*/
package jalview.gui;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
+import jalview.bin.Cache;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SeqCigar;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
import jalview.jbgui.GPCAPanel;
-import jalview.schemes.ResidueProperties;
+import jalview.math.RotatableMatrix.Axis;
+import jalview.util.ImageMaker;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.PCAModel;
import java.awt.BorderLayout;
import java.awt.Color;
+import java.awt.Dimension;
import java.awt.Graphics;
-import java.awt.GridLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.print.PageFormat;
import java.awt.print.Printable;
import java.awt.print.PrinterException;
import java.awt.print.PrinterJob;
-import java.util.Hashtable;
import javax.swing.ButtonGroup;
-import javax.swing.JButton;
-import javax.swing.JCheckBoxMenuItem;
import javax.swing.JColorChooser;
-import javax.swing.JLabel;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JProgressBar;
import javax.swing.JRadioButtonMenuItem;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
+ * The panel holding the Principal Component Analysis 3-D visualisation
*/
-public class PCAPanel extends GPCAPanel implements Runnable,
- IProgressIndicator
+public class PCAPanel extends GPCAPanel
+ implements Runnable, IProgressIndicator
{
+ private static final int MIN_WIDTH = 470;
+
+ private static final int MIN_HEIGHT = 250;
RotatableCanvas rc;
AlignmentPanel ap;
- AlignViewport av;
+ AlignmentViewport av;
PCAModel pcaModel;
int top = 0;
+ private IProgressIndicator progressBar;
+
+ private boolean working;
+
/**
- * Creates a new PCAPanel object.
+ * Constructor given sequence data, a similarity (or distance) score model
+ * name, and score calculation parameters
*
- * @param av
- * DOCUMENT ME!
- * @param s
- * DOCUMENT ME!
+ * @param alignPanel
+ * @param modelName
+ * @param params
*/
- public PCAPanel(AlignmentPanel ap)
+ public PCAPanel(AlignmentPanel alignPanel, String modelName,
+ SimilarityParamsI params)
{
- this.av = ap.av;
- this.ap = ap;
+ super();
+ this.av = alignPanel.av;
+ this.ap = alignPanel;
+ boolean nucleotide = av.getAlignment().isNucleotide();
+
+ progressBar = new ProgressBar(statusPanel, statusBar);
+
+ addInternalFrameListener(new InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(InternalFrameEvent e)
+ {
+ close_actionPerformed();
+ }
+ });
- boolean sameLength = true;
boolean selected = av.getSelectionGroup() != null
&& av.getSelectionGroup().getSize() > 0;
AlignmentView seqstrings = av.getAlignmentView(selected);
- boolean nucleotide = av.getAlignment().isNucleotide();
SequenceI[] seqs;
if (!selected)
{
{
seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
}
- SeqCigar sq[] = seqstrings.getSequences();
- int length = sq[0].getWidth();
-
- for (int i = 0; i < seqs.length; i++)
- {
- if (sq[i].getWidth() != length)
- {
- sameLength = false;
- break;
- }
- }
-
- if (!sameLength)
- {
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager.getString("label.pca_sequences_not_aligned"),
- MessageManager.getString("label.sequences_not_aligned"), JOptionPane.WARNING_MESSAGE);
- return;
- }
- pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
+ ScoreModelI scoreModel = ScoreModels.getInstance()
+ .getScoreModel(modelName, ap);
+ pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
+ params);
PaintRefresher.Register(this, av.getSequenceSetId());
- rc = new RotatableCanvas(ap);
+ rc = new RotatableCanvas(alignPanel);
this.getContentPane().add(rc, BorderLayout.CENTER);
- Thread worker = new Thread(this);
- worker.start();
+
+ addKeyListener(rc);
+ validate();
+
+ this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
}
- @Override
- protected void scoreMatrix_menuSelected()
+ /**
+ * Ensure references to potentially very large objects (the PCA matrices) are
+ * nulled when the frame is closed
+ */
+ protected void close_actionPerformed()
{
- scoreMatrixMenu.removeAll();
- for (final String sm : ResidueProperties.scoreMatrices.keySet())
- {
- if (ResidueProperties.getScoreMatrix(sm) != null)
- {
- // create an entry for this score matrix for use in PCA
- JCheckBoxMenuItem jm = new JCheckBoxMenuItem();
- jm.setText(MessageManager
- .getStringOrReturn("label.score_model", sm));
- jm.setSelected(pcaModel.getScore_matrix().equals(sm));
- if ((ResidueProperties.scoreMatrices.get(sm).isDNA() && ResidueProperties.scoreMatrices
- .get(sm).isProtein())
- || pcaModel.isNucleotide() == ResidueProperties.scoreMatrices
- .get(sm).isDNA())
- {
- final PCAPanel us = this;
- jm.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- if (!pcaModel.getScore_matrix().equals(sm))
- {
- pcaModel.setScore_matrix(sm);
- Thread worker = new Thread(us);
- worker.start();
- }
- }
- });
- scoreMatrixMenu.add(jm);
- }
- }
- }
+ pcaModel = null;
}
- public void bgcolour_actionPerformed(ActionEvent e)
+ @Override
+ protected void bgcolour_actionPerformed()
{
- Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_backgroud_colour"),
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_background_colour"),
rc.bgColour);
if (col != null)
}
/**
- * DOCUMENT ME!
