Updates the Jalview Develop 2-12 builds at https://www.jalview.org/development/jalview_develop-2-12/
Build: #2 was successful Changes by Mateusz Warowny <mmzwarowny@dundee.ac.uk> and James Procter <j.procter@dundee.ac.uk>
Code commits
Jalview Git
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James Procter <j.procter@dundee.ac.uk> b8c0c4d78deccb7901d905a248aba47ea1c87a6a
Merge branch 'JAL-1601-direct-jpred4-rest-service' into development/Release_2_12_Branch
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> c94a8b5ef45fa2fbd903130f0246370c3bb4acc7
JAL-1601 fix phmmer client js library
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> 5f4add94664f2a0f0876a09a920988064a1d7322
JAL-1601 Add jslibs for hmmer and jpred
- utils/jalviewjs/libjs/simple-http-client-site.zip (version 5f4add94664f2a0f0876a09a920988064a1d7322) (diffs)
- utils/jalviewjs/libjs/jpred-client-site.zip (version 5f4add94664f2a0f0876a09a920988064a1d7322) (diffs)
- utils/jalviewjs/libjs/hmmer-client-site.zip (version 5f4add94664f2a0f0876a09a920988064a1d7322) (diffs)
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> f1a12cfc77755bd27f7a7afc6c0ce6d352e2222c
JAL-1601 Fix broken Alignment Annotation test
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> c56d4ccb5d054775cff8bc0f518cd51cc2dc1513
JAL-1601 Patch JPred4 service tests.
- test/jalview/ws2/actions/secstructpred/SecStructPredPDBSearchTaskTest.java (version c56d4ccb5d054775cff8bc0f518cd51cc2dc1513) (diffs)
- src/jalview/ws2/client/jpred4/JPred4WSClient.java (version c56d4ccb5d054775cff8bc0f518cd51cc2dc1513) (diffs)
- src/jalview/ws2/actions/secstructpred/SecStructPredPDBSearchTask.java (version c56d4ccb5d054775cff8bc0f518cd51cc2dc1513) (diffs)
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> 65074fc4efb2d445593e16c157e25fafb4191fde
JAL-1601 Expand secondary structure prediction tests
- examples/testdata/secstrpred/alignment0.concise (version 65074fc4efb2d445593e16c157e25fafb4191fde) (diffs)
- examples/testdata/secstrpred/alignment0.fa (version 65074fc4efb2d445593e16c157e25fafb4191fde) (diffs)
- examples/testdata/secstrpred/alignment0_aln.fa (version 65074fc4efb2d445593e16c157e25fafb4191fde) (diffs)
- examples/testdata/secstrpred/alignment0a_aln.fa (version 65074fc4efb2d445593e16c157e25fafb4191fde) (diffs)
- examples/testdata/secstrpred/sequence0.align (version 65074fc4efb2d445593e16c157e25fafb4191fde) (diffs)
- examples/testdata/secstrpred/sequence0.concise (version 65074fc4efb2d445593e16c157e25fafb4191fde) (diffs)
- examples/testdata/secstrpred/sequence0_input.fa (version 65074fc4efb2d445593e16c157e25fafb4191fde) (diffs)
- src/jalview/datamodel/AlignmentAnnotation.java (version 65074fc4efb2d445593e16c157e25fafb4191fde) (diffs)
- test/jalview/testutils/ScopeFunctions.java (version 65074fc4efb2d445593e16c157e25fafb4191fde) (diffs)
- test/jalview/ws2/actions/alignment/AlignmentActionTest.java (version 65074fc4efb2d445593e16c157e25fafb4191fde) (diffs)
- test/jalview/ws2/actions/secstructpred/SecStructPredMsaTaskTest.java (version 65074fc4efb2d445593e16c157e25fafb4191fde) (diffs)
- test/jalview/ws2/actions/secstructpred/SecStructPredPDBSearchTaskTest.java (version 65074fc4efb2d445593e16c157e25fafb4191fde) (diffs)
- test/jalview/ws2/actions/secstructpred/SecStructPredTaskTest.java (version 65074fc4efb2d445593e16c157e25fafb4191fde) (diffs)
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> 8c2fad69801213e33af18b00bbeff070782191b1
JAL-1601 Change getSubJobs return type
