Build: #8 failed
Job: Clover and Tests failed
Code commits
Jalview Gitlab
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Gitlab User cc05d28187e3100fd060e6b7e3b1795477c23e62
Merge branch 'development/Release_2_11_5_Branch' into bug/JAL-4603_export_svg_files_missing_part_of_sequence
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Gitlab User e99989fb26bdc128c3e93c6d2ccaf13d9ec5e172 m
JAL-4635 - patch http->https in SHMR URL stored in jalview preferences
- src/jalview/ws/rest/RestClient.java (version e99989fb26bdc128c3e93c6d2ccaf13d9ec5e172)
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Gitlab User f26d7c074a87a9d526292ddc3be2987213875459 m
Merge branch 'bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest' into development/Release_2_11_5_Branch
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Gitlab User 6f2c311824a96fc172e1713db11e8c1cdb24e48c m
JAL-4633 attempted workaround - really need a j2stest to verify that the j2s-ed expression is correct.
- src/jalview/gui/TreeCanvas.java (version 6f2c311824a96fc172e1713db11e8c1cdb24e48c)
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Gitlab User 4c26acdffa837bb57913025f467987146508c9b8 m
JAL-4634 patch out nested stream processing so j2s transpilation works
- src/jalview/analysis/AlignmentUtils.java (version 4c26acdffa837bb57913025f467987146508c9b8)
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Gitlab User b9cef2bab75d9d5e6689e901ae49654ceb9aa4c7 m
JAL-3084 patch out Startup panel in preferences
- src/jalview/jbgui/GPreferences.java (version b9cef2bab75d9d5e6689e901ae49654ceb9aa4c7)
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Gitlab User 2776620fe32b0861edcc30a761cfb9e333a2d504 m
Merge branch 'patch/JAL-4601_stk_ss_annots_showhide' into development/Release_2_11_5_Branch
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Ben Soares <b.soares@dundee.ac.uk> c0746f1378bd64b7cf72b082eca210d21f86feff m
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).
- src/net/meyfa/sha256/Sha256.java (version c0746f1378bd64b7cf72b082eca210d21f86feff)
- src/jalview/util/StringUtils.java (version c0746f1378bd64b7cf72b082eca210d21f86feff)
- src/jalview/util/DigestUtils.java (version c0746f1378bd64b7cf72b082eca210d21f86feff)
- src/jalview/ext/htsjdk/HtsContigDb.java (version c0746f1378bd64b7cf72b082eca210d21f86feff)
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Gitlab User 3640cfb3a1a72b0a7514f5406b223cad955aa1fc m
JAL-4601 expand scope - test alignment from PF02008 which has secondary structure annotations per-sequence - show/hide ss annotations show show/hide consensus
- src/jalview/viewmodel/AlignmentViewport.java (version 3640cfb3a1a72b0a7514f5406b223cad955aa1fc)
- src/jalview/gui/PopupMenu.java (version 3640cfb3a1a72b0a7514f5406b223cad955aa1fc)
- src/jalview/gui/AnnotationLabels.java (version 3640cfb3a1a72b0a7514f5406b223cad955aa1fc)
- src/jalview/gui/AlignmentPanel.java (version 3640cfb3a1a72b0a7514f5406b223cad955aa1fc)
- src/jalview/gui/AlignFrame.java (version 3640cfb3a1a72b0a7514f5406b223cad955aa1fc)
- src/jalview/appletgui/AnnotationLabels.java (version 3640cfb3a1a72b0a7514f5406b223cad955aa1fc)
- src/jalview/api/AlignViewportI.java (version 3640cfb3a1a72b0a7514f5406b223cad955aa1fc)
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Gitlab User 296fa7802e4da3abaa3f1bdd8f8ae2e60497d62d m
JAL-4617 - updated release notes for JAL-4594 and JAL-4601
- help/markdown/whatsnew/whatsnew-2_11_5_1.md (version 296fa7802e4da3abaa3f1bdd8f8ae2e60497d62d)
- help/markdown/releases/release-2_11_5_1.md (version 296fa7802e4da3abaa3f1bdd8f8ae2e60497d62d)
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Gitlab User 6699edd3618298e5fcd92d67a61e9b175b4d444f m
