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

Class TranspathService

java.lang.Object

de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathService

All Implemented Interfaces:

FileDownloadStatusInformationProvider, BackgroundTaskStatusProvider, HelperClass

public class TranspathService
extends Object
implements BackgroundTaskStatusProvider, FileDownloadStatusInformationProvider, HelperClass

Constructor Summary

Constructors

Constructor	Description
TranspathService()

Method Summary

Modifier and Type	Method	Description
void	finishedNewDownload()
String	getCurrentStatusMessage1()	Returns a status message on what is going on.
String	getCurrentStatusMessage2()	Returns a status message on what is going on.
int	getCurrentStatusValue()	Returns the completion status.
double	getCurrentStatusValueFine()	Same as getCurrentStatusValue(), but this method should return a finer granted progress value.
String	getDescription()
static InputSource	getFileInputSource(String fileName)
static BufferedReader	getFileReader(String fileName)
static TranspathMolecule	getMolecule(String moleculeID)
static TranspathPathway	getPathway(String pathwayID)
static Collection<TranspathPathway>	getPathways()
static TranspathReaction	getReaction(String reactionID)
static String	getReleaseVersionForTranspath()
JComponent	getStatusPane(boolean showEmpty)
void	pleaseContinueRun()	This method is called as soon as the user indicates that he is comfortable to let the algorithm continue its work.
void	pleaseStop()	If this method is called on the status provider, the linked work task should stop its execution as soon as possible.
boolean	pluginWaitsForUser()
void	setCurrentStatusValue(int value)	Override this method and pass a implementor of this interface to any other service method.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

TranspathService

public TranspathService()

Method Details

finishedNewDownload

public void finishedNewDownload()

Specified by:

finishedNewDownload in interface FileDownloadStatusInformationProvider

getFileReader

public static BufferedReader getFileReader(String fileName)

getFileInputSource

public static InputSource getFileInputSource(String fileName)

getPathways

public static Collection<TranspathPathway> getPathways()

getReleaseVersionForTranspath

public static String getReleaseVersionForTranspath()

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

getDescription

public String getDescription()

Specified by:

getDescription in interface FileDownloadStatusInformationProvider

getStatusPane

public JComponent getStatusPane(boolean showEmpty)

Specified by:

getStatusPane in interface FileDownloadStatusInformationProvider

getReaction

public static TranspathReaction getReaction(String reactionID)

getPathway

public static TranspathPathway getPathway(String pathwayID)

getMolecule

public static TranspathMolecule getMolecule(String moleculeID)