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kjvdheide <kjvanderheide@dundee.ac.uk> 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?

JAL-2797 added constructor including embedded/standalone boolean

JAL-2797 the big switch, all GUI method calls now go via the AptxFrame interface

JAL-2797 standalone and embedded implementations of AptxFrame

JAL-2797 added adapter for the dummy frame listener

    • -0
    • +52
    /forester/java/src/org/forester/archaeopteryx/FrameAdapter.java
JAL-2797 added the frame and listener interfaces

JAL-2890 removed redundant variable assignment

JAL-2800 first go at new calculation frame

    • -1
    • +6
    /src/jalview/gui/TreeCalculationFrame.java
JAL-2890 minor name changes

    • -14
    • +2
    /src/jalview/ext/cipres/CipresJob.java
JAL-2826 added action performed for hiding collapsed sequences

    • -0
    • +18
    /src/jalview/ext/archaeopteryx/AptxFrame.java
    • -1
    • +1
    /src/jalview/ext/treeviewer/TreeFrameI.java
JAL-2826 added isCollapsed boolean to tree nodes

    • -0
    • +6
    /src/jalview/ext/archaeopteryx/TreeNode.java
    • -0
    • +2
    /src/jalview/ext/treeviewer/TreeNodeI.java
JAL-2890 renamed cipres job results to cipres job

    • -0
    • +109
    /src/jalview/ext/cipres/CipresJob.java
    • -109
    • +0
    /src/jalview/ext/cipres/CipresJobResults.java
JAL-2890 renamed cipres job to query builder

    • -248
    • +0
    /src/jalview/ext/cipres/CipresJob.java
    • -0
    • +248
    /src/jalview/ext/cipres/CipresQueryBuilder.java
    • -71
    • +0
    /test/jalview/ext/cipres/CipresJobTest.java
    • -0
    • +71
    /test/jalview/ext/cipres/CipresQueryBuilderTest.java
JAL-2890 added job results wrapper

    • -3
    • +3
    /src/jalview/ext/cipres/CipresJob.java
    • -0
    • +109
    /src/jalview/ext/cipres/CipresJobResults.java
    • -0
    • +1
    /test/jalview/ext/cipres/CipresJobTest.java
JAL-2890 added test

    • -0
    • +70
    /test/jalview/ext/cipres/CipresJobTest.java
JAL-2890 removed isError() check from validation job (gives NPE)

    • -4
    • +1
    /src/jalview/ext/cipres/CipresJob.java
JAL-2890 added getters for the parameters

    • -0
    • +19
    /src/jalview/ext/cipres/CipresJob.java
JAL-2890 name change

    • -0
    • +232
    /src/jalview/ext/cipres/CipresJob.java
    • -232
    • +0
    /src/jalview/ext/cipres/TreeJob.java
JAL-2890 removed tool parameter from validate/submit job methods

    • -9
    • +11
    /src/jalview/ext/cipres/TreeJob.java
JAL-2890 made CiClient static (as it should be) and added dummy umbrella clients

    • -7
    • +10
    /src/jalview/ext/cipres/TreeJob.java
JAL-2890 made the submitted job a class value and added getter for it

JAL-2890 added constructor that includes tool name & simplified others

    • -7
    • +18
    /src/jalview/ext/cipres/TreeJob.java
JAL-2890 made tool name a class value instead of method params

    • -0
    • +12
    /src/jalview/ext/cipres/TreeJob.java
JAL-2890 submit/valid jobs now return the actual job objects

    • -7
    • +44
    /src/jalview/ext/cipres/TreeJob.java
JAL-2890 added flag telling if parameters have been validated

    • -1
    • +23
    /src/jalview/ext/cipres/TreeJob.java