Merge branch 'bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus' into development/Release_2_11_5_Branch
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Gitlab User acbb7d39481e53918a63f69cd008b4f6bbd7a588 m
JAL-835 fix format list tests for a3m
- test/jalview/io/FileFormatsTest.java (version acbb7d39481e53918a63f69cd008b4f6bbd7a588)
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Gitlab User fcc56071280b5c38964437c8b723e0d1e7f1ac13 m
JAL-835 slightly faster a3m import --- can still be faster but good enough for release
- test/jalview/datamodel/SequenceTest.java (version fcc56071280b5c38964437c8b723e0d1e7f1ac13)
- src/jalview/datamodel/SequenceI.java (version fcc56071280b5c38964437c8b723e0d1e7f1ac13)
- src/jalview/datamodel/Sequence.java (version fcc56071280b5c38964437c8b723e0d1e7f1ac13)
- src/jalview/analysis/AlignmentUtils.java (version fcc56071280b5c38964437c8b723e0d1e7f1ac13)
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Gitlab User 3b1560c22adbb362d84fcfc5d61b8ce200417b46 m
JAL-4601 fix failing tests
- test/jalview/io/FileFormatsTest.java (version 3b1560c22adbb362d84fcfc5d61b8ce200417b46)
- test/jalview/analysis/AlignmentUtilsTests.java (version 3b1560c22adbb362d84fcfc5d61b8ce200417b46)
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Gitlab User 780b3934c0436f711354200a1a9b48b8b5d3fc67 m
JA-4601 - refactored the 'setSecondaryStructureSources' routine to alignmentViewportI since it is viewportlocal, and it is now called from alignmentViewport.updateSSConsensus Now there are almost certainly too many calls to uodate/refresh on import of annotations.. will try and reduce in next commit
- src/jalview/workers/SecondaryStructureConsensusThread.java (version 780b3934c0436f711354200a1a9b48b8b5d3fc67)
- src/jalview/viewmodel/AlignmentViewport.java (version 780b3934c0436f711354200a1a9b48b8b5d3fc67)
- src/jalview/api/AlignViewportI.java (version 780b3934c0436f711354200a1a9b48b8b5d3fc67)
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Ben Soares <b.soares@dundee.ac.uk> 916a3ca4dfb56bc9f62a3c626dfa5ed46e56cd18 m
JAL-4601 Enable Secondary Structure Consensus to appear immediately after annotation file load
- src/jalview/gui/AlignFrame.java (version 916a3ca4dfb56bc9f62a3c626dfa5ed46e56cd18)
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Ben Soares <b.soares@dundee.ac.uk> f401f2c455e830cc4b5f1479f74bd581ce835e61 m
Merge branch 'development/Release_2_11_5_Branch' into bug/JAL-4594_ss_consensus_overlap_other_annot
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Gitlab User d96cd12c18b602f601a84a1a90774e5a203fa154 m
JAL-4617 'whats new' for 2.11.5.1 and update fileformat docs for .a3m
- help/markdown/whatsnew/whatsnew-2_11_5_1.md (version d96cd12c18b602f601a84a1a90774e5a203fa154)
- help/help/html/io/fileformats.html (version d96cd12c18b602f601a84a1a90774e5a203fa154)
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Gitlab User 26e5206fcd793334724fa4f2127ff956d994ef72 m
JAL-4602 JAL-4617 release notes & docs for autohiding of global ss consensus for just one provider
- help/markdown/releases/release-2_11_5_1.md (version 26e5206fcd793334724fa4f2127ff956d994ef72)
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Gitlab User d0a286713116c07f50d958c9c9e06dfa29e3d494 m
JAL-4602 JAL-4617 release notes & docs for autohiding of global ss consensus for just one provider
- help/help/html/calculations/protssconsensus.html (version d0a286713116c07f50d958c9c9e06dfa29e3d494)
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Gitlab User 89d8c1d5df9f40af9bd27e1591837ad9532a67a2 m