+ * Calculates the PCA and displays the results
*/
+ @Override
public void run()
{
+ working = true;
long progId = System.currentTimeMillis();
IProgressIndicator progress = this;
String message = MessageManager.getString("label.pca_recalculating");
progress.setProgressBar(message, progId);
try
{
- calcSettings.setEnabled(false);
- pcaModel.run();
- // ////////////////
+ pcaModel.calculate();
+
xCombobox.setSelectedIndex(0);
yCombobox.setSelectedIndex(1);
zCombobox.setSelectedIndex(2);
pcaModel.updateRc(rc);
// rc.invalidate();
- nuclSetting.setSelected(pcaModel.isNucleotide());
- protSetting.setSelected(!pcaModel.isNucleotide());
- jvVersionSetting.setSelected(pcaModel.isJvCalcMode());
top = pcaModel.getTop();
} catch (OutOfMemoryError er)
{
new OOMWarning("calculating PCA", er);
+ working = false;
return;
} finally
{
progress.setProgressBar("", progId);
}
- calcSettings.setEnabled(true);
+
repaint();
if (getParent() == null)
{
- addKeyListener(rc);
- Desktop.addInternalFrame(this, MessageManager
- .getString("label.principal_component_analysis"), 475, 450);
- }
- }
-
- @Override
- protected void nuclSetting_actionPerfomed(ActionEvent arg0)
- {
- if (!pcaModel.isNucleotide())
- {
- pcaModel.setNucleotide(true);
- pcaModel.setScore_matrix("DNA");
- Thread worker = new Thread(this);
- worker.start();
+ Desktop.addInternalFrame(this,
+ MessageManager.formatMessage("label.calc_title", "PCA",
+ pcaModel.getScoreModelName()),
+ 475, 450);
}
-
- }
-
- @Override
- protected void protSetting_actionPerfomed(ActionEvent arg0)
- {
-
- if (pcaModel.isNucleotide())
- {
- pcaModel.setNucleotide(false);
- pcaModel.setScore_matrix("BLOSUM62");
- Thread worker = new Thread(this);
- worker.start();
- }
- }
-
- @Override
- protected void jvVersionSetting_actionPerfomed(ActionEvent arg0)
- {
- pcaModel.setJvCalcMode(jvVersionSetting.isSelected());
- Thread worker = new Thread(this);
- worker.start();
+ working = false;
}
/**
- * DOCUMENT ME!
+ * Updates the PCA display after a change of component to use for x, y or z
+ * axis
*/
- void doDimensionChange()
+ @Override
+ protected void doDimensionChange()
{
if (top == 0)
{
int dim2 = top - yCombobox.getSelectedIndex();
int dim3 = top - zCombobox.getSelectedIndex();
pcaModel.updateRcView(dim1, dim2, dim3);
- rc.img = null;
- rc.rotmat.setIdentity();
- rc.initAxes();
- rc.paint(rc.getGraphics());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void xCombobox_actionPerformed(ActionEvent e)
- {
- doDimensionChange();
+ rc.resetView();
}
/**
- * DOCUMENT ME!
+ * Sets the selected checkbox item index for PCA dimension (1, 2, 3...) for
+ * the given axis (X/Y/Z)
*
- * @param e
- * DOCUMENT ME!
