\r
import javax.imageio.*;\r
\r
-import javax.swing.*;\r
import java.beans.PropertyChangeEvent;\r
\r
\r
initTreePanel(av, seqVector, type, pwtype, s, e, null);\r
\r
// We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default\r
- treeCanvas.setShowDistances(true);\r
- distanceMenu.setSelected(true);\r
+ showDistances(true);\r
}\r
\r
/**\r
initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);\r
}\r
\r
+ public AlignmentI getAlignment()\r
+ {\r
+ return treeCanvas.av.getAlignment();\r
+ }\r
+\r
\r
void initTreePanel(AlignViewport av, Vector seqVector, String type,\r
String pwtype, int s, int e, NewickFile newTree)\r
{\r
// Must be outside run(), as Jalview2XML tries to\r
// update distance/bootstrap visibility at the same time\r
- treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
- bootstrapMenu.setSelected(newtree.HasBootstrap());\r
-\r
- treeCanvas.setShowDistances(newtree.HasDistances());\r
- distanceMenu.setSelected(newtree.HasDistances());\r
+ showBootstrap(newtree.HasBootstrap());\r
+ showDistances(newtree.HasDistances());\r
}\r
}\r
\r
}\r
}\r
\r
+ public void showDistances(boolean b)\r
+ {\r
+ treeCanvas.setShowDistances(b);\r
+ distanceMenu.setSelected(b);\r
+ }\r
+\r
+ public void showBootstrap(boolean b)\r
+ {\r
+ treeCanvas.setShowBootstrap(b);\r
+ bootstrapMenu.setSelected(b);\r
+ }\r
+\r
+ public void showPlaceholders(boolean b)\r
+ {\r
+ placeholdersMenu.setState(b);\r
+ treeCanvas.setMarkPlaceholders(b);\r
+ }\r
+\r
+\r
+\r
\r
/**\r
* DOCUMENT ME!\r
Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);\r
\r
jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
- cap.setText(fout.print(false, true));\r
+ cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));\r
}\r
\r
/**\r
try\r
{\r
jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
- String output = fout.print(false, true); // distances only\r
+ String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());\r
java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(\r
choice));\r
out.println(output);\r