JAL-2375 JAL-2376 First commit of implementation for Phyre2 result browsing, template...
authortcofoegbu <tcnofoegbu@dundee.ac.uk>
Fri, 20 Jan 2017 19:43:20 +0000 (19:43 +0000)
committertcofoegbu <tcnofoegbu@dundee.ac.uk>
Fri, 20 Jan 2017 19:43:20 +0000 (19:43 +0000)
commit42ca4613b0a07bab7c27a61b11acafdc9a3c27d1
treeff8c7652a70aad3109b784a14158a36eae579413
parentf1ad88cc8d9b26244086e5c24b73fb80b0ff0a38
JAL-2375 JAL-2376 First commit of implementation for Phyre2 result browsing, template parsing and structure mapping. Added fix for failing tests in SiftsClientTest, added improvement to un-offer cached option when cached data is unavailable, added improvement to include horizontal separator between structure filter options and manual input options, and other minor refactoring
500 files changed:
examples/testdata/phyre2results/56da5616b4559c93/56da5616b4559c93.job [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/PBS_jobid [new file with mode: 0644]
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examples/testdata/phyre2results/56da5616b4559c93/aligs/c1c4cA_.45.alig.txt [new file with mode: 0644]
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examples/testdata/phyre2results/56da5616b4559c93/aligs/c1ep3B_.77.alig.html [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c1ep3B_.77.alig.txt [new file with mode: 0644]
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examples/testdata/phyre2results/56da5616b4559c93/aligs/c1ffuA_.59.alig.txt [new file with mode: 0644]
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examples/testdata/phyre2results/56da5616b4559c93/aligs/c1l6vA_.42.alig.txt [new file with mode: 0644]
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examples/testdata/phyre2results/56da5616b4559c93/aligs/c1nekB_.69.alig.txt [new file with mode: 0644]
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examples/testdata/phyre2results/56da5616b4559c93/aligs/c2kanA_.95.alig.html [new file with mode: 0644]
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examples/testdata/phyre2results/56da5616b4559c93/aligs/c2mj3A_.34.alig.html [new file with mode: 0644]
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examples/testdata/phyre2results/56da5616b4559c93/aligs/c2piaA_.20.alig.html [new file with mode: 0644]
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examples/testdata/phyre2results/56da5616b4559c93/aligs/c2w3rG_.65.alig.html [new file with mode: 0644]
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examples/testdata/phyre2results/56da5616b4559c93/aligs/c2wlbB_.30.alig.html [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c2wlbB_.30.alig.txt [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c2y5cB_.28.alig.html [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c2y5cB_.28.alig.txt [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c3ah7A_.27.alig.html [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c3ah7A_.27.alig.txt [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c3b9jI_.70.alig.html [new file with mode: 0644]
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examples/testdata/phyre2results/56da5616b4559c93/aligs/c3bl5E_.99.alig.html [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c3bl5E_.99.alig.txt [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c3eubJ_.72.alig.html [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c3eubJ_.72.alig.txt [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c3hrdH_.52.alig.html [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c3hrdH_.52.alig.txt [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c3huiA_.39.alig.html [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c3huiA_.39.alig.txt [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c3hvzB_.85.alig.html [new file with mode: 0644]
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examples/testdata/phyre2results/56da5616b4559c93/aligs/c3j60I_.96.alig.html [new file with mode: 0644]
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examples/testdata/phyre2results/56da5616b4559c93/aligs/c3lxfC_.33.alig.html [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c3lxfC_.33.alig.txt [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c3p1mG_.40.alig.html [new file with mode: 0644]
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examples/testdata/phyre2results/56da5616b4559c93/aligs/c3vrbF_.66.alig.html [new file with mode: 0644]
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examples/testdata/phyre2results/56da5616b4559c93/aligs/c3zyvA_.74.alig.html [new file with mode: 0644]
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examples/testdata/phyre2results/56da5616b4559c93/aligs/c3zyyX_.25.alig.html [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c3zyyX_.25.alig.txt [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c4itkA_.15.alig.html [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c4itkA_.15.alig.txt [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c4ltuB_.36.alig.html [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c4ltuB_.36.alig.txt [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c4n58A_.1.alig.html [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c4n58A_.1.alig.txt [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c4p6vF_.24.alig.html [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c4p6vF_.24.alig.txt [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/c4uhxA_.75.alig.html [new file with mode: 0644]
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examples/testdata/phyre2results/56da5616b4559c93/aligs/c5frtC_.26.alig.html [new file with mode: 0644]
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examples/testdata/phyre2results/56da5616b4559c93/aligs/d1a70a_.2.alig.html [new file with mode: 0644]
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examples/testdata/phyre2results/56da5616b4559c93/aligs/d1awda_.10.alig.html [new file with mode: 0644]
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examples/testdata/phyre2results/56da5616b4559c93/aligs/d1dgja2.51.alig.html [new file with mode: 0644]
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examples/testdata/phyre2results/56da5616b4559c93/aligs/d1doia_.22.alig.html [new file with mode: 0644]
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examples/testdata/phyre2results/56da5616b4559c93/aligs/d1ep3b2.78.alig.html [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/d1ep3b2.78.alig.txt [new file with mode: 0644]
examples/testdata/phyre2results/56da5616b4559c93/aligs/d1ffva2.50.alig.html [new file with mode: 0644]
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resources/lang/Messages.properties
src/jalview/api/SiftsClientI.java
src/jalview/fts/core/FTSRestResponse.java
src/jalview/fts/service/pdb/PDBFTSPanel.java
src/jalview/fts/service/uniprot/UniprotFTSPanel.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AssociateStructureFileWithSeq.java [moved from src/jalview/gui/AssociatePdbFileWithSeq.java with 95% similarity]
src/jalview/gui/JvSummaryTable.java [new file with mode: 0644]
src/jalview/gui/StructureChooser.java
src/jalview/jbgui/GStructureChooser.java
src/jalview/structure/StructureMappingClient.java [new file with mode: 0644]
src/jalview/structure/StructureSelectionManager.java
src/jalview/structures/models/MappingOutputModel.java [moved from src/jalview/ws/sifts/MappingOutputPojo.java with 97% similarity]
src/jalview/ws/phyre2/Phyre2Client.java [new file with mode: 0644]
src/jalview/ws/phyre2/Phyre2SummaryPojo.java [new file with mode: 0644]
src/jalview/ws/sifts/SiftsClient.java
test/jalview/ws/phyre2/Phyre2ClientTest.java [new file with mode: 0644]
test/jalview/ws/sifts/SiftsClientTest.java