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> 3671f6391d5036f3ef37658492f053271c86f790
Merge branch 'bug/JAL-4313-make-visible-annot-fix' into JAL-1601-direct-jpred4-rest-service
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> 72e63582d51fbaa0cc5a3963abc96814f984039b m
JAL-4313 Clamp start and end ranges to array size
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> aa218da8aa3bf61463d84e478b1ed498d7d964cb m
JAL-4313 Test and patch annots trimming
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> fa529a2a75da021dd95a8b13205c2a6e4c5e460f
Merge branch 'bug/JAL-4313-make-visible-annot-fix' into JAL-1601-direct-jpred4-rest-service
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> a2e93a7f3acf8cf68ab89bc9d9af188543bdf6a3 m
JAL-4313 Test makeVisibleAnnotations
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> a95bd4060394f1f54bc9d17560cc5cf192127fa9 m
JAL-4313 Create Annotation tests
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> 2ea710eca2128ed962434e668bbf51180b6ceab8 m
JAL-4313 Create utilities to test annotations
- test/jalview/testutils/AnnotationsMatcher.java (version 2ea710eca2128ed962434e668bbf51180b6ceab8) (diffs)
- test/jalview/testutils/AnnotationsMatcherTest.java (version 2ea710eca2128ed962434e668bbf51180b6ceab8) (diffs)
- test/jalview/testutils/Matchers.java (version 2ea710eca2128ed962434e668bbf51180b6ceab8) (diffs)
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> d871e56cfedde274a256055824e8b0fc677a43fb m
JAL-4313 Change default trim end to (length - 1)
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> 614e136583b401b4273d92723fec158d84d4cb52 m
JAL-4313 Patch AnnotationsMatcher to match nulls
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> 5fe8a7444f60733f195cd812e75d7e873e688880
JAL-1601 Implement sec str pred for single sequences
- src/jalview/ws2/actions/secstructpred/SecStructPredAction.java (version 5fe8a7444f60733f195cd812e75d7e873e688880) (diffs)
- src/jalview/ws2/actions/secstructpred/SecStructPredPDBSearchTask.java (version 5fe8a7444f60733f195cd812e75d7e873e688880) (diffs)
- src/jalview/ws2/client/jpred4/JPred4WSDiscoverer.java (version 5fe8a7444f60733f195cd812e75d7e873e688880) (diffs)
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> 4826177c4126bfa7bb79eb1b7bd43f5c7cb62132
JAL-1601 Reuse existing "getNonEmptySequenceSet" method
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> c49683bef626d9c1de9d06e5f11039e6d4df55c3
JAL-1601 Rename task class to SecStructPredMsaTask
- src/jalview/ws2/actions/secstructpred/SecStructPredAction.java (version c49683bef626d9c1de9d06e5f11039e6d4df55c3) (diffs)
- src/jalview/ws2/actions/secstructpred/SecStructPredMsaTask.java (version c49683bef626d9c1de9d06e5f11039e6d4df55c3) (diffs)
- src/jalview/ws2/actions/secstructpred/SecStructPredTask.java (version c49683bef626d9c1de9d06e5f11039e6d4df55c3) (diffs)
- test/jalview/ws2/actions/secstructpred/SecStructPredTaskTest.java (version c49683bef626d9c1de9d06e5f11039e6d4df55c3) (diffs)
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> 4988ed19828c905d40e5a69d4a0fdb72f241bcad
JAL-1601 Move job class as inner task class
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> bd306b69256571ae575562d3079c842fa3be43f5
JAL-1601 Create alignment copying method in AlignmentUtils
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> 9f67f658a0f2028646b8189c57c03ffac709f27c
JAL-1601 Test alignment submitted to service
