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...
WIP
WIP
Merge branch 'bug/JAL-3806_mappingCoversSequence' into releases/Release_2_11_1_Branch

JAL-3816 JAL-3814 JAL-3813 JAL-3812 JAL-3811 JAL-3818 release notes and date for 2.11.1.4 release

This is likely an improvement on the "roll your own" pattern of setting Runnable handlers for dialog responses as hacked together for JalviewJS (JAL-3048). If so, it would be preferable (but no sma...

This is likely an improvement on the "roll your own" pattern of setting Runnable handlers for dialog responses as hacked together for JalviewJS (JAL-3048). If so, it would be preferable (but no small job) to change all dialogs to this pattern.

There are still numerous dialogs that have not been changed to either pattern (so won't work in SwingJS): see comment at https://issues.jalview.org/browse/?focusedCommentId=20525&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#JAL-3048comment-20525.

Class has some compiler warnings which could easily be resolved (typed Hashtable, unused import).

Class has some compiler warnings which could easily be resolved (typed Hashtable, unused import).

It would be good to add Javadoc to this method

It would be good to add Javadoc to this method

As an aside, I would suggest inlining (removing) the two overloaded constructors that call this one (to reduce code bloat).

As an aside, I would suggest inlining (removing) the two overloaded constructors that call this one (to reduce code bloat).

Merge branch 'bug/JAL-3818_jmolDeadlock' into releases/Release_2_11_1_Branch

Merge branch 'releases/Release_2_11_1_4_debianpatches' into releases/Release_2_11_1_Branch

JAL-3818 process Jmol callbacks in AWT thread
JAL-3818 process Jmol callbacks in AWT thread
JAL-3521 High quality file icons for jalview associated files, and associated mime-type icon references

    • binary
    /utils/debian/debian/icons/128x128/apps/jalview-icon.png
    • binary
    /utils/debian/debian/icons/16x16/apps/jalview-icon.png
    • binary
    /utils/debian/debian/icons/256x256/apps/jalview-icon.png
    • binary
    /utils/debian/debian/icons/32x32/apps/jalview-icon.png
    • binary
    /utils/debian/debian/icons/48x48/apps/jalview-icon.png
    • binary
    /utils/debian/debian/icons/512x512/apps/jalview-icon.png
    • binary
    /utils/debian/debian/icons/64x64/apps/jalview-icon.png
    • binary
    /utils/debian/debian/jalview-file.png
    • -22
    • +22
    /utils/debian/debian/jalview-mime.xml
    • -1
    • +1
    /utils/debian/file_associations_template-shared-mime-info.xml
    • -1
    • +1
    /utils/debian/mime_types_for_debian.pl
Or can it be compiled to Java 8 bytecode?

Or can it be compiled to Java 8 bytecode?