Package de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes

Class Experiment2GraphHelper

java.lang.Object
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes.Experiment2GraphHelper
All Implemented Interfaces:
BackgroundTaskStatusProvider, BackgroundTaskStatusProviderSupportingExternalCall, HelperClass
public class Experiment2GraphHelper
extends Object
implements BackgroundTaskStatusProviderSupportingExternalCall, HelperClass
Author:
klukas To change the template for this generated type comment go to Window - Preferences - Java - Code Generation - Code and Comments

  • Field Details

    • mapFolder

      public static String mapFolder

    • mapVarName

      public static String mapVarName

  • Constructor Details

    • Experiment2GraphHelper

      public Experiment2GraphHelper()

  • Method Details

    • getMappedDataListFromGraphElement

      public static ExperimentInterface getMappedDataListFromGraphElement​(GraphElement graphElement)
      Get a list of mapped xml data that has been assigned to a node (or other GraphElement).
      Returns:
      A list of mapped data or null, if no mapping data is available.

    • getMappedDataListFromGraphElement

      public static ExperimentInterface getMappedDataListFromGraphElement​(GraphElement graphElement, String mapVarName)

    • getXMLdataAttribute

      public static XMLAttribute getXMLdataAttribute​(GraphElement graphElement)

    • getMappedDataListSizeFromGraphElement

      public static Integer getMappedDataListSizeFromGraphElement​(GraphElement graphElement)

    • mapDataToGraphElements

      public MapResult mapDataToGraphElements​(boolean mapAlsoInCaseOfEmptyDataset, ExperimentInterface md, Collection<GraphElement> targetGraphElements, Graph addNewGraphElementsToThisGraph, boolean doUserMapping, String diagramStyle, int minimumLines, boolean considerEnzymeDb, boolean considerMappingToKEGGmapNodes, boolean selectResult)

    • mapDataToGraphElements

      public MapResult mapDataToGraphElements​(boolean mapAlsoInCaseOfEmptyDataset, ExperimentInterface mappingData, Collection<GraphElement> targetGraphElements, Graph addNewGraphElementsToThisGraph, boolean doUserMapping, String diagramStyle, int minimumLines, int diagramsPerRow, boolean considerEnzymeDb, boolean considerMappingToKEGGmapNodes, boolean selectResult)
      Maps the data from the XML document to the list of nodes
      Parameters:
      mapAlsoInCaseOfEmptyDataset - If true, a mapping will be done although no data points are in the data set. This creates also empty diagrams.
      doc - The XML Document with the experimental data.
      targetGraphElements - The node list where the data should be mapped.
      addNewGraphElementsToThisGraph - If not null, new nodes will be added to this graph if one or more mappings are done for a node, if set to false, each time a mapping is done, the count will be increased. Set this to true, to find out, how many nodes have data mapped.
      validTimePoints -
      validConditons -
      Returns:
      MapResult

    • addMappingData2Node

      public static void addMappingData2Node​(SubstanceInterface xmlSubstanceNode, GraphElement graphNode, String diagramStyle)

    • addMappingData2Node

      public static void addMappingData2Node​(SubstanceInterface xmlSubstanceNode, Node graphNode)

    • addExperimentNameInfoToAllLinesForThisSubstanceNode

      public static void addExperimentNameInfoToAllLinesForThisSubstanceNode​(Node xmlSubstanceNode)

    • getCurrentStatusValue

      public int getCurrentStatusValue()
      Description copied from interface: BackgroundTaskStatusProvider
      Returns the completion status. WARNING: This method must be Thread-Safe!
      Specified by:
      getCurrentStatusValue in interface BackgroundTaskStatusProvider
      Returns:
      A number from 0..100 which represents the completion status. If -1 is returned, the progress bar is set to "indeterminate", which means, that the progress bar will float from left to right and reverse. (Useful if status can not be determined) Other values let the progressbar disappear.

    • getCurrentStatusMessage1

      public String getCurrentStatusMessage1()
      Description copied from interface: BackgroundTaskStatusProvider
      Returns a status message on what is going on. WARNING: This method must be Thread-Safe!
      Specified by:
      getCurrentStatusMessage1 in interface BackgroundTaskStatusProvider
      Returns:
      A status message, or null if not needed.

    • getCurrentStatusMessage2

      public String getCurrentStatusMessage2()
      Description copied from interface: BackgroundTaskStatusProvider
      Returns a status message on what is going on. Is used the same like getCurrentStatusMessage1. This second message adds flexibility. If not needed, the first message should be used and this should return null if not needed. WARNING: This method must be Thread-Safe!
      Specified by:
      getCurrentStatusMessage2 in interface BackgroundTaskStatusProvider
      Returns:
      A status message, or null if not needed.

    • pleaseStop

      public void pleaseStop()
      Description copied from interface: BackgroundTaskStatusProvider
      If this method is called on the status provider, the linked work task should stop its execution as soon as possible.
      Specified by:
      pleaseStop in interface BackgroundTaskStatusProvider

    • getCurrentStatusValueFine

      public double getCurrentStatusValueFine()
      Description copied from interface: BackgroundTaskStatusProvider
      Same as getCurrentStatusValue(), but this method should return a finer granted progress value. If this is not needed, the code for getCurrentStatusValue() could be reused by the client.
      Specified by:
      getCurrentStatusValueFine in interface BackgroundTaskStatusProvider
      Returns:
      The current progress value (fine).

    • pluginWaitsForUser

      public boolean pluginWaitsForUser()
      Specified by:
      pluginWaitsForUser in interface BackgroundTaskStatusProvider
      Returns:
      Let this method return true in order to show a "Continue" button in the GUI. When this buttons is clicked, the method pleaseContinueRun is called. Use these two methods to let the user interact with the GUI while the algorithm is waiting for the user to be ready for the continued work of the algorithm.

    • pleaseContinueRun

      public void pleaseContinueRun()
      Description copied from interface: BackgroundTaskStatusProvider
      This method is called as soon as the user indicates that he is comfortable to let the algorithm continue its work.
      Specified by:
      pleaseContinueRun in interface BackgroundTaskStatusProvider

    • setCurrentStatusValue

      public void setCurrentStatusValue​(int value)
      Description copied from interface: BackgroundTaskStatusProvider
      Override this method and pass a implementor of this interface to any other service method. This method can use this call to update the status value.
      Specified by:
      setCurrentStatusValue in interface BackgroundTaskStatusProvider

    • setCurrentStatusValueFine

      public void setCurrentStatusValueFine​(double value)
      Specified by:
      setCurrentStatusValueFine in interface BackgroundTaskStatusProviderSupportingExternalCall

    • wantsToStop

      public boolean wantsToStop()
      Specified by:
      wantsToStop in interface BackgroundTaskStatusProviderSupportingExternalCall

    • setCurrentStatusText1

      public void setCurrentStatusText1​(String status)
      Specified by:
      setCurrentStatusText1 in interface BackgroundTaskStatusProviderSupportingExternalCall

    • setCurrentStatusText2

      public void setCurrentStatusText2​(String status)
      Specified by:
      setCurrentStatusText2 in interface BackgroundTaskStatusProviderSupportingExternalCall

    • setCurrentStatusValueFineAdd

      public void setCurrentStatusValueFineAdd​(double smallProgressStep)
      Specified by:
      setCurrentStatusValueFineAdd in interface BackgroundTaskStatusProviderSupportingExternalCall