+ * @param index
+ * @param axis
*/
- protected void yCombobox_actionPerformed(ActionEvent e)
+ public void setSelectedDimensionIndex(int index, Axis axis)
{
- doDimensionChange();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void zCombobox_actionPerformed(ActionEvent e)
- {
- doDimensionChange();
+ switch (axis)
+ {
+ case X:
+ xCombobox.setSelectedIndex(index);
+ break;
+ case Y:
+ yCombobox.setSelectedIndex(index);
+ break;
+ case Z:
+ zCombobox.setSelectedIndex(index);
+ break;
+ default:
+ }
}
- public void outputValues_actionPerformed(ActionEvent e)
+ @Override
+ protected void outputValues_actionPerformed()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
try
}
}
- public void showLabels_actionPerformed(ActionEvent e)
+ @Override
+ protected void showLabels_actionPerformed()
{
rc.showLabels(showLabels.getState());
}
- public void print_actionPerformed(ActionEvent e)
+ @Override
+ protected void print_actionPerformed()
{
PCAPrinter printer = new PCAPrinter();
printer.start();
}
- public void originalSeqData_actionPerformed(ActionEvent e)
+ /**
+ * If available, shows the data which formed the inputs for the PCA as a new
+ * alignment
+ */
+ @Override
+ public void originalSeqData_actionPerformed()
{
- // this was cut'n'pasted from the equivalent TreePanel method - we should
- // make this an abstract function of all jalview analysis windows
- if (pcaModel.getSeqtrings() == null)
+ // JAL-2647 disabled after load from project (until save to project done)
+ if (pcaModel.getInputData() == null)
{
- jalview.bin.Cache.log
- .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
+ 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
// warrant a new window to be created
- // create new alignmnt window with hidden regions (unhiding hidden regions
+ // create new alignment window with hidden regions (unhiding hidden regions
// yields unaligned seqs)
// or create a selection box around columns in alignment view
// test Alignment(SeqCigar[])
} catch (Exception ex)
{
}
- ;
- Object[] alAndColsel = pcaModel.getSeqtrings()
- .getAlignmentAndColumnSelection(gc);
+
+ Object[] alAndColsel = pcaModel.getInputData()
+ .getAlignmentAndHiddenColumns(gc);
if (alAndColsel != null && alAndColsel[0] != null)
{
// AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
- Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
- Alignment dataset = (av != null && av.getAlignment() != null) ? av
- .getAlignment().getDataset() : null;
+ AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
+ AlignmentI dataset = (av != null && av.getAlignment() != null)
+ ? av.getAlignment().getDataset()
+ : null;
if (dataset != null)
{
al.setDataset(dataset);
if (true)
{
// make a new frame!
- AlignFrame af = new AlignFrame(al,
- (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
// >>>This is a fix for the moment, until a better solution is
// found!!<<<
class PCAPrinter extends Thread implements Printable
{
+ @Override
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);
}
}
+ @Override
public int print(Graphics pg, PageFormat pf, int pi)
throws PrinterException
{
pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
- rc.drawBackground(pg, rc.bgColour);
+ rc.drawBackground(pg);
rc.drawScene(pg);
- if (rc.drawAxes == true)
+ if (rc.drawAxes)
{
rc.drawAxes(pg);
}
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Handler for 'Save as EPS' option
*/
- public void eps_actionPerformed(ActionEvent e)
+ @Override
+ protected void eps_actionPerformed()
{
- makePCAImage(jalview.util.ImageMaker.TYPE.EPS);
+ makePCAImage(ImageMaker.TYPE.EPS);
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Handler for 'Save as PNG' option
*/
- public void png_actionPerformed(ActionEvent e)
+ @Override
+ protected void png_actionPerformed()
{
- makePCAImage(jalview.util.ImageMaker.TYPE.PNG);
+ makePCAImage(ImageMaker.TYPE.PNG);
}
- void makePCAImage(jalview.util.ImageMaker.TYPE type)
+ void makePCAImage(ImageMaker.TYPE type)
{
int width = rc.getWidth();
int height = rc.getHeight();
- jalview.util.ImageMaker im;
+ 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);
- }
- else if (type == jalview.util.ImageMaker.TYPE.EPS)
+ switch (type)
{
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.EPS,
+ case PNG:
+ im = new ImageMaker(this, ImageMaker.TYPE.PNG,
