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/* |
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Copyright @ 1999-2003, The Institute for Genomic Research (TIGR). |
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All rights reserved. |
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*/ |
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/* |
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* $RCSfile: SOMInitDialog.java,v $ |
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* $Revision: 1.3 $ |
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* $Date: 2005/03/10 20:22:04 $ |
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* $Author: braistedj $ |
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* $State: Exp $ |
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*/ |
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package org.tigr.microarray.mev.cluster.gui.impl.som; |
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|
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import java.awt.BorderLayout; |
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import java.awt.Color; |
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import java.awt.Dimension; |
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import java.awt.FontMetrics; |
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import java.awt.Frame; |
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import java.awt.GridBagConstraints; |
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import java.awt.GridBagLayout; |
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import java.awt.GridLayout; |
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import java.awt.Insets; |
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import java.awt.Toolkit; |
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import java.awt.event.ActionEvent; |
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import java.awt.event.ActionListener; |
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import java.awt.event.WindowEvent; |
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|
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import javax.swing.JComboBox; |
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import javax.swing.JLabel; |
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import javax.swing.JOptionPane; |
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import javax.swing.JPanel; |
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import javax.swing.JTextField; |
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import javax.swing.UIManager; |
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import javax.swing.border.EmptyBorder; |
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|
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import org.tigr.microarray.mev.cluster.gui.impl.dialogs.AlgorithmDialog; |
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import org.tigr.microarray.mev.cluster.gui.impl.dialogs.DialogListener; |
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import org.tigr.microarray.mev.cluster.gui.impl.dialogs.DistanceMetricPanel; |
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import org.tigr.microarray.mev.cluster.gui.impl.dialogs.HCLSelectionPanel; |
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import org.tigr.microarray.mev.cluster.gui.impl.dialogs.ParameterPanel; |
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import org.tigr.microarray.mev.cluster.gui.impl.dialogs.SampleSelectionPanel; |
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import org.tigr.microarray.mev.cluster.gui.impl.dialogs.dialogHelpUtil.HelpWindow; |
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|
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public class SOMInitDialog extends AlgorithmDialog { |
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|
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private int result; |
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private SampleSelectionPanel sampleSelectionPanel; |
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private HCLSelectionPanel hclOpsPanel; |
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private DistanceMetricPanel metricPanel; |
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|
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public JTextField dimXField; |
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public JTextField dimYField; |
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public JTextField iterField; |
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public JTextField alphaField; |
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public JTextField radiusField; |
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public JComboBox initList; |
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public JComboBox neighbList; |
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public JComboBox topoList; |
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|
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/** |
