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JAL-2291 ‘Hide Insertions’ now operates on selection or if none available, the sequen...
[jalview.git]
/
src
/
jalview
/
gui
/
TreeCanvas.java
diff --git
a/src/jalview/gui/TreeCanvas.java
b/src/jalview/gui/TreeCanvas.java
index
eb4253f
..
3494fb8
100755
(executable)
--- a/
src/jalview/gui/TreeCanvas.java
+++ b/
src/jalview/gui/TreeCanvas.java
@@
-21,7
+21,7
@@
package jalview.gui;
import jalview.analysis.Conservation;
package jalview.gui;
import jalview.analysis.Conservation;
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeModel;
import jalview.api.AlignViewportI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.api.AlignViewportI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
@@
-53,6
+53,7
@@
import java.awt.print.PrinterException;
import java.awt.print.PrinterJob;
import java.util.Enumeration;
import java.util.Hashtable;
import java.awt.print.PrinterJob;
import java.util.Enumeration;
import java.util.Hashtable;
+import java.util.List;
import java.util.Vector;
import javax.swing.JColorChooser;
import java.util.Vector;
import javax.swing.JColorChooser;
@@
-73,7
+74,7
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
/** DOCUMENT ME!! */
public static final String PLACEHOLDER = " * ";
/** DOCUMENT ME!! */
public static final String PLACEHOLDER = " * ";
- NJTree tree;
+ TreeModel tree;
JScrollPane scrollPane;
JScrollPane scrollPane;
@@
-168,7
+169,7
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
* @param tree
* DOCUMENT ME!
*/
* @param tree
* DOCUMENT ME!
*/
- public void setTree(NJTree tree)
+ public void setTree(TreeModel tree)
{
this.tree = tree;
tree.findHeight(tree.getTopNode());
{
this.tree = tree;
tree.findHeight(tree.getTopNode());
@@
-549,7
+550,16
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
public void run()
{
PrinterJob printJob = PrinterJob.getPrinterJob();
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);
printJob.setPrintable(this, pf);
@@
-929,8
+939,7
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
threshold = (float) (x - offx)
/ (float) (getWidth() - labelLength - (2 * offx));
threshold = (float) (x - offx)
/ (float) (getWidth() - labelLength - (2 * offx));
- tree.getGroups().removeAllElements();
- tree.groupNodes(tree.getTopNode(), threshold);
+ List<SequenceNode> groups = tree.groupNodes(threshold);
setColor(tree.getTopNode(), Color.black);
AlignmentPanel[] aps = getAssociatedPanels();
setColor(tree.getTopNode(), Color.black);
AlignmentPanel[] aps = getAssociatedPanels();
@@
-950,7
+959,7
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
aps[a].av.getCodingComplement().clearSequenceColours();
}
}
aps[a].av.getCodingComplement().clearSequenceColours();
}
}
- colourGroups();
+ colourGroups(groups);
}
PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
}
PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
@@
-959,17
+968,16
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
}
}
- void colourGroups()
+ void colourGroups(List<SequenceNode> groups)
{
AlignmentPanel[] aps = getAssociatedPanels();
{
AlignmentPanel[] aps = getAssociatedPanels();
- for (int i = 0; i < tree.getGroups().size(); i++)
+ for (int i = 0; i < groups.size(); i++)
{
Color col = new Color((int) (Math.random() * 255),
(int) (Math.random() * 255), (int) (Math.random() * 255));
{
Color col = new Color((int) (Math.random() * 255),
(int) (Math.random() * 255), (int) (Math.random() * 255));
- setColor(tree.getGroups().elementAt(i), col.brighter());
+ setColor(groups.get(i), col.brighter());
- Vector<SequenceNode> l = tree.findLeaves(tree.getGroups()
- .elementAt(i));
+ Vector<SequenceNode> l = tree.findLeaves(groups.get(i));
Vector<SequenceI> sequences = new Vector<SequenceI>();
Vector<SequenceI> sequences = new Vector<SequenceI>();