+ "Make PNG image from PCA", width, height, null, null, null, 0,
+ false);
+ break;
+ case EPS:
+ im = new ImageMaker(this, ImageMaker.TYPE.EPS,
"Make EPS file from PCA", width, height, null,
- this.getTitle());
- }
- else
- {
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
- width, height, null, this.getTitle());
-
+ this.getTitle(), null, 0, false);
+ break;
+ default:
+ im = new ImageMaker(this, ImageMaker.TYPE.SVG,
+ "Make SVG file from PCA", width, height, null,
+ this.getTitle(), null, 0, false);
}
if (im.getGraphics() != null)
{
- rc.drawBackground(im.getGraphics(), Color.black);
+ rc.drawBackground(im.getGraphics());
rc.drawScene(im.getGraphics());
- if (rc.drawAxes == true)
+ if (rc.drawAxes)
{
rc.drawAxes(im.getGraphics());
}
}
}
- public void viewMenu_menuSelected()
+ @Override
+ protected void viewMenu_menuSelected()
{
buildAssociatedViewMenu();
}
+ /**
+ * Builds the menu showing the choice of possible views (for the associated
+ * sequence data) to which the PCA may be linked
+ */
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);
}
JRadioButtonMenuItem item;
ButtonGroup buttonGroup = new ButtonGroup();
- int i, iSize = aps.length;
- final PCAPanel thisPCAPanel = this;
- for (i = 0; i < iSize; i++)
+ int iSize = aps.length;
+
+ for (int i = 0; i < iSize; i++)
{
final AlignmentPanel ap = aps[i];
- item = new JRadioButtonMenuItem(ap.av.viewName, ap.av == rc.av);
+ item = new JRadioButtonMenuItem(ap.av.getViewName(), ap.av == rc.av);
buttonGroup.add(item);
item.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
rc.applyToAllViews = false;
- rc.av = ap.av;
- rc.ap = ap;
- PaintRefresher.Register(thisPCAPanel, ap.av.getSequenceSetId());
+ rc.av = panel.av;
+ rc.ap = panel;
+ PaintRefresher.Register(PCAPanel.this,
+ panel.av.getSequenceSetId());
}
});
associateViewsMenu.add(item);
}
- final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
+ final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
+ "All Views");
buttonGroup.add(itemf);
itemf.setSelected(rc.applyToAllViews);
itemf.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
rc.applyToAllViews = itemf.isSelected();
* jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
* )
*/
- protected void outputPoints_actionPerformed(ActionEvent e)
+ @Override
+ protected void outputPoints_actionPerformed()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
try
cap.setText(pcaModel.getPointsasCsv(false,
xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
zCombobox.getSelectedIndex()));
- Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.points_for_params", new String[]
+ Desktop.addInternalFrame(cap, MessageManager
+ .formatMessage("label.points_for_params", new String[]
{ this.getTitle() }), 500, 500);
} catch (OutOfMemoryError oom)
{
* jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
* .ActionEvent)
*/
- protected void outputProjPoints_actionPerformed(ActionEvent e)
+ @Override
+ protected void outputProjPoints_actionPerformed()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
try
}
}
- // methods for implementing IProgressIndicator
- // need to refactor to a reusable stub class
- Hashtable progressBars, progressBarHandlers;
-
/*
* (non-Javadoc)
*
@Override
public void setProgressBar(String message, long id)
{
- if (progressBars == null)
- {
- progressBars = new Hashtable();
- progressBarHandlers = new Hashtable();
- }
-
- JPanel progressPanel;
- Long lId = new Long(id);
- GridLayout layout = (GridLayout) statusPanel.getLayout();
- if (progressBars.get(lId) != null)
- {
- progressPanel = (JPanel) progressBars.get(new Long(id));
- statusPanel.remove(progressPanel);
- progressBars.remove(lId);
- progressPanel = null;
- if (message != null)
- {
- statusBar.setText(message);
- }
- if (progressBarHandlers.contains(lId))
- {
- progressBarHandlers.remove(lId);
- }
- layout.setRows(layout.getRows() - 1);
- }
- else
- {
- progressPanel = new JPanel(new BorderLayout(10, 5));
-
- JProgressBar progressBar = new JProgressBar();
- progressBar.setIndeterminate(true);
-
- progressPanel.add(new JLabel(message), BorderLayout.WEST);
- progressPanel.add(progressBar, BorderLayout.CENTER);
-
- layout.setRows(layout.getRows() + 1);
- statusPanel.add(progressPanel);
-
- progressBars.put(lId, progressPanel);
- }
- // update GUI
