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mev-4.0.01/source/org/tigr/microarray/mev/cluster/gui/impl/ptm/PTMInitDialog.java

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Rev	Date	Author	Line
2	26 Feb 07	jari	1	/*
2	26 Feb 07	jari	2	Copyright @ 1999-2006, The Institute for Genomic Research (TIGR).
2	26 Feb 07	jari	3	All rights reserved.
2	26 Feb 07	jari	4	*/
2	26 Feb 07	jari	5	/*
2	26 Feb 07	jari	6	* $RCSfile: PTMInitDialog.java,v $
2	26 Feb 07	jari	7	* $Revision: 1.7 $
2	26 Feb 07	jari	8	* $Date: 2006/02/24 16:15:29 $
2	26 Feb 07	jari	9	* $Author: wwang67 $
2	26 Feb 07	jari	10	* $State: Exp $
2	26 Feb 07	jari	11	*/
2	26 Feb 07	jari	12	package org.tigr.microarray.mev.cluster.gui.impl.ptm;
2	26 Feb 07	jari	13
2	26 Feb 07	jari	14	import java.awt.Color;
2	26 Feb 07	jari	15	import java.awt.Dimension;
2	26 Feb 07	jari	16	import java.awt.GridBagConstraints;
2	26 Feb 07	jari	17	import java.awt.GridBagLayout;
2	26 Feb 07	jari	18	import java.awt.Insets;
2	26 Feb 07	jari	19	import java.awt.Toolkit;
2	26 Feb 07	jari	20	import java.awt.event.ActionEvent;
2	26 Feb 07	jari	21	import java.awt.event.ActionListener;
2	26 Feb 07	jari	22	import java.awt.event.FocusEvent;
2	26 Feb 07	jari	23	import java.awt.event.FocusListener;
2	26 Feb 07	jari	24	import java.awt.event.ItemEvent;
2	26 Feb 07	jari	25	import java.awt.event.ItemListener;
2	26 Feb 07	jari	26	import java.io.BufferedReader;
2	26 Feb 07	jari	27	import java.io.BufferedWriter;
2	26 Feb 07	jari	28	import java.io.EOFException;
2	26 Feb 07	jari	29	import java.io.File;
2	26 Feb 07	jari	30	import java.io.FileWriter;
2	26 Feb 07	jari	31	import java.io.IOException;
2	26 Feb 07	jari	32	import java.util.Hashtable;
2	26 Feb 07	jari	33	import java.util.Vector;
2	26 Feb 07	jari	34
2	26 Feb 07	jari	35	import javax.swing.BorderFactory;
2	26 Feb 07	jari	36	import javax.swing.ButtonGroup;
2	26 Feb 07	jari	37	import javax.swing.DefaultListModel;
2	26 Feb 07	jari	38	import javax.swing.JButton;
2	26 Feb 07	jari	39	import javax.swing.JCheckBox;
2	26 Feb 07	jari	40	import javax.swing.JFileChooser;
2	26 Feb 07	jari	41	import javax.swing.JFrame;
2	26 Feb 07	jari	42	import javax.swing.JLabel;
2	26 Feb 07	jari	43	import javax.swing.JList;
2	26 Feb 07	jari	44	import javax.swing.JOptionPane;
2	26 Feb 07	jari	45	import javax.swing.JPanel;
2	26 Feb 07	jari	46	import javax.swing.JRadioButton;
2	26 Feb 07	jari	47	import javax.swing.JScrollPane;
2	26 Feb 07	jari	48	import javax.swing.JSlider;
2	26 Feb 07	jari	49	import javax.swing.JSplitPane;
2	26 Feb 07	jari	50	import javax.swing.JTabbedPane;
2	26 Feb 07	jari	51	import javax.swing.JTextField;
2	26 Feb 07	jari	52	import javax.swing.ListSelectionModel;
2	26 Feb 07	jari	53	import javax.swing.ScrollPaneConstants;
2	26 Feb 07	jari	54	import javax.swing.SwingConstants;
2	26 Feb 07	jari	55	import javax.swing.border.BevelBorder;
2	26 Feb 07	jari	56	import javax.swing.border.EtchedBorder;
2	26 Feb 07	jari	57	import javax.swing.event.ChangeEvent;
2	26 Feb 07	jari	58	import javax.swing.event.ChangeListener;
2	26 Feb 07	jari	59	import javax.swing.event.ListSelectionEvent;
2	26 Feb 07	jari	60	import javax.swing.event.ListSelectionListener;
2	26 Feb 07	jari	61
2	26 Feb 07	jari	62	import org.tigr.graph.GraphCanvas;
2	26 Feb 07	jari	63	import org.tigr.graph.GraphLine;
2	26 Feb 07	jari	64	import org.tigr.graph.GraphPoint;
2	26 Feb 07	jari	65	import org.tigr.microarray.mev.TMEV;
2	26 Feb 07	jari	66	import org.tigr.microarray.mev.cluster.gui.impl.GUIFactory;
2	26 Feb 07	jari	67	import org.tigr.microarray.mev.cluster.gui.impl.dialogs.AlgorithmDialog;
2	26 Feb 07	jari	68	import org.tigr.microarray.mev.cluster.gui.impl.dialogs.dialogHelpUtil.HelpWindow;
2	26 Feb 07	jari	69	import org.tigr.util.FloatMatrix;
2	26 Feb 07	jari	70
2	26 Feb 07	jari	71
2	26 Feb 07	jari	72	public class PTMInitDialog extends AlgorithmDialog {
2	26 Feb 07	jari	73
2	26 Feb 07	jari	74	String[] SampleNames;
2	26 Feb 07	jari	75	Vector sampleNamesVector;
2	26 Feb 07	jari	76	Vector uniqueIDs;
2	26 Feb 07	jari	77	Vector clusters; //THIS IS A VECTOR OF VECTORS (EACH SUB-VECTOR CONTAINS THE INDICES OF UNIQUEIDS IN THAT CLUSTER)
2	26 Feb 07	jari	78	Vector expClusters;
2	26 Feb 07	jari	79	Color[] clusterColors;
2	26 Feb 07	jari	80	Color[] expClusterColors;
2	26 Feb 07	jari	81	GeneSelector geneSelectPanel;
2	26 Feb 07	jari	82	GeneClusterSelector geneClusterSelectPanel;
2	26 Feb 07	jari	83	ExperimentSelector expSelectPanel;
2	26 Feb 07	jari	84	ExperimentClusterSelector clusterSelectPanel;
2	26 Feb 07	jari	85	SavedTemplateSelector templateSelectPanel;
2	26 Feb 07	jari	86	TemplatePanel tempPanel;
2	26 Feb 07	jari	87	ThresholdPanel thresh;
2	26 Feb 07	jari	88	FloatMatrix expMatrix;
2	26 Feb 07	jari	89	JCheckBox drawTreesBox;
2	26 Feb 07	jari	90	private JRadioButton sigOnly, allClusters;
2	26 Feb 07	jari	91	JPanel drawTreesPane;
2	26 Feb 07	jari	92	JTabbedPane tabbedPane;
2	26 Feb 07	jari	93	JButton saveTemplateButton;
2	26 Feb 07	jari	94	Vector template = new Vector();
2	26 Feb 07	jari	95
2	26 Feb 07	jari	96	FloatMatrix templateMatrix;
2	26 Feb 07	jari	97	boolean setTemplate = false;
2	26 Feb 07	jari	98	boolean clusterGenes = true;
2	26 Feb 07	jari	99
2	26 Feb 07	jari	100	int numberOfExperiments;
2	26 Feb 07	jari	101	private boolean okPressed = false;
2	26 Feb 07	jari	102
2	26 Feb 07	jari	103	public PTMInitDialog(JFrame parentFrame, boolean modality, FloatMatrix expMatrix, Vector uniqueIDs, Vector sampleNamesVector, Vector clusters, Vector expClusters, Color[] clusterColors, Color[] expClusterColors) {
2	26 Feb 07	jari	104	super(parentFrame, "PTM: Pavlidis Template Matching", modality);
2	26 Feb 07	jari	105	this.expMatrix = expMatrix;
2	26 Feb 07	jari	106	this.numberOfExperiments = expMatrix.getColumnDimension();
2	26 Feb 07	jari	107	this.uniqueIDs = uniqueIDs;
2	26 Feb 07	jari	108	this.sampleNamesVector = sampleNamesVector;
2	26 Feb 07	jari	109	this.clusters = clusters;
2	26 Feb 07	jari	110	this.clusterColors = clusterColors;
2	26 Feb 07	jari	111	this.expClusters = expClusters;
2	26 Feb 07	jari	112	this.expClusterColors = expClusterColors;
2	26 Feb 07	jari	113	SampleNames = getSampleNames();
2	26 Feb 07	jari	114	// setBounds(0, 0, 1000, 800); // may need to tinker with this, to set the right size and position of the frame
2	26 Feb 07	jari	115	setBounds(0,0,890,700);
2	26 Feb 07	jari	116	setSize(890, 700);
2	26 Feb 07	jari	117	setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
2	26 Feb 07	jari	118	GridBagLayout gridbag = new GridBagLayout();
2	26 Feb 07	jari	119	GridBagConstraints constraints = new GridBagConstraints();
2	26 Feb 07	jari	120	constraints.fill = GridBagConstraints.BOTH;
2	26 Feb 07	jari	121	JPanel pane = new JPanel();
2	26 Feb 07	jari	122	pane.setLayout(gridbag);
2	26 Feb 07	jari	123
2	26 Feb 07	jari	124	buildConstraints(constraints, 0, 0, 2, 1, 0, 10);
2	26 Feb 07	jari	125	tabbedPane = new JTabbedPane();
2	26 Feb 07	jari	126	geneSelectPanel = new GeneSelector();
2	26 Feb 07	jari	127	geneClusterSelectPanel = new GeneClusterSelector();
2	26 Feb 07	jari	128	expSelectPanel = new ExperimentSelector();
2	26 Feb 07	jari	129	clusterSelectPanel = new ExperimentClusterSelector();
2	26 Feb 07	jari	130	templateSelectPanel = new SavedTemplateSelector();
2	26 Feb 07	jari	131
2	26 Feb 07	jari	132	tabbedPane.addTab("Gene Templates", geneSelectPanel);
2	26 Feb 07	jari	133	tabbedPane.addTab("Gene Cluster Templates", geneClusterSelectPanel);
2	26 Feb 07	jari	134	tabbedPane.addTab("Sample Templates", expSelectPanel);
2	26 Feb 07	jari	135	tabbedPane.addTab("Sample Cluster Templates", clusterSelectPanel);
2	26 Feb 07	jari	136	tabbedPane.addTab("Select a Saved Template", templateSelectPanel);
2	26 Feb 07	jari	137	tabbedPane.setSelectedIndex(0);
2	26 Feb 07	jari	138
2	26 Feb 07	jari	139	gridbag.setConstraints(tabbedPane, constraints);
2	26 Feb 07	jari	140	pane.add(tabbedPane);
2	26 Feb 07	jari	141
2	26 Feb 07	jari	142	//placeholder button for top panel
2	26 Feb 07	jari	143	buildConstraints(constraints, 0, 1, 2, 1, 0, 10);
2	26 Feb 07	jari	144	tempPanel = new TemplatePanel();
2	26 Feb 07	jari	145	tempPanel.setPreferredSize(new Dimension(80, 400));
2	26 Feb 07	jari	146	//JButton button1 = new JButton("Enter template");
2	26 Feb 07	jari	147	gridbag.setConstraints(tempPanel, constraints);
2	26 Feb 07	jari	148	pane.add(tempPanel);
2	26 Feb 07	jari	149
2	26 Feb 07	jari	150	tabbedPane.addChangeListener(new ChangeListener(){
2	26 Feb 07	jari	151
2	26 Feb 07	jari	152	public void stateChanged(ChangeEvent evt){
2	26 Feb 07	jari	153	int index = tabbedPane.getSelectedIndex();
2	26 Feb 07	jari	154	if(index > 1){
2	26 Feb 07	jari	155	tempPanel.setEnabled(false);
2	26 Feb 07	jari	156	tempPanel.setVisible(false);
2	26 Feb 07	jari	157	}
2	26 Feb 07	jari	158	else{
2	26 Feb 07	jari	159	tempPanel.setEnabled(true);
2	26 Feb 07	jari	160	tempPanel.setVisible(true);
2	26 Feb 07	jari	161	}
2	26 Feb 07	jari	162	}
2	26 Feb 07	jari	163
2	26 Feb 07	jari	164	});
2	26 Feb 07	jari	165
2	26 Feb 07	jari	166	// threshold prob panel
2	26 Feb 07	jari	167	buildConstraints(constraints, 0, 2, 1, 1, 20, 0);
2	26 Feb 07	jari	168	thresh = new ThresholdPanel();
2	26 Feb 07	jari	169	gridbag.setConstraints(thresh, constraints);
2	26 Feb 07	jari	170	pane.add(thresh);
2	26 Feb 07	jari	171
2	26 Feb 07	jari	172	buildConstraints(constraints, 1,2, 1, 1, 5, 0);
2	26 Feb 07	jari	173
2	26 Feb 07	jari	174	drawTreesPane = new JPanel();
2	26 Feb 07	jari	175	drawTreesPane.setLayout(new GridBagLayout());
2	26 Feb 07	jari	176	drawTreesBox = new JCheckBox("Construct Hierarchical Trees for:");
2	26 Feb 07	jari	177	drawTreesBox.setFocusPainted(false);
2	26 Feb 07	jari	178
2	26 Feb 07	jari	179	sigOnly = new JRadioButton("Matched genes only", true);
2	26 Feb 07	jari	180	//sigOnly.setBackground(Color.white);
2	26 Feb 07	jari	181	//sigOnly.setForeground(UIManager.getColor("Label.foreground"));
2	26 Feb 07	jari	182
2	26 Feb 07	jari	183	allClusters = new JRadioButton("All clusters", false);
2	26 Feb 07	jari	184	//allClusters.setBackground(Color.white);
2	26 Feb 07	jari	185	//allClusters.setForeground(UIManager.getColor("Label.foreground"));
2	26 Feb 07	jari	186
2	26 Feb 07	jari	187	sigOnly.setEnabled(false);
2	26 Feb 07	jari	188	allClusters.setEnabled(false);
2	26 Feb 07	jari	189
2	26 Feb 07	jari	190	ButtonGroup allOrSig = new ButtonGroup();
2	26 Feb 07	jari	191	allOrSig.add(sigOnly);
2	26 Feb 07	jari	192	allOrSig.add(allClusters);
2	26 Feb 07	jari	193
2	26 Feb 07	jari	194	saveTemplateButton = new JButton("Save Current Template", GUIFactory.getIcon("save16.gif"));
2	26 Feb 07	jari	195	saveTemplateButton.setToolTipText("Saves template to file");
2	26 Feb 07	jari	196	saveTemplateButton.setFocusPainted(false);
2	26 Feb 07	jari	197	saveTemplateButton.setActionCommand("save-template-to-file-command");
2	26 Feb 07	jari	198	saveTemplateButton.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED));
2	26 Feb 07	jari	199	saveTemplateButton.setMargin(new Insets(2,50,2,5));
2	26 Feb 07	jari	200	saveTemplateButton.setPreferredSize(new Dimension(175,30));
2	26 Feb 07	jari	201	saveTemplateButton.addActionListener(new ActionListener(){
2	26 Feb 07	jari	202	public void actionPerformed(ActionEvent evt) {
2	26 Feb 07	jari	203	if (evt.getSource() == saveTemplateButton) {
2	26 Feb 07	jari	204	String dataPath = TMEV.getDataPath();
2	26 Feb 07	jari	205	File fileLoc = TMEV.getFile("data/");
2	26 Feb 07	jari	206	// if the data path is null go to default, if not null and not exist then to to default
2	26 Feb 07	jari	207	// else use the dataPath
2	26 Feb 07	jari	208	if(dataPath != null) {
2	26 Feb 07	jari	209	fileLoc = new File(dataPath);
2	26 Feb 07	jari	210	if(!fileLoc.exists()) {
2	26 Feb 07	jari	211	fileLoc = TMEV.getFile("data/");
2	26 Feb 07	jari	212	}
2	26 Feb 07	jari	213	}
2	26 Feb 07	jari	214	JFileChooser fc = new JFileChooser(fileLoc);
2	26 Feb 07	jari	215
2	26 Feb 07	jari	216	int returnVal = fc.showSaveDialog(PTMInitDialog.this);
2	26 Feb 07	jari	217	if (returnVal == JFileChooser.APPROVE_OPTION) {
2	26 Feb 07	jari	218	File file = fc.getSelectedFile();
2	26 Feb 07	jari	219	try {
2	26 Feb 07	jari	220	// DataOutputStream templateData = new DataOutputStream(new FileOutputStream(file.getPath(), true));
2	26 Feb 07	jari	221	BufferedWriter bw = new BufferedWriter(new FileWriter(file.getPath()));
2	26 Feb 07	jari	222	if(tabbedPane.getSelectedIndex() < 2){
2	26 Feb 07	jari	223	for(int i = 0; i < tempPanel.tempScr.tempGrid.length; i++) {
2	26 Feb 07	jari	224	String s = tempPanel.tempScr.tempGrid[i].templateField.getText();
2	26 Feb 07	jari	225	float f = Float.parseFloat(s);
2	26 Feb 07	jari	226	// templateData.writeFloat(f);
2	26 Feb 07	jari	227	bw.write(Float.toString(f)+"\n");
2	26 Feb 07	jari	228	}
2	26 Feb 07	jari	229	}
2	26 Feb 07	jari	230	else{
2	26 Feb 07	jari	231	for(int i = 0; i < template.size() ; i++){
2	26 Feb 07	jari	232	bw.write(((Float)template.elementAt(i)).toString()+"\n");
2	26 Feb 07	jari	233	//templateData.writeFloat(((Float)template.elementAt(i)).floatValue());
2	26 Feb 07	jari	234	}
2	26 Feb 07	jari	235	}
2	26 Feb 07	jari	236	bw.flush();
2	26 Feb 07	jari	237	bw.close();
2	26 Feb 07	jari	238	// templateData.close();
2	26 Feb 07	jari	239	} catch (IOException e) {
2	26 Feb 07	jari	240	System.out.println("Error: " + e.toString());
2	26 Feb 07	jari	241	}
2	26 Feb 07	jari	242	}
2	26 Feb 07	jari	243	}
2	26 Feb 07	jari	244	}
2	26 Feb 07	jari	245	});
2	26 Feb 07	jari	246
2	26 Feb 07	jari	247	drawTreesBox.addItemListener(new ItemListener() {
2	26 Feb 07	jari	248	public void itemStateChanged(ItemEvent e) {
2	26 Feb 07	jari	249	if (e.getStateChange() == ItemEvent.DESELECTED) {
2	26 Feb 07	jari	250	sigOnly.setEnabled(false);
2	26 Feb 07	jari	251	allClusters.setEnabled(false);
2	26 Feb 07	jari	252	} else {
2	26 Feb 07	jari	253	sigOnly.setEnabled(true);
2	26 Feb 07	jari	254	allClusters.setEnabled(true);
2	26 Feb 07	jari	255	}
2	26 Feb 07	jari	256	}
2	26 Feb 07	jari	257	});
2	26 Feb 07	jari	258
2	26 Feb 07	jari	259	drawTreesPane.add(saveTemplateButton, new GridBagConstraints(0,0,1,1,0,0,GridBagConstraints.CENTER,GridBagConstraints.BOTH,new Insets(0,30,0,20),0,0));
2	26 Feb 07	jari	260	drawTreesPane.add(drawTreesBox, new GridBagConstraints(1,0,1,1,0,0,GridBagConstraints.CENTER,GridBagConstraints.BOTH,new Insets(0,30,0,20),0,0));
2	26 Feb 07	jari	261	drawTreesPane.add(sigOnly, new GridBagConstraints(1,1,1,1,0,0,GridBagConstraints.WEST,GridBagConstraints.NONE,new Insets(0,30,0,20),0,0));
