jalview

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removed useless flag (was always null for button press) to ensure default view colouring behaviour for JAL-824 when sequence colouring is chosen

JAL-823 and JAL-824 - seqColour no longer the default colouring state unless PDB file opened from alignment window

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    /src/jalview/gui/AppJmol.java
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    /src/jalview/jbgui/GStructureViewer.java
comments re JAL-823 legacy issue

clarify tooltip

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    /src/jalview/gui/ViewSelectionMenu.java
moved loadingFromArchive flag modification to after GUI refreshes are completed and javadoc.

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
option for enabling Jmol colouring mode JAL-824

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    /src/jalview/appletgui/AppletJmol.java
in progress

JAL-641 patch

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    /src/jalview/gui/ViewSelectionMenu.java
patch for JAL-733

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    /src/jalview/gui/ViewSelectionMenu.java
patch for JAL-820 and JAL-821

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    /src/jalview/gui/AnnotationLabels.java
separated alignment annotation height calculation from panel height adjustment

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    /src/jalview/gui/AlignmentPanel.java
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    /src/jalview/gui/AnnotationPanel.java
moved to same place as in jalview.gui

save and recover graph height, visibility and row position for autocalculated annotation rows (JAL-785) and column label formatting attributes (JAL-817 and JAL-818).

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    /src/jalview/gui/Jalview2XML.java
allow an alignment annotation row to be removed and re-inserted without losing any of its sequence or group associations (JAL-784)

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    /src/jalview/datamodel/AlignmentI.java
allow an existing alignment annotation row to be bound to a sequenceGroup as its consensus or conservation row (JAL-784)

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    /src/jalview/datamodel/SequenceGroup.java
added graphHeight attribute to schema (JAL-784)

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    /src/jalview/schemabinding/version2/Annotation.java
  1. … 67 more files in changeset.
refactored

  1. … 11 more files in changeset.
avoid race condition when featureRenderer for structure is updated by its associated view.

patched XML parser to ensure it properly escapes non-html friendly characters prior to tooltip generation (resolves JAL-808)

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    /src/jalview/ws/EnfinEnvision2OneWay.java
in progress

in progress

in progress

in progress

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    • +133
    /forester/java/src/org/forester/ws/uniprot/UniProtEntry.java
in progress

in progress

updated to pfam25

simple

updated to pfam25

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    /forester/ruby/evoruby/exe/run_phylo_pipeline.rb
added display of some basic data