cytoscape
Class CyProject

java.lang.Object
  cytoscape.CyProject

Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

public class CyProject
extends Object

This class is constructed from a project file, and contains string values associated with various meaningful variable names that identify the component of a CyNetwork object or various customization options. See the documentation for the readProjectFile method for the recognized file formats.

Field Summary

protected String	bioDataDirectory Deprecated.
protected boolean	canonicalize Deprecated.
protected String	defaultLayoutStrategy Deprecated.
protected String	defaultSpeciesName Deprecated.
protected List	edgeAttributeFilenames Deprecated.
protected String	expressionFilename Deprecated.
protected String	geometryFilename Deprecated.
protected String	interactionsFilename Deprecated.
protected String[]	layoutStrategies Deprecated.
protected List	nodeAttributeFilenames Deprecated.
protected String[]	otherArgs Deprecated.
protected String	projectFilename Deprecated.
protected String	projectPropsFileName Deprecated.
protected String	projectVizmapPropsFileName Deprecated.

Constructor Summary

CyProject(String fileLocation)
Deprecated. Constructs a Project object by reading the file at the supplied location, by calling readProjectFile with the argument.

Method Summary

protected String	absolutizeFilename(File parentDirectory, String filename) Deprecated. Helper method to reconstruct the absolute path to a file.
String	getBioDataDirectory() Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
boolean	getCanonicalize() Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
String	getDefaultLayoutStrategy() Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
String	getDefaultSpeciesName() Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
String[]	getEdgeAttributeFilenames() Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
String	getExpressionFilename() Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
String	getGeometryFilename() Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
String	getInteractionsFilename() Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
String[]	getNodeAttributeFilenames() Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
int	getNumberOfEdgeAttributeFiles() Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
int	getNumberOfNodeAttributeFiles() Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
String[]	getOtherArgs() Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
String	getProjectFilename() Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
String	getProjectPropsFileName() Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
String	getProjectVizmapPropsFileName() Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
protected String[]	parseProjectFileText(String[] lines, String key) Deprecated. Helper method that, given an array of text lines, searches for lines of the form "key=value", where the key is the second argument, and returns an array of all the values.
protected void	readProjectFile(String fileLocation) Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

Methods inherited from class java.lang.Object

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

Field Detail

projectFilename

protected String projectFilename

Deprecated.

interactionsFilename

protected String interactionsFilename

Deprecated.

geometryFilename

protected String geometryFilename

Deprecated.

expressionFilename

protected String expressionFilename

Deprecated.

nodeAttributeFilenames

protected List nodeAttributeFilenames

Deprecated.

edgeAttributeFilenames

protected List edgeAttributeFilenames

Deprecated.

bioDataDirectory

protected String bioDataDirectory

Deprecated.

defaultSpeciesName

protected String defaultSpeciesName

Deprecated.

layoutStrategies

protected String[] layoutStrategies

Deprecated.

defaultLayoutStrategy

protected String defaultLayoutStrategy

Deprecated.

projectPropsFileName

protected String projectPropsFileName

Deprecated.

projectVizmapPropsFileName

protected String projectVizmapPropsFileName

Deprecated.

canonicalize

protected boolean canonicalize

Deprecated.

otherArgs

protected String[] otherArgs

Deprecated.

Constructor Detail

CyProject

public CyProject(String fileLocation)

Deprecated.

Constructs a Project object by reading the file at the supplied location, by calling readProjectFile with the argument.

Method Detail

getProjectFilename

public String getProjectFilename()

Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

getInteractionsFilename

public String getInteractionsFilename()

Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

getGeometryFilename

public String getGeometryFilename()

Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

getExpressionFilename

public String getExpressionFilename()

Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

getNumberOfNodeAttributeFiles

public int getNumberOfNodeAttributeFiles()

Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

getNumberOfEdgeAttributeFiles

public int getNumberOfEdgeAttributeFiles()

Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

getNodeAttributeFilenames

public String[] getNodeAttributeFilenames()

Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

getEdgeAttributeFilenames

public String[] getEdgeAttributeFilenames()

Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

getBioDataDirectory

public String getBioDataDirectory()

Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

getDefaultSpeciesName

public String getDefaultSpeciesName()

Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

getDefaultLayoutStrategy

public String getDefaultLayoutStrategy()

Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

getProjectPropsFileName

public String getProjectPropsFileName()

Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

getProjectVizmapPropsFileName

public String getProjectVizmapPropsFileName()

Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

getCanonicalize

public boolean getCanonicalize()

Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

getOtherArgs

public String[] getOtherArgs()

Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

readProjectFile

protected void readProjectFile(String fileLocation)

Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

Reads the project file at the specified location. Currently, the location can either be a local file (in which case the location should be an absolute or relative path to the file), or a file in a jar archive, in which case the location should be the name of the file in the jar archive, prefaced with the header string "jar://". For example: fileLocation = "/users/me/projects/project" (local text file) fileLocation = "jar://jarProject" (jar archive, presumably in path) Support could be added for reading files from web pages using the TextHttpReader helper class, but I'm not sure what issues would be involved with this. In any case, the actual file should be a project file, which is a sequence of lines of the general form "key=value", where the keys are particular recognized strings. For most keys, any occurances after the first are ignored. The exceptions are the "noa", "eda", and "arg" keys, for which multiple occurances are saved as an array of String values. Other lines are ignored, so reading a file that isn't a project file simply produces empty values for every field. The known keys are as follows: "sif" specifies the location of a graph file in interactions format "gml" specifies the location of a graph file in GML format. it is not strictly an error to include both the "sif" and "gml" keys in the project file, but many classes that try to use this information do not expect both "noa" specifies the location of a node attributes file. "eda" specifies the location of an edge attributes file. "expr" specifies the location of an expression data file "dataserver" specifies the location of a data server "species" specifies a default species name "layout" specifies a default layout algorithm "props" specifies the locatipn of a customization properties file (ex: cytoscape.props) "vprops" specifies the location of a properties file containing specifications of visual mappings (ex: vizmap.props) "canonicalize" determines whether the data server is used to get canonical names from the supplied names that may be common names or synonyms "args" a catch=all category for any other String values that may be significant to some class that uses this project information For information on the formats of the different data files mentioned here and the classes that read them, see the following classes: graph interactions file format: cytoscape.data.readers.InteractionsReader graph GML file format: cytoscape.data.readers.GMLReader customization properties file: cytoscape.CytoscapeConfig visual mappings properties file: cytoscape.visual.CalculatorIO

absolutizeFilename

protected String absolutizeFilename(File parentDirectory,
                                    String filename)

Deprecated.

Helper method to reconstruct the absolute path to a file.

parseProjectFileText

protected String[] parseProjectFileText(String[] lines,
                                        String key)

Deprecated.

Helper method that, given an array of text lines, searches for lines of the form "key=value", where the key is the second argument, and returns an array of all the values.