2	26 Feb 07	jari	262	drawTreesPane.add(allClusters, new GridBagConstraints(1,2,1,1,0,0,GridBagConstraints.WEST,GridBagConstraints.NONE,new Insets(0,30,0,20),0,0));
2	26 Feb 07	jari	263
2	26 Feb 07	jari	264	constraints.anchor = GridBagConstraints.CENTER;
2	26 Feb 07	jari	265	gridbag.setConstraints(drawTreesPane, constraints);
2	26 Feb 07	jari	266	buildConstraints(constraints, 1, 2, 1, 1, 5, 0);
2	26 Feb 07	jari	267	gridbag.setConstraints(drawTreesPane, constraints);
2	26 Feb 07	jari	268	pane.add(drawTreesPane);
2	26 Feb 07	jari	269	addContent(pane);
2	26 Feb 07	jari	270	setActionListeners(new EventListener());
2	26 Feb 07	jari	271	}
2	26 Feb 07	jari	272
2	26 Feb 07	jari	273
2	26 Feb 07	jari	274	public void setVisible(boolean visible) {
2	26 Feb 07	jari	275
2	26 Feb 07	jari	276	Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
2	26 Feb 07	jari	277	setLocation((screenSize.width - getSize().width)/2, (screenSize.height - getSize().height)/2);
2	26 Feb 07	jari	278
2	26 Feb 07	jari	279	super.setVisible(visible);
2	26 Feb 07	jari	280	}
2	26 Feb 07	jari	281
2	26 Feb 07	jari	282	public boolean isGeneTemplate(){
2	26 Feb 07	jari	283	return this.clusterGenes;
2	26 Feb 07	jari	284	}
2	26 Feb 07	jari	285
2	26 Feb 07	jari	286	void buildConstraints(GridBagConstraints gbc, int gx, int gy,
2	26 Feb 07	jari	287	int gw, int gh, int wx, int wy) {
2	26 Feb 07	jari	288
2	26 Feb 07	jari	289	gbc.gridx = gx;
2	26 Feb 07	jari	290	gbc.gridy = gy;
2	26 Feb 07	jari	291	gbc.gridwidth = gw;
2	26 Feb 07	jari	292	gbc.gridheight = gh;
2	26 Feb 07	jari	293	gbc.weightx = wx;
2	26 Feb 07	jari	294	gbc.weighty = wy;
2	26 Feb 07	jari	295	}
2	26 Feb 07	jari	296
2	26 Feb 07	jari	297
2	26 Feb 07	jari	298	String[] getSampleNames() {
2	26 Feb 07	jari	299	String[] SampleNames = new String[sampleNamesVector.size()];
2	26 Feb 07	jari	300	for(int i = 0; i < sampleNamesVector.size(); i++){
2	26 Feb 07	jari	301	SampleNames[i] = (String)sampleNamesVector.get(i);
2	26 Feb 07	jari	302	}
2	26 Feb 07	jari	303	return SampleNames;
2	26 Feb 07	jari	304	}
2	26 Feb 07	jari	305
2	26 Feb 07	jari	306
2	26 Feb 07	jari	307	class ExperimentSelector extends JPanel{
2	26 Feb 07	jari	308	JList expList;
2	26 Feb 07	jari	309	GraphCanvas profileDisplayPanel;
2	26 Feb 07	jari	310	JScrollPane listScrollPane;
2	26 Feb 07	jari	311	JButton selectButton;
2	26 Feb 07	jari	312	int maxIndex = -1;
2	26 Feb 07	jari	313	int minIndex = -1;
2	26 Feb 07	jari	314
2	26 Feb 07	jari	315	JSplitPane expSplitPane;
2	26 Feb 07	jari	316
2	26 Feb 07	jari	317	ExperimentSelector() {
2	26 Feb 07	jari	318	GridBagLayout gridbag = new GridBagLayout();
2	26 Feb 07	jari	319	GridBagConstraints constraints = new GridBagConstraints();
2	26 Feb 07	jari	320	this.setLayout(gridbag);
2	26 Feb 07	jari	321
2	26 Feb 07	jari	322	expList = new JList(sampleNamesVector);
2	26 Feb 07	jari	323	expList.setSelectedIndex(0);
2	26 Feb 07	jari	324
2	26 Feb 07	jari	325	//AIS -- Use the graph classes
2	26 Feb 07	jari	326	profileDisplayPanel = new GraphCanvas();
2	26 Feb 07	jari	327	profileDisplayPanel.setGraphBounds(0, expMatrix.getRowDimension(), -3, 3);
2	26 Feb 07	jari	328	profileDisplayPanel.setGraphSpacing(20, 20, 20, 20);
2	26 Feb 07	jari	329	profileDisplayPanel.setXAxisValue(0);
2	26 Feb 07	jari	330	profileDisplayPanel.setYAxisValue(0);
2	26 Feb 07	jari	331
2	26 Feb 07	jari	332	//AIS -- Use the graph classes
2	26 Feb 07	jari	333	/* expProfileDisplayPanel = new GraphCanvas();
2	26 Feb 07	jari	334	expProfileDisplayPanel.setGraphBounds(0, expMatrix.getRowDimension(), -3, 3);
2	26 Feb 07	jari	335	expProfileDisplayPanel.setGraphSpacing(20, 20, 20, 20);
2	26 Feb 07	jari	336	expProfileDisplayPanel.setXAxisValue(0);
2	26 Feb 07	jari	337	expProfileDisplayPanel.setYAxisValue(0);
2	26 Feb 07	jari	338	*/
2	26 Feb 07	jari	339	expList.addListSelectionListener(new ListSelectionListener(){
2	26 Feb 07	jari	340	public void valueChanged(ListSelectionEvent e) {
2	26 Feb 07	jari	341	refreshGraph();
2	26 Feb 07	jari	342	}
2	26 Feb 07	jari	343	});
2	26 Feb 07	jari	344	//-- AIS
2	26 Feb 07	jari	345
2	26 Feb 07	jari	346	listScrollPane = new JScrollPane(expList);
2	26 Feb 07	jari	347	expSplitPane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, listScrollPane, profileDisplayPanel);
2	26 Feb 07	jari	348	expSplitPane.setOneTouchExpandable(true);
2	26 Feb 07	jari	349	expSplitPane.setDividerLocation(200);
2	26 Feb 07	jari	350
2	26 Feb 07	jari	351	Dimension minimumSize = new Dimension(100,50);
2	26 Feb 07	jari	352	expList.setMinimumSize(minimumSize);
2	26 Feb 07	jari	353	profileDisplayPanel.setMinimumSize(minimumSize);
2	26 Feb 07	jari	354
2	26 Feb 07	jari	355	//uIDSplitPane.setPreferredSize(new Dimension(700,150));
2	26 Feb 07	jari	356
2	26 Feb 07	jari	357	buildConstraints(constraints, 0, 0, 1, 1, 1, 1);
2	26 Feb 07	jari	358	constraints.fill = GridBagConstraints.BOTH;
2	26 Feb 07	jari	359	gridbag.setConstraints(expSplitPane, constraints);
2	26 Feb 07	jari	360	this.add(expSplitPane);
2	26 Feb 07	jari	361
2	26 Feb 07	jari	362	buildConstraints(constraints, 0, 1, 1, 1, 0, 0);
2	26 Feb 07	jari	363	constraints.fill = GridBagConstraints.NONE;
2	26 Feb 07	jari	364	constraints.anchor = GridBagConstraints.CENTER;
2	26 Feb 07	jari	365	constraints.insets = new Insets(10,0,10,0);
2	26 Feb 07	jari	366	selectButton = new JButton("Select highlighted samples from above list to use as template", GUIFactory.getIcon("select_check24.gif"));
2	26 Feb 07	jari	367	selectButton.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED));
2	26 Feb 07	jari	368	selectButton.setMargin(new Insets(10,10,10,10));
2	26 Feb 07	jari	369	selectButton.setPreferredSize(new Dimension(400,30));
2	26 Feb 07	jari	370	selectButton.setFocusPainted(false);
2	26 Feb 07	jari	371	selectButton.addActionListener(new ActionListener(){
2	26 Feb 07	jari	372
2	26 Feb 07	jari	373	public void actionPerformed(ActionEvent e) {
2	26 Feb 07	jari	374	int [] index = expList.getSelectedIndices();
2	26 Feb 07	jari	375	Vector expProfile = new Vector();
2	26 Feb 07	jari	376	Vector expProfiles = new Vector();
2	26 Feb 07	jari	377
2	26 Feb 07	jari	378	for(int j = 0; j < index.length; j++){
2	26 Feb 07	jari	379	expProfile = getExperiment(index[j]);
2	26 Feb 07	jari	380	float max = getMax(expProfile);
2	26 Feb 07	jari	381	float min = getMin(expProfile);
2	26 Feb 07	jari	382
2	26 Feb 07	jari	383	if ((max - min) == 0) {
2	26 Feb 07	jari	384	for(int i = 0; i < expProfile.size(); i++) {
2	26 Feb 07	jari	385	expProfile.set(i, new Float(0.5));
2	26 Feb 07	jari	386	}
2	26 Feb 07	jari	387	} else {
2	26 Feb 07	jari	388	for(int i = 0; i < expProfile.size(); i++) {
2	26 Feb 07	jari	389	float f = (((Float)expProfile.get(i)).floatValue()- min)/(max - min);
2	26 Feb 07	jari	390	expProfile.set(i, new Float(f));
2	26 Feb 07	jari	391	}
2	26 Feb 07	jari	392	}
2	26 Feb 07	jari	393	expProfiles.add(expProfile);
2	26 Feb 07	jari	394	}
2	26 Feb 07	jari	395
2	26 Feb 07	jari	396	template = getMeanProfile(expProfiles);
2	26 Feb 07	jari	397	setTemplate = true;
2	26 Feb 07	jari	398	clusterGenes = false;
2	26 Feb 07	jari	399	refreshGraph();
2	26 Feb 07	jari	400	}
2	26 Feb 07	jari	401
2	26 Feb 07	jari	402	});
2	26 Feb 07	jari	403
2	26 Feb 07	jari	404	gridbag.setConstraints(selectButton, constraints);
2	26 Feb 07	jari	405	this.add(selectButton);
2	26 Feb 07	jari	406	refreshGraph();
2	26 Feb 07	jari	407	}
2	26 Feb 07	jari	408
2	26 Feb 07	jari	409
2	26 Feb 07	jari	410	private void refreshGraph() {
2	26 Feb 07	jari	411	profileDisplayPanel.removeAllGraphElements();
2	26 Feb 07	jari	412	// int index = expList.getSelectedIndex();
2	26 Feb 07	jari	413	int [] indices = expList.getSelectedIndices();
2	26 Feb 07	jari	414	Vector expProfile;
2	26 Feb 07	jari	415	Vector expProfiles = new Vector();
2	26 Feb 07	jari	416	float max = Float.NEGATIVE_INFINITY;
2	26 Feb 07	jari	417	float min = Float.POSITIVE_INFINITY;
2	26 Feb 07	jari	418	float maxRange;
2	26 Feb 07	jari	419	for(int exp = 0; exp < indices.length; exp++){
2	26 Feb 07	jari	420	expProfile = getExperiment(indices[exp]);
2	26 Feb 07	jari	421	expProfiles.add(expProfile);
2	26 Feb 07	jari	422	max = Math.max(max, getMax(expProfile));
2	26 Feb 07	jari	423	min = Math.min(min, getMin(expProfile));
2	26 Feb 07	jari	424	maxRange = Math.max(max, Math.abs(min));
2	26 Feb 07	jari	425	profileDisplayPanel.setGraphBounds(0,expProfile.size(),-maxRange,maxRange);
2	26 Feb 07	jari	426
2	26 Feb 07	jari	427	for (int i = 0; i < expProfile.size(); i++) {
2	26 Feb 07	jari	428	if (!Float.isNaN(((Float) expProfile.elementAt(i)).floatValue())) {
2	26 Feb 07	jari	429	GraphPoint gp = new GraphPoint(i /+ 1/, ((Float) expProfile.elementAt(i)).floatValue(), Color.red, 5);
2	26 Feb 07	jari	430	profileDisplayPanel.addGraphElement(gp);
2	26 Feb 07	jari	431	}
2	26 Feb 07	jari	432	}
2	26 Feb 07	jari	433
2	26 Feb 07	jari	434	for (int i = 0; i < expProfile.size() - 1; i++) {
2	26 Feb 07	jari	435	if ((Float.isNaN(((Float) expProfile.elementAt(i)).floatValue())) \|\| (Float.isNaN(((Float) expProfile.elementAt(i+1)).floatValue()))) {
2	26 Feb 07	jari	436	continue;
2	26 Feb 07	jari	437	}
2	26 Feb 07	jari	438	GraphLine gl = new GraphLine(i /+ 1/, ((Float) expProfile.elementAt(i)).floatValue(),
2	26 Feb 07	jari	439	i + 1, ((Float) expProfile.elementAt(i + 1)).floatValue(), Color.blue);
2	26 Feb 07	jari	440	profileDisplayPanel.addGraphElement(gl);
2	26 Feb 07	jari	441	}
2	26 Feb 07	jari	442	}
2	26 Feb 07	jari	443
2	26 Feb 07	jari	444	expProfile = getMeanProfile(expProfiles);
2	26 Feb 07	jari	445
2	26 Feb 07	jari	446	if(setTemplate){
2	26 Feb 07	jari	447
2	26 Feb 07	jari	448	for (int i = 0; i < expProfile.size() - 1; i++) {
2	26 Feb 07	jari	449	if ((Float.isNaN(((Float) expProfile.elementAt(i)).floatValue())) \|\| (Float.isNaN(((Float) expProfile.elementAt(i+1)).floatValue()))) {
2	26 Feb 07	jari	450	continue;
2	26 Feb 07	jari	451	}
2	26 Feb 07	jari	452	GraphLine gl = new GraphLine(i /+ 1/, ((Float) expProfile.elementAt(i)).floatValue(),
2	26 Feb 07	jari	453	i + 1, ((Float) expProfile.elementAt(i + 1)).floatValue(), Color.green);
2	26 Feb 07	jari	454	profileDisplayPanel.addGraphElement(gl);
2	26 Feb 07	jari	455	}
2	26 Feb 07	jari	456	}
2	26 Feb 07	jari	457	profileDisplayPanel.repaint();
2	26 Feb 07	jari	458	}
2	26 Feb 07	jari	459
2	26 Feb 07	jari	460	public void reset(){
2	26 Feb 07	jari	461	expList.setSelectedIndex(0);
2	26 Feb 07	jari	462	setTemplate = false;
2	26 Feb 07	jari	463	refreshGraph();
2	26 Feb 07	jari	464	}
2	26 Feb 07	jari	465	}
2	26 Feb 07	jari	466
2	26 Feb 07	jari	467	Vector getMeanProfile(Vector expInCluster) {
2	26 Feb 07	jari	468
2	26 Feb 07	jari	469	Vector meanProfile = new Vector();
2	26 Feb 07	jari	470
2	26 Feb 07	jari	471	//if empty just return a NaN profile
2	26 Feb 07	jari	472	if(expInCluster.size() == 0) {
2	26 Feb 07	jari	473	Vector v = new Vector(this.numberOfExperiments);
2	26 Feb 07	jari	474	for(int i = 0; i < numberOfExperiments; i++) {
2	26 Feb 07	jari	475	v.add(new Float(Float.NaN));
2	26 Feb 07	jari	476	}
2	26 Feb 07	jari	477	return v;
2	26 Feb 07	jari	478	}
2	26 Feb 07	jari	479
2	26 Feb 07	jari	480	float[][] expMatrix = this.convertToFloatMatrix(expInCluster);
2	26 Feb 07	jari	481	float[] meanArray;
2	26 Feb 07	jari	482	int n = 0;
2	26 Feb 07	jari	483	float mean;
2	26 Feb 07	jari	484
2	26 Feb 07	jari	485	for (int i = 0; i < expMatrix[0].length; i++){
2	26 Feb 07	jari	486	float sum = 0;
2	26 Feb 07	jari	487	n = 0;
2	26 Feb 07	jari	488	for (int j = 0; j < expMatrix.length; j++){
2	26 Feb 07	jari	489	if (!Float.isNaN(expMatrix[j][i])){
2	26 Feb 07	jari	490	sum += expMatrix[j][i];
2	26 Feb 07	jari	491	n++;
2	26 Feb 07	jari	492	}
2	26 Feb 07	jari	493	}
2	26 Feb 07	jari	494	mean = (n > 0) ? (sum / (float)n) : 0;
2	26 Feb 07	jari	495	meanProfile.add(new Float(mean));
2	26 Feb 07	jari	496	}
2	26 Feb 07	jari	497	return meanProfile;
2	26 Feb 07	jari	498	}
2	26 Feb 07	jari	499
2	26 Feb 07	jari	500
2	26 Feb 07	jari	501	float[][] convertToFloatMatrix(Vector geneCluster) {
2	26 Feb 07	jari	502	float[][] matrix = new float[geneCluster.size()][];
2	26 Feb 07	jari	503
2	26 Feb 07	jari	504	for (int i = 0; i < geneCluster.size(); i++) {
2	26 Feb 07	jari	505	Vector currentGene = (Vector) ((Vector) geneCluster.get(i)).clone();
2	26 Feb 07	jari	506	matrix[i] = new float[currentGene.size()];
2	26 Feb 07	jari	507	for (int j = 0; j < currentGene.size(); j++) {
2	26 Feb 07	jari	508	matrix[i][j] = ((Float)currentGene.get(j)).floatValue();
2	26 Feb 07	jari	509	}
2	26 Feb 07	jari	510	}
2	26 Feb 07	jari	511	return matrix;
2	26 Feb 07	jari	512	}
2	26 Feb 07	jari	513
2	26 Feb 07	jari	514
2	26 Feb 07	jari	515	private Vector getExperiment(int index) {
2	26 Feb 07	jari	516	Vector exp = new Vector();
2	26 Feb 07	jari	517	int rows = expMatrix.getRowDimension();
2	26 Feb 07	jari	518	for (int i = 0; i < rows; i++) {
2	26 Feb 07	jari	519	exp.add(new Float(expMatrix.get(i, index)));
2	26 Feb 07	jari	520	}
2	26 Feb 07	jari	521	return exp;
2	26 Feb 07	jari	522	}
2	26 Feb 07	jari	523
2	26 Feb 07	jari	524
2	26 Feb 07	jari	525	private float getMax(Vector element) {
2	26 Feb 07	jari	526	float max = Float.NEGATIVE_INFINITY;
2	26 Feb 07	jari	527
2	26 Feb 07	jari	528	for(int i = 0; i < element.size(); i++) {
2	26 Feb 07	jari	529	if (! Float.isNaN(((Float)element.get(i)).floatValue())) {
2	26 Feb 07	jari	530	float current = ((Float)element.get(i)).floatValue();
2	26 Feb 07	jari	531	if (current > max) max = current;
2	26 Feb 07	jari	532	}
2	26 Feb 07	jari	533	}
2	26 Feb 07	jari	534
2	26 Feb 07	jari	535	return max;
2	26 Feb 07	jari	536	}
2	26 Feb 07	jari	537
2	26 Feb 07	jari	538
2	26 Feb 07	jari	539	private float getMin(Vector element) {
2	26 Feb 07	jari	540	float min = Float.MAX_VALUE;
2	26 Feb 07	jari	541
2	26 Feb 07	jari	542	for(int i = 0; i < element.size(); i++) {
2	26 Feb 07	jari	543	if (! Float.isNaN(((Float)element.get(i)).floatValue())) {
2	26 Feb 07	jari	544	float current = ((Float)element.get(i)).floatValue();
2	26 Feb 07	jari	545	if (current < min) min = current;
2	26 Feb 07	jari	546	}
2	26 Feb 07	jari	547	}
2	26 Feb 07	jari	548	return min;
2	26 Feb 07	jari	549	}
2	26 Feb 07	jari	550
2	26 Feb 07	jari	551
2	26 Feb 07	jari	552
2	26 Feb 07	jari	553	class ExperimentClusterSelector extends JPanel {
2	26 Feb 07	jari	554	JList clusterList;
2	26 Feb 07	jari	555	GraphCanvas profileDisplayPanel;
2	26 Feb 07	jari	556	JScrollPane listScrollPane;
2	26 Feb 07	jari	557	JButton selectButton;
2	26 Feb 07	jari	558
2	26 Feb 07	jari	559	Vector clusterNames; // JUST THE NAMES OF THE CLUSTERS, i.e., "CLUSTER 1", "CLUSTER 2", ETC.
