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jprocter <jim procter> in jalview

not related to JAL-3765 ! Actually related to JAL-3675!

not related to JAL-3765 ! Actually related to JAL-3675!

relevant issue is JAL-3626

relevant issue is JAL-3626

Would be nicer. Currently the getdown-launcher is agnostic of which CHANNEL the Jalview version it's in was created with. This seemed like a quick way to achieve almost the same, but longer term a ...

Would be nicer. Currently the getdown-launcher is agnostic of which CHANNEL the Jalview version it's in was created with.
This seemed like a quick way to achieve almost the same, but longer term a getdown created visibile indicator would be ideal. I'll create an issue.

Hi Ben Soares - maybe nicer to have these generated by the getdown launcher in the future ? Worth an issue perhaps ?

Hi Ben Soares - maybe nicer to have these generated by the getdown launcher in the future ? Worth an issue perhaps ?

Ben Soares reported JAL-3514 about this build

Ben Soares reported JAL-3514 about this build

why are loops in removeAlreadyRetrievedSeqs now backwards?

why are loops in removeAlreadyRetrievedSeqs now backwards?

uncommentable debug message for JAL-771

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    • +3
    /src/jalview/datamodel/SearchResults.java
html tags

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

    • -2138
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    /src/jalview/bin/JalviewLite.java
separation of jmol script command generation from jmol binding

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    /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

    • -3560
    • +3575
    /src/jalview/appletgui/AlignFrame.java
ensure feature renderer settings come from the given view

added simple stdout debug function

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

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

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

documentation for JAL-732

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

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

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    • +1
    /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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    • +12
    /src/jalview/appletgui/AppletJmol.java
JAL-641 patch

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    • +2
    /src/jalview/gui/ViewSelectionMenu.java
patch for JAL-733

    • -29
    • +95
    /src/jalview/gui/ViewSelectionMenu.java
patch for JAL-820 and JAL-821

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    • +5
    /src/jalview/gui/AnnotationLabels.java