC › #219 | 2 months ago |
Merge branch 'development/Release_2_11_5_Branch' into bug/JAL-4594_ss_consensus_overlap_other_annot
JAL-4604 removed a line marked REMOVE THIS LINE
JAL-4603 An example file needed for ImageExporterTest.java
JAL-4581 Switched to using https://github.com/meyfa/java-sha256 which has MIT license
JAL-4581 Updated commons-codec jar and switched SHA256 hash to use it
JAL-4581. Added an MD5 hash for jalview.ext.htsjdk.HtsContigDb. Made jalview.util.DigestUtils for MD5 and SHA256 digest. Adapted net.meyfa.sha256.Sha256 to not use java.nio.IntBuffer and java.nio.ByteBuffer (not supported by SwingJS).
JAL-4603 adjustments to the test
JAL-4607 minor changes required for install4j 11.0.5 gradle plugin
JAL-4607 Fix background colour of install4j wizard in dark mode, with update to 11.0.5
Merge branch 'bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection' into development/Release_2_11_5_Branch
JAL-4581 added MIT license listed for https://github.com/meyfa/java-sha256
JAL-4603 Use the disableInput() and enableInput() methods for the AlignFrame while exporting SVG/EPS
JAL-4603 prevent other ways of resizing the AlignFrame
JAL-4603 Removed the not-working-test for release patch
JAL-4604 Changes to getdown/LaunchUtils to fix the arguments bug, and also detect being launched with the spurious arguments and remove them
JAL-4604 Fixed Console logger being initiated too early and log level in props file not being set. This was causing jalview.util.Log4jTest.testLog4j to fail. Neatened the args in that test to use '--' to prevent mixed argstyle warning.
JAL-4604 Bug in LaunchUtils not removing previous 'appbase' 'appid' arguments
JAL-4604 getdown upgrade bug avert in GetdownApp.java
JAL-4604 Allow getdown to use its own version in jar comparison
JAL-4601 Enable Secondary Structure Consensus to appear immediately after annotation file load
JAL-4581 Include com.dyspersja.Sha256MessageDigest to use a builtin hashing algorithm that j2s can transpile. No change in colours generated.
JAL-4604 Ensure getdownappdir is now set and passed through. Some indentation fixes in getdown...Application.java
Merge branch 'development/Release_2_11_5_Branch' into bug/JAL-4594_ss_consensus_overlap_other_annot
JAL-4604 This needed for some old installations. Normally set in getdown separately
JAL-4603 Nail down the number of wrappedWidths being rendered for an image export
JAL-4603 Add glass pane methods to AlignFrame to disable/re-enable user input
Modernised CLI arguments in jvlfiles.html help file.
JAL-4603 grey panel on the glasspane now changes with size of AlignFrame
JAL-4604 Now ensure non-buggy arguments are passed as-is
JAL-4604 Check for old install4j set property for appdir to swap in new getdown-launcher.jar
JAL-4603 Optionally don't grey out the status bar when calling AlignFrame.disableInput()
|
Testless build |
| JB › GDL › #78 | 2 months ago |
Merge branch 'development/Release_2_11_5_Branch' into bug/JAL-4594_ss_consensus_overlap_other_annot
JAL-4603 An example file needed for ImageExporterTest.java
JAL-4604 removed a line marked REMOVE THIS LINE
JAL-4581 Updated commons-codec jar and switched SHA256 hash to use it
JAL-4581 Switched to using https://github.com/meyfa/java-sha256 which has MIT license
JAL-4603 adjustments to the test
JAL-4607 Fix background colour of install4j wizard in dark mode, with update to 11.0.5
JAL-4581. Added an MD5 hash for jalview.ext.htsjdk.HtsContigDb. Made jalview.util.DigestUtils for MD5 and SHA256 digest. Adapted net.meyfa.sha256.Sha256 to not use java.nio.IntBuffer and java.nio.ByteBuffer (not supported by SwingJS).
