Mateusz Warowny

WIP

JAL-3878 Use slivka client's URL when building web service

JAL-3878 Add conservation service discovery

JAL-3878 Build interactive services menu

    • -2
    • +206
    /src/jalview/ws2/gui/WebServicesMenuManager.java
JAL-3878 Implement prot. seq. an. discovery for slivka.

JAL-3878 Implement gui elements for annotation servicces

    • -0
    • +120
    /src/jalview/ws2/gui/AnnotationServiceGuiHandler.java
JAL-3878 Create SlivkaAnnotationWSClient

JAL-3878 Add full name getter to ActionI

    • -0
    • +17
    /src/jalview/ws2/actions/api/ActionI.java
JAL-3878 Log status changes in annotation task

JAL-3878 Allow null value for action name

    • -2
    • +1
    /src/jalview/ws2/actions/BaseAction.java
JAL-3878 Add action and task for annotation services

    • -0
    • +88
    /src/jalview/util/Pair.java
    • -0
    • +128
    /src/jalview/ws2/actions/annotation/AnnotationAction.java
    • -0
    • +144
    /src/jalview/ws2/actions/annotation/AnnotationJob.java
    • -0
    • +56
    /src/jalview/ws2/actions/annotation/AnnotationResult.java
    • -0
    • +573
    /src/jalview/ws2/actions/annotation/AnnotationTask.java
    • -0
    • +16
    /src/jalview/ws2/client/api/AnnotationWebServiceClientI.java
JAL-3878 Introduce IProgressIndicator#addProgressBar

addProgressBar adds a bar to the panel if it doesn't exist

ensuring that the bar is present after the call contrary

to setProgressBar which toggles the progress bar on and off.

    • -1
    • +15
    /src/jalview/gui/IProgressIndicator.java
    • -41
    • +60
    /src/jalview/gui/ProgressBar.java
    • -0
    • +6
    /src/jalview/gui/StructureChooser.java
JAL-3878 Fix method name to fireTaskRestarted

JAL-3878 Add char[] constructor to Sequence

    • -0
    • +15
    /src/jalview/datamodel/Sequence.java
JAL-3878 Make BaseJob setters public so they can be accessed by other tasks.

JAL-3878 Add fullName to BaseAction class which combines service and action name

    • -0
    • +14
    /src/jalview/ws2/actions/BaseAction.java
JAL-3878 Move status precedence list to JobStatus class

    • -0
    • +19
    /src/jalview/ws2/api/JobStatus.java
JAL-3878 Add uid to WS Tasks

    • -2
    • +7
    /src/jalview/ws2/actions/api/TaskI.java
JAL-3878 Patch preferences window to use new discoverer.

    • -34
    • +37
    /src/jalview/gui/SlivkaPreferences.java
JAL-3878 Fix discoverer being stuck on BEGIN state if task was cancelled.

JAL-3878 Add slivka discoverer and menu to AlignFrame

JAL-3878 Change align frame added to desktop to correct one

JAL-3878 Wrap infoPanel updates with SwingUtilities.invokeLater

JAL-3878 Fix re-alignment-capable services detection.

JAL-3878 Clear services list on reload.

JAL-3878 Fix task status precedence calculation

Task status could only go up from the current status.

JAL-3878 Fix NullPointerExceptions caused by nulls in arrays

    • -3
    • +12
    /src/jalview/ws/params/simple/Option.java
JAL3878 Implement slivka service discoverer

    • -0
    • +224
    /src/jalview/ws2/client/slivka/SlivkaParamStoreFactory.java
    • -0
    • +190
    /src/jalview/ws2/client/slivka/SlivkaWSDiscoverer.java
JAL-3878 Move action name initialization to its own setter.

    • -2
    • +7
    /src/jalview/ws2/actions/BaseAction.java
JAL-3878 Add builders to each service parameter class

    • -0
    • +53
    /src/jalview/ws/params/simple/BooleanOption.java
    • -1
    • +19
    /src/jalview/ws/params/simple/FileParameter.java
    • -5
    • +104
    /src/jalview/ws/params/simple/Option.java