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* Constructs the dialog with predefined parameters. |
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*/ |
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public SOMInitDialog(Frame frame, int dimX, int dimY, long iterations, |
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float alpha, float radius, |
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int initType, int neighborhood, int topology, String globalFunctionName, boolean globalAbsoluteValue) { |
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super(frame, "SOM: Self Organizing Maps", true); |
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this.setSize(520, 343); |
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this.setResizable(false); |
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|
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Listener listener = new Listener(); |
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addWindowListener(listener); |
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|
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sampleSelectionPanel = new SampleSelectionPanel(Color.white, UIManager.getColor("Label.foreground"),true,"Sample Selection"); |
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|
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sampleSelectionPanel.setExperimentButtonActionListener(new ActionListener(){ |
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public void actionPerformed( ActionEvent e ){ |
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if( sampleSelectionPanel.isClusterGenesSelected() ) |
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return; |
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int sel = initList.getSelectedIndex(); |
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initList.removeItemAt(1); |
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initList.insertItemAt("Random Samples", 1); |
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initList.setSelectedIndex(sel); |
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} |
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}); |
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sampleSelectionPanel.setGeneButtonActionListener(new ActionListener(){ |
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public void actionPerformed( ActionEvent e ){ |
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if( !sampleSelectionPanel.isClusterGenesSelected() ) |
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return; |
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int sel = initList.getSelectedIndex(); |
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initList.removeItemAt(1); |
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initList.insertItemAt("Random Genes", 1); |
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initList.setSelectedIndex(sel); |
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} |
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}); |
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|
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|
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metricPanel = new DistanceMetricPanel(globalFunctionName, globalAbsoluteValue, "Euclidean Distance", "SOM", true, true); |
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|
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JPanel parameters1 = new JPanel(); |
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parameters1.setBorder(new EmptyBorder(5, 10, 20, 0)); |
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parameters1.setBackground(Color.white); |
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parameters1.setForeground(Color.black); |
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parameters1.setLayout(new GridBagLayout()); |
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|
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GridBagConstraints gbc = new GridBagConstraints(); |
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gbc.insets.right = 10; |
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gbc.gridx = 0; |
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gbc.gridy = 0; |
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gbc.anchor = GridBagConstraints.WEST; |
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|
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parameters1.add(new JLabel("Dimension X"), gbc); |
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gbc.gridy = 1; |
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parameters1.add(new JLabel("Dimension Y"), gbc); |
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gbc.gridy = 2; |
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parameters1.add(new JLabel("Iterations") , gbc); |
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gbc.gridy = 3; |
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parameters1.add(new JLabel("Alpha"), gbc); |
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gbc.gridy = 4; |
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parameters1.add(new JLabel("Radius"), gbc); |
