import jalview.datamodel.AlignmentView;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
+import jalview.gui.ImageExporter.ImageWriterI;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
import jalview.jbgui.GPCAPanel;
+import jalview.util.ImageMaker;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.PCAModel;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
import javax.swing.JMenuItem;
import javax.swing.JRadioButtonMenuItem;
import javax.swing.event.InternalFrameAdapter;
* @author $author$
* @version $Revision$
*/
-public class PCAPanel extends GPCAPanel implements Runnable,
- IProgressIndicator
+public class PCAPanel extends GPCAPanel
+ implements Runnable, IProgressIndicator
{
private IProgressIndicator progressBar;
int top = 0;
+ private boolean working;
+
/**
* Creates a new PCAPanel object using default score model and parameters
*
*/
public PCAPanel(AlignmentPanel alignPanel)
{
- this(alignPanel, ScoreModels.getInstance()
- .getDefaultModel(!alignPanel.av.getAlignment().isNucleotide())
- .getName(), SimilarityParams.SeqSpace);
+ this(alignPanel,
+ ScoreModels.getInstance()
+ .getDefaultModel(
+ !alignPanel.av.getAlignment().isNucleotide())
+ .getName(),
+ SimilarityParams.SeqSpace);
}
/**
seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
}
- ScoreModelI scoreModel = ScoreModels.getInstance().getScoreModel(
- modelName, ap);
+ ScoreModelI scoreModel = ScoreModels.getInstance()
+ .getScoreModel(modelName, ap);
pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
params);
PaintRefresher.Register(this, av.getSequenceSetId());
{
if (!pcaModel.getScoreModelName().equals(name))
{
- ScoreModelI sm2 = ScoreModels.getInstance().getScoreModel(
- name, ap);
+ ScoreModelI sm2 = ScoreModels.getInstance()
+ .getScoreModel(name, ap);
pcaModel.setScoreModel(sm2);
Thread worker = new Thread(PCAPanel.this);
worker.start();
@Override
public void bgcolour_actionPerformed(ActionEvent e)
{
- Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_background_colour"),
- rc.bgColour);
-
- if (col != null)
+ String ttl = MessageManager.getString("label.select_background_colour");
+ ColourChooserListener listener = new ColourChooserListener()
{
- rc.bgColour = col;
- }
- rc.repaint();
+ @Override
+ public void colourSelected(Color c)
+ {
+ rc.bgColour = c;
+ rc.repaint();
+ }
+ };
+ JalviewColourChooser.showColourChooser(this, ttl, rc.bgColour,
+ listener);
}
/**
message = MessageManager.getString("label.pca_calculating");
}
progress.setProgressBar(message, progId);
+ working = true;
try
{
calcSettings.setEnabled(false);
} catch (OutOfMemoryError er)
{
new OOMWarning("calculating PCA", er);
+ working = false;
return;
} finally
{
.getString("label.principal_component_analysis"), 475, 450);
this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
}
+ working = false;
}
@Override
if (!pcaModel.isNucleotide())
{
pcaModel.setNucleotide(true);
- pcaModel.setScoreModel(ScoreModels.getInstance().getDefaultModel(
- false));
+ pcaModel.setScoreModel(
+ ScoreModels.getInstance().getDefaultModel(false));
Thread worker = new Thread(this);
worker.start();
}
if (pcaModel.isNucleotide())
{
pcaModel.setNucleotide(false);
- pcaModel.setScoreModel(ScoreModels.getInstance()
- .getDefaultModel(true));
+ pcaModel.setScoreModel(
+ ScoreModels.getInstance().getDefaultModel(true));
Thread worker = new Thread(this);
worker.start();
}
// make this an abstract function of all jalview analysis windows
if (pcaModel.getSeqtrings() == null)
{
- jalview.bin.Cache.log
- .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
+ jalview.bin.Cache.log.info(
+ "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
return;
}
// decide if av alignment is sufficiently different to original data to
// AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
- AlignmentI dataset = (av != null && av.getAlignment() != null) ? av
- .getAlignment().getDataset() : null;
+ AlignmentI dataset = (av != null && av.getAlignment() != null)
+ ? av.getAlignment().getDataset()
+ : null;
if (dataset != null)
{
al.setDataset(dataset);
{
// make a new frame!
AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
// >>>This is a fix for the moment, until a better solution is
// found!!<<<
// msaorder);
Desktop.addInternalFrame(af, MessageManager.formatMessage(
- "label.original_data_for_params",
- new String[] { this.title }), AlignFrame.DEFAULT_WIDTH,
+ "label.original_data_for_params", new String[]
+ { this.title }), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
}
}
public void run()
{
PrinterJob printJob = PrinterJob.getPrinterJob();
- PageFormat pf = printJob.pageDialog(printJob.defaultPage());
+ PageFormat defaultPage = printJob.defaultPage();
+ PageFormat pf = printJob.pageDialog(defaultPage);
+
+ if (defaultPage == pf)
+ {
+ /*
+ * user cancelled
+ */
+ return;
+ }
printJob.setPrintable(this, pf);
}
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void eps_actionPerformed(ActionEvent e)
- {
- makePCAImage(jalview.util.ImageMaker.TYPE.EPS);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void png_actionPerformed(ActionEvent e)
- {
- makePCAImage(jalview.util.ImageMaker.TYPE.PNG);
- }
-
- void makePCAImage(jalview.util.ImageMaker.TYPE type)
+ public void makePCAImage(ImageMaker.TYPE type)
{
int width = rc.getWidth();
int height = rc.getHeight();
-
- jalview.util.ImageMaker im;
-
- if (type == jalview.util.ImageMaker.TYPE.PNG)
- {
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from PCA",
- width, height, null, null, null, 0, false);
- }
- else if (type == jalview.util.ImageMaker.TYPE.EPS)
- {
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from PCA",
- width, height, null, this.getTitle(), null, 0, false);
- }
- else
- {
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
- width, height, null, this.getTitle(), null, 0, false);
-
- }
-
- if (im.getGraphics() != null)
+ ImageWriterI writer = new ImageWriterI()
{
- rc.drawBackground(im.getGraphics(), Color.black);
- rc.drawScene(im.getGraphics());
- if (rc.drawAxes == true)
+ @Override
+ public void exportImage(Graphics g) throws Exception
{
- rc.drawAxes(im.getGraphics());
+ rc.drawBackground(g, Color.black);
+ rc.drawScene(g);
+ if (rc.drawAxes)
+ {
+ rc.drawAxes(g);
+ }
}
- im.writeImage();
- }
+ };
+ String pca = MessageManager.getString("label.pca");
+ ImageExporter exporter = new ImageExporter(writer, null, type, pca);
+ exporter.doExport(null, this, width, height, pca);
}
@Override
void buildAssociatedViewMenu()
{
- AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
- .getSequenceSetId());
+ AlignmentPanel[] aps = PaintRefresher
+ .getAssociatedPanels(av.getSequenceSetId());
if (aps.length == 1 && rc.av == aps[0].av)
{
associateViewsMenu.setVisible(false);
associateViewsMenu.setVisible(true);
- if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
+ if ((viewMenu
+ .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
{
viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
}
associateViewsMenu.add(item);
}
- final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
+ final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
+ "All Views");
buttonGroup.add(itemf);
cap.setText(pcaModel.getPointsasCsv(false,
xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
zCombobox.getSelectedIndex()));
- Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.points_for_params", new String[] { this.getTitle() }),
- 500, 500);
+ Desktop.addInternalFrame(cap, MessageManager
+ .formatMessage("label.points_for_params", new String[]
+ { this.getTitle() }), 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("exporting PCA points", oom);
xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
zCombobox.getSelectedIndex()));
Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.transformed_points_for_params",
- new String[] { this.getTitle() }), 500, 500);
+ "label.transformed_points_for_params", new String[]
+ { this.getTitle() }), 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("exporting transformed PCA points", oom);
top = t;
zCombobox.setSelectedIndex(2);
}
+
+ /**
+ * Answers true if PCA calculation is in progress, else false
+ *
+ * @return
+ */
+ public boolean isWorking()
+ {
+ return working;
+ }
}
git://source.jalview.org / jalview.git / blobdiff