[Jtreeview-cvs] jtreeview commit notification

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Update of /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/model
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12946/src/edu/stanford/genetics/treeview/model

Modified Files:
      Tag: SpellmanBeta
	TVModelLoader.java TVModel.java KnnModel.java 
	FlatFileParser.java ProgressTrackable.java LoadProgress.java 
	LoadProgress2.java FlatFileStreamTokenizer.java 
Added Files:
      Tag: SpellmanBeta
	AtrTVModelLoader.java AtrTVModel.java 
Log Message:

--- NEW FILE: AtrTVModelLoader.java ---
/* BEGIN_HEADER                                              Java TreeView
 *
 * $Author: avsegal
 * $RCSfile: AtrTVModelLoader.java
 * $Revision: 
 * $Date: Jun 25, 2004
 * $Name:  
 *
 * This file is part of Java TreeView
 * Copyright (C) 2001-2003 Alok Saldanha, All Rights Reserved.
 *
 * This software is provided under the GNU GPL Version 2. In particular,
 *
 * 1) If you modify a source file, make a comment in it containing your name and the date.
 * 2) If you distribute a modified version, you must do it under the GPL 2.
 * 3) Developers are encouraged but not required to notify the Java TreeView maintainers at al...@ge... when they make a useful addition. It would be nice if significant contributions could be merged into the main distribution.
 *
 * A full copy of the license can be found in gpl.txt or online at
 * http://www.gnu.org/licenses/gpl.txt
 *
 * END_HEADER
 */

package edu.stanford.genetics.treeview.model;

import edu.stanford.genetics.treeview.LoadException;
import java.awt.Frame;
import java.util.Vector;
import java.io.*;

/**
 * @author avsegal
 *
 * To change the template for this generated type comment go to
 * Window&gt;Preferences&gt;Java&gt;Code Generation&gt;Code and Comments
 */
public class AtrTVModelLoader extends TVModelLoader {

	/**
	 * @param targetModel
	 */
	public AtrTVModelLoader(AtrTVModel targetModel) {
		super(targetModel);
	}

	protected void  parseCDT(Vector tempVector) throws LoadException {
		super.findCdtDimensions(tempVector);
		super.loadArrayAnnotation(tempVector);
		super.loadGeneAnnotation(tempVector);
	}

}

Index: TVModelLoader.java
===================================================================
RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/model/TVModelLoader.java,v
retrieving revision 1.13
retrieving revision 1.13.2.1
diff -C2 -d -r1.13 -r1.13.2.1
*** TVModelLoader.java	5 Apr 2004 17:50:31 -0000	1.13
--- TVModelLoader.java	1 Jul 2004 20:36:19 -0000	1.13.2.1
***************
*** 336,340 ****
  	// finds ngene, nexpr, nArrayPrefix, nGenePrefix
  	// 
! 	private void findCdtDimensions(Vector tempVector)  {
  		println("Finding Cdt Dimensions");
  		int ngene, nexpr, nArrayPrefix, nGenePrefix;
--- 336,340 ----
  	// finds ngene, nexpr, nArrayPrefix, nGenePrefix
  	// 
! 	protected void findCdtDimensions(Vector tempVector)  {
  		println("Finding Cdt Dimensions");
  		int ngene, nexpr, nArrayPrefix, nGenePrefix;
***************
*** 393,397 ****
  	}

! 	private void loadArrayAnnotation(Vector tempVector) {
  		// cols to skip over before arrays begin...
  		int nGenePrefix  = targetModel.getNGenePrefix();
--- 393,397 ----
  	}

! 	protected void loadArrayAnnotation(Vector tempVector) {
  		// cols to skip over before arrays begin...
  		int nGenePrefix  = targetModel.getNGenePrefix();
***************
*** 415,419 ****
  	}

! 	private void loadGeneAnnotation(Vector tempVector) {
  		// how many cols of annotation?
  		int nGenePrefix  = targetModel.getNGenePrefix();
--- 415,419 ----
  	}

! 	protected void loadGeneAnnotation(Vector tempVector) {
  		// how many cols of annotation?
  		int nGenePrefix  = targetModel.getNGenePrefix();

--- NEW FILE: AtrTVModel.java ---
/* BEGIN_HEADER                                              Java TreeView
 *
 * $Author: avsegal
 * $RCSfile: AtrTVModel.java
 * $Revision: 
 * $Date: Jun 25, 2004
 * $Name:  
 *
 * This file is part of Java TreeView
 * Copyright (C) 2001-2003 Alok Saldanha, All Rights Reserved.
 *
 * This software is provided under the GNU GPL Version 2. In particular,
 *
 * 1) If you modify a source file, make a comment in it containing your name and the date.
 * 2) If you distribute a modified version, you must do it under the GPL 2.
 * 3) Developers are encouraged but not required to notify the Java TreeView maintainers at al...@ge... when they make a useful addition. It would be nice if significant contributions could be merged into the main distribution.
 *
 * A full copy of the license can be found in gpl.txt or online at
 * http://www.gnu.org/licenses/gpl.txt
 *
 * END_HEADER
 */

package edu.stanford.genetics.treeview.model;

