Package de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.kegg_reaction

Class ReactionService

java.lang.Object
de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.kegg_reaction.ReactionService
All Implemented Interfaces:
FileDownloadStatusInformationProvider, BackgroundTaskStatusProvider, HelperClass
public class ReactionService
extends Object
implements BackgroundTaskStatusProvider, FileDownloadStatusInformationProvider, HelperClass

  • Constructor Details

    • ReactionService

      public ReactionService()

  • Method Details

    • finishedNewDownload

      public void finishedNewDownload()
      Specified by:
      finishedNewDownload in interface FileDownloadStatusInformationProvider

    • getReactionFromId

      public static ReactionEntry getReactionFromId​(String reactionID)

    • getInformationLazy

      public static ReactionEntry getInformationLazy​(String reactionID)

    • getReleaseVersionForEnzymeInformation

      public static String getReleaseVersionForEnzymeInformation()
      Returns:
      The release information of the compound file. Read out of ligant.txt.

    • 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

    • 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

    • getAllReactionIds

      public static Collection<String> getAllReactionIds()

    • getDescription

      public String getDescription()
      Specified by:
      getDescription in interface FileDownloadStatusInformationProvider

    • getStatusPane

      public JComponent getStatusPane​(boolean showEmpty)
      Specified by:
      getStatusPane in interface FileDownloadStatusInformationProvider