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.HiddenColumns;
import jalview.datamodel.SequenceI;
import jalview.jbgui.GPCAPanel;
+import jalview.math.RotatableMatrix.Axis;
import jalview.util.ImageMaker;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import javax.swing.event.InternalFrameEvent;
/**
- * The panel holding the Principal Component Analysis 3-d visualisation
+ * The panel holding the Principal Component Analysis 3-D visualisation
*/
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;
int top = 0;
- private static final int MIN_WIDTH = 470;
-
- private static final int MIN_HEIGHT = 250;
-
private IProgressIndicator progressBar;
private boolean working;
rc = new RotatableCanvas(alignPanel);
this.getContentPane().add(rc, BorderLayout.CENTER);
- /*
- * perform calculation in a new Thread
- */
- Thread worker = new Thread(this);
- worker.start();
+ addKeyListener(rc);
+ validate();
+
+ this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
}
/**
try
{
pcaModel.calculate();
- // ////////////////
+
xCombobox.setSelectedIndex(0);
yCombobox.setSelectedIndex(1);
zCombobox.setSelectedIndex(2);
repaint();
if (getParent() == null)
{
- addKeyListener(rc);
Desktop.addInternalFrame(this,
MessageManager.formatMessage("label.calc_title", "PCA",
pcaModel.getScoreModelName()),
475, 450);
- this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
}
working = false;
}
int dim3 = top - zCombobox.getSelectedIndex();
pcaModel.updateRcView(dim1, dim2, dim3);
rc.resetView();
- rc.paint(rc.getGraphics());
+ }
+
+ /**
+ * Sets the selected checkbox item index for PCA dimension (1, 2, 3...) for
+ * the given axis (X/Y/Z)
+ *
+ * @param index
+ * @param axis
+ */
+ public void setSelectedDimensionIndex(int index, Axis axis)
+ {
+ switch (axis)
+ {
+ case X:
+ xCombobox.setSelectedIndex(index);
+ break;
+ case Y:
+ yCombobox.setSelectedIndex(index);
+ break;
+ case Z:
+ zCombobox.setSelectedIndex(index);
+ break;
+ default:
+ }
}
@Override
// make this an abstract function of all jalview analysis windows
if (pcaModel.getSeqtrings() == null)
{
- jalview.bin.Cache.log.info(
+ Cache.log.info(
"Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
return;
}
{
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);
+ }
}