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/* |
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* NumberOfAlterationsViewer.java |
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* |
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* Created on May 19, 2003, 4:18 AM |
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*/ |
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|
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package org.tigr.microarray.mev.cgh.CGHGuiObj.AlgorithmResultsViewers.NumberOfAlterationsViewers; |
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|
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import java.awt.BorderLayout; |
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import java.awt.image.BufferedImage; |
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import java.beans.Expression; |
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import java.util.EventObject; |
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import java.util.Iterator; |
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import java.util.Vector; |
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|
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import javax.swing.JComponent; |
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import javax.swing.JScrollPane; |
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import javax.swing.JTable; |
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|
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import org.tigr.microarray.mev.MultipleArrayData; |
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import org.tigr.microarray.mev.cgh.CGHDataObj.ICGHDataRegion; |
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import org.tigr.microarray.mev.cgh.CGHGuiObj.GuiUtil.GenomeBrowserLauncher; |
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import org.tigr.microarray.mev.cgh.CGHListenerObj.IDataRegionSelectionListener; |
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import org.tigr.microarray.mev.cgh.CGHUtil.TableDataWriter; |
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import org.tigr.microarray.mev.cluster.gui.Experiment; |
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import org.tigr.microarray.mev.cluster.gui.ICGHDisplayMenu; |
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import org.tigr.microarray.mev.cluster.gui.IData; |
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import org.tigr.microarray.mev.cluster.gui.IDisplayMenu; |
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import org.tigr.microarray.mev.cluster.gui.IFramework; |
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import org.tigr.microarray.mev.cluster.gui.IViewer; |
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|
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/** |
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* |
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* @author Adam Margolin |
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* @author Raktim Sinha |
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*/ |
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|
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public class NumberOfAlterationsViewer extends javax.swing.JPanel implements IViewer{ |
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NumberOfAlterationsDataModel dataModel; |
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JTable resultsTable = new JTable(); |
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|
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Vector listeners = new Vector(); |
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//CGHMultipleArrayDataFcd fcd; |
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IData data; |
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|
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/** Creates new form NumberOfAlterationsViewer */ |
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public NumberOfAlterationsViewer() { |
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initComponents(); |
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initCustomComponents(); |
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} |
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|
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/** This method is called from within the constructor to |
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* initialize the form. |
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* WARNING: Do NOT modify this code. The content of this method is |
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* always regenerated by the Form Editor. |
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*/ |
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private void initComponents() {//GEN-BEGIN:initComponents |
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menubar = new javax.swing.JMenuBar(); |
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mnuFile = new javax.swing.JMenu(); |
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itmSave = new javax.swing.JMenuItem(); |
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mnuAnnotations = new javax.swing.JMenu(); |
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itmAnnotateSelected = new javax.swing.JMenuItem(); |
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mnuLinks = new javax.swing.JMenu(); |
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btnEnsembl = new javax.swing.JMenuItem(); |
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btnGoldenPath = new javax.swing.JMenuItem(); |
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btnNcbi = new javax.swing.JMenuItem(); |
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|
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mnuFile.setText("File"); |
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itmSave.setText("Save"); |
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itmSave.addActionListener(new java.awt.event.ActionListener() { |
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public void actionPerformed(java.awt.event.ActionEvent evt) { |
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itmSaveActionPerformed(evt); |
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} |
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}); |
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|
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mnuFile.add(itmSave); |
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menubar.add(mnuFile); |
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mnuAnnotations.setText("Annotations"); |
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itmAnnotateSelected.setText("Annotate Selected"); |
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itmAnnotateSelected.addActionListener(new java.awt.event.ActionListener() { |