2	26 Feb 07	jari	560	//Vector clusterContents; // THIS IS A VECTOR OF VECTORS (= THE INDICES OF THE UNIQUE IDS IN A CLUSTER)
2	26 Feb 07	jari	561	Vector expDataInClusters; // THIS IS A VECTOR OF VECTORS ( = CLUSTERS) OF VECTORS ( = EXPRESSION PROFILES OF GENES IN THAT CLUSTER).
2	26 Feb 07	jari	562	Vector averageClusterProfiles;
2	26 Feb 07	jari	563
2	26 Feb 07	jari	564	JSplitPane clusterSplitPane;
2	26 Feb 07	jari	565
2	26 Feb 07	jari	566	ExperimentClusterSelector() {
2	26 Feb 07	jari	567
2	26 Feb 07	jari	568	clusterNames = new Vector();
2	26 Feb 07	jari	569
2	26 Feb 07	jari	570	if (expClusters.size() == 0) {
2	26 Feb 07	jari	571	clusterNames.add("No sample clusters to show");
2	26 Feb 07	jari	572	} else {
2	26 Feb 07	jari	573	for (int i = 0; i < expClusters.size(); i++) {
2	26 Feb 07	jari	574	clusterNames.add("Exp. Cluster " + (i+1));
2	26 Feb 07	jari	575	}
2	26 Feb 07	jari	576
2	26 Feb 07	jari	577	expDataInClusters = new Vector();
2	26 Feb 07	jari	578	averageClusterProfiles = new Vector();
2	26 Feb 07	jari	579	int index;
2	26 Feb 07	jari	580	for(int j = 0; j < expClusters.size(); j++) {//IN THIS "FOR" LOOP, CURRENT CLUSTER INITIALLY CONTAINS THE INDICES OF THE GENES IN THE CLUSTER, BUT THESE ARE REPLACED BY THE ACUALLY EXPRESSION VECTORS
2	26 Feb 07	jari	581	Vector currentCluster = (Vector)expClusters.get(j);
2	26 Feb 07	jari	582	Vector cluster = new Vector();
2	26 Feb 07	jari	583	for (int k = 0; k < currentCluster.size(); k++) {
2	26 Feb 07	jari	584	index = ((Integer)currentCluster.get(k)).intValue();
2	26 Feb 07	jari	585	Vector currentGene = getExperiment(index);
2	26 Feb 07	jari	586	//currentCluster.set(k, currentGene);
2	26 Feb 07	jari	587	cluster.add(currentGene);
2	26 Feb 07	jari	588	}
2	26 Feb 07	jari	589
2	26 Feb 07	jari	590	expDataInClusters.add(cluster);
2	26 Feb 07	jari	591	Vector meanOfCurrentCluster = getMeanProfile(cluster);
2	26 Feb 07	jari	592	averageClusterProfiles.add(meanOfCurrentCluster);
2	26 Feb 07	jari	593	}
2	26 Feb 07	jari	594
2	26 Feb 07	jari	595	}
2	26 Feb 07	jari	596
2	26 Feb 07	jari	597	GridBagLayout gridbag = new GridBagLayout();
2	26 Feb 07	jari	598	GridBagConstraints constraints = new GridBagConstraints();
2	26 Feb 07	jari	599	//constraints.fill = GridBagConstraints.NONE;
2	26 Feb 07	jari	600	this.setLayout(gridbag);
2	26 Feb 07	jari	601
2	26 Feb 07	jari	602	clusterList = new JList(clusterNames);
2	26 Feb 07	jari	603	clusterList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
2	26 Feb 07	jari	604	clusterList.setSelectedIndex(0);
2	26 Feb 07	jari	605
2	26 Feb 07	jari	606	//AIS -- Use the graph classes
2	26 Feb 07	jari	607	profileDisplayPanel = new GraphCanvas();
2	26 Feb 07	jari	608	profileDisplayPanel.setGraphBounds(0, sampleNamesVector.size(), -3, 3);
2	26 Feb 07	jari	609	profileDisplayPanel.setGraphSpacing(20, 20, 20, 20);
2	26 Feb 07	jari	610	profileDisplayPanel.setXAxisValue(0);
2	26 Feb 07	jari	611	profileDisplayPanel.setYAxisValue(0);
2	26 Feb 07	jari	612
2	26 Feb 07	jari	613	clusterList.addListSelectionListener(new ListSelectionListener(){
2	26 Feb 07	jari	614	public void valueChanged(ListSelectionEvent e) {
2	26 Feb 07	jari	615	refreshGraph();
2	26 Feb 07	jari	616	}
2	26 Feb 07	jari	617	});
2	26 Feb 07	jari	618	//-- AIS
2	26 Feb 07	jari	619
2	26 Feb 07	jari	620	listScrollPane = new JScrollPane(clusterList);
2	26 Feb 07	jari	621
2	26 Feb 07	jari	622	clusterSplitPane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, listScrollPane, profileDisplayPanel);
2	26 Feb 07	jari	623	clusterSplitPane.setOneTouchExpandable(true);
2	26 Feb 07	jari	624	clusterSplitPane.setDividerLocation(200);
2	26 Feb 07	jari	625
2	26 Feb 07	jari	626	Dimension minimumSize = new Dimension(100,50);
2	26 Feb 07	jari	627	clusterList.setMinimumSize(minimumSize);
2	26 Feb 07	jari	628	profileDisplayPanel.setMinimumSize(minimumSize);
2	26 Feb 07	jari	629
2	26 Feb 07	jari	630	buildConstraints(constraints, 0, 0, 1, 1, 1, 1);
2	26 Feb 07	jari	631	constraints.fill = GridBagConstraints.BOTH;
2	26 Feb 07	jari	632	gridbag.setConstraints(clusterSplitPane, constraints);
2	26 Feb 07	jari	633	this.add(clusterSplitPane);
2	26 Feb 07	jari	634
2	26 Feb 07	jari	635	buildConstraints(constraints, 0, 1, 1, 1, 0, 0);
2	26 Feb 07	jari	636	constraints.fill = GridBagConstraints.NONE;
2	26 Feb 07	jari	637	constraints.anchor = GridBagConstraints.CENTER;
2	26 Feb 07	jari	638	constraints.insets = new Insets(10,0,10,0);
2	26 Feb 07	jari	639	selectButton = new JButton("Select highlighted cluster from above list to use its mean as template", GUIFactory.getIcon("select_check24.gif"));
2	26 Feb 07	jari	640	selectButton.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED));
2	26 Feb 07	jari	641	selectButton.setMargin(new Insets(10,10,10,10));
2	26 Feb 07	jari	642	selectButton.setPreferredSize(new Dimension(430,30));
2	26 Feb 07	jari	643	selectButton.setFocusPainted(false);
2	26 Feb 07	jari	644	selectButton.addActionListener(new ActionListener(){
2	26 Feb 07	jari	645
2	26 Feb 07	jari	646	public void actionPerformed(ActionEvent e) {
2	26 Feb 07	jari	647	if (expClusters.size() == 0){
2	26 Feb 07	jari	648	JOptionPane.showMessageDialog(null, "No sample clusters to select");
2	26 Feb 07	jari	649	} else {
2	26 Feb 07	jari	650	int c = clusterList.getSelectedIndex();
2	26 Feb 07	jari	651	Vector v = (Vector)(expClusters.elementAt(c));
2	26 Feb 07	jari	652	int [] index = new int[v.size()];
2	26 Feb 07	jari	653	for(int i = 0; i < index.length; i++)
2	26 Feb 07	jari	654	index[i] = ((Integer)v.elementAt(i)).intValue();
2	26 Feb 07	jari	655
2	26 Feb 07	jari	656	Vector expProfile = new Vector();
2	26 Feb 07	jari	657	Vector expProfiles = new Vector();
2	26 Feb 07	jari	658
2	26 Feb 07	jari	659	for(int j = 0; j < index.length; j++){
2	26 Feb 07	jari	660	expProfile = getExperiment(index[j]);
2	26 Feb 07	jari	661	float max = getMax(expProfile);
2	26 Feb 07	jari	662	float min = getMin(expProfile);
2	26 Feb 07	jari	663
2	26 Feb 07	jari	664	if ((max - min) == 0) {
2	26 Feb 07	jari	665	for(int i = 0; i < expProfile.size(); i++) {
2	26 Feb 07	jari	666	expProfile.set(i, new Float(0.5));
2	26 Feb 07	jari	667	}
2	26 Feb 07	jari	668	} else {
2	26 Feb 07	jari	669	for(int i = 0; i < expProfile.size(); i++) {
2	26 Feb 07	jari	670	float f = (((Float)expProfile.get(i)).floatValue()- min)/(max - min);
2	26 Feb 07	jari	671	expProfile.set(i, new Float(f));
2	26 Feb 07	jari	672	}
2	26 Feb 07	jari	673	}
2	26 Feb 07	jari	674	expProfiles.add(expProfile);
2	26 Feb 07	jari	675	}
2	26 Feb 07	jari	676
2	26 Feb 07	jari	677	template = getMeanProfile(expProfiles);
2	26 Feb 07	jari	678	setTemplate = true;
2	26 Feb 07	jari	679	clusterGenes = false;
2	26 Feb 07	jari	680	okButton.setEnabled(true);
2	26 Feb 07	jari	681	}
2	26 Feb 07	jari	682	}
2	26 Feb 07	jari	683
2	26 Feb 07	jari	684	});
2	26 Feb 07	jari	685
2	26 Feb 07	jari	686	gridbag.setConstraints(selectButton, constraints);
2	26 Feb 07	jari	687	this.add(selectButton);
2	26 Feb 07	jari	688	refreshGraph();
2	26 Feb 07	jari	689	}
2	26 Feb 07	jari	690
2	26 Feb 07	jari	691	private void refreshGraph() {
2	26 Feb 07	jari	692
2	26 Feb 07	jari	693	int index = clusterList.getSelectedIndex();
2	26 Feb 07	jari	694	if (expClusters.size() <= 0) return;
2	26 Feb 07	jari	695	Vector meanProfile = (Vector) averageClusterProfiles.elementAt(index);
2	26 Feb 07	jari	696	Vector currExp;
2	26 Feb 07	jari	697	GraphLine gL;
2	26 Feb 07	jari	698	float min = Float.POSITIVE_INFINITY;
2	26 Feb 07	jari	699	float max = Float.NEGATIVE_INFINITY;
2	26 Feb 07	jari	700	float maxRange;
2	26 Feb 07	jari	701	profileDisplayPanel.removeAllGraphElements();
2	26 Feb 07	jari	702	Vector selectedCluster = (Vector)expDataInClusters.get(index);
2	26 Feb 07	jari	703
2	26 Feb 07	jari	704	for (int j = 0; j < selectedCluster.size(); j++) {
2	26 Feb 07	jari	705
2	26 Feb 07	jari	706	currExp = (Vector)selectedCluster.get(j);
2	26 Feb 07	jari	707
2	26 Feb 07	jari	708	max = Math.max(max, getMax(currExp));
2	26 Feb 07	jari	709	min = Math.min(min, getMin(currExp));
2	26 Feb 07	jari	710	maxRange = Math.max(max, Math.abs(min));
2	26 Feb 07	jari	711	profileDisplayPanel.setGraphBounds(0, currExp.size(), -maxRange, maxRange);
2	26 Feb 07	jari	712
2	26 Feb 07	jari	713	for (int i = 0; i < currExp.size() - 1; i++) {
2	26 Feb 07	jari	714	if ((Float.isNaN(((Float) currExp.elementAt(i)).floatValue()))\|\|(Float.isNaN(((Float) currExp.elementAt(i+1)).floatValue()))) {
2	26 Feb 07	jari	715	continue;
2	26 Feb 07	jari	716	}
2	26 Feb 07	jari	717	gL = new GraphLine(i /+ 1/, ((Float) currExp.elementAt(i)).floatValue(),
2	26 Feb 07	jari	718	i + 1, ((Float) currExp.elementAt(i + 1)).floatValue(), expClusterColors[index]);
2	26 Feb 07	jari	719	profileDisplayPanel.addGraphElement(gL);
2	26 Feb 07	jari	720	}
2	26 Feb 07	jari	721	}
2	26 Feb 07	jari	722
2	26 Feb 07	jari	723	for (int i = 0; i < meanProfile.size(); i++) {
2	26 Feb 07	jari	724	if (!Float.isNaN(((Float) meanProfile.elementAt(i)).floatValue())) {
2	26 Feb 07	jari	725	GraphPoint gp = new GraphPoint(i/* + 1*/, ((Float) meanProfile.elementAt(i)).floatValue(), Color.red, 5);
2	26 Feb 07	jari	726	profileDisplayPanel.addGraphElement(gp);
2	26 Feb 07	jari	727	}
2	26 Feb 07	jari	728	}
2	26 Feb 07	jari	729
2	26 Feb 07	jari	730	for (int i = 0; i < meanProfile.size() - 1; i++) {
2	26 Feb 07	jari	731	gL = new GraphLine(i /+ 1/, ((Float) meanProfile.elementAt(i)).floatValue(),
2	26 Feb 07	jari	732	i + 1, ((Float) meanProfile.elementAt(i + 1)).floatValue(), Color.blue);
2	26 Feb 07	jari	733	profileDisplayPanel.addGraphElement(gL);
2	26 Feb 07	jari	734	}
2	26 Feb 07	jari	735
2	26 Feb 07	jari	736	if(setTemplate){
2	26 Feb 07	jari	737
2	26 Feb 07	jari	738	for (int i = 0; i < meanProfile.size() - 1; i++) {
2	26 Feb 07	jari	739	if ((Float.isNaN(((Float) meanProfile.elementAt(i)).floatValue())) \|\| (Float.isNaN(((Float) meanProfile.elementAt(i+1)).floatValue()))) {
2	26 Feb 07	jari	740	continue;
2	26 Feb 07	jari	741	}
2	26 Feb 07	jari	742	gL = new GraphLine(i /+ 1/, ((Float) meanProfile.elementAt(i)).floatValue(),
2	26 Feb 07	jari	743	i + 1, ((Float) meanProfile.elementAt(i + 1)).floatValue(), Color.green);
2	26 Feb 07	jari	744	profileDisplayPanel.addGraphElement(gL);
2	26 Feb 07	jari	745	}
2	26 Feb 07	jari	746	}
2	26 Feb 07	jari	747	profileDisplayPanel.repaint();
2	26 Feb 07	jari	748	}
2	26 Feb 07	jari	749
2	26 Feb 07	jari	750	public void reset(){
2	26 Feb 07	jari	751	clusterList.setSelectedIndex(0);
2	26 Feb 07	jari	752	setTemplate = false;
2	26 Feb 07	jari	753	refreshGraph();
2	26 Feb 07	jari	754	}
2	26 Feb 07	jari	755
2	26 Feb 07	jari	756	}
2	26 Feb 07	jari	757
2	26 Feb 07	jari	758	/*
2	26 Feb 07	jari	759	class AbsolutePanel extends JPanel {
2	26 Feb 07	jari	760
2	26 Feb 07	jari	761	JCheckBox absBox;
2	26 Feb 07	jari	762	JLabel absLabel1;
2	26 Feb 07	jari	763	JLabel absLabel2;
2	26 Feb 07	jari	764
2	26 Feb 07	jari	765	AbsolutePanel() {
2	26 Feb 07	jari	766
2	26 Feb 07	jari	767	GridBagLayout gridbag = new GridBagLayout();
2	26 Feb 07	jari	768	GridBagLayout gridbag2 = new GridBagLayout();
2	26 Feb 07	jari	769	GridBagConstraints constraints = new GridBagConstraints();
2	26 Feb 07	jari	770	constraints.fill = GridBagConstraints.NONE;
2	26 Feb 07	jari	771	//constraints.anchor = GridBagConstraints.WEST;
2	26 Feb 07	jari	772	this.setLayout(gridbag);
2	26 Feb 07	jari	773
2	26 Feb 07	jari	774	buildConstraints(constraints, 0, 0, 1, 2, 30, 0);
2	26 Feb 07	jari	775	absBox = new JCheckBox(" Match to Absolute R");
2	26 Feb 07	jari	776	gridbag.setConstraints(absBox, constraints);
2	26 Feb 07	jari	777	this.add(absBox);
2	26 Feb 07	jari	778
2	26 Feb 07	jari	779	JPanel tipPanel = new JPanel();
2	26 Feb 07	jari	780	tipPanel.setBorder(new TitledBorder(new EtchedBorder(EtchedBorder.LOWERED), "Tip on Using Absolute R"));
2	26 Feb 07	jari	781	// tipPanel.setLayout(gridbag2);
2	26 Feb 07	jari	782
2	26 Feb 07	jari	783	JTextArea text = new JTextArea("If checked, both positively and negatively correlated profiles\n"+
2	26 Feb 07	jari	784	"will be matched.\n"+
2	26 Feb 07	jari	785	"If not checked, only negatively correlated profiles will be matched");
2	26 Feb 07	jari	786	text.setBackground(new Color(208,208,208));
2	26 Feb 07	jari	787
2	26 Feb 07	jari	788	text.setFont(new Font("Dialog", Font.PLAIN, 12));
2	26 Feb 07	jari	789	// buildConstraints(constraints, 0, 0, 1, 1, 70, 50);
2	26 Feb 07	jari	790	// absLabel1 = new JLabel("Yes: both +vely and -vely correlated expression profiles will be matched");
2	26 Feb 07	jari	791	// constraints.anchor = GridBagConstraints.WEST;
2	26 Feb 07	jari	792	// gridbag2.setConstraints(absLabel1, constraints);
2	26 Feb 07	jari	793	// tipPanel.add(absLabel1);
2	26 Feb 07	jari	794
2	26 Feb 07	jari	795	// buildConstraints(constraints, 0, 1, 1, 1, 0, 50);
2	26 Feb 07	jari	796	// absLabel2 = new JLabel("No: only +vely correlated expression profiles will be matched");
2	26 Feb 07	jari	797	// constraints.anchor = GridBagConstraints.NORTHWEST;
2	26 Feb 07	jari	798	// gridbag2.setConstraints(absLabel2, constraints);
2	26 Feb 07	jari	799	// tipPanel.add(absLabel2);
2	26 Feb 07	jari	800	tipPanel.add(text);
2	26 Feb 07	jari	801
2	26 Feb 07	jari	802
2	26 Feb 07	jari	803	buildConstraints(constraints, 1, 0, 1, 2, 30, 0);
2	26 Feb 07	jari	804	gridbag.setConstraints(tipPanel, constraints);
2	26 Feb 07	jari	805	this.add(tipPanel);
2	26 Feb 07	jari	806	}
2	26 Feb 07	jari	807
2	26 Feb 07	jari	808	}*/
2	26 Feb 07	jari	809
2	26 Feb 07	jari	810
2	26 Feb 07	jari	811	class SavedTemplateSelector extends JPanel{