JAL-4607 minor changes required for install4j 11.0.5 gradle plugin
Merge branch 'bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection' into development/Release_2_11_5_Branch
JAL-4581 added MIT license listed for https://github.com/meyfa/java-sha256
JAL-4603 prevent other ways of resizing the AlignFrame
JAL-4603 Use the disableInput() and enableInput() methods for the AlignFrame while exporting SVG/EPS
JAL-4603 Removed the not-working-test for release patch
JAL-4604 This needed for some old installations. Normally set in getdown separately
JAL-4604 Changes to getdown/LaunchUtils to fix the arguments bug, and also detect being launched with the spurious arguments and remove them
JAL-4604 Bug in LaunchUtils not removing previous 'appbase' 'appid' arguments
JAL-4601 Enable Secondary Structure Consensus to appear immediately after annotation file load
JAL-4604 Ensure getdownappdir is now set and passed through. Some indentation fixes in getdown...Application.java
JAL-4604 Allow getdown to use its own version in jar comparison
JAL-4603 Nail down the number of wrappedWidths being rendered for an image export
Merge branch 'development/Release_2_11_5_Branch' into bug/JAL-4594_ss_consensus_overlap_other_annot
JAL-4603 Add glass pane methods to AlignFrame to disable/re-enable user input
JAL-4581 Include com.dyspersja.Sha256MessageDigest to use a builtin hashing algorithm that j2s can transpile. No change in colours generated.
Modernised CLI arguments in jvlfiles.html help file.
JAL-4603 grey panel on the glasspane now changes with size of AlignFrame
JAL-4604 Check for old install4j set property for appdir to swap in new getdown-launcher.jar
JAL-4604 Now ensure non-buggy arguments are passed as-is
JAL-4604 getdown upgrade bug avert in GetdownApp.java
JAL-4604 Fixed Console logger being initiated too early and log level in props file not being set. This was causing jalview.util.Log4jTest.testLog4j to fail. Neatened the args in that test to use '--' to prevent mixed argstyle warning.
JAL-4603 Optionally don't grey out the status bar when calling AlignFrame.disableInput()
|
Testless build |
| JB › GPC › #358 | 2 months ago |
JAL-4581 added MIT license listed for https://github.com/meyfa/java-sha256
Merge branch 'development/Release_2_11_5_Branch' into bug/JAL-4594_ss_consensus_overlap_other_annot
JAL-4604 removed a line marked REMOVE THIS LINE
JAL-4603 An example file needed for ImageExporterTest.java
JAL-4581 Switched to using https://github.com/meyfa/java-sha256 which has MIT license
JAL-4581. Added an MD5 hash for jalview.ext.htsjdk.HtsContigDb. Made jalview.util.DigestUtils for MD5 and SHA256 digest. Adapted net.meyfa.sha256.Sha256 to not use java.nio.IntBuffer and java.nio.ByteBuffer (not supported by SwingJS).
JAL-4603 adjustments to the test
JAL-4603 Add glass pane methods to AlignFrame to disable/re-enable user input
JAL-4603 prevent other ways of resizing the AlignFrame
Merge branch 'bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection' into development/Release_2_11_5_Branch
JAL-4607 minor changes required for install4j 11.0.5 gradle plugin
JAL-4581 Updated commons-codec jar and switched SHA256 hash to use it
JAL-4603 Use the disableInput() and enableInput() methods for the AlignFrame while exporting SVG/EPS
JAL-4604 Bug in LaunchUtils not removing previous 'appbase' 'appid' arguments
JAL-4604 This needed for some old installations. Normally set in getdown separately
JAL-4601 Enable Secondary Structure Consensus to appear immediately after annotation file load
JAL-4604 Allow getdown to use its own version in jar comparison
JAL-4604 Ensure getdownappdir is now set and passed through. Some indentation fixes in getdown...Application.java
JAL-4604 Changes to getdown/LaunchUtils to fix the arguments bug, and also detect being launched with the spurious arguments and remove them
JAL-4603 Removed the not-working-test for release patch
JAL-4603 Nail down the number of wrappedWidths being rendered for an image export
JAL-4581 Include com.dyspersja.Sha256MessageDigest to use a builtin hashing algorithm that j2s can transpile. No change in colours generated.