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public void actionPerformed(java.awt.event.ActionEvent evt) { |
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itmAnnotateSelectedActionPerformed(evt); |
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} |
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}); |
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|
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mnuAnnotations.add(itmAnnotateSelected); |
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menubar.add(mnuAnnotations); |
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mnuLinks.setText("Links"); |
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btnEnsembl.setText("Ensembl"); |
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btnEnsembl.addActionListener(new java.awt.event.ActionListener() { |
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public void actionPerformed(java.awt.event.ActionEvent evt) { |
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btnEnsemblActionPerformed(evt); |
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} |
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}); |
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|
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mnuLinks.add(btnEnsembl); |
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btnGoldenPath.setText("Golden Path"); |
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btnGoldenPath.addActionListener(new java.awt.event.ActionListener() { |
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public void actionPerformed(java.awt.event.ActionEvent evt) { |
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btnGoldenPathActionPerformed(evt); |
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} |
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}); |
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mnuLinks.add(btnGoldenPath); |
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|
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btnNcbi.setText("NCBI"); |
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btnNcbi.addActionListener(new java.awt.event.ActionListener() { |
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public void actionPerformed(java.awt.event.ActionEvent evt) { |
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btnNCBIActionPerformed(evt); |
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} |
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}); |
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mnuLinks.add(btnNcbi); |
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|
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menubar.add(mnuLinks); |
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|
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setLayout(new java.awt.BorderLayout()); |
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|
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}//GEN-END:initComponents |
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|
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|
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private void btnNCBIActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_btnGoldenPathActionPerformed |
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// Add your handling code here: |
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int[] selectedRow = resultsTable.getSelectedRows(); |
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|
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if(selectedRow.length != 0){ |
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ICGHDataRegion[] dataRegions = dataModel.getDataRegionAt(selectedRow); |
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GenomeBrowserLauncher.launchNCBIMapViewer(dataRegions, data.getCGHSpecies()); |
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} |
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}//GEN-LAST:event_btnGoldenPathActionPerformed |
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|
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private void btnGoldenPathActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_btnGoldenPathActionPerformed |
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// Add your handling code here: |
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int selectedRow = resultsTable.getSelectedRow(); |
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if(selectedRow != -1){ |
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ICGHDataRegion dataRegion = dataModel.getDataRegionAt(selectedRow); |
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GenomeBrowserLauncher.launchGoldenPath(dataRegion, data.getCGHSpecies()); |
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} |
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}//GEN-LAST:event_btnGoldenPathActionPerformed |
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|
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private void btnEnsemblActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_btnEnsemblActionPerformed |
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// Add your handling code here: |
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int selectedRow = resultsTable.getSelectedRow(); |
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if(selectedRow != -1){ |
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ICGHDataRegion dataRegion = dataModel.getDataRegionAt(selectedRow); |
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GenomeBrowserLauncher.launchEnsembl(dataRegion, data.getCGHSpecies()); |
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} |
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}//GEN-LAST:event_btnEnsemblActionPerformed |
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|
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private void itmSaveActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_itmSaveActionPerformed |
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// Add your handling code here: |
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TableDataWriter writer = new TableDataWriter(); |
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writer.writeTable(dataModel); |
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}//GEN-LAST:event_itmSaveActionPerformed |
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|
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private void itmAnnotateSelectedActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_itmAnnotateSelectedActionPerformed |
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// Add your handling code here: |
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//ICGHDataRegion[] AnnotationRegions = new AnnotationRegion[fcd.getData().getNumChromosomes()]; |
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Vector[] vecAnnotationRegions = new Vector[data.getNumChromosomes()]; |
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for(int i = 0; i < vecAnnotationRegions.length; i++){ |