2	26 Feb 07	jari	812	JList templateList;
2	26 Feb 07	jari	813	GraphCanvas profileDisplayPanel;
2	26 Feb 07	jari	814	JScrollPane listScrollPane;
2	26 Feb 07	jari	815	JButton selectButton;
2	26 Feb 07	jari	816	JButton loadButton;
2	26 Feb 07	jari	817	Vector templatesVector = new Vector();
2	26 Feb 07	jari	818	DefaultListModel listModel;
2	26 Feb 07	jari	819
2	26 Feb 07	jari	820	Vector templates;
2	26 Feb 07	jari	821
2	26 Feb 07	jari	822	JSplitPane templateSplitPane;
2	26 Feb 07	jari	823	JPanel templateButtonPanel;
2	26 Feb 07	jari	824	boolean savedTemplateSelected;
2	26 Feb 07	jari	825
2	26 Feb 07	jari	826	SavedTemplateSelector() {
2	26 Feb 07	jari	827
2	26 Feb 07	jari	828	listModel = new DefaultListModel();
2	26 Feb 07	jari	829
2	26 Feb 07	jari	830	//
2	26 Feb 07	jari	831	//templates = new Vector();
2	26 Feb 07	jari	832	//for(int i = 0; i < templateArray.length; i++) {
2	26 Feb 07	jari	833	// templates.add(templateArray[i]);
2	26 Feb 07	jari	834	//}
2	26 Feb 07	jari	835	//
2	26 Feb 07	jari	836
2	26 Feb 07	jari	837	GridBagLayout gridbag = new GridBagLayout();
2	26 Feb 07	jari	838	GridBagConstraints constraints = new GridBagConstraints();
2	26 Feb 07	jari	839	//constraints.fill = GridBagConstraints.NONE;
2	26 Feb 07	jari	840	this.setLayout(gridbag);
2	26 Feb 07	jari	841
2	26 Feb 07	jari	842	templateList = new JList(listModel);
2	26 Feb 07	jari	843	templateList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
2	26 Feb 07	jari	844	templateList.setSelectedIndex(-1);
2	26 Feb 07	jari	845
2	26 Feb 07	jari	846	//AIS -- Use the graph classes
2	26 Feb 07	jari	847	profileDisplayPanel = new GraphCanvas();
2	26 Feb 07	jari	848	profileDisplayPanel.setGraphBounds(0, sampleNamesVector.size(), -3, 3);
2	26 Feb 07	jari	849	profileDisplayPanel.setGraphSpacing(20, 20, 20, 20);
2	26 Feb 07	jari	850	profileDisplayPanel.setXAxisValue(0);
2	26 Feb 07	jari	851	profileDisplayPanel.setYAxisValue(0);
2	26 Feb 07	jari	852
2	26 Feb 07	jari	853	templateList.addListSelectionListener(new ListSelectionListener(){
2	26 Feb 07	jari	854	public void valueChanged(ListSelectionEvent e) {
2	26 Feb 07	jari	855	if(templatesVector.size() > 0){
2	26 Feb 07	jari	856	Vector temp = (Vector)templatesVector.elementAt(templateList.getSelectedIndex());
2	26 Feb 07	jari	857	if(temp.size() == numberOfExperiments){
2	26 Feb 07	jari	858	tempPanel.setVisible(true);
2	26 Feb 07	jari	859	tempPanel.setEnabled(true);
2	26 Feb 07	jari	860	} else {
2	26 Feb 07	jari	861	tempPanel.setVisible(false);
2	26 Feb 07	jari	862	tempPanel.setEnabled(false);
2	26 Feb 07	jari	863	}
2	26 Feb 07	jari	864	}
2	26 Feb 07	jari	865	savedTemplateSelected = false;
2	26 Feb 07	jari	866	refreshGraph();
2	26 Feb 07	jari	867	}
2	26 Feb 07	jari	868	});
2	26 Feb 07	jari	869	//-- AIS
2	26 Feb 07	jari	870
2	26 Feb 07	jari	871	//uniqueIDList.addListSelectionListener(new listSelectionListener(){}); //IMPLEMENT THIS LATER
2	26 Feb 07	jari	872
2	26 Feb 07	jari	873	listScrollPane = new JScrollPane(templateList);
2	26 Feb 07	jari	874
2	26 Feb 07	jari	875	//profileDisplayPanel = new JPanel();
2	26 Feb 07	jari	876	templateSplitPane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, listScrollPane, profileDisplayPanel);
2	26 Feb 07	jari	877	templateSplitPane.setOneTouchExpandable(true);
2	26 Feb 07	jari	878	templateSplitPane.setDividerLocation(200);
2	26 Feb 07	jari	879
2	26 Feb 07	jari	880	Dimension minimumSize = new Dimension(100,50);
2	26 Feb 07	jari	881	templateList.setMinimumSize(minimumSize);
2	26 Feb 07	jari	882	profileDisplayPanel.setMinimumSize(minimumSize);
2	26 Feb 07	jari	883
2	26 Feb 07	jari	884	templateSplitPane.setPreferredSize(new Dimension(700,150));
2	26 Feb 07	jari	885
2	26 Feb 07	jari	886	buildConstraints(constraints, 0, 0, 1, 1, 1, 1);
2	26 Feb 07	jari	887
2	26 Feb 07	jari	888	constraints.fill = GridBagConstraints.BOTH;
2	26 Feb 07	jari	889	constraints.anchor = GridBagConstraints.CENTER;
2	26 Feb 07	jari	890	constraints.insets = new Insets(5,5,5,5);
2	26 Feb 07	jari	891	gridbag.setConstraints(templateSplitPane, constraints);
2	26 Feb 07	jari	892	this.add(templateSplitPane);
2	26 Feb 07	jari	893
2	26 Feb 07	jari	894	loadButton = new JButton("Load saved template", GUIFactory.getIcon("Open24.gif"));
2	26 Feb 07	jari	895	loadButton.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED));
2	26 Feb 07	jari	896	loadButton.setMargin(new Insets(10,10,10,10));
2	26 Feb 07	jari	897	loadButton.setFocusPainted(false);
2	26 Feb 07	jari	898	loadButton.setPreferredSize(new Dimension(200, 30));
2	26 Feb 07	jari	899	loadButton.addActionListener(new ActionListener(){
2	26 Feb 07	jari	900	public void actionPerformed(ActionEvent evt) {
2	26 Feb 07	jari	901	if (evt.getSource() == loadButton) {
2	26 Feb 07	jari	902	JFileChooser fc = new JFileChooser(TMEV.getFile("data/"));
2	26 Feb 07	jari	903
2	26 Feb 07	jari	904	int returnVal = fc.showOpenDialog(SavedTemplateSelector.this);
2	26 Feb 07	jari	905	if (returnVal == JFileChooser.APPROVE_OPTION) {
2	26 Feb 07	jari	906	// listModel.removeAllElements();
2	26 Feb 07	jari	907	File file = fc.getSelectedFile();
2	26 Feb 07	jari	908	try {
2	26 Feb 07	jari	909	// DataInputStream in = new DataInputStream(new FileInputStream(file.getPath()));
2	26 Feb 07	jari	910	BufferedReader br = new BufferedReader(new java.io.FileReader(file.getPath()));
2	26 Feb 07	jari	911	try {
2	26 Feb 07	jari	912	//*****READING OF INPUT DATA TAKES PLACE IN THIS BLOCK
2	26 Feb 07	jari	913	// templatesVector = new Vector();
2	26 Feb 07	jari	914	int index = templatesVector.size();
2	26 Feb 07	jari	915	String value;
2	26 Feb 07	jari	916	Vector currentTemplate = new Vector();
2	26 Feb 07	jari	917	while ((value = br.readLine())!= null) {
2	26 Feb 07	jari	918	currentTemplate.add(new Float((value)));
2	26 Feb 07	jari	919	}
2	26 Feb 07	jari	920	listModel.addElement(file.getName());
2	26 Feb 07	jari	921	templatesVector.add(currentTemplate);
2	26 Feb 07	jari	922	templateList.setSelectedIndex(templatesVector.size()-1);
2	26 Feb 07	jari	923	br.close();
2	26 Feb 07	jari	924	refreshGraph();
2	26 Feb 07	jari	925	profileDisplayPanel.setGraphBounds(0, currentTemplate.size(), -3, 3);
2	26 Feb 07	jari	926	} catch (EOFException exc) {
2	26 Feb 07	jari	927	br.close();
2	26 Feb 07	jari	928	}
2	26 Feb 07	jari	929	} catch (IOException e){
2	26 Feb 07	jari	930	System.out.println("Error: " + e.toString());
2	26 Feb 07	jari	931	JOptionPane.showMessageDialog(null, e.toString());
2	26 Feb 07	jari	932	}
2	26 Feb 07	jari	933	}
2	26 Feb 07	jari	934	}
2	26 Feb 07	jari	935	}
2	26 Feb 07	jari	936	});
2	26 Feb 07	jari	937
2	26 Feb 07	jari	938	selectButton = new JButton("Select Displayed Template", GUIFactory.getIcon("select_check24.gif"));
2	26 Feb 07	jari	939	selectButton.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED));
2	26 Feb 07	jari	940	selectButton.setMargin(new Insets(10,10,10,10));
2	26 Feb 07	jari	941	selectButton.setFocusPainted(false);
2	26 Feb 07	jari	942	selectButton.setPreferredSize(new Dimension(200, 30));
2	26 Feb 07	jari	943	selectButton.addActionListener(new ActionListener(){
2	26 Feb 07	jari	944	public void actionPerformed(ActionEvent e) {
2	26 Feb 07	jari	945	if (listModel.size() == 0){
2	26 Feb 07	jari	946	JOptionPane.showMessageDialog(null, "No templates to select");
2	26 Feb 07	jari	947	} else {
2	26 Feb 07	jari	948	savedTemplateSelected = true;
2	26 Feb 07	jari	949	int index = templateList.getSelectedIndex();
2	26 Feb 07	jari	950	Vector expProfile = (Vector) ((Vector) templatesVector.get(index)).clone();
2	26 Feb 07	jari	951
2	26 Feb 07	jari	952	float max = getMax(expProfile);
2	26 Feb 07	jari	953	float min = getMin(expProfile);
2	26 Feb 07	jari	954
2	26 Feb 07	jari	955	if ((max - min) == 0) {
2	26 Feb 07	jari	956	for(int i = 0; i < expProfile.size(); i++) {
2	26 Feb 07	jari	957	expProfile.set(i, new Float(0.5));
2	26 Feb 07	jari	958	}
2	26 Feb 07	jari	959
2	26 Feb 07	jari	960	} else {
2	26 Feb 07	jari	961
2	26 Feb 07	jari	962	for(int i = 0; i < expProfile.size(); i++) {
2	26 Feb 07	jari	963	float f = (((Float)expProfile.get(i)).floatValue()- min)/(max - min);
2	26 Feb 07	jari	964	expProfile.set(i, new Float(f));
2	26 Feb 07	jari	965	}
2	26 Feb 07	jari	966	}
2	26 Feb 07	jari	967	if(expProfile.size() == numberOfExperiments){
2	26 Feb 07	jari	968	clusterGenes = true;
2	26 Feb 07	jari	969	for(int i = 0; i < tempPanel.tempScr.tempGrid.length; i++){
2	26 Feb 07	jari	970	tempPanel.tempScr.tempGrid[i].templateSlider.setValue((int) Math.floor(((Float)expProfile.get(i)).floatValue()*100));
2	26 Feb 07	jari	971	tempPanel.tempScr.tempGrid[i].templateField.setText("" + ((Float)expProfile.get(i)).floatValue());
2	26 Feb 07	jari	972	}
2	26 Feb 07	jari	973	}
2	26 Feb 07	jari	974	else{
2	26 Feb 07	jari	975	clusterGenes = false;
2	26 Feb 07	jari	976	template = expProfile;
2	26 Feb 07	jari	977	}
2	26 Feb 07	jari	978	}
2	26 Feb 07	jari	979	refreshGraph();
2	26 Feb 07	jari	980	}
2	26 Feb 07	jari	981
2	26 Feb 07	jari	982	});
2	26 Feb 07	jari	983
2	26 Feb 07	jari	984	gridbag.setConstraints(selectButton, constraints);
2	26 Feb 07	jari	985	this.add(selectButton);
2	26 Feb 07	jari	986	buildConstraints(constraints, 0, 1, 1, 1, 0, 0);
2	26 Feb 07	jari	987	templateButtonPanel = new JPanel();
2	26 Feb 07	jari	988	templateButtonPanel.add(loadButton);
2	26 Feb 07	jari	989	templateButtonPanel.add(selectButton);
2	26 Feb 07	jari	990	gridbag.setConstraints(templateButtonPanel, constraints);
2	26 Feb 07	jari	991	this.add(templateButtonPanel);
2	26 Feb 07	jari	992	refreshGraph();
2	26 Feb 07	jari	993
2	26 Feb 07	jari	994	}
2	26 Feb 07	jari	995
2	26 Feb 07	jari	996	private void refreshGraph() {
2	26 Feb 07	jari	997	float maxRange;
2	26 Feb 07	jari	998	float min = Float.POSITIVE_INFINITY;
2	26 Feb 07	jari	999	float max = Float.NEGATIVE_INFINITY;
2	26 Feb 07	jari	1000	int index = templateList.getSelectedIndex();
2	26 Feb 07	jari	1001	Color lineColor = Color.blue;
2	26 Feb 07	jari	1002	if(savedTemplateSelected == true)
2	26 Feb 07	jari	1003	lineColor = Color.green;
2	26 Feb 07	jari	1004
2	26 Feb 07	jari	1005	if (index < 0) return;
2	26 Feb 07	jari	1006	Vector expProfile = (Vector) ((Vector) templatesVector.get(index)).clone();
2	26 Feb 07	jari	1007
2	26 Feb 07	jari	1008	max = Math.max(max, getMax(expProfile));
2	26 Feb 07	jari	1009	min = Math.min(min, getMin(expProfile));
2	26 Feb 07	jari	1010	maxRange = Math.max(max, Math.abs(min));
2	26 Feb 07	jari	1011	profileDisplayPanel.setGraphBounds(0,expProfile.size(),-maxRange,maxRange);
2	26 Feb 07	jari	1012
2	26 Feb 07	jari	1013	profileDisplayPanel.removeAllGraphElements();
2	26 Feb 07	jari	1014	for (int i = 0; i < expProfile.size(); i++) {
2	26 Feb 07	jari	1015	GraphPoint gp = new GraphPoint(i + 1, ((Float) expProfile.elementAt(i)).floatValue(), Color.red, 2);
2	26 Feb 07	jari	1016	profileDisplayPanel.addGraphElement(gp);
2	26 Feb 07	jari	1017	}
2	26 Feb 07	jari	1018
2	26 Feb 07	jari	1019	for (int i = 0; i < expProfile.size() - 1; i++) {
2	26 Feb 07	jari	1020	GraphLine gl = new GraphLine(i + 1, ((Float) expProfile.elementAt(i)).floatValue(),
2	26 Feb 07	jari	1021	i + 2, ((Float) expProfile.elementAt(i + 1)).floatValue(), lineColor);
2	26 Feb 07	jari	1022	profileDisplayPanel.addGraphElement(gl);
2	26 Feb 07	jari	1023	}
2	26 Feb 07	jari	1024
2	26 Feb 07	jari	1025	profileDisplayPanel.repaint();
2	26 Feb 07	jari	1026	}
2	26 Feb 07	jari	1027
2	26 Feb 07	jari	1028	public void reset(){
2	26 Feb 07	jari	1029	savedTemplateSelected = false;
2	26 Feb 07	jari	1030	refreshGraph();
2	26 Feb 07	jari	1031	}
2	26 Feb 07	jari	1032
2	26 Feb 07	jari	1033	}
2	26 Feb 07	jari	1034
2	26 Feb 07	jari	1035
2	26 Feb 07	jari	1036
2	26 Feb 07	jari	1037	class ThresholdPanel extends JPanel {
2	26 Feb 07	jari	1038
2	26 Feb 07	jari	1039	JLabel threshLabel1;
2	26 Feb 07	jari	1040	JLabel threshLabel2;
2	26 Feb 07	jari	1041	JTextField threshInputField;
2	26 Feb 07	jari	1042	JRadioButton chooseR;
2	26 Feb 07	jari	1043	JRadioButton chooseP;
2	26 Feb 07	jari	1044	JCheckBox useAbsolute;
2	26 Feb 07	jari	1045	JLabel inputLabel;
2	26 Feb 07	jari	1046
2	26 Feb 07	jari	1047	ThresholdPanel() {
2	26 Feb 07	jari	1048
2	26 Feb 07	jari	1049	GridBagLayout gridbag = new GridBagLayout();
2	26 Feb 07	jari	1050	GridBagConstraints constraints = new GridBagConstraints();
2	26 Feb 07	jari	1051	constraints.fill = GridBagConstraints.NONE;
2	26 Feb 07	jari	1052	constraints.insets = new Insets(10, 30, 10, 0);
2	26 Feb 07	jari	1053	this.setLayout(gridbag);
2	26 Feb 07	jari	1054	this.setBorder(BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED), "Threshold Parameters"));
2	26 Feb 07	jari	1055
2	26 Feb 07	jari	1056
2	26 Feb 07	jari	1057	useAbsolute = new JCheckBox("Use Absolute R");
2	26 Feb 07	jari	1058	useAbsolute.setFocusPainted(false);
2	26 Feb 07	jari	1059	buildConstraints(constraints, 0, 0, 3, 1, 0, 0);
2	26 Feb 07	jari	1060	constraints.anchor = GridBagConstraints.WEST;
2	26 Feb 07	jari	1061	gridbag.setConstraints(useAbsolute, constraints);
2	26 Feb 07	jari	1062	this.add(useAbsolute);
2	26 Feb 07	jari	1063
2	26 Feb 07	jari	1064	constraints.insets = new Insets(0, 30, 0, 0);
2	26 Feb 07	jari	1065
2	26 Feb 07	jari	1066	ButtonGroup chooseRorP = new ButtonGroup();
2	26 Feb 07	jari	1067	chooseR = new JRadioButton("Use Threshold R",false);
2	26 Feb 07	jari	1068	chooseR.setFocusPainted(false);
2	26 Feb 07	jari	1069	chooseRorP.add(chooseR);
2	26 Feb 07	jari	1070	chooseP = new JRadioButton("Use Threshold p-Value",true);
2	26 Feb 07	jari	1071	chooseP.setFocusPainted(false);
