use of uk.ac.babraham.SeqMonk.Displays.Report.InteractionReport.InteractionReportOptions in project SeqMonk by s-andrews.
the class HeatmapProbeListWindow method actionPerformed.
/* (non-Javadoc)
* @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
*/
public void actionPerformed(ActionEvent ae) {
if (ae.getActionCommand().equals("close")) {
setVisible(false);
dispose();
} else if (ae.getActionCommand().equals("save_image")) {
ImageSaver.saveImage(heatmapPanel);
} else if (ae.getActionCommand().equals("cluster")) {
if (clusterButton.getText().equals("Cluster Interactions")) {
// First we need to make up an interaction cluster matrix which we
// can then feed to the generic hierarchical clustering program
InteractionClusterMatrix clusterMatrix = new InteractionClusterMatrix(matrix.filteredInteractions(), matrix.probeCount());
clusterMatrix.addListener(new ProgressDialog(this, "HiC Interaction Clustering", clusterMatrix));
clusterMatrix.addListener(this);
clusterMatrix.startCorrelating();
clusterButton.setEnabled(false);
} else {
matrix.setCluster(null);
saveClustersButton.setEnabled(false);
clusterButton.setText("Cluster Interactions");
}
} else if (ae.getActionCommand().equals("save_probes")) {
ProbeList newList = matrix.createProbeListFromCurrentInteractions();
// Ask for a name for the list
String groupName = null;
while (true) {
groupName = (String) JOptionPane.showInputDialog(this, "Enter list name", "Found " + newList.getAllProbes().length + " probes", JOptionPane.QUESTION_MESSAGE, null, null, newList.name());
if (groupName == null) {
// Since the list will automatically have been added to
// the ProbeList tree we actively need to delete it if
// they choose to cancel at this point.
newList.delete();
// They cancelled
return;
}
if (groupName.length() == 0)
// Try again
continue;
break;
}
newList.setName(groupName);
} else if (ae.getActionCommand().equals("save_clusters")) {
if (matrix.cluster() == null)
return;
// Get a limit for how many probes per cluster
String howManyProbes = JOptionPane.showInputDialog(this, "Minimum number of probes per cluster", "10");
if (howManyProbes == null)
return;
int minProbes;
try {
minProbes = Integer.parseInt(howManyProbes);
} catch (NumberFormatException nfe) {
JOptionPane.showMessageDialog(this, howManyProbes + " was not an integer", "Error", JOptionPane.ERROR_MESSAGE);
return;
}
ProbeList newList = matrix.createProbeListsFromClusters(minProbes, heatmapPanel.probeListPanel().currentYStartIndex(), heatmapPanel.probeListPanel().currentYEndIndex());
// This was called before clustering had completed.
if (newList == null)
return;
// Ask for a name for the list
String groupName = null;
while (true) {
groupName = (String) JOptionPane.showInputDialog(this, "Enter list name", "Found " + newList.getAllProbes().length + " probes", JOptionPane.QUESTION_MESSAGE, null, null, newList.name());
if (groupName == null) {
// Since the list will automatically have been added to
// the ProbeList tree we actively need to delete it if
// they choose to cancel at this point.
newList.delete();
// They cancelled
return;
}
if (groupName.length() == 0)
// Try again
continue;
break;
}
newList.setName(groupName);
} else if (ae.getActionCommand().equals("make_report")) {
new InteractionReportOptions(SeqMonkApplication.getInstance(), new AnnotatedInteractionReport(SeqMonkApplication.getInstance().dataCollection(), matrix));
}
}
use of uk.ac.babraham.SeqMonk.Displays.Report.InteractionReport.InteractionReportOptions in project SeqMonk by s-andrews.
the class HeatmapGenomeWindow method actionPerformed.
