jalview

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improved javascript callback execution thread and provided 'large string' asynchronous retrieval interface (JAL-735)

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    /src/jalview/bin/JalviewLite.java
separation of jmol script command generation from jmol binding

    • -1623
    • +1532
    /src/jalview/ext/jmol/JalviewJmolBinding.java
    • -0
    • +135
    /src/jalview/ext/jmol/JmolCommands.java
javadoc and informative error message when external binding to PDB fails

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    • +3575
    /src/jalview/appletgui/AlignFrame.java
ensure feature renderer settings come from the given view

added simple stdout debug function

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JAL-824 - additional methods to allow jmol colouring state indicator to be passed in and modified on an instantiated view

JAL-824 - patch to schema to allow jmol colouring state to be stored

toggle of inclusion/exclusion of views for colouring was't working

    • -1
    • +6
    /src/jalview/gui/ViewSelectionMenu.java
JAL-824 - ensure Jmol colouring is a radio button

    • -1
    • +1
    /src/jalview/appletgui/AppletJmol.java
documentation for JAL-824 and JAL-621

documentation for JAL-732

    • -2
    • +14
    /help/html/features/viewingpdbs.html
htmlfix

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in progress...

    • -0
    • +31
    /forester/java/src/org/forester/development/Hello3d.java
    • -0
    • +72
    /forester/java/src/org/forester/ws/uniprot/DatabaseTools.java
    • -0
    • +137
    /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

    • -27
    • +107
    /src/jalview/gui/AppJmol.java
    • -2
    • +21
    /src/jalview/jbgui/GStructureViewer.java
comments re JAL-823 legacy issue

clarify tooltip

    • -1
    • +1
    /src/jalview/gui/ViewSelectionMenu.java
moved loadingFromArchive flag modification to after GUI refreshes are completed and javadoc.

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    • +11
    /src/jalview/ext/jmol/JalviewJmolBinding.java
option for enabling Jmol colouring mode JAL-824

    • -3
    • +12
    /src/jalview/appletgui/AppletJmol.java
in progress