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-3842 fix automatic what's new link for custom version builds

WIP
WIP
JAL-3842 JAL-3746 (need to cherry pick to develop) - automatically generate link to latest release notes in what's new

JAL-3842 2.11.1.5 what’s new, release notes, and version bump

Merge branch 'patch/JAL-3840_2_11_1_4' into releases/Release_2_11_1_Branch

JAL-3840 don’t update the modal residue count for gaps

    • -1
    • +6
    /src/jalview/datamodel/ResidueCount.java
fixes JAL-3840

    • -9
    • +1
    /src/jalview/datamodel/ResidueCount.java
JAL-3840 failing test - show that addGaps overflows

    • -1
    • +1
    /src/jalview/datamodel/ResidueCount.java
JAL-3248 Archived old README. Added new README to point user to doc/building.md

    • -0
    • +47
    /doc/old_ant_build_README
JAL-3743 Fixed NullPointerExceptions happening with linkCheck task when gradle >= 6.6

JAL-3833 cap the scaling used by HiDPISetting for incorrect DPI values or incorrect height/width values

JAL-3816 release date updated to 9th March

JAL-3816 release date set for 8th March and updated what's new

JAL-3816 new known defects JAL-3705 and JAL-3806