Merge branch 'feature/JAL-4602_Hide_All_SS_consensus_for_single_provider' into development/Release_2_11_5_Branch
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Ben Soares <b.soares@dundee.ac.uk> d92ec98a32dc75a9fd0c635c803d00d60ce92f97 m
JAL-4581 added MIT license listed for https://github.com/meyfa/java-sha256
- THIRDPARTYLIBS (version d92ec98a32dc75a9fd0c635c803d00d60ce92f97)
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Ben Soares <b.soares@dundee.ac.uk> 5916d4ddba097390cb43ca16a412af5a54a607b1 m
JAL-4581 Switched to using https://github.com/meyfa/java-sha256 which has MIT license
- test/jalview/util/StringUtilsTest.java (version 5916d4ddba097390cb43ca16a412af5a54a607b1)
- src/net/meyfa/sha256/Sha256.java (version 5916d4ddba097390cb43ca16a412af5a54a607b1)
- src/jalview/util/StringUtils.java (version 5916d4ddba097390cb43ca16a412af5a54a607b1)
- src/com/dyspersja/Sha256MessageDigest.java (version 5916d4ddba097390cb43ca16a412af5a54a607b1)
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Ben Soares <b.soares@dundee.ac.uk> 5f8ff8c1e6213da20874cd2274dd4ec70567240b m
Merge branch 'development/Release_2_11_5_Branch' into bug/JAL-4594_ss_consensus_overlap_other_annot
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Ben Soares <b.soares@dundee.ac.uk> df9575c2108ec7ce106fab874d3d82101381b18e m
JAL-4581 Include com.dyspersja.Sha256MessageDigest to use a builtin hashing algorithm that j2s can transpile. No change in colours generated.
- src/jalview/util/StringUtils.java (version df9575c2108ec7ce106fab874d3d82101381b18e)
- src/com/dyspersja/Sha256MessageDigest.java (version df9575c2108ec7ce106fab874d3d82101381b18e)
- j8lib/commons-codec-1.20.0.jar (version df9575c2108ec7ce106fab874d3d82101381b18e)
- j11lib/commons-codec-1.20.0.jar (version df9575c2108ec7ce106fab874d3d82101381b18e)
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Gitlab User b0fd08a15bfaff92e5d6c81412f82b5902ac284e m
JAL-4617 release notes for JAL-4626,JAL-835
- help/markdown/releases/release-2_11_5_1.md (version b0fd08a15bfaff92e5d6c81412f82b5902ac284e)
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Gitlab User f78fcddb036b7af746d360ab4253c44958640ff4 m
Merge branch 'feature/JAL-835_hhsuite_a3m_support' into development/Release_2_11_5_Branch
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Gitlab User ca386e6bc36dc5a22b753f9a7417b26e1f5ea349 m
Merge branch 'patch/JAL-4626_alphafoldVersionTracker' into development/Release_2_11_5_Branch
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Gitlab User 2c607230589b9dd93f77cf07e9e7c0004f23a9a5 m
JAL-4617 release notes for JAL-4606 JAL-4521
- help/markdown/releases/release-2_11_5_1.md (version 2c607230589b9dd93f77cf07e9e7c0004f23a9a5)
- .settings/org.eclipse.buildship.core.prefs (version 2c607230589b9dd93f77cf07e9e7c0004f23a9a5)
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Renia Correya 4a5185652a9c0450b46184af8a5fb7233e8b707f m
JAL-4606 Bug fix for Jmol incorrect path interpretation on windows
- src/jalview/structure/StructureSelectionManager.java (version 4a5185652a9c0450b46184af8a5fb7233e8b707f)
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Ben Soares <b.soares@dundee.ac.uk> a9267ce9a9c38d37b3b1674702fc7b9bb4f6a8d5 m
JAL-4581 Updated commons-codec jar and switched SHA256 hash to use it
- src/jalview/util/StringUtils.java (version a9267ce9a9c38d37b3b1674702fc7b9bb4f6a8d5)
- j8lib/commons-codec-1.3.jar (version a9267ce9a9c38d37b3b1674702fc7b9bb4f6a8d5)
- j8lib/commons-codec-1.20.0.jar (version a9267ce9a9c38d37b3b1674702fc7b9bb4f6a8d5)
- j11lib/commons-codec-1.3.jar (version a9267ce9a9c38d37b3b1674702fc7b9bb4f6a8d5)
- j11lib/commons-codec-1.20.0.jar (version a9267ce9a9c38d37b3b1674702fc7b9bb4f6a8d5)