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> 8fda5a627c8066bf3939cb97fc358ba1389e92d2
JAL-1601 Propagate hidden columns to the output alignment
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> 5bf9dbf63ff6ea586fd92ca01b6b24be6b39421d
JAL-1601 Propagate representative sequence to the final output alignment
- src/jalview/ws2/actions/secstructpred/SecStructPredJob.java (version 5bf9dbf63ff6ea586fd92ca01b6b24be6b39421d) (diffs)
- src/jalview/ws2/actions/secstructpred/SecStructPredTask.java (version 5bf9dbf63ff6ea586fd92ca01b6b24be6b39421d) (diffs)
- src/jalview/ws2/gui/SearchServiceGuiHandler.java (version 5bf9dbf63ff6ea586fd92ca01b6b24be6b39421d) (diffs)
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> 66f174b1f1371d93ef9bef55be4a99255efab305
JAL-1601 Set job status to server error if collecting results throws an uncaught exception
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> d01453133dd3b6247e4d0a12a6dd6886d6053a6c
JAL-1601 Create SecStructPredTask class
- src/jalview/datamodel/AlignmentView.java (version d01453133dd3b6247e4d0a12a6dd6886d6053a6c) (diffs)
- src/jalview/ws2/actions/secstructpred/SecStructPredJob.java (version d01453133dd3b6247e4d0a12a6dd6886d6053a6c) (diffs)
- src/jalview/ws2/actions/secstructpred/SecStructPredTask.java (version d01453133dd3b6247e4d0a12a6dd6886d6053a6c) (diffs)
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> 96d1dabfb3cf7a879ef9f1b3bfce3d2fe8c46954
JAL-1601 Load and display JPred4 service in AlignFrame
- src/jalview/gui/AlignFrame.java (version 96d1dabfb3cf7a879ef9f1b3bfce3d2fe8c46954) (diffs)
- src/jalview/gui/Desktop.java (version 96d1dabfb3cf7a879ef9f1b3bfce3d2fe8c46954) (diffs)
- src/jalview/ws2/actions/BaseAction.java (version 96d1dabfb3cf7a879ef9f1b3bfce3d2fe8c46954) (diffs)
- src/jalview/ws2/gui/WebServicesMenuManager.java (version 96d1dabfb3cf7a879ef9f1b3bfce3d2fe8c46954) (diffs)
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> f2ae581a7c93c7c92a574d6c92ee7e0d9fb7b775
JAL-1601 Implement JPred4 WS client and discoverer
- j11lib/jpred-client-1.0-SNAPSHOT.jar (version f2ae581a7c93c7c92a574d6c92ee7e0d9fb7b775) (diffs)
- src/jalview/ws2/client/jpred4/JPred4WSClient.java (version f2ae581a7c93c7c92a574d6c92ee7e0d9fb7b775) (diffs)
- src/jalview/ws2/client/jpred4/JPred4WSDiscoverer.java (version f2ae581a7c93c7c92a574d6c92ee7e0d9fb7b775) (diffs)
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> 589fd82e772d0f17cdb49eb995f6a45603d87176
JAL-1601 Create action and task for sec. str. pred. jobs
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> c2bf9f8908abdf8e3604800b20e443f5bc73393b
JAL-1601 Implement JPred4 client and discoverer
- j11lib/jpred-client-1.0-SNAPSHOT.jar (version c2bf9f8908abdf8e3604800b20e443f5bc73393b) (diffs)
- src/jalview/ws2/client/jpred4/JPred4WSClient.java (version c2bf9f8908abdf8e3604800b20e443f5bc73393b) (diffs)
- src/jalview/ws2/client/jpred4/JPred4WSDiscoverer.java (version c2bf9f8908abdf8e3604800b20e443f5bc73393b) (diffs)
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> 0cffc343e997247a84774b57ba41ad6e62b2c231
JAL-1601 Update javadoc of getAlignmentAndHiddenColumns
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> 852ce759351d72bfb696b8cc3e806a156a2fbbd7
JAL-1601 Add sec str pred provider and client interfaces
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Mateusz Warowny <mmzwarowny@dundee.ac.uk> 8899690eec8b1e2b4c74da42ed02d0453c5b7141
JAL-1601 Test getVisibleCongigMapFor