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vecAnnotationRegions[i] = new Vector(); |
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} |
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|
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int[] selectedRows = resultsTable.getSelectedRows(); |
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|
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for(int i = 0; i < selectedRows.length; i++){ |
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ICGHDataRegion dataRegion = dataModel.getDataRegionAt(selectedRows[i]); |
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int chromosomeIndex = dataRegion.getChromosomeIndex(); |
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vecAnnotationRegions[chromosomeIndex].add(dataRegion); |
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} |
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|
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//ICGHDataRegion[][] annotationRegions = new ICGHDataRegion[fcd.getData().getNumChromosomes()][]; |
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ICGHDataRegion[][] annotationRegions = new ICGHDataRegion[data.getNumChromosomes()][]; |
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for(int i = 0; i < annotationRegions.length; i++){ |
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Vector chromRegions = vecAnnotationRegions[i]; |
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annotationRegions[i] = new ICGHDataRegion[chromRegions.size()]; |
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for(int j = 0; j < chromRegions.size(); j++){ |
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annotationRegions[i][j] = (ICGHDataRegion)chromRegions.get(j); |
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} |
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} |
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|
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((MultipleArrayData)data).setAnnotations(annotationRegions); |
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fireAnnotationsSelected(new EventObject(annotationRegions)); |
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|
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}//GEN-LAST:event_itmAnnotateSelectedActionPerformed |
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|
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private void fireAnnotationsSelected(EventObject eventObject){ |
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Iterator it = listeners.iterator(); |
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while(it.hasNext()){ |
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Object obj = it.next(); |
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if(obj instanceof IDataRegionSelectionListener){ |
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((IDataRegionSelectionListener)obj).onAnnotationsSelected(eventObject); |
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} |
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} |
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} |
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|
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private void initCustomComponents(){ |
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setLayout(new BorderLayout()); |
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JScrollPane scrResults = new JScrollPane(); |
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scrResults.setViewportView(resultsTable); |
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add(scrResults, BorderLayout.CENTER); |
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|
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} |
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|
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/** Returns a component to be inserted into scroll pane view port. |
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*/ |
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public JComponent getContentComponent() { |
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return this; |
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} |
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|
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/** Returns a component to be inserted into scroll pane header. |
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*/ |
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public JComponent getHeaderComponent() { |
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return menubar; |
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} |
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|
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/** Invoked by the framework to save or to print viewer image. |
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*/ |
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public BufferedImage getImage() { |
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return null; |
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} |
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|
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/** Invoked when the framework is going to be closed. |
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*/ |
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public void onClosed() { |
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} |
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|
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/** Invoked by the framework when data is changed, |
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* if this viewer is selected. |
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* @see IData |
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*/ |
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public void onDataChanged(IData data) { |
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} |
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|
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/** Invoked by the framework when this viewer was deselected. |
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*/ |
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public void onDeselected() { |
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} |
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|
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/** Invoked by the framework when display menu is changed, |
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* if this viewer is selected. |
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* @see IDisplayMenu |
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*/ |
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public void onMenuChanged(IDisplayMenu menu) { |
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} |