2	26 Feb 07	jari	1072	chooseRorP.add(chooseP);
2	26 Feb 07	jari	1073
2	26 Feb 07	jari	1074	buildConstraints(constraints, 0, 1, 1, 1, 10, 0);
2	26 Feb 07	jari	1075	//constraints.anchor = GridBagConstraints.WEST;
2	26 Feb 07	jari	1076	//constraints.fill = GridBagConstraints.NONE;
2	26 Feb 07	jari	1077	gridbag.setConstraints(chooseR, constraints);
2	26 Feb 07	jari	1078	this.add(chooseR);
2	26 Feb 07	jari	1079
2	26 Feb 07	jari	1080	buildConstraints(constraints, 0, 2, 1, 1, 0, 0);
2	26 Feb 07	jari	1081	// constraints.anchor = GridBagConstraints.WEST;
2	26 Feb 07	jari	1082	gridbag.setConstraints(chooseP, constraints);
2	26 Feb 07	jari	1083	this.add(chooseP);
2	26 Feb 07	jari	1084
2	26 Feb 07	jari	1085	buildConstraints(constraints, 1, 0, 1, 1, 80, 0);
2	26 Feb 07	jari	1086	threshLabel1 = new JLabel("Enter magnitude of threshold R or p-Value (between 0 and 1 inclusive)");
2	26 Feb 07	jari	1087	buildConstraints(constraints, 1, 1, 1, 1, 0, 0);
2	26 Feb 07	jari	1088	threshLabel2 = new JLabel("at which selected profiles should be correlated to template");
2	26 Feb 07	jari	1089	constraints.insets = new Insets(15, 5, 0, 0);
2	26 Feb 07	jari	1090
2	26 Feb 07	jari	1091	JPanel thresholdInputPanel = new JPanel(new GridBagLayout());
2	26 Feb 07	jari	1092
2	26 Feb 07	jari	1093	// buildConstraints(constraints, 1, 0, 1, 3, 10, 0);
2	26 Feb 07	jari	1094	inputLabel = new JLabel("Enter p-value [0,1] :");
2	26 Feb 07	jari	1095	inputLabel.setForeground(Color.black);
2	26 Feb 07	jari	1096	inputLabel.setAlignmentX(JLabel.RIGHT_ALIGNMENT);
2	26 Feb 07	jari	1097	inputLabel.setSize(150, 40);
2	26 Feb 07	jari	1098	inputLabel.setMinimumSize( new Dimension(150,40));
2	26 Feb 07	jari	1099	gridbag.setConstraints(inputLabel, constraints);
2	26 Feb 07	jari	1100	thresholdInputPanel.add(inputLabel, new GridBagConstraints(0,0,1,1,0,0,GridBagConstraints.CENTER,GridBagConstraints.BOTH,new Insets(0,0,0,0),0,0));
2	26 Feb 07	jari	1101
2	26 Feb 07	jari	1102	chooseR.addChangeListener(new ChangeListener(){
2	26 Feb 07	jari	1103
2	26 Feb 07	jari	1104	public void stateChanged(ChangeEvent evt){
2	26 Feb 07	jari	1105	if(chooseR.isSelected())
2	26 Feb 07	jari	1106	inputLabel.setText("Enter R [0,1] :");
2	26 Feb 07	jari	1107	else
2	26 Feb 07	jari	1108	inputLabel.setText("Enter p-value [0,1] :");
2	26 Feb 07	jari	1109	}
2	26 Feb 07	jari	1110
2	26 Feb 07	jari	1111	});
2	26 Feb 07	jari	1112
2	26 Feb 07	jari	1113	threshInputField = new JTextField("", 7);
2	26 Feb 07	jari	1114	threshInputField.addActionListener(new ActionListener(){
2	26 Feb 07	jari	1115	public void actionPerformed(ActionEvent evt) {
2	26 Feb 07	jari	1116
2	26 Feb 07	jari	1117	if(evt.getSource() == threshInputField){
2	26 Feb 07	jari	1118	try {
2	26 Feb 07	jari	1119	String s = threshInputField.getText();
2	26 Feb 07	jari	1120	double r = Double.parseDouble(s);
2	26 Feb 07	jari	1121	if ((r > 1)\|\|(r < 0)) {
2	26 Feb 07	jari	1122	JOptionPane.showMessageDialog(null, "Threshold R value must be between 0 and 1 (inclusive)");
2	26 Feb 07	jari	1123	threshInputField.selectAll();
2	26 Feb 07	jari	1124	threshInputField.requestFocus();
2	26 Feb 07	jari	1125	}
2	26 Feb 07	jari	1126	} catch (Exception exc) {
2	26 Feb 07	jari	1127	JOptionPane.showMessageDialog(null, "Input Format Error: Threshold R value must be between 0 and 1 (inclusive)");
2	26 Feb 07	jari	1128	threshInputField.selectAll();
2	26 Feb 07	jari	1129	threshInputField.requestFocus();
2	26 Feb 07	jari	1130	}
2	26 Feb 07	jari	1131
2	26 Feb 07	jari	1132	}
2	26 Feb 07	jari	1133
2	26 Feb 07	jari	1134	}
2	26 Feb 07	jari	1135	});
2	26 Feb 07	jari	1136
2	26 Feb 07	jari	1137	thresholdInputPanel.add(threshInputField, new GridBagConstraints(1,0,1,1,5,0,GridBagConstraints.CENTER,GridBagConstraints.BOTH,new Insets(0,10,0,0),0,0));
2	26 Feb 07	jari	1138
2	26 Feb 07	jari	1139	buildConstraints(constraints, 1, 0, 1, 3, 10, 0);
2	26 Feb 07	jari	1140	constraints.anchor = GridBagConstraints.CENTER;
2	26 Feb 07	jari	1141	constraints.fill = GridBagConstraints.BOTH;
2	26 Feb 07	jari	1142
2	26 Feb 07	jari	1143	gridbag.setConstraints(thresholdInputPanel, constraints);
2	26 Feb 07	jari	1144
2	26 Feb 07	jari	1145	this.add(thresholdInputPanel);
2	26 Feb 07	jari	1146	}
2	26 Feb 07	jari	1147
2	26 Feb 07	jari	1148	}
2	26 Feb 07	jari	1149
2	26 Feb 07	jari	1150
2	26 Feb 07	jari	1151	class TemplatePanel extends JPanel {
2	26 Feb 07	jari	1152
2	26 Feb 07	jari	1153	TemplateScroller tempScr;
2	26 Feb 07	jari	1154
2	26 Feb 07	jari	1155	TemplatePanel() {
2	26 Feb 07	jari	1156	GridBagLayout gridbag = new GridBagLayout();
2	26 Feb 07	jari	1157	GridBagConstraints constraints = new GridBagConstraints();
2	26 Feb 07	jari	1158	constraints.fill = GridBagConstraints.BOTH;
2	26 Feb 07	jari	1159	this.setLayout(gridbag);
2	26 Feb 07	jari	1160
2	26 Feb 07	jari	1161	tempScr = new TemplateScroller();
2	26 Feb 07	jari	1162	JScrollPane scroller = tempScr.createTemplateScroller();
2	26 Feb 07	jari	1163	buildConstraints(constraints, 0, 0, 1, 1, 100, 95);
2	26 Feb 07	jari	1164	gridbag.setConstraints(scroller, constraints);
2	26 Feb 07	jari	1165	this.add(scroller);
2	26 Feb 07	jari	1166
2	26 Feb 07	jari	1167	buildConstraints(constraints, 0, 1, 1, 1, 100, 5);
2	26 Feb 07	jari	1168	constraints.fill = GridBagConstraints.NONE;
2	26 Feb 07	jari	1169	setMaximumSize(new Dimension(600,100));
2	26 Feb 07	jari	1170	setSize(600,100);
2	26 Feb 07	jari	1171	}
2	26 Feb 07	jari	1172
2	26 Feb 07	jari	1173	public void reset(){
2	26 Feb 07	jari	1174	tempScr.reset();
2	26 Feb 07	jari	1175	}
2	26 Feb 07	jari	1176
2	26 Feb 07	jari	1177
2	26 Feb 07	jari	1178	class TemplateScroller extends JPanel {
2	26 Feb 07	jari	1179
2	26 Feb 07	jari	1180	TemplateElementGrid[] tempGrid = new TemplateElementGrid[SampleNames.length];
2	26 Feb 07	jari	1181
2	26 Feb 07	jari	1182	JScrollPane createTemplateScroller() {
2	26 Feb 07	jari	1183	GridBagLayout gridbag = new GridBagLayout();
2	26 Feb 07	jari	1184	GridBagConstraints constraints = new GridBagConstraints();
2	26 Feb 07	jari	1185	constraints.fill = GridBagConstraints.BOTH;
2	26 Feb 07	jari	1186	this.setLayout(gridbag);
2	26 Feb 07	jari	1187
2	26 Feb 07	jari	1188	for (int i = 0; i < SampleNames.length; i++) {
2	26 Feb 07	jari	1189	tempGrid[i] = new TemplateElementGrid(SampleNames[i]);
2	26 Feb 07	jari	1190	buildConstraints(constraints, i, 0, 1, 1, 100, 100);
2	26 Feb 07	jari	1191	gridbag.setConstraints(tempGrid[i], constraints);
2	26 Feb 07	jari	1192	this.add(tempGrid[i]);
2	26 Feb 07	jari	1193	}
2	26 Feb 07	jari	1194
2	26 Feb 07	jari	1195	JScrollPane scroller = new JScrollPane(this);
2	26 Feb 07	jari	1196	scroller.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_AS_NEEDED);
2	26 Feb 07	jari	1197	scroller.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_NEVER);
2	26 Feb 07	jari	1198	return scroller;
2	26 Feb 07	jari	1199	}
2	26 Feb 07	jari	1200
2	26 Feb 07	jari	1201	public void reset(){
2	26 Feb 07	jari	1202	for(int i = 0; i < tempGrid.length; i++)
2	26 Feb 07	jari	1203	tempGrid[i].reset();
2	26 Feb 07	jari	1204	}
2	26 Feb 07	jari	1205
2	26 Feb 07	jari	1206
2	26 Feb 07	jari	1207	class TemplateElementGrid extends JPanel {
2	26 Feb 07	jari	1208
2	26 Feb 07	jari	1209	JLabel exptName;
2	26 Feb 07	jari	1210	JTextField templateField;
2	26 Feb 07	jari	1211	JSlider templateSlider;
2	26 Feb 07	jari	1212	JCheckBox activeBox;
2	26 Feb 07	jari	1213
2	26 Feb 07	jari	1214	TemplateElementGrid(String SampleName) {
2	26 Feb 07	jari	1215	GridBagLayout templateElement = new GridBagLayout();
2	26 Feb 07	jari	1216	GridBagConstraints constraints = new GridBagConstraints();
2	26 Feb 07	jari	1217	constraints.fill = GridBagConstraints.BOTH;
2	26 Feb 07	jari	1218	this.setLayout(templateElement);
2	26 Feb 07	jari	1219
2	26 Feb 07	jari	1220	buildConstraints(constraints, 0, 0, 1, 1, 50, 10);
2	26 Feb 07	jari	1221	exptName = new JLabel(SampleName, SwingConstants.CENTER);
2	26 Feb 07	jari	1222	templateElement.setConstraints(exptName, constraints);
2	26 Feb 07	jari	1223	this.add(exptName);
2	26 Feb 07	jari	1224
2	26 Feb 07	jari	1225	buildConstraints(constraints, 1, 0, 1, 1, 50, 0);
2	26 Feb 07	jari	1226	activeBox = new JCheckBox();
2	26 Feb 07	jari	1227	activeBox.setSelected(true);
2	26 Feb 07	jari	1228	activeBox.addItemListener(new ItemListener() {
2	26 Feb 07	jari	1229	public void itemStateChanged(ItemEvent e) {
2	26 Feb 07	jari	1230	if (e.getStateChange() == ItemEvent.DESELECTED) {
2	26 Feb 07	jari	1231	//templateField.setText("NULL");
2	26 Feb 07	jari	1232	templateField.setBackground(Color.gray);
2	26 Feb 07	jari	1233	templateField.setEnabled(false);
2	26 Feb 07	jari	1234	templateSlider.setEnabled(false);
2	26 Feb 07	jari	1235	}
2	26 Feb 07	jari	1236
2	26 Feb 07	jari	1237	if (e.getStateChange() == ItemEvent.SELECTED) {
2	26 Feb 07	jari	1238	//templateField.setText("NULL");
2	26 Feb 07	jari	1239	templateField.setBackground(Color.white);
2	26 Feb 07	jari	1240	templateField.setEnabled(true);
2	26 Feb 07	jari	1241	templateSlider.setEnabled(true);
2	26 Feb 07	jari	1242	}
2	26 Feb 07	jari	1243
2	26 Feb 07	jari	1244	}
2	26 Feb 07	jari	1245	});
2	26 Feb 07	jari	1246	templateElement.setConstraints(activeBox, constraints);
2	26 Feb 07	jari	1247	this.add(activeBox);
2	26 Feb 07	jari	1248
2	26 Feb 07	jari	1249	buildConstraints(constraints, 0, 1, 2, 1, 0, 5);
2	26 Feb 07	jari	1250	templateField = new JTextField("0.5", 4);
2	26 Feb 07	jari	1251	templateField.addActionListener(new ActionListener(){
2	26 Feb 07	jari	1252	public void actionPerformed(ActionEvent e) {
2	26 Feb 07	jari	1253	int sliderValue;
2	26 Feb 07	jari	1254	if(e.getSource() == templateField){
2	26 Feb 07	jari	1255	try {
2	26 Feb 07	jari	1256	String s = templateField.getText();
2	26 Feb 07	jari	1257	double d = Double.parseDouble(s);
2	26 Feb 07	jari	1258	sliderValue = (int)Math.floor(d*100);
2	26 Feb 07	jari	1259	if ((d > 1)\|\|(d < 0)) {
2	26 Feb 07	jari	1260
2	26 Feb 07	jari	1261	sliderValue = 50;
2	26 Feb 07	jari	1262	templateField.setText("0.5");
2	26 Feb 07	jari	1263	JOptionPane.showMessageDialog(null, "Template values must be between 0 and 1 (inclusive)");
2	26 Feb 07	jari	1264
2	26 Feb 07	jari	1265	}
2	26 Feb 07	jari	1266	} catch (Exception exc) {
2	26 Feb 07	jari	1267
2	26 Feb 07	jari	1268	templateField.setText("0.5");
2	26 Feb 07	jari	1269	sliderValue = 50;
2	26 Feb 07	jari	1270	JOptionPane.showMessageDialog(null, "Input Format Error: Template values must be between 0 and 1 (inclusive)");
2	26 Feb 07	jari	1271
2	26 Feb 07	jari	1272	}
2	26 Feb 07	jari	1273
2	26 Feb 07	jari	1274	templateSlider.setValue(sliderValue);
2	26 Feb 07	jari	1275	}
2	26 Feb 07	jari	1276
2	26 Feb 07	jari	1277	}
2	26 Feb 07	jari	1278	});
2	26 Feb 07	jari	1279
2	26 Feb 07	jari	1280	templateField.addFocusListener(new FocusListener(){
2	26 Feb 07	jari	1281	public void focusLost(FocusEvent e) {
2	26 Feb 07	jari	1282	int sliderValue;
2	26 Feb 07	jari	1283	if(e.getSource() == templateField){
2	26 Feb 07	jari	1284	try {
2	26 Feb 07	jari	1285	String s = templateField.getText();
2	26 Feb 07	jari	1286	double d = Double.parseDouble(s);
2	26 Feb 07	jari	1287	sliderValue = (int)Math.floor(d*100);
2	26 Feb 07	jari	1288	if ((d > 1)\|\|(d < 0)) {
2	26 Feb 07	jari	1289
2	26 Feb 07	jari	1290	sliderValue = 50;
2	26 Feb 07	jari	1291	templateField.setText("0.5");
2	26 Feb 07	jari	1292	JOptionPane.showMessageDialog(null, "Template values must be between 0 and 1 (inclusive)");
2	26 Feb 07	jari	1293
2	26 Feb 07	jari	1294	}
2	26 Feb 07	jari	1295	} catch (Exception exc) {
2	26 Feb 07	jari	1296
2	26 Feb 07	jari	1297	templateField.setText("0.5");
2	26 Feb 07	jari	1298	sliderValue = 50;
2	26 Feb 07	jari	1299	JOptionPane.showMessageDialog(null, "Template values must be between 0 and 1 (inclusive)");
2	26 Feb 07	jari	1300
2	26 Feb 07	jari	1301	}
2	26 Feb 07	jari	1302
2	26 Feb 07	jari	1303	templateSlider.setValue(sliderValue);
2	26 Feb 07	jari	1304	}
2	26 Feb 07	jari	1305	}
2	26 Feb 07	jari	1306
2	26 Feb 07	jari	1307
2	26 Feb 07	jari	1308	public void focusGained(FocusEvent e) {
2	26 Feb 07	jari	1309	}
2	26 Feb 07	jari	1310	});
2	26 Feb 07	jari	1311
2	26 Feb 07	jari	1312	templateElement.setConstraints(templateField, constraints);
2	26 Feb 07	jari	1313	this.add(templateField);
2	26 Feb 07	jari	1314
2	26 Feb 07	jari	1315	buildConstraints(constraints, 0, 2, 2, 1, 0, 85);
2	26 Feb 07	jari	1316	templateSlider = new JSlider(JSlider.VERTICAL, 0, 100, 50); templateSlider.setPreferredSize(new Dimension(30,50));
2	26 Feb 07	jari	1317	templateSlider.setMajorTickSpacing(20);
2	26 Feb 07	jari	1318	templateSlider.setMinorTickSpacing(10);
2	26 Feb 07	jari	1319	//templateSlider.setPaintTicks(true);
2	26 Feb 07	jari	1320	Hashtable labelTable = new Hashtable();
2	26 Feb 07	jari	1321	labelTable.put( new Integer( 0 ), new JLabel("Min") );
2	26 Feb 07	jari	1322	labelTable.put( new Integer( 100 ), new JLabel("Max") );
2	26 Feb 07	jari	1323	templateSlider.setLabelTable( labelTable );
2	26 Feb 07	jari	1324	templateSlider.setPaintLabels(true);
2	26 Feb 07	jari	1325	templateSlider.addChangeListener(new ChangeListener(){
2	26 Feb 07	jari	1326	public void stateChanged(ChangeEvent e) {
2	26 Feb 07	jari	1327	JSlider source = (JSlider)e.getSource();
2	26 Feb 07	jari	1328	if (!source.getValueIsAdjusting()) {
2	26 Feb 07	jari	1329	int value = (int)source.getValue();
2	26 Feb 07	jari	1330
2	26 Feb 07	jari	1331	if (value == 100) {
2	26 Feb 07	jari	1332	templateField.setText("1.0"); //CLUMSY WAY OF DISPLAYING INTEGER AS DOUBLE? MAYBE CHANGE?