Merge branch 'development/Release_2_11_5_Branch' into bug/JAL-4594_ss_consensus_overlap_other_annot
JAL-4603 Optionally don't grey out the status bar when calling AlignFrame.disableInput()
Modernised CLI arguments in jvlfiles.html help file.
JAL-4604 Check for old install4j set property for appdir to swap in new getdown-launcher.jar
JAL-4603 grey panel on the glasspane now changes with size of AlignFrame
JAL-4607 Fix background colour of install4j wizard in dark mode, with update to 11.0.5
JAL-4604 Now ensure non-buggy arguments are passed as-is
JAL-4604 getdown upgrade bug avert in GetdownApp.java
JAL-4604 Fixed Console logger being initiated too early and log level in props file not being set. This was causing jalview.util.Log4jTest.testLog4j to fail. Neatened the args in that test to use '--' to prevent mixed argstyle warning.
|
Testless build |
| JB › GDB › #706 | 2 months ago |
JAL-4581 added MIT license listed for https://github.com/meyfa/java-sha256
Modernised CLI arguments in jvlfiles.html help file.
JAL-4604 removed a line marked REMOVE THIS LINE
JAL-4581 Switched to using https://github.com/meyfa/java-sha256 which has MIT license
JAL-4603 An example file needed for ImageExporterTest.java
Merge branch 'bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection' into development/Release_2_11_5_Branch
JAL-4603 grey panel on the glasspane now changes with size of AlignFrame
JAL-4603 adjustments to the test
JAL-4581 Updated commons-codec jar and switched SHA256 hash to use it
Merge branch 'development/Release_2_11_5_Branch' into bug/JAL-4594_ss_consensus_overlap_other_annot
JAL-4603 Use the disableInput() and enableInput() methods for the AlignFrame while exporting SVG/EPS
JAL-4603 Removed the not-working-test for release patch
JAL-4603 Add glass pane methods to AlignFrame to disable/re-enable user input
JAL-4604 This needed for some old installations. Normally set in getdown separately
Merge branch 'development/Release_2_11_5_Branch' into bug/JAL-4594_ss_consensus_overlap_other_annot
JAL-4601 Enable Secondary Structure Consensus to appear immediately after annotation file load
JAL-4604 Allow getdown to use its own version in jar comparison
JAL-4607 minor changes required for install4j 11.0.5 gradle plugin
JAL-4604 Ensure getdownappdir is now set and passed through. Some indentation fixes in getdown...Application.java
JAL-4604 Changes to getdown/LaunchUtils to fix the arguments bug, and also detect being launched with the spurious arguments and remove them
JAL-4603 Nail down the number of wrappedWidths being rendered for an image export
JAL-4604 Now ensure non-buggy arguments are passed as-is
JAL-4581 Include com.dyspersja.Sha256MessageDigest to use a builtin hashing algorithm that j2s can transpile. No change in colours generated.
JAL-4603 prevent other ways of resizing the AlignFrame
JAL-4604 Check for old install4j set property for appdir to swap in new getdown-launcher.jar
JAL-4581. Added an MD5 hash for jalview.ext.htsjdk.HtsContigDb. Made jalview.util.DigestUtils for MD5 and SHA256 digest. Adapted net.meyfa.sha256.Sha256 to not use java.nio.IntBuffer and java.nio.ByteBuffer (not supported by SwingJS).
JAL-4604 getdown upgrade bug avert in GetdownApp.java
JAL-4604 Fixed Console logger being initiated too early and log level in props file not being set. This was causing jalview.util.Log4jTest.testLog4j to fail. Neatened the args in that test to use '--' to prevent mixed argstyle warning.
