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edu.stanford.genetics.treeview
Class FileSet  

java.lang.Object
  edu.stanford.genetics.treeview.FileSet

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public class FileSet

extends java.lang.Object

Encapsulates a set of files corresponding to a typical hieararichal cluster analysis. Such things are always based upon a cdt or pcl file.

The following attributes are meaningful to the FileSet:

• dir: The directory of the fileset
• root: The root of the fileset
• cdt: The extension for the generalized cdt file
• atr: The extension for the atr
• jtv: The extension for the jtv

Version:

$Revision: 1.6 $ $Date: 2003/09/25 04:53:37 $ Note: Should be flexible enough to have a url base instead of dir (1/16/2003)

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Field Summary
static int	AUTO_STYLE
static int	CLASSIC_STYLE
static int	KMEANS_STYLE
static int	LINKED_STYLE
private  ConfigNode	node

 

Constructor Summary

FileSet(ConfigNode configNode)           Constructor for the FileSet object

FileSet(java.lang.String string1, java.lang.String string2)           Make fileset based upon unrooted DummyConfigNode with the specified values

 

Method Summary
void	copyState(FileSet fileSet)           Copies state from another fileset
boolean	equals(FileSet fileSet)           Determines equality by looking at the cdt base alone.
java.lang.String	getAtr()
java.lang.String	getCdt()
ConfigNode	getConfigNode()           Gets the configNode attribute of the FileSet object
java.lang.String	getDir()
java.lang.String	getExt()
java.lang.String	getGtr()
java.lang.String	getJtv()
java.lang.String	getKag()           Used to display array clusters for knn clustering
java.lang.String	getKgg()           Used to display gene clusters for knn clustering
java.lang.String	getName()
java.lang.String	getRoot()
int	getStyle()
boolean	hasMoved()
boolean	isUrl()
void	setCdt(java.lang.String string1)           Sets the base of the FileSet object.
void	setDir(java.lang.String string)           Sets the dir in which this fileset can be found
void	setExt(java.lang.String string)           Sets the extension associated with the base of the fileset.
void	setName(java.lang.String string)
void	setRoot(java.lang.String string)           Sets the root of the FileSet object.
void	setStyle(int newStyle)
java.lang.String	toString()           Convert this Object to a human-readable String.

 

Methods inherited from class java.lang.Object

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

 

Field Detail

node

private ConfigNode node

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AUTO_STYLE

public static final int AUTO_STYLE

See Also:

Constant Field Values

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CLASSIC_STYLE

public static final int CLASSIC_STYLE

See Also:

Constant Field Values

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KMEANS_STYLE

public static final int KMEANS_STYLE

See Also:

Constant Field Values

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LINKED_STYLE

public static final int LINKED_STYLE

See Also:

Constant Field Values

Constructor Detail

FileSet

public FileSet(ConfigNode configNode)

Constructor for the FileSet object

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FileSet

public FileSet(java.lang.String string1,
               java.lang.String string2)

Make fileset based upon unrooted DummyConfigNode with the specified values

Method Detail

isUrl

public boolean isUrl()

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hasMoved

public boolean hasMoved()

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getConfigNode

public ConfigNode getConfigNode()

Gets the configNode attribute of the FileSet object

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copyState

public void copyState(FileSet fileSet)

Copies state from another fileset

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toString

public java.lang.String toString()

Description copied from class: java.lang.Object

Convert this Object to a human-readable String. There are no limits placed on how long this String should be or what it should contain. We suggest you make it as intuitive as possible to be able to place it into System.out.println() 55 and such.

It is typical, but not required, to ensure that this method never completes abruptly with a java.lang.RuntimeException.

This method will be called when performing string concatenation with this object. If the result is null, string concatenation will instead use "null".

The default implementation returns getClass().getName() + "@" + Integer.toHexString(hashCode()).

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equals

public boolean equals(FileSet fileSet)

Determines equality by looking at the cdt base alone.

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getAtr

public java.lang.String getAtr()

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getCdt

public java.lang.String getCdt()

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getDir

public java.lang.String getDir()

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getGtr

public java.lang.String getGtr()

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getJtv

public java.lang.String getJtv()

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getRoot

public java.lang.String getRoot()

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getExt

public java.lang.String getExt()

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getName

public java.lang.String getName()

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setCdt

public void setCdt(java.lang.String string1)

Sets the base of the FileSet object. Parses out extension, root

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setRoot

public void setRoot(java.lang.String string)

Sets the root of the FileSet object. i.e. the filename without extendsion.

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setDir

public void setDir(java.lang.String string)

Sets the dir in which this fileset can be found

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setExt

public void setExt(java.lang.String string)

Sets the extension associated with the base of the fileset.

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setName

public void setName(java.lang.String string)

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getKgg

public java.lang.String getKgg()

Used to display gene clusters for knn clustering

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getKag

public java.lang.String getKag()

Used to display array clusters for knn clustering

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getStyle

public int getStyle()

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setStyle

public void setStyle(int newStyle)

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> edu >> stanford >> genetics >> [ treeview overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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