2	26 Feb 07	jari	1333	} else if (value > 0 && value < 10) {
2	26 Feb 07	jari	1334	templateField.setText("0.0" + value);
2	26 Feb 07	jari	1335	} else {
2	26 Feb 07	jari	1336	templateField.setText("0." + value);
2	26 Feb 07	jari	1337	}
2	26 Feb 07	jari	1338	}
2	26 Feb 07	jari	1339	}
2	26 Feb 07	jari	1340
2	26 Feb 07	jari	1341	});
2	26 Feb 07	jari	1342	templateElement.setConstraints(templateSlider, constraints);
2	26 Feb 07	jari	1343	this.add(templateSlider);
2	26 Feb 07	jari	1344
2	26 Feb 07	jari	1345
2	26 Feb 07	jari	1346	}
2	26 Feb 07	jari	1347
2	26 Feb 07	jari	1348	public void reset() {
2	26 Feb 07	jari	1349	templateSlider.setValue(50);
2	26 Feb 07	jari	1350	templateField.setText("0.5");
2	26 Feb 07	jari	1351	}
2	26 Feb 07	jari	1352	}
2	26 Feb 07	jari	1353	}
2	26 Feb 07	jari	1354	}
2	26 Feb 07	jari	1355
2	26 Feb 07	jari	1356
2	26 Feb 07	jari	1357
2	26 Feb 07	jari	1358	public Vector getTemplate() {
2	26 Feb 07	jari	1359	Vector geneTemplate = new Vector();
2	26 Feb 07	jari	1360	int paneIndex = tabbedPane.getSelectedIndex();
2	26 Feb 07	jari	1361
2	26 Feb 07	jari	1362	//if a gene, gene cluster, or stored gene template
2	26 Feb 07	jari	1363	if(paneIndex == 0 \|\| paneIndex == 1 \|\| ( paneIndex == 4 && tempPanel.isVisible() )){
2	26 Feb 07	jari	1364
2	26 Feb 07	jari	1365	int numExp = this.expMatrix.getColumnDimension();
2	26 Feb 07	jari	1366
2	26 Feb 07	jari	1367	for(int i = 0; i < numExp; i++) {
2	26 Feb 07	jari	1368	String s = tempPanel.tempScr.tempGrid[i].templateField.getText();
2	26 Feb 07	jari	1369	if (s.equals("NaN")\|\|(s.equals("NULL"))\|\|(!(tempPanel.tempScr.tempGrid[i].activeBox.isSelected()))) {
2	26 Feb 07	jari	1370	geneTemplate.add(new Float(Float.NaN));
2	26 Feb 07	jari	1371	} else {
2	26 Feb 07	jari	1372	geneTemplate.add(new Float(s));
2	26 Feb 07	jari	1373	}
2	26 Feb 07	jari	1374	}
2	26 Feb 07	jari	1375	return geneTemplate;
2	26 Feb 07	jari	1376	}
2	26 Feb 07	jari	1377	return template;
2	26 Feb 07	jari	1378	}
2	26 Feb 07	jari	1379
2	26 Feb 07	jari	1380
2	26 Feb 07	jari	1381
2	26 Feb 07	jari	1382	public FloatMatrix convertTemplateVectorToFloatMatrix() {
2	26 Feb 07	jari	1383	template = getTemplate();
2	26 Feb 07	jari	1384	FloatMatrix templateMatrix = new FloatMatrix(1, template.size());
2	26 Feb 07	jari	1385	for (int i = 0; i < template.size(); i++) {
2	26 Feb 07	jari	1386	templateMatrix.A[0][i] = ((Float) (template.get(i))).floatValue();
2	26 Feb 07	jari	1387	}
2	26 Feb 07	jari	1388	return templateMatrix;
2	26 Feb 07	jari	1389	}
2	26 Feb 07	jari	1390
2	26 Feb 07	jari	1391
2	26 Feb 07	jari	1392	protected void fireOkButtonEvent() {
2	26 Feb 07	jari	1393	templateMatrix = convertTemplateVectorToFloatMatrix();
2	26 Feb 07	jari	1394	boolean absoluteSelected = thresh.useAbsolute.isSelected();
2	26 Feb 07	jari	1395	boolean drawTreesSelected = drawTreesBox.isSelected();
2	26 Feb 07	jari	1396	boolean rSelected = thresh.chooseR.isSelected();
2	26 Feb 07	jari	1397	String s = thresh.threshInputField.getText();
2	26 Feb 07	jari	1398	double threshR = Double.parseDouble(s);
2	26 Feb 07	jari	1399
2	26 Feb 07	jari	1400	Hashtable hash = new Hashtable();
2	26 Feb 07	jari	1401	hash.put(new String("drawTrees"), new Boolean(drawTreesSelected)); //Should be a checkbox in the init dialog
2	26 Feb 07	jari	1402	hash.put(new String("useAbsolute"), new Boolean(absoluteSelected));
2	26 Feb 07	jari	1403	hash.put(new String("useR"), new Boolean(rSelected));
2	26 Feb 07	jari	1404	hash.put(new String("template"), getTemplate());
2	26 Feb 07	jari	1405	hash.put(new String("thresholdR"), new Double(threshR));
2	26 Feb 07	jari	1406
2	26 Feb 07	jari	1407	// fireEvent(new ActionInfoEvent(this, hash));
2	26 Feb 07	jari	1408
2	26 Feb 07	jari	1409	}
2	26 Feb 07	jari	1410
2	26 Feb 07	jari	1411	public boolean isDrawTrees() {
2	26 Feb 07	jari	1412	return drawTreesBox.isSelected();
2	26 Feb 07	jari	1413	}
2	26 Feb 07	jari	1414
2	26 Feb 07	jari	1415	public boolean drawSigTreesOnly() {
2	26 Feb 07	jari	1416	return sigOnly.isSelected();
2	26 Feb 07	jari	1417	}
2	26 Feb 07	jari	1418
2	26 Feb 07	jari	1419	public boolean isUseAbsolute() {
2	26 Feb 07	jari	1420	return thresh.useAbsolute.isSelected();
2	26 Feb 07	jari	1421	}
2	26 Feb 07	jari	1422
2	26 Feb 07	jari	1423	public boolean isUseR() {
2	26 Feb 07	jari	1424	return thresh.chooseR.isSelected();
2	26 Feb 07	jari	1425	}
2	26 Feb 07	jari	1426
2	26 Feb 07	jari	1427	public FloatMatrix getTemplateMatrix() {
2	26 Feb 07	jari	1428	return convertTemplateVectorToFloatMatrix();
2	26 Feb 07	jari	1429	}
2	26 Feb 07	jari	1430
2	26 Feb 07	jari	1431	public double getThresholdR() {
2	26 Feb 07	jari	1432	return Double.parseDouble(thresh.threshInputField.getText());
2	26 Feb 07	jari	1433	}
2	26 Feb 07	jari	1434
2	26 Feb 07	jari	1435	public boolean isOkPressed() {return this.okPressed;}
2	26 Feb 07	jari	1436
2	26 Feb 07	jari	1437	protected class EventListener implements ActionListener {
2	26 Feb 07	jari	1438
2	26 Feb 07	jari	1439	public void actionPerformed(ActionEvent event) {
2	26 Feb 07	jari	1440
2	26 Feb 07	jari	1441	String command = event.getActionCommand();
2	26 Feb 07	jari	1442	if (command.equals("ok-command")) {
2	26 Feb 07	jari	1443	try {
2	26 Feb 07	jari	1444	String s = thresh.threshInputField.getText();
2	26 Feb 07	jari	1445	double r = Double.parseDouble(s);
2	26 Feb 07	jari	1446	if ((r > 1)\|\|(r < 0)) {
2	26 Feb 07	jari	1447	JOptionPane.showMessageDialog(null, "Threshold R value must be between 0 and 1 (inclusive)");
2	26 Feb 07	jari	1448	thresh.threshInputField.selectAll();
2	26 Feb 07	jari	1449	thresh.threshInputField.requestFocus();
2	26 Feb 07	jari	1450	}
2	26 Feb 07	jari	1451	else {
2	26 Feb 07	jari	1452	okPressed = true;
2	26 Feb 07	jari	1453	fireOkButtonEvent();
2	26 Feb 07	jari	1454	setVisible(false);
2	26 Feb 07	jari	1455	}
2	26 Feb 07	jari	1456	} catch (Exception exc) {
2	26 Feb 07	jari	1457	// exc.printStackTrace();
2	26 Feb 07	jari	1458	JOptionPane.showMessageDialog(null, "Input Format Error: Requires value between 0 and 1 (inclusive)");
2	26 Feb 07	jari	1459	thresh.threshInputField.selectAll();
2	26 Feb 07	jari	1460	thresh.threshInputField.requestFocus();
2	26 Feb 07	jari	1461	}
2	26 Feb 07	jari	1462	}
2	26 Feb 07	jari	1463	else if (command.equals("reset-command")){
2	26 Feb 07	jari	1464	template = new Vector();
2	26 Feb 07	jari	1465	expSelectPanel.reset();
2	26 Feb 07	jari	1466	clusterSelectPanel.reset();
2	26 Feb 07	jari	1467	geneSelectPanel.reset();
2	26 Feb 07	jari	1468	geneClusterSelectPanel.reset();
2	26 Feb 07	jari	1469	tempPanel.reset();
2	26 Feb 07	jari	1470	templateSelectPanel.reset();
2	26 Feb 07	jari	1471	thresh.useAbsolute.setSelected(false);
2	26 Feb 07	jari	1472	thresh.chooseP.setSelected(true);
2	26 Feb 07	jari	1473	thresh.threshInputField.setText("0.01");
2	26 Feb 07	jari	1474	okPressed = false;
2	26 Feb 07	jari	1475	}
2	26 Feb 07	jari	1476	else if (command.equals("cancel-command")){
2	26 Feb 07	jari	1477	hide();
2	26 Feb 07	jari	1478	dispose();
2	26 Feb 07	jari	1479	}
2	26 Feb 07	jari	1480	else if (command.equals("info-command")){
2	26 Feb 07	jari	1481	HelpWindow hw = new HelpWindow(PTMInitDialog.this, "PTM Initialization Dialog");
2	26 Feb 07	jari	1482	if(hw.getWindowContent()){
2	26 Feb 07	jari	1483	hw.setSize(450,650);
2	26 Feb 07	jari	1484	hw.setLocation();
2	26 Feb 07	jari	1485	hw.show();
2	26 Feb 07	jari	1486	}
2	26 Feb 07	jari	1487	else {
2	26 Feb 07	jari	1488	hw.setVisible(false);
2	26 Feb 07	jari	1489	hw.dispose();
2	26 Feb 07	jari	1490	}
2	26 Feb 07	jari	1491	}
2	26 Feb 07	jari	1492	else if (command.equals("save-template-command")){
2	26 Feb 07	jari	1493
2	26 Feb 07	jari	1494	}
2	26 Feb 07	jari	1495	}
2	26 Feb 07	jari	1496	}
2	26 Feb 07	jari	1497
2	26 Feb 07	jari	1498
2	26 Feb 07	jari	1499	/*********************************************************************
2	26 Feb 07	jari	1500	*
2	26 Feb 07	jari	1501	*
2	26 Feb 07	jari	1502	*
2	26 Feb 07	jari	1503	* Gene related code
2	26 Feb 07	jari	1504	*
2	26 Feb 07	jari	1505	*
2	26 Feb 07	jari	1506	*
2	26 Feb 07	jari	1507	*
2	26 Feb 07	jari	1508	*
2	26 Feb 07	jari	1509	*/
2	26 Feb 07	jari	1510
2	26 Feb 07	jari	1511	class GeneSelector extends JPanel{
2	26 Feb 07	jari	1512	JList uniqueIDList;
2	26 Feb 07	jari	1513	GraphCanvas profileDisplayPanel;
2	26 Feb 07	jari	1514	JScrollPane listScrollPane;
2	26 Feb 07	jari	1515	JButton selectButton;
2	26 Feb 07	jari	1516	int maxIndex = -1;
2	26 Feb 07	jari	1517	int minIndex = -1;
2	26 Feb 07	jari	1518
2	26 Feb 07	jari	1519
2	26 Feb 07	jari	1520	JSplitPane uIDSplitPane;
2	26 Feb 07	jari	1521
2	26 Feb 07	jari	1522	GeneSelector() {
2	26 Feb 07	jari	1523
2	26 Feb 07	jari	1524	GridBagLayout gridbag = new GridBagLayout();
2	26 Feb 07	jari	1525	GridBagConstraints constraints = new GridBagConstraints();
2	26 Feb 07	jari	1526	//constraints.fill = GridBagConstraints.NONE;
2	26 Feb 07	jari	1527	this.setLayout(gridbag);
2	26 Feb 07	jari	1528
2	26 Feb 07	jari	1529	uniqueIDList = new JList(uniqueIDs);
2	26 Feb 07	jari	1530	uniqueIDList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
2	26 Feb 07	jari	1531	uniqueIDList.setSelectedIndex(0);
2	26 Feb 07	jari	1532
2	26 Feb 07	jari	1533	//AIS -- Use the graph classes
2	26 Feb 07	jari	1534	profileDisplayPanel = new GraphCanvas();
2	26 Feb 07	jari	1535	profileDisplayPanel.setGraphBounds(0, sampleNamesVector.size(), -3, 3);
2	26 Feb 07	jari	1536	profileDisplayPanel.setGraphSpacing(20, 20, 20, 20);
2	26 Feb 07	jari	1537	profileDisplayPanel.setXAxisValue(0);
2	26 Feb 07	jari	1538	profileDisplayPanel.setYAxisValue(0);
2	26 Feb 07	jari	1539
2	26 Feb 07	jari	1540	uniqueIDList.addListSelectionListener(new ListSelectionListener(){
2	26 Feb 07	jari	1541	public void valueChanged(ListSelectionEvent e) {
2	26 Feb 07	jari	1542	refreshGraph();
2	26 Feb 07	jari	1543	}
2	26 Feb 07	jari	1544	});
2	26 Feb 07	jari	1545	//-- AIS
2	26 Feb 07	jari	1546
2	26 Feb 07	jari	1547	listScrollPane = new JScrollPane(uniqueIDList);
2	26 Feb 07	jari	1548
2	26 Feb 07	jari	1549	uIDSplitPane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, listScrollPane, profileDisplayPanel);
2	26 Feb 07	jari	1550	uIDSplitPane.setOneTouchExpandable(true);
2	26 Feb 07	jari	1551	uIDSplitPane.setDividerLocation(200);
2	26 Feb 07	jari	1552
2	26 Feb 07	jari	1553	Dimension minimumSize = new Dimension(100,50);
2	26 Feb 07	jari	1554	uniqueIDList.setMinimumSize(minimumSize);
2	26 Feb 07	jari	1555	profileDisplayPanel.setMinimumSize(minimumSize);
2	26 Feb 07	jari	1556
2	26 Feb 07	jari	1557	//uIDSplitPane.setPreferredSize(new Dimension(700,150));
2	26 Feb 07	jari	1558
2	26 Feb 07	jari	1559	buildConstraints(constraints, 0, 0, 1, 1, 1, 1);
2	26 Feb 07	jari	1560	constraints.fill = GridBagConstraints.BOTH;
2	26 Feb 07	jari	1561	constraints.anchor = GridBagConstraints.NORTH;
2	26 Feb 07	jari	1562	gridbag.setConstraints(uIDSplitPane, constraints);
2	26 Feb 07	jari	1563	this.add(uIDSplitPane);
2	26 Feb 07	jari	1564
2	26 Feb 07	jari	1565	buildConstraints(constraints, 0, 1, 1, 1, 1, 0);
2	26 Feb 07	jari	1566	constraints.fill = GridBagConstraints.NONE;
2	26 Feb 07	jari	1567	constraints.anchor = GridBagConstraints.CENTER;
2	26 Feb 07	jari	1568	constraints.insets = new Insets(10,10,10,10);
2	26 Feb 07	jari	1569	selectButton = new JButton("Select highlighted gene from above list to use as template", GUIFactory.getIcon("select_check24.gif"));
2	26 Feb 07	jari	1570	selectButton.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED));
2	26 Feb 07	jari	1571	selectButton.setMargin(new Insets(10,10,10,10));
2	26 Feb 07	jari	1572	selectButton.setPreferredSize(new Dimension(400,30));
2	26 Feb 07	jari	1573	selectButton.setFocusPainted(false);
2	26 Feb 07	jari	1574
2	26 Feb 07	jari	1575	selectButton.addActionListener(new ActionListener(){
2	26 Feb 07	jari	1576
2	26 Feb 07	jari	1577
2	26 Feb 07	jari	1578	public void actionPerformed(ActionEvent e) {
2	26 Feb 07	jari	1579	int index = uniqueIDList.getSelectedIndex();
2	26 Feb 07	jari	1580	Vector expProfile = getGene(index);
2	26 Feb 07	jari	1581	float max = getMax(expProfile);
2	26 Feb 07	jari	1582	float min = getMin(expProfile);