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gbc.gridx = 1; |
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gbc.gridy = 0; |
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gbc.insets.right = 0; |
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gbc.fill = GridBagConstraints.HORIZONTAL; |
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dimXField = new JTextField(String.valueOf(dimX), 5); |
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parameters1.add(dimXField , gbc); |
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gbc.gridy = 1; |
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dimYField = new JTextField(String.valueOf(dimY), 5); |
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parameters1.add(dimYField , gbc); |
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gbc.gridy = 2; |
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iterField = new JTextField(String.valueOf(iterations), 5); |
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parameters1.add(iterField , gbc); |
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gbc.gridy = 3; |
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alphaField = new JTextField(String.valueOf(alpha), 5); |
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parameters1.add(alphaField , gbc); |
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gbc.gridy = 4; |
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radiusField = new JTextField(String.valueOf(radius), 5); |
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parameters1.add(radiusField, gbc); |
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gbc.gridx = 0; |
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gbc.gridy = 5; |
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gbc.gridwidth = 2; |
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|
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JPanel parameters2 = new JPanel(); |
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parameters2.setLayout(new GridLayout(0, 1, 0, 10)); |
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parameters2.setBorder(new EmptyBorder(5, 25, 15, 10)); |
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parameters2.setBackground(Color.white); |
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|
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parameters2.add(new JLabel("Initialization"), BorderLayout.WEST); |
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parameters2.add(new JLabel("Neighborhood"), BorderLayout.WEST); |
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parameters2.add(new JLabel("Topology"), BorderLayout.WEST); |
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|
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JPanel parameters3 = new JPanel(); |
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parameters3.setLayout(new GridLayout(0, 1, 10, 10)); |
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parameters3.setBorder(new EmptyBorder(10, 0, 15, 10)); |
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parameters3.setBackground(Color.white); |
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|
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initList = new JComboBox(new String[] {"Random Vector", "Random Genes"}); |
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initList.setSelectedIndex(initType); |
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|
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FontMetrics fm = initList.getFontMetrics(initList.getFont()); |
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int width = fm.stringWidth("Random Samples"); |
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initList.setPreferredSize( new Dimension(width + 40, initList.getHeight())); |
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|
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neighbList = new JComboBox(new String[] {"Bubble", "Gaussian"}); |
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neighbList.setSelectedIndex(neighborhood); |
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neighbList.setPreferredSize( new Dimension(width, initList.getHeight())); |
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|
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topoList = new JComboBox(new String[] {"Hexagonal", "Rectangular"}); |
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topoList.setSelectedIndex(topology); |
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|
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initList.setBackground(Color.white); |
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neighbList.setBackground(Color.white); |
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topoList.setBackground(Color.white); |
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|
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parameters3.add(initList); |
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parameters3.add(neighbList); |
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parameters3.add(topoList); |
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|