/**
 * @author avsegal
 *
 * To change the template for this generated type comment go to
 * Window&gt;Preferences&gt;Java&gt;Code Generation&gt;Code and Comments
 */

import edu.stanford.genetics.treeview.*;
import java.util.*;
import java.awt.*;
import java.io.*;
import java.awt.event.*;
import javax.swing.*;

public class AtrTVModel extends TVModel {

	/**
	 * 
	 */
	public AtrTVModel() {
		super();
	}

	public double getValue(int x, int y) {
		return -1;
	}
	public void setExprData(double [] newData) {
	}

	public XmlConfig getDocumentConfig() {
		return null;
	}

	public void setDocumentConfig(XmlConfig newVal) {
	}

	public void setFrame(Frame f) {
	}

	public Frame getFrame() {
			return null;
	}

	public MenuItem getStatMenuItem() {
		return null;
	}

	public void loadNew(FileSet fileSet) throws LoadException {
		resetState();
		setSource(fileSet);
		final AtrTVModelLoader loader = new AtrTVModelLoader(this);
		loader.loadInto(); 
	}

}
Index: TVModel.java
===================================================================
RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/model/TVModel.java,v
retrieving revision 1.11
retrieving revision 1.11.2.1
diff -C2 -d -r1.11 -r1.11.2.1
*** TVModel.java	18 May 2004 18:17:16 -0000	1.11
--- TVModel.java	1 Jul 2004 20:36:19 -0000	1.11.2.1
***************
*** 159,162 ****
--- 159,277 ----
  		 return target;
  	 }
+ 	 /**
+ 	  * Reorders all the arrays in the new ordering.
+ 	  * @param ordering the new ordering of arrays, must have size equal to number of arrays
+ 	  */
+ 	public void reorderArrays(int [] ordering)
+ 	{
+ 		if(ordering == null || ordering.length != aHeaders.length) // make sure input to function makes sense
+ 		{
+ 			return;
+ 		}
+ 	
+ 	
+ 		DataMatrix data = getDataMatrix();
+ 	
+ 		for(int j = 0; j < data.getNumRow(); j++)
+ 		{
+ 			double [] temp = new double[data.getNumCol()];
+ 			for(int i = 0; i < data.getNumCol(); i++)
+ 			{
+ 				temp[i] = data.getValue(ordering[i], j);
+ 			}
+ 			for(int i = 0; i < data.getNumCol(); i++)
+ 			{
+ 				data.setValue(temp[i], i, j);
+ 			}
+ 		}
+ 	
+ 		String [][] temp2 = new String[aHeaders.length][];
+ 	
+ 		for(int i = 0; i < aHeaders.length; i++)
+ 		{
+ 			temp2[i] = aHeaders[ordering[i]];		
+ 		}
+ 		setArrayHeaders(temp2);
+ 		hashAIDs();
+ 		
+ 					
+ 		setChanged();
+ 	}
+ 	
+ 	/**
+ 	 * Reset order in config file to the identity ordering.
+ 	 */
+ 	public void clearOrder()
+ 	{
+ 		ConfigNode order = documentConfig.getNode("ArrayOrder");
+ 
+ 		for(int i = 0; i < aHeaders.length; i++)
+ 		{
+ 			order.setAttribute("Position" + i, i, i);
+ 		}		
+ 	}
+ 	
+ 	
+ 	/**
+ 	 * Save a reordering to the config node.
+ 	 * @param ordering the ordering to save
+ 	 */
+ 	public void saveOrder(int [] ordering)
+ 	{
+ 		ConfigNode order = documentConfig.getNode("ArrayOrder");
+ 			
+ 		int prevVal = 0;
+ 		int [] temp = new int[aHeaders.length];
+ 		
+ 		for(int i = 0; i < aHeaders.length; i++)
+ 		{
+ 			prevVal = order.getAttribute("Position" + ordering[i], -1);
+ 			if(prevVal == -1)
+ 			{
+ 				temp[i] = ordering[i];
+ 			}
+ 			else
+ 			{
+ 				temp[i] = prevVal;
+ 			}
+ 		}
+ 		
+ 		//System.out.print("Saved ordering:  ");
+ 		for(int i = 0; i < aHeaders.length; i++)
+ 		{
+ 			order.setAttribute("Position" + i, temp[i], -1);
+ 		//	System.out.print(order.getAttribute("Position" + i, -1) + " ");
+ 		}
+ 		//System.out.println();
+ 		
+ 	}
+ 	
+ 	/**
+ 	 * Load array order from the config node.
+ 	 */
+ 	public void loadOrder()
+ 	{
+ 		if(documentConfig == null)
+ 		{
+ 			return;
+ 		}
+ 		
+ 		ConfigNode order = documentConfig.getNode("ArrayOrder");
+ 		
+ 		int [] ordering = new int[aHeaders.length];
+ 		
+ 		int prevVal = 0;
+ 		
+ 		
+ 		//System.out.print("Loaded ordering:  ");
+ 		for(int i = 0; i < ordering.length; i++)
+ 		{
+ 			ordering[i] = order.getAttribute("Position" + i, i);
+ 		//	System.out.print(ordering[i] + " ");
+ 		}
+ 		//System.out.println();
+ 		
+ 		reorderArrays(ordering);
+ 	}

  	 public void resetState () {
***************
*** 324,327 ****
--- 439,447 ----
  			}
  		}
+ 		public void setValue(double value, int x, int y)
+ 		{
+ 			exprData[x + y*nexpr] = value;
+ 			setChanged();
+ 		}
  		public int getNumRow() {
  			return ngene;