jalview

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htmlfix

in progress...

in progress...

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    /forester/java/src/org/forester/development/Hello3d.java
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    /forester/java/src/org/forester/ws/uniprot/DatabaseTools.java
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    /forester/java/src/org/forester/ws/uniprot/EbiDbEntry.java
in progress

pattern match for up added....

pattern match for up added....

formatting

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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    • +17
    /src/jalview/ws/EnfinEnvision2OneWay.java
in progress

in progress

in progress