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hclOpsPanel = new HCLSelectionPanel(); |
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|
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ParameterPanel paramPanel = new ParameterPanel(); |
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paramPanel.setLayout(new BorderLayout()); |
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|
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paramPanel.add(parameters1, BorderLayout.WEST); |
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paramPanel.add(parameters2, BorderLayout.CENTER); |
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paramPanel.add(parameters3, BorderLayout.EAST); |
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|
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JPanel panel3 = new JPanel(new GridBagLayout()); |
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panel3.add(sampleSelectionPanel, new GridBagConstraints(0,0,1,1,1,0,GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0)); |
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panel3.add(metricPanel, new GridBagConstraints(0,1,1,1,1,0,GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0)); |
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panel3.add(paramPanel, new GridBagConstraints(0,2,1,1,1,0,GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0)); |
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panel3.add(hclOpsPanel, new GridBagConstraints(0,3,1,1,1,0,GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0)); |
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|
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setActionListeners(listener); |
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addContent(panel3); |
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pack(); |
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// panel1.add(topPanel, BorderLayout.CENTER); |
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|
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// this.getContentPane().add(panel1, BorderLayout.CENTER); |
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} |
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|
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/** |
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* Shows the dialog. |
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*/ |
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public int showModal() { |
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Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); |
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setLocation((screenSize.width - getSize().width)/2, (screenSize.height - getSize().height)/2); |
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show(); |
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return result; |
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} |
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|
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/** |
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* Returns if clustering Genes is true |
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*/ |
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public boolean isClusterGenes(){ |
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return sampleSelectionPanel.isClusterGenesSelected(); |
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} |
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|
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|
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/** |
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* Returns the x dimension. |
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*/ |
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public int getDimensionX() { |
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return Integer.parseInt(dimXField.getText()); |
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} |
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|
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/** |
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* Returns the y dimension. |
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*/ |
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public int getDimensionY() { |
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return Integer.parseInt(dimYField.getText()); |
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} |
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|
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/** |
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* Returns count of iterations. |
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*/ |
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public long getIterations() { |
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return Long.parseLong(iterField.getText()); |
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} |
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|
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/** |