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Renia Correya e0ed80e7c5755b4fbc2c1a6976f9666e246ac59d m
JAL-4602 Hide 'All' ss consensus annotation when one type is available
- src/jalview/workers/SecondaryStructureConsensusThread.java (version e0ed80e7c5755b4fbc2c1a6976f9666e246ac59d)
- src/jalview/viewmodel/AlignmentViewport.java (version e0ed80e7c5755b4fbc2c1a6976f9666e246ac59d)
- src/jalview/gui/AlignFrame.java (version e0ed80e7c5755b4fbc2c1a6976f9666e246ac59d)
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Gitlab User 377f1f52a15db66fd5768669a50bfda03250a6c7 m
Merge branch 'development/Release_2_11_5_Branch' into patch/JAL-4626_alphafoldVersionTracker
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Gitlab User 9c98e9d9d1171c8085ed2ca1db4ffeb8b606c616 m
JAL-4626 pick up AF_VERSION when first referred to
- test/jalview/ws/dbsources/EBIAlphaFoldTest.java (version 9c98e9d9d1171c8085ed2ca1db4ffeb8b606c616)
- src/jalview/ws/dbsources/EBIAlfaFold.java (version 9c98e9d9d1171c8085ed2ca1db4ffeb8b606c616)
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Ben Soares f306b783e2b09b813cffc5c6cd4bab2c46d74f12 m
Merge branch 'feature/JAL-4521_Allow_PCA_tree_for_one_seq_mul_ss' into 'development/Release_2_11_5_Branch'
JAL-4521 Allow tree calculation for one sequence multiple structure
See merge request jalview/jalview!23 -
Ben Soares <b.soares@dundee.ac.uk> 9369deda21dc14b2f5921ce5208142e89f295600 m
Merge branch 'bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection' into development/Release_2_11_5_Branch
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Ben Soares <b.soares@dundee.ac.uk> 0d10b35174aa38a4a48c5965e683dabe47dcd553 m
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.
- test/jalview/util/Log4jTest.java (version 0d10b35174aa38a4a48c5965e683dabe47dcd553)
- src/jalview/bin/Jalview.java (version 0d10b35174aa38a4a48c5965e683dabe47dcd553)
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Renia Correya e3c46fcd8ca84107f389e7e5bf51d3fc4f10dbc3 m
JAL-4521 Allow tree calculation for SS for 1 seq and muliple structures
Allow calculation dialog/score model to be selected for secondary
structure when working with 1 sequence + many structures.- src/jalview/gui/CalculationChooser.java (version e3c46fcd8ca84107f389e7e5bf51d3fc4f10dbc3)
- src/jalview/gui/AlignFrame.java (version e3c46fcd8ca84107f389e7e5bf51d3fc4f10dbc3)
- resources/lang/Messages.properties (version e3c46fcd8ca84107f389e7e5bf51d3fc4f10dbc3)
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Gitlab User 1e51a6fea55e3be2947e7bcd5018494754acb92b m
JAL-835 hook in A3mFile as an importable type and recognise filenames that have .a3m suffixes as an A3m file
- src/jalview/io/IdentifyFile.java (version 1e51a6fea55e3be2947e7bcd5018494754acb92b)
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Gitlab User 754034afa3c6d7859c83cd9d6f2c8f11276e6cef m
JAL-835 support a3m file import
- src/jalview/io/FileFormat.java (version 754034afa3c6d7859c83cd9d6f2c8f11276e6cef)
- src/jalview/io/FastaFile.java (version 754034afa3c6d7859c83cd9d6f2c8f11276e6cef)
- src/jalview/io/A3mFile.java (version 754034afa3c6d7859c83cd9d6f2c8f11276e6cef)
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Gitlab User 407915ca3bba33d94b3529b49b52175efdc71dce m
Merge branch 'development/Release_2_11_5_Branch' into feature/JAL-835_hhsuite_a3m_support
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Gitlab User 3bf9d58d0cd1b768503f644d8126520f565af95e m
JAL-4243 JAL-4617 release notes for bio-tools record update
- help/markdown/releases/release-2_11_5_1.md (version 3bf9d58d0cd1b768503f644d8126520f565af95e)
