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

Class KeggService

java.lang.Object
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg.KeggService
All Implemented Interfaces:
BackgroundTaskStatusProvider, HelperClass
public class KeggService
extends Object
implements BackgroundTaskStatusProvider, HelperClass

  • Constructor Details

    • KeggService

      public KeggService()

  • Method Details

    • loadKeggPathwayIntoEditor

      public static boolean loadKeggPathwayIntoEditor​(KeggPathwayEntry myEntry, Graph loadBlockingIntoThisGraph, Color enzymeColor, boolean separateClusters)
      If loadBlockingIntoThisGraph is != null, this method adds the loaded graph to the given graph instance. If this parameter is NULL (default), then this method returns immediately and opens a new graph window editor.
      Parameters:
      myEntry -
      loadBlockingIntoThisGraph -

    • mergeKeggGraphs

      public static void mergeKeggGraphs​(Graph mergeIntoThisGraph, Graph newGraph, Vector2d centerOfNewGraph, boolean linkToExistingMaps, boolean clusterSeparation)

    • loadPathway

      public static void loadPathway​(KeggPathwayEntry myEntry, boolean processLabels)

    • loadPathway

      public static void loadPathway​(KeggPathwayEntry myEntry, Graph targetGraph, boolean processLabels)

    • loadPathway

      public static void loadPathway​(KeggPathwayEntry myEntry, Graph targetGraph, Node initialMapNode, boolean processLabels)

    • loadPathway

      public static void loadPathway​(KeggPathwayEntry myEntry, Graph targetGraph, Node initialMapNode, boolean askForNewWindow, boolean separateClusters)

    • getKeggPathwayGravistoGraph

      public static Graph getKeggPathwayGravistoGraph​(KeggPathwayEntry myEntry, boolean showErrorMessages, Color enzymeColors) throws org.jdom2.JDOMException, IOException, MalformedURLException
      Throws:
      org.jdom2.JDOMException
      IOException
      MalformedURLException

    • getKeggPathwayGravistoGraph

      public static Graph getKeggPathwayGravistoGraph​(KeggPathwayEntry myEntry, boolean showErrorMessages, Color enzymeColors, boolean includeMapNodes) throws org.jdom2.JDOMException, IOException, MalformedURLException
      Throws:
      org.jdom2.JDOMException
      IOException
      MalformedURLException

    • colorizeEnzymesGlycansCompounds

      public static void colorizeEnzymesGlycansCompounds​(Graph graph, String mapName, Color enzymeColor, boolean markNotPresent, boolean orthologs, boolean enzymes, boolean glycans, boolean compounds, boolean convertTypeToGeneWhenProcessingOrthologs)

    • processKeggTree

      public void processKeggTree​(JTree keggTree, HashMap<KeggPathwayEntry,​DefaultMutableTreeNode> pathwayToTreeNodeMap)
      Parameters:
      keggTree -
      keggTree -

    • 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.

    • 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).

    • 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

    • 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

    • loadKeggPathwayIntoGraph

      public static void loadKeggPathwayIntoGraph​(InputStream in, Graph g, Color enzymeColor)

    • 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

    • getDefaultEnzymeColor

      public static Color getDefaultEnzymeColor()