JAL-4603 Optionally don't grey out the status bar when calling AlignFrame.disableInput()
JAL-4607 Fix background colour of install4j wizard in dark mode, with update to 11.0.5
JAL-4604 Bug in LaunchUtils not removing previous 'appbase' 'appid' arguments
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1915 passed |
| JB › GTC › #18 | 7 months ago | Testless build | |
| JB › GDC › #218 | 7 months ago | Testless build | |
| JB › GDL › #77 | 7 months ago | Testless build | |
| JB › GPC › #357 | 7 months ago | Testless build |
| Build | Completed | Code commits | Tests |
|---|---|---|---|
| JB › GGR › #7 | 3 years ago |
JAL-629 Made ArgValuesMap helper class, simplifies readability/writing of the code and will allow arg position lookups
JAL-629 Add debug messages for more failing tests
JAL-4125 Additions to JvOptionPane and QuitHandler with StructureViewerBase handling closed frame during quit differently. Still not working as dialog content does not appear until after quithandling thread has finished (it's blocking EDT). Need to break the doDesktopQuit Callable up into sections, that add another bit to the end when necessary.
JAL-4088 Updated j8libs/*.jar in THIRDPARTYLIBS
JAL-629 bootstrap args and properties. Remember index of args for 'previous structure' defaulting of other args
JAL-629 test fixing
JAL-629 refactoring TFType. Remove i18n identification of annotation.
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629
JAL-4128 Catch RasterFormatException caused whilst resizing Overview window, recalculate OverviewDimensions od instead. Prevent negative OverviewDimensions being set to avoid problem with vertically fully shrunk overview window 'losing' the alignement canvas.
JAL-1988 Add a sleep to file save test to give time for file to save
JAL-629 nf-core sample alignment files and a2m versions
JAL-629 Fasta sequence id reading whitespace fix. Flexioble pae json keys and structure. Headless fixes. Logging fixes (MessageManager -- test broken). ArgParser and Console helper methods. Commands added e.g. --colour=gecos:flower.
JAL-3416 Fix file permissions on bundled macOS JREs
JAL-629 "updated" json-simple
Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629
JAL-3416 No longer needed
JAL-4064 JAL-4054 Corrected the tgz top-level dir from './Contents' to 'Contents' for mac JRE bundles for install4j (not strictly used, but might be in the future).
JAL-629 Attempts to add PAE to structure. --headless working. Make HTML output single threaded in headless mode. Delete an editor temp file.
JAL-4118 fix a small buglet in BackupFiles exhibited in tests on build server. Possible problem with filename with dirs in passed to BackupFiles.
JAL-629 added Alphafold cif, pdb and PAE json files to examples/AlphaFold
JAL-629 fix a PAEMatrix casting error
Merge branch 'develop' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
JAL-629 make sequence id key 'seqid'
JAL-629 better test fixes. --props=... instead of --debug
Merge branch 'develop' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
JAL-4125 Spanish translations
JAL-629 fixed a Log4j test by adding --debug arg
JAL-3416 Upgraded FlatLaf to 3.0 and added macOS theme for macOS
JAL-1988 Make sensible choices if only the opening file has been opened, and alter the message if an alignment has been fetched but not changed
JAL-4118 remove unnecessary sleep from QuitHandlerTest
JAL-629 example files from nf-core
JAL-629 adjust arg type for tempfac-shading -- was grabbing next argument
JAL-629 helper eclipse CLI run
JAL-4125 Move confirmation of closing external viewer windows into the quit handler, and allow all to close or not in closeViewer whilst quitting.
JAL-3416 Turn off (partial) flatlaf scaling for HiDPI in Linux and Java 8 - Some GUI parts unusable
Merge branch 'develop' into improvement/JAL-4111_suffixed_DEVELOP_channels
JAL-3416 remove a missed panel titlebar icon in TreePanel
JAL-3416 More explicit setting of FlatLaf macOS theme
JAL-3416 More tweaking of FlatLaf. Problem with macOS themed FlatLaf solved with new DesktopManager
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Testless build |
| Build | Completed | Code commits | Tests |
|---|