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Gitlab User 665ae4644ceccd2ff2d5e70181c6baa189f3797d m
Merge branch 'update/JAL-4243_biotools_json_record' into development/Release_2_11_5_Branch
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Gitlab User f92e7a119f2371146d45a90940f3ff6cc0e63a1c m
Merge branch 'development/Release_2_11_5_Branch' into bug/JAL-4594_ss_consensus_overlap_other_annot
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Gitlab User 94dd8e493d9351cfeb5a07c4a13583aa225cf21a m
JAL-4607 release notes for 2.11.5.1 (JAL-4617)
- help/markdown/releases/release-2_11_5_1.md (version 94dd8e493d9351cfeb5a07c4a13583aa225cf21a)
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Gitlab User 28d0eb545da3936b9c0fda00bd49eea577a1ebee m
Merge branch 'improvement/JAL-4607_install4j_dark_mode_background_colour' into development/Release_2_11_5_Branch
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Gitlab User 7875d21f5c728fc242817aa1020e2cff18e41300 m
JAL-4604 plus JAL-4617 release notes and version bump
- help/markdown/whatsnew/whatsnew-2_11_5_1.md (version 7875d21f5c728fc242817aa1020e2cff18e41300)
- help/markdown/releases/release-2_11_5_1.md (version 7875d21f5c728fc242817aa1020e2cff18e41300)
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Gitlab User 33005ea58c7b9583772afb479c7f3289f932d0d3 m
Merge branch 'bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection' into development/Release_2_11_5_Branch
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Renia Correya 99d6b27f309d96c096bbab9840128888ce769e78 m
JAL-4594 Fix for ss consensus appears to overlap with other annotation
- src/jalview/workers/SecondaryStructureConsensusThread.java (version 99d6b27f309d96c096bbab9840128888ce769e78)
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Gitlab User de404214a47d594b38f4d5ce869e357f3a36ff6b m
JAL-835 enhanced ShiftList to support a3m insert expansion via AlignmentUtils.a3mToMSA and provided a groovy script PoC
- test/jalview/util/ShiftListTest.java (version de404214a47d594b38f4d5ce869e357f3a36ff6b)
- test/jalview/analysis/AlignmentUtilsTests.java (version de404214a47d594b38f4d5ce869e357f3a36ff6b)
- src/jalview/util/ShiftList.java (version de404214a47d594b38f4d5ce869e357f3a36ff6b)
- src/jalview/analysis/AlignmentUtils.java (version de404214a47d594b38f4d5ce869e357f3a36ff6b)
- examples/testdata/query.a3m.fa (version de404214a47d594b38f4d5ce869e357f3a36ff6b)
- examples/testdata/query.a3m (version de404214a47d594b38f4d5ce869e357f3a36ff6b)
- examples/groovy/a3mtoFasta.groovy (version de404214a47d594b38f4d5ce869e357f3a36ff6b)
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Ben Soares <b.soares@dundee.ac.uk> c662cdbcf8253d09fe5f7215ba99385e9e9be2ae m
JAL-4607 minor changes required for install4j 11.0.5 gradle plugin
- build.gradle (version c662cdbcf8253d09fe5f7215ba99385e9e9be2ae)
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Ben Soares <b.soares@dundee.ac.uk> 6221773ca9538a097b31b1d6f53097774c2485a1 m
JAL-4607 Fix background colour of install4j wizard in dark mode, with update to 11.0.5
- utils/install4j/install4j11_template.install4j (version 6221773ca9538a097b31b1d6f53097774c2485a1)
- build.gradle (version 6221773ca9538a097b31b1d6f53097774c2485a1)
-
Ben Soares <b.soares@dundee.ac.uk> 01b48f04818d683d5d0f90d7833ae0c6d4191a8c m
JAL-4604 Allow getdown to use its own version in jar comparison
- src/jalview/util/LaunchUtils.java (version 01b48f04818d683d5d0f90d7833ae0c6d4191a8c)
- j8lib/getdown-core.jar (version 01b48f04818d683d5d0f90d7833ae0c6d4191a8c)
- j11lib/getdown-core.jar (version 01b48f04818d683d5d0f90d7833ae0c6d4191a8c)