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* Returns the alpha value. |
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*/ |
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public float getAlpha() { |
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return Float.parseFloat(alphaField.getText()); |
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} |
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|
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/** |
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* Returns the radius value. |
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*/ |
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public float getRadius() { |
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return Float.parseFloat(radiusField.getText()); |
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} |
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|
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/** |
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* Returns the initialization type. |
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*/ |
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public int getInitType() { |
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return initList.getSelectedIndex(); |
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} |
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|
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/** |
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* Returns the neighborhood index. |
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*/ |
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public int getNeighborhood() { |
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return neighbList.getSelectedIndex(); |
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} |
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|
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/** |
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* Returns the topology index. |
2 |
26 Feb 07 |
jari |
270 |
*/ |
2 |
26 Feb 07 |
jari |
271 |
public int getTopology() { |
2 |
26 Feb 07 |
jari |
272 |
return topoList.getSelectedIndex(); |
2 |
26 Feb 07 |
jari |
273 |
} |
2 |
26 Feb 07 |
jari |
274 |
|
2 |
26 Feb 07 |
jari |
275 |
/** |
2 |
26 Feb 07 |
jari |
* Returns true if the hierarchical checkbox is selected. |
2 |
26 Feb 07 |
jari |
277 |
*/ |
2 |
26 Feb 07 |
jari |
278 |
public boolean isHierarchicalTree() { |
2 |
26 Feb 07 |
jari |
279 |
return hclOpsPanel.isHCLSelected(); |
2 |
26 Feb 07 |
jari |
280 |
} |
2 |
26 Feb 07 |
jari |
281 |
|
2 |
26 Feb 07 |
jari |
282 |
/** |
2 |
26 Feb 07 |
jari |
* Returns the currently selected metric |
2 |
26 Feb 07 |
jari |
284 |
*/ |
2 |
26 Feb 07 |
jari |
285 |
public int getDistanceMetric() { |
2 |
26 Feb 07 |
jari |
286 |
return metricPanel.getMetricIndex(); |
2 |
26 Feb 07 |
jari |
287 |
} |
2 |
26 Feb 07 |
jari |
288 |
|
2 |
26 Feb 07 |
jari |
289 |
/** |
2 |
26 Feb 07 |
jari |
* Returns true if the absolute checkbox is selected, else false |
2 |
26 Feb 07 |
jari |
291 |
*/ |
2 |
26 Feb 07 |
jari |
292 |
public boolean isAbsoluteDistance() { |
2 |
26 Feb 07 |
jari |
293 |
return metricPanel.getAbsoluteSelection(); |
2 |
26 Feb 07 |
jari |
294 |
} |
2 |
26 Feb 07 |
jari |
295 |
|
2 |
26 Feb 07 |
jari |
296 |
|
2 |
26 Feb 07 |
jari |
297 |
/** |
2 |
26 Feb 07 |
jari |
* Resets the controls to default |
2 |
26 Feb 07 |
jari |
299 |
*/ |
2 |
26 Feb 07 |
jari |
300 |
private void resetControls(){ |
2 |
26 Feb 07 |
jari |
301 |
this.dimXField.setText("3"); |
2 |
26 Feb 07 |
jari |
302 |
this.dimYField.setText("3"); |
2 |
26 Feb 07 |
jari |
303 |
this.iterField.setText("2000"); |
2 |
26 Feb 07 |
jari |
304 |
this.alphaField.setText("0.05"); |
2 |
26 Feb 07 |
jari |
305 |
this.radiusField.setText("3.0"); |
2 |
26 Feb 07 |
jari |
306 |
initList.removeItemAt(1); |
2 |
26 Feb 07 |
jari |
307 |
initList.insertItemAt("Random Genes", 1); |
2 |
26 Feb 07 |
jari |
308 |
this.initList.setSelectedIndex(1); |
2 |
26 Feb 07 |
jari |
309 |
this.neighbList.setSelectedIndex(1); |
2 |
26 Feb 07 |
jari |
310 |
this.topoList.setSelectedIndex(0); |
2 |
26 Feb 07 |
jari |
311 |
this.sampleSelectionPanel.setClusterGenesSelected(true); |
2 |
26 Feb 07 |
jari |
312 |
this.hclOpsPanel.setHCLSelected(false); |
2 |
26 Feb 07 |
jari |
313 |
this.initList.setSelectedIndex(1); |
2 |
26 Feb 07 |
jari |
314 |
this.neighbList.setSelectedIndex(1); |
2 |
26 Feb 07 |
jari |
315 |
this.topoList.setSelectedIndex(0); |
2 |
26 Feb 07 |
jari |
316 |
this.metricPanel.reset(); |
2 |
26 Feb 07 |
jari |
317 |
} |
2 |
26 Feb 07 |
jari |
318 |
|
2 |
26 Feb 07 |
jari |
319 |
/** |
2 |
26 Feb 07 |
jari |
* Validates input values |
2 |
26 Feb 07 |
jari |
321 |
*/ |
2 |
26 Feb 07 |
jari |
322 |
private boolean validInput(int x, int y, long i, float a, float r){ |
2 |
26 Feb 07 |
jari |
323 |
boolean valid = true; |
2 |
26 Feb 07 |
jari |
324 |
if(x < 1 ){ |
2 |
26 Feb 07 |
jari |
325 |
JOptionPane.showMessageDialog(SOMInitDialog.this, "x Dimension must be > 0", "Input Error!", JOptionPane.ERROR_MESSAGE); |
2 |
26 Feb 07 |
jari |
326 |
this.dimXField.requestFocus(); |