/* (non-Javadoc)
* @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
*/
public void actionPerformed(ActionEvent ae) {
if (ae.getActionCommand().equals("close")) {
setVisible(false);
dispose();
} else if (ae.getActionCommand().equals("save_image")) {
ImageSaver.saveImage(heatmapPanel);
} else if (ae.getActionCommand().equals("cluster")) {
if (clusterButton.getText().equals("Cluster Interactions")) {
// First we need to make up an interaction cluster matrix which we
// can then feed to the generic hierarchical clustering program
InteractionClusterMatrix clusterMatrix = new InteractionClusterMatrix(matrix.filteredInteractions(), matrix.probeCount());
clusterMatrix.addListener(new ProgressDialog(this, "HiC Interaction Clustering", clusterMatrix));
clusterMatrix.addListener(this);
clusterMatrix.startCorrelating();
clusterButton.setEnabled(false);
} else {
matrix.setCluster(null);
saveClustersButton.setEnabled(false);
clusterButton.setText("Cluster Interactions");
}
} else if (ae.getActionCommand().equals("save_probes")) {
ProbeList newList = matrix.createProbeListFromCurrentInteractions();
// Ask for a name for the list
String groupName = null;
while (true) {
groupName = (String) JOptionPane.showInputDialog(this, "Enter list name", "Found " + newList.getAllProbes().length + " probes", JOptionPane.QUESTION_MESSAGE, null, null, newList.name());
if (groupName == null) {
// Since the list will automatically have been added to
// the ProbeList tree we actively need to delete it if
// they choose to cancel at this point.
newList.delete();
// They cancelled
return;
}
if (groupName.length() == 0)
// Try again
continue;
break;
}
newList.setName(groupName);
} else if (ae.getActionCommand().equals("save_clusters")) {
if (matrix.cluster() == null)
return;
// Get a limit for how many probes per cluster
String howManyProbes = JOptionPane.showInputDialog(this, "Minimum number of probes per cluster", "10");
if (howManyProbes == null)
return;
int minProbes;
try {
minProbes = Integer.parseInt(howManyProbes);
} catch (NumberFormatException nfe) {
JOptionPane.showMessageDialog(this, howManyProbes + " was not an integer", "Error", JOptionPane.ERROR_MESSAGE);
return;
}
ProbeList newList = matrix.createProbeListsFromClusters(minProbes, heatmapPanel.genomePanel().currentYStartIndex(), heatmapPanel.genomePanel().currentYEndIndex());
// This was called before clustering had completed.
if (newList == null)
return;
// Ask for a name for the list
String groupName = null;
while (true) {
groupName = (String) JOptionPane.showInputDialog(this, "Enter list name", "Found " + newList.getAllProbes().length + " probes", JOptionPane.QUESTION_MESSAGE, null, null, newList.name());
if (groupName == null) {
// Since the list will automatically have been added to
// the ProbeList tree we actively need to delete it if
// they choose to cancel at this point.
newList.delete();
// They cancelled
return;
}
if (groupName.length() == 0)
// Try again
continue;
break;
}
newList.setName(groupName);
} else if (ae.getActionCommand().equals("send_x")) {
DisplayPreferences.getInstance().setLocation(xChr, SequenceRead.packPosition(xStart, xEnd, Location.UNKNOWN));
} else if (ae.getActionCommand().equals("send_y")) {
DisplayPreferences.getInstance().setLocation(yChr, SequenceRead.packPosition(yStart, yEnd, Location.UNKNOWN));
} else if (ae.getActionCommand().equals("match")) {
Chromosome chr = DisplayPreferences.getInstance().getCurrentChromosome();
int start = SequenceRead.start(DisplayPreferences.getInstance().getCurrentLocation());
int end = SequenceRead.end(DisplayPreferences.getInstance().getCurrentLocation());
heatmapPanel.genomePanel().setCurrentPosition(chr, start, end);
} else if (ae.getActionCommand().equals("make_report")) {
new InteractionReportOptions(SeqMonkApplication.getInstance(), new AnnotatedInteractionReport(SeqMonkApplication.getInstance().dataCollection(), matrix));
}
}
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