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Code commits
Jalview Gitlab
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Gitlab User c5863647f151f0f4e2100adc983690b4e60bbfbf
Merge branch 'development/Release_2_11_5_Branch' into releases/Release_2_11_5_Branch
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Gitlab User fae900933e918d9f3670c0c005d2c2a75190058e m
JAL-4617 bump release date to 3rd Dec (TODAY!)
- help/markdown/releases/release-2_11_5_1.md (version fae900933e918d9f3670c0c005d2c2a75190058e)
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Gitlab User 72e73571c0279e78742be5633019c09594a391f1 m
JAL-4617 release notes for JAL-2991,JAL-3084,JAL-4601,JAL-4603,JAL-4633,JAL-4634,JAL-4635
- help/markdown/releases/release-2_11_5_1.md (version 72e73571c0279e78742be5633019c09594a391f1)
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Gitlab User 1c6a6fa010faed5256f1dba8c8f5ebff001cc9f3 m
JAL-4633 JAL-4517 make sure sequence node 'isPlaceholder' is updated so sort by mechanism works correctly when tree restored from project or imported directly
- src/jalview/gui/TreePanel.java (version 1c6a6fa010faed5256f1dba8c8f5ebff001cc9f3)
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Gitlab User 03922b799e1683743f9e361271c15ab6ac652f37 m
JAL-4603 remove unused test data
- examples/PF03760.fa (version 03922b799e1683743f9e361271c15ab6ac652f37)
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Gitlab User aa9b04d454c094e49d21b391333c4abf661ee162 m
JAL-4635 redo patching of zeus URL to fix failing test
- test/jalview/ws/rest/RestClientTest.java (version aa9b04d454c094e49d21b391333c4abf661ee162)
- src/jalview/ws/rest/RestClient.java (version aa9b04d454c094e49d21b391333c4abf661ee162)
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Gitlab User cc05d28187e3100fd060e6b7e3b1795477c23e62 m
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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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> 5579c7411432a1b978a885bb1addf5853f0f3fd4 m
JAL-4603 Removed the not-working-test for release patch
- test/jalview/gui/ImageExporterTest.java (version 5579c7411432a1b978a885bb1addf5853f0f3fd4)
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Ben Soares <b.soares@dundee.ac.uk> bb7ec8ab8e1322cf4c632cf2e4ab278c5e380c83 m
JAL-4603 prevent other ways of resizing the AlignFrame
- src/jalview/gui/AlignFrame.java (version bb7ec8ab8e1322cf4c632cf2e4ab278c5e380c83)
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Ben Soares <b.soares@dundee.ac.uk> 013e5919ec7e940eef65a31635eee06671fa1b9b m
JAL-4603 grey panel on the glasspane now changes with size of AlignFrame
- src/jalview/gui/AlignFrame.java (version 013e5919ec7e940eef65a31635eee06671fa1b9b)
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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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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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Ben Soares <b.soares@dundee.ac.uk> afd28f2d71ea0f42474a3778145464f7438db890 m
JAL-4603 An example file needed for ImageExporterTest.java
- examples/PF03760.fa (version afd28f2d71ea0f42474a3778145464f7438db890)
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Ben Soares <b.soares@dundee.ac.uk> 87d35730f5e4c4caea99770d207ca7fafd37c3b8 m
JAL-4603 adjustments to the test
- test/jalview/gui/ImageExporterTest.java (version 87d35730f5e4c4caea99770d207ca7fafd37c3b8)
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Ben Soares <b.soares@dundee.ac.uk> cc043854810f31ff56d5ceaba4946ff998134151 m
JAL-4603 Optionally don't grey out the status bar when calling AlignFrame.disableInput()
- src/jalview/gui/ImageExporter.java (version cc043854810f31ff56d5ceaba4946ff998134151)
- src/jalview/gui/AlignFrame.java (version cc043854810f31ff56d5ceaba4946ff998134151)
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Ben Soares <b.soares@dundee.ac.uk> ec8d3f9c843ef349b4826e800134d6b9a28f3c6b m
JAL-4603 Use the disableInput() and enableInput() methods for the AlignFrame while exporting SVG/EPS
- src/jalview/gui/ImageExporter.java (version ec8d3f9c843ef349b4826e800134d6b9a28f3c6b)
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Ben Soares <b.soares@dundee.ac.uk> 891fa1368a556f6ac97bcc1a2e5753dbaf975e15 m
JAL-4603 Add glass pane methods to AlignFrame to disable/re-enable user input
- src/jalview/gui/AlignFrame.java (version 891fa1368a556f6ac97bcc1a2e5753dbaf975e15)
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Ben Soares <b.soares@dundee.ac.uk> d62b00e47e08c2f62f2fb18c77aad606e7c37e77 m
JAL-4603 Nail down the number of wrappedWidths being rendered for an image export
- src/jalview/gui/SeqCanvas.java (version d62b00e47e08c2f62f2fb18c77aad606e7c37e77)
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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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Renia Correya 99d6b27f309d96c096bbab9840128888ce769e78 m
JAL-4594 Fix for ss consensus appears to overlap with other annotation
- src/jalview/workers/SecondaryStructureConsensusThread.java (version 99d6b27f309d96c096bbab9840128888ce769e78)