2 |
26 Feb 07 |
jari |
327 |
this.dimXField.selectAll(); |
2 |
26 Feb 07 |
jari |
328 |
valid = false; |
2 |
26 Feb 07 |
jari |
329 |
} |
2 |
26 Feb 07 |
jari |
330 |
else if( y < 1){ |
2 |
26 Feb 07 |
jari |
331 |
JOptionPane.showMessageDialog(SOMInitDialog.this, "y Dimension must be > 0", "Input Error!", JOptionPane.ERROR_MESSAGE); |
2 |
26 Feb 07 |
jari |
332 |
this.dimYField.requestFocus(); |
2 |
26 Feb 07 |
jari |
333 |
this.dimYField.selectAll(); |
2 |
26 Feb 07 |
jari |
334 |
valid = false; |
2 |
26 Feb 07 |
jari |
335 |
} |
2 |
26 Feb 07 |
jari |
336 |
else if( i < 1 ){ |
2 |
26 Feb 07 |
jari |
337 |
JOptionPane.showMessageDialog(SOMInitDialog.this, "Number of Iterations must be > 0", "Input Error!", JOptionPane.ERROR_MESSAGE); |
2 |
26 Feb 07 |
jari |
338 |
this.iterField.requestFocus(); |
2 |
26 Feb 07 |
jari |
339 |
this.iterField.selectAll(); |
2 |
26 Feb 07 |
jari |
340 |
valid = false; |
2 |
26 Feb 07 |
jari |
341 |
} |
2 |
26 Feb 07 |
jari |
342 |
else if( a <= 0 ){ |
2 |
26 Feb 07 |
jari |
343 |
JOptionPane.showMessageDialog(SOMInitDialog.this, "Alpha value must be > 0", "Input Error!", JOptionPane.ERROR_MESSAGE); |
2 |
26 Feb 07 |
jari |
344 |
this.alphaField.requestFocus(); |
2 |
26 Feb 07 |
jari |
345 |
this.alphaField.selectAll(); |
2 |
26 Feb 07 |
jari |
346 |
valid = false; |
2 |
26 Feb 07 |
jari |
347 |
} |
2 |
26 Feb 07 |
jari |
348 |
else if(r <= 0){ |
2 |
26 Feb 07 |
jari |
349 |
JOptionPane.showMessageDialog(SOMInitDialog.this, "Radius value must be > 0", "Input Error!", JOptionPane.ERROR_MESSAGE); |
2 |
26 Feb 07 |
jari |
350 |
this.radiusField.requestFocus(); |
2 |
26 Feb 07 |
jari |
351 |
this.radiusField.selectAll(); |
2 |
26 Feb 07 |
jari |
352 |
valid = false; |
2 |
26 Feb 07 |
jari |
353 |
} |
2 |
26 Feb 07 |
jari |
354 |
return valid; |
2 |
26 Feb 07 |
jari |
355 |
} |
2 |
26 Feb 07 |
jari |
356 |
|
2 |
26 Feb 07 |
jari |
357 |
/** |
2 |
26 Feb 07 |
jari |
* The class to listen to the dialog events. |
2 |
26 Feb 07 |
jari |
359 |
*/ |
2 |
26 Feb 07 |
jari |
360 |
private class Listener extends DialogListener { |
2 |
26 Feb 07 |
jari |
361 |
|
2 |
26 Feb 07 |
jari |
362 |
public void actionPerformed(ActionEvent e) { |
2 |
26 Feb 07 |
jari |
363 |
String command = e.getActionCommand(); |
2 |
26 Feb 07 |
jari |
364 |
if (command.equals("ok-command")) { |
2 |
26 Feb 07 |
jari |
365 |
int x,y; |
2 |
26 Feb 07 |
jari |
366 |
long i; |
2 |
26 Feb 07 |
jari |
367 |
float a,r; |
2 |
26 Feb 07 |
jari |
368 |
try { |
2 |
26 Feb 07 |
jari |
369 |
x = Integer.parseInt(dimXField.getText()); |
2 |
26 Feb 07 |
jari |
370 |
y = Integer.parseInt(dimYField.getText()); |
2 |
26 Feb 07 |
jari |
371 |
i = Long.parseLong(iterField.getText()); |
2 |
26 Feb 07 |
jari |
372 |
a = Float.parseFloat(alphaField.getText()); |
2 |
26 Feb 07 |
jari |
373 |
r = Float.parseFloat(radiusField.getText()); |
2 |
26 Feb 07 |
jari |
374 |
if(validInput(x,y,i,a,r)){ |
2 |
26 Feb 07 |
jari |
375 |
result = JOptionPane.OK_OPTION; |
2 |
26 Feb 07 |
jari |
376 |
dispose(); |
2 |
26 Feb 07 |
jari |
377 |
} |
2 |
26 Feb 07 |
jari |
378 |
} catch (NumberFormatException nfe) { |
2 |
26 Feb 07 |
jari |
379 |
JOptionPane.showMessageDialog(SOMInitDialog.this, "Input value " + nfe.getMessage() +" is not valid input. \nPlease enter a new value or view the parameter information help page for this algorithm.", "Input Error!", JOptionPane.ERROR_MESSAGE); |
2 |
26 Feb 07 |
jari |
380 |
result = JOptionPane.CANCEL_OPTION; |
2 |
26 Feb 07 |
jari |
381 |
} |
2 |
26 Feb 07 |
jari |
382 |
|
2 |
26 Feb 07 |
jari |
383 |
} else if (command.equals("cancel-command")) { |
2 |
26 Feb 07 |
jari |
384 |
result = JOptionPane.CANCEL_OPTION; |
2 |
26 Feb 07 |
jari |
385 |
dispose(); |
2 |
26 Feb 07 |
jari |
386 |
}else if (command.equals("reset-command")){ |
2 |
26 Feb 07 |
jari |
387 |
resetControls(); |
2 |
26 Feb 07 |
jari |
388 |
}else if(command.equals("info-command")){ |
2 |
26 Feb 07 |
jari |
389 |
HelpWindow helpWindow = new HelpWindow(SOMInitDialog.this, "SOM Initialization Dialog"); |
2 |
26 Feb 07 |
jari |
390 |
if(helpWindow.getWindowContent()){ |
2 |
26 Feb 07 |
jari |
391 |
helpWindow.setSize(450, 600); |
2 |
26 Feb 07 |
jari |
392 |
helpWindow.setLocation(); |
2 |
26 Feb 07 |
jari |
393 |
helpWindow.show(); |
2 |
26 Feb 07 |
jari |
394 |
} |
2 |
26 Feb 07 |
jari |
395 |
else{ |
2 |
26 Feb 07 |
jari |
396 |
helpWindow.dispose(); |
2 |
26 Feb 07 |
jari |
397 |
} |
2 |
26 Feb 07 |
jari |
398 |
} |
2 |
26 Feb 07 |
jari |
399 |
} |
2 |
26 Feb 07 |
jari |
400 |
|
2 |
26 Feb 07 |
jari |
401 |
public void windowClosing(WindowEvent e) { |
2 |
26 Feb 07 |
jari |
402 |
result = JOptionPane.CLOSED_OPTION; |
2 |
26 Feb 07 |
jari |
403 |
dispose(); |
2 |
26 Feb 07 |
jari |
404 |
} |
2 |
26 Feb 07 |
jari |
405 |
} |
2 |
26 Feb 07 |
jari |
406 |
|
2 |
26 Feb 07 |
jari |
407 |
public static void main(String[] args) { |
2 |
26 Feb 07 |
jari |
408 |
SOMInitDialog dlg = new SOMInitDialog(new Frame(), 0 ,0, 0, 0, 0, 1, 0, 0, "Euclidean Distance", false); |
2 |
26 Feb 07 |
jari |
409 |
dlg.showModal(); |
2 |
26 Feb 07 |
jari |
410 |
System.exit(0); |
2 |
26 Feb 07 |
jari |
411 |
} |
2 |
26 Feb 07 |
jari |
412 |
} |