- getdown/src/getdown/core/src/main/java/jalview/util/LaunchUtils.java (version 01b48f04818d683d5d0f90d7833ae0c6d4191a8c)
- getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java (version 01b48f04818d683d5d0f90d7833ae0c6d4191a8c)
- getdown/lib/getdown-launcher.jar (version 01b48f04818d683d5d0f90d7833ae0c6d4191a8c)
- getdown/lib/getdown-launcher-local.jar (version 01b48f04818d683d5d0f90d7833ae0c6d4191a8c)
- getdown/lib/getdown-core.jar (version 01b48f04818d683d5d0f90d7833ae0c6d4191a8c)
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Ben Soares <b.soares@dundee.ac.uk> 473e3dd1153b3493888e8841a5fec30eed205b92 m
JAL-4604 removed a line marked REMOVE THIS LINE
- j8lib/getdown-core.jar (version 473e3dd1153b3493888e8841a5fec30eed205b92)
- j11lib/getdown-core.jar (version 473e3dd1153b3493888e8841a5fec30eed205b92)
- getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/GetdownApp.java (version 473e3dd1153b3493888e8841a5fec30eed205b92)
- getdown/lib/getdown-launcher.jar (version 473e3dd1153b3493888e8841a5fec30eed205b92)
- getdown/lib/getdown-launcher-local.jar (version 473e3dd1153b3493888e8841a5fec30eed205b92)
- getdown/lib/getdown-core.jar (version 473e3dd1153b3493888e8841a5fec30eed205b92)
-
Ben Soares <b.soares@dundee.ac.uk> c7ec2412ae67d38a9306a4f68e946b8eeecabff2 m
JAL-4604 This needed for some old installations. Normally set in getdown separately
- gradle.properties (version c7ec2412ae67d38a9306a4f68e946b8eeecabff2)
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Ben Soares <b.soares@dundee.ac.uk> 4659cdba6eac42181072c7437e2f2742a2333cb3 m
JAL-4604 Now ensure non-buggy arguments are passed as-is
- j8lib/getdown-core.jar (version 4659cdba6eac42181072c7437e2f2742a2333cb3)
- j11lib/getdown-core.jar (version 4659cdba6eac42181072c7437e2f2742a2333cb3)
- getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/GetdownApp.java (version 4659cdba6eac42181072c7437e2f2742a2333cb3)
- getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java (version 4659cdba6eac42181072c7437e2f2742a2333cb3)
- getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java (version 4659cdba6eac42181072c7437e2f2742a2333cb3)
- getdown/lib/getdown-launcher.jar (version 4659cdba6eac42181072c7437e2f2742a2333cb3)
- getdown/lib/getdown-launcher-local.jar (version 4659cdba6eac42181072c7437e2f2742a2333cb3)
- getdown/lib/getdown-core.jar (version 4659cdba6eac42181072c7437e2f2742a2333cb3)
-
Ben Soares <b.soares@dundee.ac.uk> 28fb06e0e3779a4a52075ac7957a8d953256bfef m
JAL-4604 Ensure getdownappdir is now set and passed through. Some indentation fixes in getdown...Application.java
- src/jalview/bin/Jalview.java (version 28fb06e0e3779a4a52075ac7957a8d953256bfef)
- j8lib/getdown-core.jar (version 28fb06e0e3779a4a52075ac7957a8d953256bfef)
- j11lib/getdown-core.jar (version 28fb06e0e3779a4a52075ac7957a8d953256bfef)
- getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java (version 28fb06e0e3779a4a52075ac7957a8d953256bfef)
- getdown/lib/getdown-launcher.jar (version 28fb06e0e3779a4a52075ac7957a8d953256bfef)
- getdown/lib/getdown-launcher-local.jar (version 28fb06e0e3779a4a52075ac7957a8d953256bfef)
- getdown/lib/getdown-core.jar (version 28fb06e0e3779a4a52075ac7957a8d953256bfef)
-
Ben Soares <b.soares@dundee.ac.uk> b4309df8f01a5abf9d7d73cea76b1f9b9aa3a3f6 m
JAL-4604 Check for old install4j set property for appdir to swap in new getdown-launcher.jar
- src/jalview/bin/Jalview.java (version b4309df8f01a5abf9d7d73cea76b1f9b9aa3a3f6)
-
Ben Soares <b.soares@dundee.ac.uk> 7feb4abf2fc4dd85712b5824af621206ca5603eb m
JAL-4604 Changes to getdown/LaunchUtils to fix the arguments bug, and also detect being launched with the spurious arguments and remove them
