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jprocter <jim procter> in jalview

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2,039 commits
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  • First commit: 12 January 2005
  • Last commit: 05 May 2011
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Monday 19 Oct 2020
11:59 am

Jim Procter

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

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

Friday 22 May 2020
11:37 am

Jim Procter

relevant issue is JAL-3626

relevant issue is JAL-3626

Thursday 09 Apr 2020
2:34 pm

Ben Soares

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.

12:07 pm

Jim Procter

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 ?

Wednesday 05 Feb 2020
11:50 am

Jim Procter

Ben Soares reported JAL-3514 about this build

Ben Soares reported JAL-3514 about this build

Friday 01 Feb 2019
2:23 pm

Mungo Carstairs

why are loops in removeAlreadyRetrievedSeqs now backwards?

why are loops in removeAlreadyRetrievedSeqs now backwards?

Thursday 05 May 2011
3:07 pm

jprocter <Jim Procter>

uncommentable debug message for JAL-771

Options
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    /src/jalview/datamodel/SearchResults.java
3:02 pm

jprocter <Jim Procter>

html tags

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    • +2
    /doc/building.html
3:01 pm

jprocter <Jim Procter>

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

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    • -2138
    • +2254
    /src/jalview/bin/JalviewLite.java
    • -236
    • +239
    /src/jalview/javascript/JSFunctionExec.java
    • -86
    • +253
    /src/jalview/javascript/MouseOverStructureListener.java
2:56 pm

jprocter <Jim Procter>

separation of jmol script command generation from jmol binding

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    • +1532
    /src/jalview/ext/jmol/JalviewJmolBinding.java
    • -0
    • +135
    /src/jalview/ext/jmol/JmolCommands.java
2:55 pm

jprocter <Jim Procter>

javadoc and informative error message when external binding to PDB fails

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    • -3560
    • +3575
    /src/jalview/appletgui/AlignFrame.java
2:53 pm

jprocter <Jim Procter>

ensure feature renderer settings come from the given view

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    • +2
    /src/jalview/gui/AppJmolBinding.java
2:40 pm

jprocter <Jim Procter>

added simple stdout debug function

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    • +15
    /src/jalview/structure/StructureSelectionManager.java
Monday 25 Apr 2011
5:22 pm

jprocter <Jim Procter>

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

Options
    • -6
    • +28
    /src/jalview/gui/AppJmol.java
5:21 pm

jprocter <Jim Procter>

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

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    • +5
    /schemas/jalview.xsd
    • -4
    • +7
    /src/jalview/gui/Jalview2XML.java
    • -1
    • +1
    /src/jalview/schemabinding/version2/.castor.cdr
    • -1
    • +73
    /src/jalview/schemabinding/version2/StructureState.java
    • -0
    • +41
    /src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java
2:55 pm

jprocter <Jim Procter>

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

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    • +14
    /src/jalview/gui/AppJmol.java
    • -1
    • +6
    /src/jalview/gui/ViewSelectionMenu.java
2:08 pm

jprocter <Jim Procter>

JAL-824 - ensure Jmol colouring is a radio button

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    • +1
    /src/jalview/appletgui/AppletJmol.java
1:57 pm

jprocter <Jim Procter>

documentation for JAL-824 and JAL-621

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    /help/html/features/jmol.html
1:56 pm

jprocter <Jim Procter>

documentation for JAL-732

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    • +14
    /help/html/features/viewingpdbs.html
1:54 pm

jprocter <Jim Procter>

htmlfix

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    /help/html/webServices/urllinks.html
Friday 22 Apr 2011
3:26 pm

jprocter <Jim Procter>

formatting

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    • +2
    /src/jalview/gui/AppJmol.java
3:24 pm

jprocter <Jim Procter>

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

Options
    • -31
    • +1
    /src/jalview/gui/AppJmol.java
12:41 pm

jprocter <Jim Procter>

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

Options
    • -27
    • +107
    /src/jalview/gui/AppJmol.java
    • -1
    • +1
    /src/jalview/gui/AppJmolBinding.java
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    • +21
    /src/jalview/jbgui/GStructureViewer.java
12:40 pm

jprocter <Jim Procter>

comments re JAL-823 legacy issue

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    /src/jalview/gui/Jalview2XML.java
12:39 pm

jprocter <Jim Procter>

clarify tooltip

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    /src/jalview/gui/ViewSelectionMenu.java
12:39 pm

jprocter <Jim Procter>

moved loadingFromArchive flag modification to after GUI refreshes are completed and javadoc.

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    • -1
    • +11
    /src/jalview/ext/jmol/JalviewJmolBinding.java
12:37 pm

jprocter <Jim Procter>

option for enabling Jmol colouring mode JAL-824

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    • +12
    /src/jalview/appletgui/AppletJmol.java
Thursday 21 Apr 2011
5:55 pm

jprocter <Jim Procter>

JAL-641 patch

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    • +2
    /src/jalview/gui/ViewSelectionMenu.java
5:54 pm

jprocter <Jim Procter>

patch for JAL-733

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    • +95
    /src/jalview/gui/ViewSelectionMenu.java
3:51 pm

jprocter <Jim Procter>

patch for JAL-820 and JAL-821

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