jalview

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patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available

patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available

semantics for determining if a PDB file has a SIFTs mapping - could be absorbed into the PDB metadata object

semantics for determining if a PDB file has a SIFTs mapping - could be absorbed into the PDB metadata object

magic logic to recognise which structure database provider client to use - PDB or AlphaFold - ensures metadata and annotation rows are propagates

magic logic to recognise which structure database provider client to use - PDB or AlphaFold - ensures metadata and annotation rows are propagates

Reviewing the alphafold + contact matrix patch for 2.11.2
Reviewing the alphafold + contact matrix patch for 2.11.2
remove debugging printlns

remove debugging printlns

aim is normally to avoid creating query-specific data containers on the core query response class

aim is normally to avoid creating query-specific data containers on the core query response class

? not sure this is correct

? not sure this is correct

Needs additionally: model_category created sequence_identity uniprot_start uniprot_end resolution coverage qmean_version ? model_version

Needs additionally:
model_category
created
sequence_identity
uniprot_start
uniprot_end
resolution
coverage
qmean_version ?
model_version

Evaluate 3D-Beacons dev path based on Arnaud's ERASMUS+ project code
Evaluate 3D-Beacons dev path based on Arnaud's ERASMUS+ project code
JAL-3851 start a listener with -testlistener and suggest a port with -testlistener_port. wget -S -O...
JAL-3851 start a listener with -testlistener and suggest a port with -testlistener_port. wget -S -O...
JAL-3854 patched SeqSeqUtils.deUniquify to not use instanceOf - seems to work

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    /src/jalview/analysis/SeqsetUtils.java
JAL-2994 disable tests for FileUtils path search methods on bamboo

JAL-3848 slivka preferences in javascript

JAL-3848 reinstate Fetch DB References submenu

JAL-3848 add compbio and jalview to direct connection list for J2S

JAL-3848 update jalview core with slivka classes, example file import and structure view

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    /utils/jalviewjs/classlists/jalview.txt
JAL-3853 - tweak test again - since failed a few commits after f6cb90d43782ca99cf2b1cbee2dc76bca3d1d466

JAL-3848 update swingJS runtime and transpiler to 3.3.1

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    /swingjs/ver/3.3.1-j11/DEV_NOTES.txt
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    /swingjs/ver/3.3.1-j11/SwingJS-site.zip
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    /swingjs/ver/3.3.1-j11/_j2sclasslist.txt
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    /swingjs/ver/3.3.1-j11/differences.txt
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    /swingjs/ver/3.3.1-j11/net.sf.j2s.core-j11.jar
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    /swingjs/ver/3.3.1-j11/timestamp
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    /swingjs/ver/3.3.1/DEV_NOTES.txt
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    /swingjs/ver/3.3.1/SwingJS-site.zip
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    /swingjs/ver/3.3.1/_j2sclasslist.txt
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    /swingjs/ver/3.3.1/differences.txt
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    /swingjs/ver/3.3.1/net.sf.j2s.core.jar
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    /swingjs/ver/3.3.1/timestamp
Merge branch 'improvement/JAL-3848_slivka_0.8' of https://source.jalview.org/git/jalview into improvement/JAL-3848_slivka_0.8

JAL-3848 Update slivka client javajs library.

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    /utils/jalviewjs/libjs/slivka-client-site.zip
JAL-3848 enable slivka services dialog in JalviewJS

JAL-3853 JAL-1870 toggle to enable/disable posterior probability transparency when rendering per sequence annotation row scores .. needs more work

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    /src/jalview/gui/AnnotationColourChooser.java
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    /src/jalview/gui/AnnotationRowFilter.java
JAL-3853 JAL-1870 patch tests for annotation colour gradient without transparency/per sequence annotation score encoding

JAL-1950 patch groovy bootstrap for importing hmmer3 json

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    /examples/groovy/hmmertestimport.groovy
JAL-3853 patch sequence annotation report code and tweak the test. When merging from 2.11.2 develop there will be conflicts that need merging re HTMLXML tags