- // setMenusForViewport();
- validate();
+ progressBar.setProgressBar(message, id);
+ // if (progressBars == null)
+ // {
+ // progressBars = new Hashtable();
+ // progressBarHandlers = new Hashtable();
+ // }
+ //
+ // JPanel progressPanel;
+ // Long lId = new Long(id);
+ // GridLayout layout = (GridLayout) statusPanel.getLayout();
+ // if (progressBars.get(lId) != null)
+ // {
+ // progressPanel = (JPanel) progressBars.get(new Long(id));
+ // statusPanel.remove(progressPanel);
+ // progressBars.remove(lId);
+ // progressPanel = null;
+ // if (message != null)
+ // {
+ // statusBar.setText(message);
+ // }
+ // if (progressBarHandlers.contains(lId))
+ // {
+ // progressBarHandlers.remove(lId);
+ // }
+ // layout.setRows(layout.getRows() - 1);
+ // }
+ // else
+ // {
+ // progressPanel = new JPanel(new BorderLayout(10, 5));
+ //
+ // JProgressBar progressBar = new JProgressBar();
+ // progressBar.setIndeterminate(true);
+ //
+ // progressPanel.add(new JLabel(message), BorderLayout.WEST);
+ // progressPanel.add(progressBar, BorderLayout.CENTER);
+ //
+ // layout.setRows(layout.getRows() + 1);
+ // statusPanel.add(progressPanel);
+ //
+ // progressBars.put(lId, progressPanel);
+ // }
+ // // update GUI
+ // // setMenusForViewport();
+ // validate();
}
@Override
public void registerHandler(final long id,
final IProgressIndicatorHandler handler)
{
- if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
- {
- throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
- }
- progressBarHandlers.put(new Long(id), handler);
- final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
- if (handler.canCancel())
- {
- JButton cancel = new JButton(
- MessageManager.getString("action.cancel"));
- final IProgressIndicator us = this;
- cancel.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- handler.cancelActivity(id);
- us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
- }
- });
- progressPanel.add(cancel, BorderLayout.EAST);
- }
+ progressBar.registerHandler(id, handler);
+ // if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
+ // {
+ // throw new
+ // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
+ // }
+ // progressBarHandlers.put(new Long(id), handler);
+ // final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
+ // if (handler.canCancel())
+ // {
+ // JButton cancel = new JButton(
+ // MessageManager.getString("action.cancel"));
+ // final IProgressIndicator us = this;
+ // cancel.addActionListener(new ActionListener()
+ // {
+ //
+ // @Override
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // handler.cancelActivity(id);
+ // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
+ // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
+ // }
+ // });
+ // progressPanel.add(cancel, BorderLayout.EAST);
+ // }
}
/**
@Override
public boolean operationInProgress()
{
- if (progressBars != null && progressBars.size() > 0)
- {
- return true;
- }
- return false;
+ return progressBar.operationInProgress();
}
@Override
- protected void resetButton_actionPerformed(ActionEvent e)
+ protected void resetButton_actionPerformed()
{
int t = top;
top = 0; // ugly - prevents dimensionChanged events from being processed
top = t;
zCombobox.setSelectedIndex(2);
}
+
+ /**
+ * Answers true if PCA calculation is in progress, else false
+ *
+ * @return
+ */
+ public boolean isWorking()
+ {
+ return working;
+ }
+
+ /**
+ * Answers the selected checkbox item index for PCA dimension for the X, Y or
+ * Z axis of the display
+ *
+ * @param axis
+ * @return
+ */
+ public int getSelectedDimensionIndex(Axis axis)
+ {
+ switch (axis)
+ {
+ case X:
+ return xCombobox.getSelectedIndex();
+ case Y:
+ return yCombobox.getSelectedIndex();
+ default:
+ return zCombobox.getSelectedIndex();
+ }
+ }
+
+ public void setShowLabels(boolean show)
+ {
+ showLabels.setSelected(show);
+ }
+
+ /**
+ * Sets the input data used to calculate the PCA. This is provided for
+ * 'restore from project', which does not currently support this (AL-2647), so
+ * sets the value to null, and hides the menu option for "Input Data...". J
+ *
+ * @param data
+ */
+ public void setInputData(AlignmentView data)
+ {
+ pcaModel.setInputData(data);
+ originalSeqData.setVisible(data != null);
+ }
}
git://source.jalview.org / jalview.git / blobdiff