2	26 Feb 07	jari	1583
2	26 Feb 07	jari	1584	if ((max - min) == 0) {
2	26 Feb 07	jari	1585
2	26 Feb 07	jari	1586	for(int i = 0; i < expProfile.size(); i++) {
2	26 Feb 07	jari	1587	expProfile.set(i, new Float(0.5));
2	26 Feb 07	jari	1588	}
2	26 Feb 07	jari	1589
2	26 Feb 07	jari	1590	} else {
2	26 Feb 07	jari	1591
2	26 Feb 07	jari	1592	for(int i = 0; i < expProfile.size(); i++) {
2	26 Feb 07	jari	1593	float f = (((Float)expProfile.get(i)).floatValue()- min)/(max - min);
2	26 Feb 07	jari	1594	expProfile.set(i, new Float(f));
2	26 Feb 07	jari	1595	}
2	26 Feb 07	jari	1596	}
2	26 Feb 07	jari	1597
2	26 Feb 07	jari	1598	for(int i = 0; i < tempPanel.tempScr.tempGrid.length; i++){
2	26 Feb 07	jari	1599	if (!Float.isNaN(((Float)expProfile.get(i)).floatValue())) {
2	26 Feb 07	jari	1600	tempPanel.tempScr.tempGrid[i].activeBox.setSelected(true);
2	26 Feb 07	jari	1601	tempPanel.tempScr.tempGrid[i].templateSlider.setEnabled(true);
2	26 Feb 07	jari	1602	tempPanel.tempScr.tempGrid[i].templateSlider.setValue((int) Math.floor(((Float)expProfile.get(i)).floatValue()*100));
2	26 Feb 07	jari	1603	tempPanel.tempScr.tempGrid[i].templateField.setEnabled(true);
2	26 Feb 07	jari	1604	tempPanel.tempScr.tempGrid[i].templateField.setBackground(Color.white);
2	26 Feb 07	jari	1605	tempPanel.tempScr.tempGrid[i].templateField.setText("" + ((Float)expProfile.get(i)).floatValue());
2	26 Feb 07	jari	1606	} else {
2	26 Feb 07	jari	1607	tempPanel.tempScr.tempGrid[i].activeBox.setSelected(false);
2	26 Feb 07	jari	1608	tempPanel.tempScr.tempGrid[i].templateSlider.setEnabled(false);
2	26 Feb 07	jari	1609	tempPanel.tempScr.tempGrid[i].templateField.setText("NULL");
2	26 Feb 07	jari	1610	tempPanel.tempScr.tempGrid[i].templateField.setBackground(Color.gray);
2	26 Feb 07	jari	1611	tempPanel.tempScr.tempGrid[i].templateField.setEnabled(false);
2	26 Feb 07	jari	1612	}
2	26 Feb 07	jari	1613	}
2	26 Feb 07	jari	1614	template = expProfile;
2	26 Feb 07	jari	1615	setTemplate = true;
2	26 Feb 07	jari	1616	clusterGenes = true;
2	26 Feb 07	jari	1617	okButton.setEnabled(true);
2	26 Feb 07	jari	1618	}
2	26 Feb 07	jari	1619
2	26 Feb 07	jari	1620	});
2	26 Feb 07	jari	1621
2	26 Feb 07	jari	1622	gridbag.setConstraints(selectButton, constraints);
2	26 Feb 07	jari	1623	this.add(selectButton);
2	26 Feb 07	jari	1624	refreshGraph();
2	26 Feb 07	jari	1625	}
2	26 Feb 07	jari	1626
2	26 Feb 07	jari	1627	private void refreshGraph() {
2	26 Feb 07	jari	1628
2	26 Feb 07	jari	1629	int index = uniqueIDList.getSelectedIndex();
2	26 Feb 07	jari	1630	Vector expProfile = getGene(index);
2	26 Feb 07	jari	1631	float max = getMax(expProfile);
2	26 Feb 07	jari	1632	float min = getMin(expProfile);
2	26 Feb 07	jari	1633	float maxRange = Math.max(max, Math.abs(min));
2	26 Feb 07	jari	1634	profileDisplayPanel.removeAllGraphElements();
2	26 Feb 07	jari	1635	profileDisplayPanel.setGraphBounds(0, expProfile.size(), -maxRange, maxRange);
2	26 Feb 07	jari	1636
2	26 Feb 07	jari	1637	for (int i = 0; i < expProfile.size(); i++) {
2	26 Feb 07	jari	1638	if (!Float.isNaN(((Float) expProfile.elementAt(i)).floatValue())) {
2	26 Feb 07	jari	1639	GraphPoint gp = new GraphPoint(i /+ 1/, ((Float) expProfile.elementAt(i)).floatValue(), Color.red, 5);
2	26 Feb 07	jari	1640	profileDisplayPanel.addGraphElement(gp);
2	26 Feb 07	jari	1641	}
2	26 Feb 07	jari	1642	}
2	26 Feb 07	jari	1643
2	26 Feb 07	jari	1644	for (int i = 0; i < expProfile.size() - 1; i++) {
2	26 Feb 07	jari	1645	if ((Float.isNaN(((Float) expProfile.elementAt(i)).floatValue())) \|\| (Float.isNaN(((Float) expProfile.elementAt(i+1)).floatValue()))) {
2	26 Feb 07	jari	1646	continue;
2	26 Feb 07	jari	1647	}
2	26 Feb 07	jari	1648	GraphLine gl = new GraphLine(i /+ 1/, ((Float) expProfile.elementAt(i)).floatValue(),
2	26 Feb 07	jari	1649	i + 1, ((Float) expProfile.elementAt(i + 1)).floatValue(), Color.blue);
2	26 Feb 07	jari	1650	profileDisplayPanel.addGraphElement(gl);
2	26 Feb 07	jari	1651
2	26 Feb 07	jari	1652	}
2	26 Feb 07	jari	1653
2	26 Feb 07	jari	1654	profileDisplayPanel.repaint();
2	26 Feb 07	jari	1655	}
2	26 Feb 07	jari	1656
2	26 Feb 07	jari	1657	public void reset(){
2	26 Feb 07	jari	1658	uniqueIDList.setSelectedIndex(0);
2	26 Feb 07	jari	1659	setTemplate = false;
2	26 Feb 07	jari	1660	refreshGraph();
2	26 Feb 07	jari	1661	}
2	26 Feb 07	jari	1662	}
2	26 Feb 07	jari	1663
2	26 Feb 07	jari	1664	private Vector getGene(int index) {
2	26 Feb 07	jari	1665	Vector gene = new Vector();
2	26 Feb 07	jari	1666
2	26 Feb 07	jari	1667	for (int i = 0; i < sampleNamesVector.size(); i++) {
2	26 Feb 07	jari	1668	gene.add(new Float(expMatrix.get(index, i)));
2	26 Feb 07	jari	1669	}
2	26 Feb 07	jari	1670
2	26 Feb 07	jari	1671	return gene;
2	26 Feb 07	jari	1672	}
2	26 Feb 07	jari	1673
2	26 Feb 07	jari	1674
2	26 Feb 07	jari	1675	class GeneClusterSelector extends JPanel {
2	26 Feb 07	jari	1676	JList clusterList;
2	26 Feb 07	jari	1677	GraphCanvas profileDisplayPanel;
2	26 Feb 07	jari	1678	JScrollPane listScrollPane;
2	26 Feb 07	jari	1679	JButton selectButton;
2	26 Feb 07	jari	1680
2	26 Feb 07	jari	1681	Vector clusterNames; // JUST THE NAMES OF THE CLUSTERS, i.e., "CLUSTER 1", "CLUSTER 2", ETC.
2	26 Feb 07	jari	1682	//Vector clusterContents; // THIS IS A VECTOR OF VECTORS (= THE INDICES OF THE UNIQUE IDS IN A CLUSTER)
2	26 Feb 07	jari	1683	Vector geneDataInClusters; // THIS IS A VECTOR OF VECTORS ( = CLUSTERS) OF VECTORS ( = EXPRESSION PROFILES OF GENES IN THAT CLUSTER).
2	26 Feb 07	jari	1684	Vector averageClusterProfiles;
2	26 Feb 07	jari	1685
2	26 Feb 07	jari	1686	JSplitPane clusterSplitPane;
2	26 Feb 07	jari	1687
2	26 Feb 07	jari	1688	GeneClusterSelector() {
2	26 Feb 07	jari	1689
2	26 Feb 07	jari	1690	clusterNames = new Vector();
2	26 Feb 07	jari	1691
2	26 Feb 07	jari	1692	if (clusters.size() == 0) {
2	26 Feb 07	jari	1693	clusterNames.add("No clusters to show");
2	26 Feb 07	jari	1694	} else {
2	26 Feb 07	jari	1695
2	26 Feb 07	jari	1696	for (int i = 0; i < clusters.size(); i++) {
2	26 Feb 07	jari	1697	clusterNames.add("Cluster " + (i+1));
2	26 Feb 07	jari	1698	}
2	26 Feb 07	jari	1699
2	26 Feb 07	jari	1700	geneDataInClusters = new Vector();
2	26 Feb 07	jari	1701	averageClusterProfiles = new Vector();
2	26 Feb 07	jari	1702
2	26 Feb 07	jari	1703	for(int j = 0; j < clusters.size(); j++) {//IN THIS "FOR" LOOP, CURRENT CLUSTER INITIALLY CONTAINS THE INDICES OF THE GENES IN THE CLUSTER, BUT THESE ARE REPLACED BY THE ACUALLY EXPRESSION VECTORS
2	26 Feb 07	jari	1704	Vector currentCluster = (Vector)clusters.get(j);
2	26 Feb 07	jari	1705
2	26 Feb 07	jari	1706	for (int k = 0; k < currentCluster.size(); k++) {
2	26 Feb 07	jari	1707	int index = ((Integer)currentCluster.get(k)).intValue();
2	26 Feb 07	jari	1708	Vector currentGene = getGene(index);
2	26 Feb 07	jari	1709	currentCluster.set(k, currentGene);
2	26 Feb 07	jari	1710	}
2	26 Feb 07	jari	1711
2	26 Feb 07	jari	1712	geneDataInClusters.add(currentCluster);
2	26 Feb 07	jari	1713
2	26 Feb 07	jari	1714	Vector meanOfCurrentCluster = getMeanProfile(currentCluster);
2	26 Feb 07	jari	1715
2	26 Feb 07	jari	1716	averageClusterProfiles.add(meanOfCurrentCluster);
2	26 Feb 07	jari	1717	}
2	26 Feb 07	jari	1718	}
2	26 Feb 07	jari	1719
2	26 Feb 07	jari	1720
2	26 Feb 07	jari	1721	GridBagLayout gridbag = new GridBagLayout();
2	26 Feb 07	jari	1722	GridBagConstraints constraints = new GridBagConstraints();
2	26 Feb 07	jari	1723	//constraints.fill = GridBagConstraints.NONE;
2	26 Feb 07	jari	1724	this.setLayout(gridbag);
2	26 Feb 07	jari	1725
2	26 Feb 07	jari	1726	clusterList = new JList(clusterNames);
2	26 Feb 07	jari	1727	clusterList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
2	26 Feb 07	jari	1728	clusterList.setSelectedIndex(0);
2	26 Feb 07	jari	1729
2	26 Feb 07	jari	1730	//AIS -- Use the graph classes
2	26 Feb 07	jari	1731	profileDisplayPanel = new GraphCanvas();
2	26 Feb 07	jari	1732	profileDisplayPanel.setGraphBounds(0, sampleNamesVector.size(), -3, 3);
2	26 Feb 07	jari	1733	profileDisplayPanel.setGraphSpacing(20, 20, 20, 20);
2	26 Feb 07	jari	1734	profileDisplayPanel.setXAxisValue(0);
2	26 Feb 07	jari	1735	profileDisplayPanel.setYAxisValue(0);
2	26 Feb 07	jari	1736
2	26 Feb 07	jari	1737	clusterList.addListSelectionListener(new ListSelectionListener(){
2	26 Feb 07	jari	1738	public void valueChanged(ListSelectionEvent e) {
2	26 Feb 07	jari	1739	refreshGraph();
2	26 Feb 07	jari	1740	}
2	26 Feb 07	jari	1741	});
2	26 Feb 07	jari	1742	//-- AIS
2	26 Feb 07	jari	1743
2	26 Feb 07	jari	1744	listScrollPane = new JScrollPane(clusterList);
2	26 Feb 07	jari	1745
2	26 Feb 07	jari	1746	clusterSplitPane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, listScrollPane, profileDisplayPanel);
2	26 Feb 07	jari	1747	clusterSplitPane.setOneTouchExpandable(true);
2	26 Feb 07	jari	1748	clusterSplitPane.setDividerLocation(200);
2	26 Feb 07	jari	1749
2	26 Feb 07	jari	1750	Dimension minimumSize = new Dimension(100,50);
2	26 Feb 07	jari	1751	clusterList.setMinimumSize(minimumSize);
2	26 Feb 07	jari	1752	profileDisplayPanel.setMinimumSize(minimumSize);
2	26 Feb 07	jari	1753
2	26 Feb 07	jari	1754	//clusterSplitPane.setMinimumSize(new Dimension(700,150));
2	26 Feb 07	jari	1755
2	26 Feb 07	jari	1756	buildConstraints(constraints, 0, 0, 1, 1, 1, 80);
2	26 Feb 07	jari	1757	constraints.fill = GridBagConstraints.BOTH;
2	26 Feb 07	jari	1758	gridbag.setConstraints(clusterSplitPane, constraints);
2	26 Feb 07	jari	1759	this.add(clusterSplitPane);
2	26 Feb 07	jari	1760
2	26 Feb 07	jari	1761	buildConstraints(constraints, 0, 1, 1, 1, 0, 20);
2	26 Feb 07	jari	1762	constraints.fill = GridBagConstraints.NONE;
2	26 Feb 07	jari	1763	//constraints.anchor = GridBagConstraints.WEST;
2	26 Feb 07	jari	1764	selectButton = new JButton("Select highlighted cluster from above list to use its mean as template", GUIFactory.getIcon("select_check24.gif"));
2	26 Feb 07	jari	1765	selectButton.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED));
2	26 Feb 07	jari	1766	selectButton.setMargin(new Insets(10,10,10,10));
2	26 Feb 07	jari	1767	selectButton.setPreferredSize(new Dimension(430,30));
2	26 Feb 07	jari	1768	selectButton.setFocusPainted(false);
2	26 Feb 07	jari	1769
2	26 Feb 07	jari	1770	selectButton.addActionListener(new ActionListener(){
2	26 Feb 07	jari	1771	public void actionPerformed(ActionEvent e) {
2	26 Feb 07	jari	1772	if (clusters.size() == 0){
2	26 Feb 07	jari	1773	JOptionPane.showMessageDialog(null, "No clusters to select");
2	26 Feb 07	jari	1774	} else {
2	26 Feb 07	jari	1775	int index = clusterList.getSelectedIndex();
2	26 Feb 07	jari	1776	Vector expProfile = (Vector) ((Vector) averageClusterProfiles.get(index)).clone();
2	26 Feb 07	jari	1777	float max = getMax(expProfile);
2	26 Feb 07	jari	1778	float min = getMin(expProfile);
2	26 Feb 07	jari	1779
2	26 Feb 07	jari	1780	if ((max - min) == 0) {
2	26 Feb 07	jari	1781
2	26 Feb 07	jari	1782	for(int i = 0; i < expProfile.size(); i++) {
2	26 Feb 07	jari	1783	expProfile.set(i, new Float(0.5));
2	26 Feb 07	jari	1784	}
2	26 Feb 07	jari	1785
2	26 Feb 07	jari	1786	} else {
2	26 Feb 07	jari	1787
2	26 Feb 07	jari	1788	for(int i = 0; i < expProfile.size(); i++) {
2	26 Feb 07	jari	1789	float f = (((Float)expProfile.get(i)).floatValue()- min)/(max - min);
2	26 Feb 07	jari	1790	expProfile.set(i, new Float(f));
2	26 Feb 07	jari	1791	}
2	26 Feb 07	jari	1792	}
2	26 Feb 07	jari	1793
2	26 Feb 07	jari	1794	for(int i = 0; i < tempPanel.tempScr.tempGrid.length; i++){
2	26 Feb 07	jari	1795	tempPanel.tempScr.tempGrid[i].templateSlider.setValue((int) Math.floor(((Float)expProfile.get(i)).floatValue()*100));
2	26 Feb 07	jari	1796	tempPanel.tempScr.tempGrid[i].templateField.setText("" + ((Float)expProfile.get(i)).floatValue());
2	26 Feb 07	jari	1797	}
2	26 Feb 07	jari	1798	if(setTemplate){
2	26 Feb 07	jari	1799	for (int i = 0; i < expProfile.size() - 1; i++) {
2	26 Feb 07	jari	1800	if ((Float.isNaN(((Float) expProfile.elementAt(i)).floatValue())) \|\| (Float.isNaN(((Float) expProfile.elementAt(i+1)).floatValue()))) {
2	26 Feb 07	jari	1801	continue;
2	26 Feb 07	jari	1802	}