- src/jalview/util/LaunchUtils.java (version 7feb4abf2fc4dd85712b5824af621206ca5603eb)
- j8lib/getdown-core.jar (version 7feb4abf2fc4dd85712b5824af621206ca5603eb)
- j11lib/getdown-core.jar (version 7feb4abf2fc4dd85712b5824af621206ca5603eb)
- getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/GetdownApp.java (version 7feb4abf2fc4dd85712b5824af621206ca5603eb)
- getdown/src/getdown/core/src/main/java/jalview/util/LaunchUtils.java (version 7feb4abf2fc4dd85712b5824af621206ca5603eb)
- getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java (version 7feb4abf2fc4dd85712b5824af621206ca5603eb)
- getdown/lib/getdown-launcher.jar (version 7feb4abf2fc4dd85712b5824af621206ca5603eb)
- getdown/lib/getdown-launcher-local.jar (version 7feb4abf2fc4dd85712b5824af621206ca5603eb)
- getdown/lib/getdown-core.jar (version 7feb4abf2fc4dd85712b5824af621206ca5603eb)
-
Ben Soares <b.soares@dundee.ac.uk> ba4e65d505f158f9a0397a6b669b392155ca1cb8 m
JAL-4604 Bug in LaunchUtils not removing previous 'appbase' 'appid' arguments
- src/jalview/util/LaunchUtils.java (version ba4e65d505f158f9a0397a6b669b392155ca1cb8)
- j8lib/getdown-core.jar (version ba4e65d505f158f9a0397a6b669b392155ca1cb8)
- j11lib/getdown-core.jar (version ba4e65d505f158f9a0397a6b669b392155ca1cb8)
- getdown/src/getdown/core/src/main/java/jalview/util/LaunchUtils.java (version ba4e65d505f158f9a0397a6b669b392155ca1cb8)
- getdown/lib/getdown-launcher.jar (version ba4e65d505f158f9a0397a6b669b392155ca1cb8)
- getdown/lib/getdown-launcher-local.jar (version ba4e65d505f158f9a0397a6b669b392155ca1cb8)
- getdown/lib/getdown-core.jar (version ba4e65d505f158f9a0397a6b669b392155ca1cb8)
-
Ben Soares <b.soares@dundee.ac.uk> ce46f05124d94cb4f54117bc98e9a295b4c1199d m
JAL-4604 getdown upgrade bug avert in GetdownApp.java
- src/jalview/util/StringUtils.java (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
- j8lib/getdown-core.jar (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
- j11lib/getdown-core.jar (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
- help/markdown/whatsnew/whatsnew-2_11_5_1.md (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
- help/markdown/releases/release-2_11_5_1.md (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
- getdown/src/getdown/pom.xml (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
- getdown/src/getdown/mvn_cmd (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
- getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/GetdownApp.java (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
- getdown/src/getdown/launcher/pom.xml (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
- getdown/src/getdown/core/src/main/java/jalview/util/StringUtils.java (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
- getdown/src/getdown/core/pom.xml (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
- getdown/src/getdown/ant/pom.xml (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
- getdown/lib/getdown-launcher.jar (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
- getdown/lib/getdown-launcher-local.jar (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
- getdown/lib/getdown-core.jar (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
- getdown/lib/JVL_VERSION (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
- getdown/lib/FJVL_VERSION (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
- RELEASE (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
-
Ben Soares <b.soares@dundee.ac.uk> 59b555ddd49df7b78598773826980346e320f232 m
JAL-4243 Bio.tools JSON record updated for 2.11.5.0 and added to Bio.tools
- utils/biotools/Jalview.json (version 59b555ddd49df7b78598773826980346e320f232)