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|
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public void onMenuChanged(ICGHDisplayMenu menu) { |
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} |
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|
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/** Invoked by the framework when this viewer is selected. |
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*/ |
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public void onSelected(IFramework framework) { |
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} |
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|
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public void onThresholdsChanged(ICGHDisplayMenu menu) { |
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} |
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|
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/** Getter for property dataModel. |
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* @return Value of property dataModel. |
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*/ |
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public NumberOfAlterationsDataModel getDataModel() { |
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return dataModel; |
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} |
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|
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/** Setter for property dataModel. |
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* @param dataModel New value of property dataModel. |
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*/ |
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public void setDataModel(NumberOfAlterationsDataModel dataModel) { |
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this.dataModel = dataModel; |
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resultsTable.setModel(dataModel); |
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} |
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|
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26 Feb 07 |
jari |
/** Getter for property fcd. |
2 |
26 Feb 07 |
jari |
* @return Value of property fcd. |
2 |
26 Feb 07 |
jari |
273 |
|
2 |
26 Feb 07 |
jari |
public CGHMultipleArrayDataFcd getFcd() { |
2 |
26 Feb 07 |
jari |
return fcd; |
2 |
26 Feb 07 |
jari |
276 |
} |
2 |
26 Feb 07 |
jari |
277 |
*/ |
2 |
26 Feb 07 |
jari |
278 |
|
2 |
26 Feb 07 |
jari |
279 |
public IData getData() { |
2 |
26 Feb 07 |
jari |
280 |
return data; |
2 |
26 Feb 07 |
jari |
281 |
} |
2 |
26 Feb 07 |
jari |
/** Setter for property fcd. |
2 |
26 Feb 07 |
jari |
* @param fcd New value of property fcd. |
2 |
26 Feb 07 |
jari |
284 |
|
2 |
26 Feb 07 |
jari |
public void setFcd(CGHMultipleArrayDataFcd fcd) { |
2 |
26 Feb 07 |
jari |
this.fcd = fcd; |
2 |
26 Feb 07 |
jari |
287 |
} |
2 |
26 Feb 07 |
jari |
288 |
*/ |
2 |
26 Feb 07 |
jari |
289 |
|
2 |
26 Feb 07 |
jari |
290 |
public void setData(IData dat){ |
2 |
26 Feb 07 |
jari |
291 |
data = dat; |
2 |
26 Feb 07 |
jari |
292 |
} |
2 |
26 Feb 07 |
jari |
293 |
public void addDrsListener(IDataRegionSelectionListener listener){ |
2 |
26 Feb 07 |
jari |
294 |
this.listeners.add(listener); |
2 |
26 Feb 07 |
jari |
295 |
} |
2 |
26 Feb 07 |
jari |
296 |
|
2 |
26 Feb 07 |
jari |
// Variables declaration - do not modify//GEN-BEGIN:variables |
2 |
26 Feb 07 |
jari |
298 |
private javax.swing.JMenu mnuAnnotations; |
2 |
26 Feb 07 |
jari |
299 |
private javax.swing.JMenuBar menubar; |
2 |
26 Feb 07 |
jari |
300 |
private javax.swing.JMenu mnuLinks; |
2 |
26 Feb 07 |
jari |
301 |
private javax.swing.JMenuItem btnEnsembl; |
2 |
26 Feb 07 |
jari |
302 |
private javax.swing.JMenuItem btnGoldenPath; |
2 |
26 Feb 07 |
jari |
303 |
private javax.swing.JMenuItem btnNcbi; |
2 |
26 Feb 07 |
jari |
304 |
private javax.swing.JMenuItem itmSave; |
2 |
26 Feb 07 |
jari |
305 |
private javax.swing.JMenuItem itmAnnotateSelected; |
2 |
26 Feb 07 |
jari |
306 |
private javax.swing.JMenu mnuFile; |
2 |
26 Feb 07 |
jari |
// End of variables declaration//GEN-END:variables |
2 |
26 Feb 07 |
jari |
308 |
|
2 |
26 Feb 07 |
jari |
309 |
public JComponent getRowHeaderComponent() { |
2 |
26 Feb 07 |
jari |
// TODO Auto-generated method stub |
2 |
26 Feb 07 |
jari |
311 |
return null; |
2 |
26 Feb 07 |
jari |
312 |
} |
2 |
26 Feb 07 |
jari |
313 |
|
2 |
26 Feb 07 |
jari |
314 |
public JComponent getCornerComponent(int cornerIndex) { |
2 |
26 Feb 07 |
jari |
// TODO Auto-generated method stub |
2 |
26 Feb 07 |
jari |
316 |
return null; |
2 |
26 Feb 07 |
jari |
317 |
} |
2 |
26 Feb 07 |
jari |
318 |
|
2 |
26 Feb 07 |
jari |
319 |
public int[][] getClusters() { |
2 |
26 Feb 07 |
jari |
// TODO Auto-generated method stub |
2 |
26 Feb 07 |
jari |
321 |
return null; |
2 |
26 Feb 07 |
jari |
322 |
} |
2 |
26 Feb 07 |
jari |
323 |
|
2 |
26 Feb 07 |
jari |
324 |
public Experiment getExperiment() { |
2 |
26 Feb 07 |
jari |
// TODO Auto-generated method stub |
2 |
26 Feb 07 |
jari |
326 |
return null; |
2 |
26 Feb 07 |
jari |
327 |
} |
2 |
26 Feb 07 |
jari |
328 |
|
2 |
26 Feb 07 |
jari |
329 |
public int getViewerType() { |
2 |
26 Feb 07 |
jari |
// TODO Auto-generated method stub |
2 |
26 Feb 07 |
jari |
331 |
return 0; |
2 |
26 Feb 07 |
jari |
332 |
} |
2 |
26 Feb 07 |
jari |
333 |
|
2 |
26 Feb 07 |
jari |
/* (non-Javadoc) |
2 |
26 Feb 07 |
jari |
* @see org.tigr.microarray.mev.cluster.gui.IViewer#setExperiment(org.tigr.microarray.mev.cluster.gui.Experiment) |
2 |
26 Feb 07 |
jari |
336 |
*/ |
2 |
26 Feb 07 |
jari |
337 |
public void setExperiment(Experiment e) { |
2 |
26 Feb 07 |
jari |
// TODO Auto-generated method stub |
2 |
26 Feb 07 |
jari |
339 |
|
2 |
26 Feb 07 |
jari |
340 |
} |
2 |
26 Feb 07 |
jari |
341 |
|
2 |
26 Feb 07 |
jari |
/* (non-Javadoc) |
2 |
26 Feb 07 |
jari |
* @see org.tigr.microarray.mev.cluster.gui.IViewer#getExperimentID() |
2 |
26 Feb 07 |
jari |
344 |
*/ |
2 |
26 Feb 07 |
jari |
345 |
public int getExperimentID() { |
2 |
26 Feb 07 |
jari |
// TODO Auto-generated method stub |
2 |
26 Feb 07 |
jari |
347 |
return 0; |
2 |
26 Feb 07 |
jari |
348 |
} |
2 |
26 Feb 07 |
jari |
349 |
|
2 |
26 Feb 07 |
jari |
/* (non-Javadoc) |
2 |
26 Feb 07 |
jari |
* @see org.tigr.microarray.mev.cluster.gui.IViewer#setExperimentID(int) |
2 |
26 Feb 07 |
jari |
352 |
*/ |
2 |
26 Feb 07 |
jari |
353 |
public void setExperimentID(int id) { |
2 |
26 Feb 07 |
jari |
// TODO Auto-generated method stub |
2 |
26 Feb 07 |
jari |
355 |
|
2 |
26 Feb 07 |
jari |
356 |
} |
2 |
26 Feb 07 |
jari |
357 |
|
2 |
26 Feb 07 |
jari |
/* (non-Javadoc) |
2 |
26 Feb 07 |
jari |
* @see org.tigr.microarray.mev.cluster.gui.IViewer#getExpression() |
2 |
26 Feb 07 |
jari |
360 |
*/ |
2 |
26 Feb 07 |
jari |
361 |
public Expression getExpression() { |
2 |
26 Feb 07 |
jari |
// TODO Auto-generated method stub |
2 |
26 Feb 07 |
jari |
363 |
return null; |
2 |
26 Feb 07 |
jari |
364 |
} |
2 |
26 Feb 07 |
jari |
365 |
|
2 |
26 Feb 07 |
jari |
366 |
} |