2	26 Feb 07	jari	1803	GraphLine gl = new GraphLine(i /+ 1/, ((Float) expProfile.elementAt(i)).floatValue(),
2	26 Feb 07	jari	1804	i + 1, ((Float) expProfile.elementAt(i + 1)).floatValue(), Color.green);
2	26 Feb 07	jari	1805	profileDisplayPanel.addGraphElement(gl);
2	26 Feb 07	jari	1806	}
2	26 Feb 07	jari	1807	}
2	26 Feb 07	jari	1808	template = expProfile;
2	26 Feb 07	jari	1809	setTemplate = true;
2	26 Feb 07	jari	1810	clusterGenes = true;
2	26 Feb 07	jari	1811	okButton.setEnabled(true);
2	26 Feb 07	jari	1812	}
2	26 Feb 07	jari	1813	}
2	26 Feb 07	jari	1814	});
2	26 Feb 07	jari	1815
2	26 Feb 07	jari	1816	gridbag.setConstraints(selectButton, constraints);
2	26 Feb 07	jari	1817	this.add(selectButton);
2	26 Feb 07	jari	1818	refreshGraph();
2	26 Feb 07	jari	1819	}
2	26 Feb 07	jari	1820
2	26 Feb 07	jari	1821	private void refreshGraph() {
2	26 Feb 07	jari	1822
2	26 Feb 07	jari	1823	int index = clusterList.getSelectedIndex();
2	26 Feb 07	jari	1824	if (clusters.size() <= 0) return;
2	26 Feb 07	jari	1825	Vector meanProfile = (Vector) averageClusterProfiles.elementAt(index);
2	26 Feb 07	jari	1826	float min = Float.POSITIVE_INFINITY;
2	26 Feb 07	jari	1827	float max = Float.NEGATIVE_INFINITY;
2	26 Feb 07	jari	1828	float maxRange;
2	26 Feb 07	jari	1829	profileDisplayPanel.removeAllGraphElements();
2	26 Feb 07	jari	1830	Vector selectedCluster = (Vector)geneDataInClusters.get(index);
2	26 Feb 07	jari	1831
2	26 Feb 07	jari	1832	for (int j = 0; j < selectedCluster.size(); j++) {
2	26 Feb 07	jari	1833
2	26 Feb 07	jari	1834	Vector currGene = (Vector)selectedCluster.get(j);
2	26 Feb 07	jari	1835
2	26 Feb 07	jari	1836	max = Math.max(max, getMax(currGene));
2	26 Feb 07	jari	1837	min = Math.min(min, getMin(currGene));
2	26 Feb 07	jari	1838	maxRange = Math.max(max, Math.abs(min));
2	26 Feb 07	jari	1839	profileDisplayPanel.setGraphBounds(0, currGene.size(), -maxRange, maxRange);
2	26 Feb 07	jari	1840
2	26 Feb 07	jari	1841	for (int i = 0; i < currGene.size(); i++) {
2	26 Feb 07	jari	1842	}
2	26 Feb 07	jari	1843
2	26 Feb 07	jari	1844	for (int i = 0; i < currGene.size() - 1; i++) {
2	26 Feb 07	jari	1845	if ((Float.isNaN(((Float) currGene.elementAt(i)).floatValue()))\|\|(Float.isNaN(((Float) currGene.elementAt(i+1)).floatValue()))) {
2	26 Feb 07	jari	1846	continue;
2	26 Feb 07	jari	1847	}
2	26 Feb 07	jari	1848
2	26 Feb 07	jari	1849	GraphLine gl = new GraphLine(i /+ 1/, ((Float) currGene.elementAt(i)).floatValue(),
2	26 Feb 07	jari	1850	i + 1, ((Float) currGene.elementAt(i + 1)).floatValue(), clusterColors[index]);
2	26 Feb 07	jari	1851	profileDisplayPanel.addGraphElement(gl);
2	26 Feb 07	jari	1852
2	26 Feb 07	jari	1853	}
2	26 Feb 07	jari	1854	}
2	26 Feb 07	jari	1855
2	26 Feb 07	jari	1856	for (int i = 0; i < meanProfile.size(); i++) {
2	26 Feb 07	jari	1857	if (!Float.isNaN(((Float) meanProfile.elementAt(i)).floatValue())) {
2	26 Feb 07	jari	1858	GraphPoint gp = new GraphPoint(i/* + 1*/, ((Float) meanProfile.elementAt(i)).floatValue(), Color.red, 5);
2	26 Feb 07	jari	1859	profileDisplayPanel.addGraphElement(gp);
2	26 Feb 07	jari	1860	}
2	26 Feb 07	jari	1861	}
2	26 Feb 07	jari	1862
2	26 Feb 07	jari	1863	for (int i = 0; i < meanProfile.size() - 1; i++) {
2	26 Feb 07	jari	1864	GraphLine gl = new GraphLine(i /+ 1/, ((Float) meanProfile.elementAt(i)).floatValue(),
2	26 Feb 07	jari	1865	i + 1, ((Float) meanProfile.elementAt(i + 1)).floatValue(), Color.blue);
2	26 Feb 07	jari	1866	profileDisplayPanel.addGraphElement(gl);
2	26 Feb 07	jari	1867	}
2	26 Feb 07	jari	1868
2	26 Feb 07	jari	1869	profileDisplayPanel.repaint();
2	26 Feb 07	jari	1870	}
2	26 Feb 07	jari	1871
2	26 Feb 07	jari	1872	public void reset(){
2	26 Feb 07	jari	1873	clusterList.setSelectedIndex(0);
2	26 Feb 07	jari	1874	setTemplate = false;
2	26 Feb 07	jari	1875	refreshGraph();
2	26 Feb 07	jari	1876	}
2	26 Feb 07	jari	1877	}
2	26 Feb 07	jari	1878
2	26 Feb 07	jari	1879	class TemplateElementGrid extends JPanel {
2	26 Feb 07	jari	1880
2	26 Feb 07	jari	1881	JLabel exptName;
2	26 Feb 07	jari	1882	JTextField templateField;
2	26 Feb 07	jari	1883	JSlider templateSlider;
2	26 Feb 07	jari	1884	JCheckBox activeBox;
2	26 Feb 07	jari	1885
2	26 Feb 07	jari	1886	TemplateElementGrid(String SampleName) {
2	26 Feb 07	jari	1887	GridBagLayout templateElement = new GridBagLayout();
2	26 Feb 07	jari	1888	GridBagConstraints constraints = new GridBagConstraints();
2	26 Feb 07	jari	1889	constraints.fill = GridBagConstraints.BOTH;
2	26 Feb 07	jari	1890	this.setLayout(templateElement);
2	26 Feb 07	jari	1891
2	26 Feb 07	jari	1892	buildConstraints(constraints, 0, 0, 1, 1, 50, 10);
2	26 Feb 07	jari	1893	exptName = new JLabel(SampleName, SwingConstants.CENTER);
2	26 Feb 07	jari	1894	templateElement.setConstraints(exptName, constraints);
2	26 Feb 07	jari	1895	this.add(exptName);
2	26 Feb 07	jari	1896
2	26 Feb 07	jari	1897	buildConstraints(constraints, 1, 0, 1, 1, 50, 0);
2	26 Feb 07	jari	1898	activeBox = new JCheckBox();
2	26 Feb 07	jari	1899	activeBox.setSelected(true);
2	26 Feb 07	jari	1900	activeBox.addItemListener(new ItemListener() {
2	26 Feb 07	jari	1901	public void itemStateChanged(ItemEvent e) {
2	26 Feb 07	jari	1902	if (e.getStateChange() == ItemEvent.DESELECTED) {
2	26 Feb 07	jari	1903	//templateField.setText("NULL");
2	26 Feb 07	jari	1904	templateField.setBackground(Color.gray);
2	26 Feb 07	jari	1905	templateField.setEnabled(false);
2	26 Feb 07	jari	1906	templateSlider.setEnabled(false);
2	26 Feb 07	jari	1907	}
2	26 Feb 07	jari	1908
2	26 Feb 07	jari	1909	if (e.getStateChange() == ItemEvent.SELECTED) {
2	26 Feb 07	jari	1910	//templateField.setText("NULL");
2	26 Feb 07	jari	1911	templateField.setBackground(Color.white);
2	26 Feb 07	jari	1912	templateField.setEnabled(true);
2	26 Feb 07	jari	1913	templateSlider.setEnabled(true);
2	26 Feb 07	jari	1914	}
2	26 Feb 07	jari	1915
2	26 Feb 07	jari	1916	}
2	26 Feb 07	jari	1917	});
2	26 Feb 07	jari	1918	templateElement.setConstraints(activeBox, constraints);
2	26 Feb 07	jari	1919	this.add(activeBox);
2	26 Feb 07	jari	1920
2	26 Feb 07	jari	1921	buildConstraints(constraints, 0, 1, 2, 1, 0, 5);
2	26 Feb 07	jari	1922	templateField = new JTextField("0.5", 4);
2	26 Feb 07	jari	1923	templateField.addActionListener(new ActionListener(){
2	26 Feb 07	jari	1924	public void actionPerformed(ActionEvent e) {
2	26 Feb 07	jari	1925	int sliderValue;
2	26 Feb 07	jari	1926	if(e.getSource() == templateField){
2	26 Feb 07	jari	1927	try {
2	26 Feb 07	jari	1928	String s = templateField.getText();
2	26 Feb 07	jari	1929	double d = Double.parseDouble(s);
2	26 Feb 07	jari	1930	sliderValue = (int)Math.floor(d*100);
2	26 Feb 07	jari	1931	if ((d > 1)\|\|(d < 0)) {
2	26 Feb 07	jari	1932
2	26 Feb 07	jari	1933	sliderValue = 50;
2	26 Feb 07	jari	1934	templateField.setText("0.5");
2	26 Feb 07	jari	1935	JOptionPane.showMessageDialog(null, "Template values must be between 0 and 1 (inclusive)");
2	26 Feb 07	jari	1936
2	26 Feb 07	jari	1937	}
2	26 Feb 07	jari	1938	} catch (Exception exc) {
2	26 Feb 07	jari	1939
2	26 Feb 07	jari	1940	templateField.setText("0.5");
2	26 Feb 07	jari	1941	sliderValue = 50;
2	26 Feb 07	jari	1942	JOptionPane.showMessageDialog(null, "Template values must be between 0 and 1 (inclusive)");
2	26 Feb 07	jari	1943
2	26 Feb 07	jari	1944	}
2	26 Feb 07	jari	1945
2	26 Feb 07	jari	1946	templateSlider.setValue(sliderValue);
2	26 Feb 07	jari	1947	}
2	26 Feb 07	jari	1948
2	26 Feb 07	jari	1949	}
2	26 Feb 07	jari	1950	});
2	26 Feb 07	jari	1951
2	26 Feb 07	jari	1952	templateField.addFocusListener(new FocusListener(){
2	26 Feb 07	jari	1953	public void focusLost(FocusEvent e) {
2	26 Feb 07	jari	1954	int sliderValue;
2	26 Feb 07	jari	1955	if(e.getSource() == templateField){
2	26 Feb 07	jari	1956	try {
2	26 Feb 07	jari	1957	String s = templateField.getText();
2	26 Feb 07	jari	1958	double d = Double.parseDouble(s);
2	26 Feb 07	jari	1959	sliderValue = (int)Math.floor(d*100);
2	26 Feb 07	jari	1960	if ((d > 1)\|\|(d < 0)) {
2	26 Feb 07	jari	1961
2	26 Feb 07	jari	1962	sliderValue = 50;
2	26 Feb 07	jari	1963	templateField.setText("0.5");
2	26 Feb 07	jari	1964	JOptionPane.showMessageDialog(null, "Template values must be between 0 and 1 (inclusive)");
2	26 Feb 07	jari	1965
2	26 Feb 07	jari	1966	}
2	26 Feb 07	jari	1967	} catch (Exception exc) {
2	26 Feb 07	jari	1968
2	26 Feb 07	jari	1969	templateField.setText("0.5");
2	26 Feb 07	jari	1970	sliderValue = 50;
2	26 Feb 07	jari	1971	JOptionPane.showMessageDialog(null, "Input Format Error: Template values must be between 0 and 1 (inclusive)");
2	26 Feb 07	jari	1972
2	26 Feb 07	jari	1973	}
2	26 Feb 07	jari	1974
2	26 Feb 07	jari	1975	templateSlider.setValue(sliderValue);
2	26 Feb 07	jari	1976	}
2	26 Feb 07	jari	1977	}
2	26 Feb 07	jari	1978
2	26 Feb 07	jari	1979
2	26 Feb 07	jari	1980	public void focusGained(FocusEvent e) {
2	26 Feb 07	jari	1981	}
2	26 Feb 07	jari	1982	});
2	26 Feb 07	jari	1983
2	26 Feb 07	jari	1984	templateElement.setConstraints(templateField, constraints);
2	26 Feb 07	jari	1985	this.add(templateField);
2	26 Feb 07	jari	1986
2	26 Feb 07	jari	1987	buildConstraints(constraints, 0, 2, 1, 2, 0, 85);
2	26 Feb 07	jari	1988	templateSlider = new JSlider(JSlider.VERTICAL, 0, 100, 50);
2	26 Feb 07	jari	1989	templateSlider.setMajorTickSpacing(20);
2	26 Feb 07	jari	1990	templateSlider.setMinorTickSpacing(10);
2	26 Feb 07	jari	1991	//templateSlider.setPaintTicks(true);
2	26 Feb 07	jari	1992	Hashtable labelTable = new Hashtable();
2	26 Feb 07	jari	1993	labelTable.put( new Integer( 0 ), new JLabel("Min") );
2	26 Feb 07	jari	1994	labelTable.put( new Integer( 100 ), new JLabel("Max") );
2	26 Feb 07	jari	1995	templateSlider.setLabelTable( labelTable );
2	26 Feb 07	jari	1996	templateSlider.setPaintLabels(true);
2	26 Feb 07	jari	1997	templateSlider.addChangeListener(new ChangeListener(){
2	26 Feb 07	jari	1998	public void stateChanged(ChangeEvent e) {
2	26 Feb 07	jari	1999	JSlider source = (JSlider)e.getSource();
2	26 Feb 07	jari	2000	if (!source.getValueIsAdjusting()) {
2	26 Feb 07	jari	2001	int value = (int)source.getValue();
2	26 Feb 07	jari	2002
2	26 Feb 07	jari	2003	if (value == 100) {
2	26 Feb 07	jari	2004	templateField.setText("1.0"); //CLUMSY WAY OF DISPLAYING INTEGER AS DOUBLE? MAYBE CHANGE?
2	26 Feb 07	jari	2005	} else if (value > 0 && value < 10) {
2	26 Feb 07	jari	2006	templateField.setText("0.0" + value);
2	26 Feb 07	jari	2007	} else {
2	26 Feb 07	jari	2008	templateField.setText("0." + value);
2	26 Feb 07	jari	2009	}
2	26 Feb 07	jari	2010	}
2	26 Feb 07	jari	2011	}
2	26 Feb 07	jari	2012
2	26 Feb 07	jari	2013	});
2	26 Feb 07	jari	2014	templateElement.setConstraints(templateSlider, constraints);
2	26 Feb 07	jari	2015	this.add(templateSlider);
2	26 Feb 07	jari	2016
2	26 Feb 07	jari	2017
2	26 Feb 07	jari	2018	}
2	26 Feb 07	jari	2019
2	26 Feb 07	jari	2020	public void reset() {
2	26 Feb 07	jari	2021	templateSlider.setValue(50);
2	26 Feb 07	jari	2022	templateField.setText("0.5");
2	26 Feb 07	jari	2023	}
2	26 Feb 07	jari	2024
2	26 Feb 07	jari	2025
2	26 Feb 07	jari	2026	}
2	26 Feb 07	jari	2027
2	26 Feb 07	jari	2028	public static void main(String [] args){
2	26 Feb 07	jari	2029	FloatMatrix expMatrix = new FloatMatrix(100,10);
2	26 Feb 07	jari	2030	Vector uniqueIDs = new Vector();
2	26 Feb 07	jari	2031	Vector sampleNamesVector = new Vector();
2	26 Feb 07	jari	2032	Color [] colors = null;
2	26 Feb 07	jari	2033	for(int i = 0; i < 100; i++)
2	26 Feb 07	jari	2034	uniqueIDs.add(String.valueOf(i));
2	26 Feb 07	jari	2035	for(int i = 0; i < 10; i++)
2	26 Feb 07	jari	2036	sampleNamesVector.add(("Exp "+String.valueOf(i)));
2	26 Feb 07	jari	2037	// public (JFrame parentFrame, boolean modality, FloatMatrix expMatrix, Vector uniqueIDs, Vector sampleNamesVector, Vector clusters, Vector expClusters, Color[] clusterColors, Color [] expClusterColors) {
2	26 Feb 07	jari	2038
2	26 Feb 07	jari	2039	PTMInitDialog box = new PTMInitDialog(new JFrame(), true, expMatrix, uniqueIDs, sampleNamesVector, new Vector(), new Vector(), colors, colors);
2	26 Feb 07	jari	2040	box.setVisible(true);
2	26 Feb 07	jari	2041	System.exit(0);
2	26 Feb 07	jari	2042	}
2	26 Feb 07	jari	2043
2	26 Feb 07	jari	2044	}