*/\r
public class TreePanel extends GTreePanel\r
{\r
- SequenceI[] seq;\r
String type;\r
String pwtype;\r
- int start;\r
- int end;\r
TreeCanvas treeCanvas;\r
NJTree tree;\r
+ AlignViewport av;\r
\r
/**\r
* Creates a new TreePanel object.\r
* @param s DOCUMENT ME!\r
* @param e DOCUMENT ME!\r
*/\r
- public TreePanel(AlignViewport av, Vector seqVector, String type,\r
- String pwtype, int s, int e)\r
+ public TreePanel(AlignViewport av, String type, String pwtype)\r
{\r
super();\r
- initTreePanel(av, seqVector, type, pwtype, s, e, null);\r
+ initTreePanel(av, type, pwtype, null);\r
\r
// We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default\r
- showDistances(true);\r
+ // showDistances(true);\r
}\r
\r
/**\r
* @param type DOCUMENT ME!\r
* @param pwtype DOCUMENT ME!\r
*/\r
- public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
- String type, String pwtype)\r
+ public TreePanel(AlignViewport av,\r
+ String type,\r
+ String pwtype,\r
+ NewickFile newtree)\r
{\r
super();\r
- initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);\r
+ initTreePanel(av, type, pwtype, newtree);\r
}\r
\r
public AlignmentI getAlignment()\r
}\r
\r
\r
- void initTreePanel(AlignViewport av, Vector seqVector, String type,\r
- String pwtype, int s, int e, NewickFile newTree)\r
+ void initTreePanel(AlignViewport av, String type, String pwtype,\r
+ NewickFile newTree)\r
{\r
\r
this.type = type;\r
this.pwtype = pwtype;\r
\r
- start = s;\r
- end = e;\r
-\r
- seq = new Sequence[seqVector.size()];\r
- seqVector.toArray(seq);\r
-\r
-\r
treeCanvas = new TreeCanvas(av, scrollPane);\r
scrollPane.setViewportView(treeCanvas);\r
\r
}\r
});\r
\r
+ this.av = av;\r
+\r
\r
TreeLoader tl = new TreeLoader(newTree);\r
tl.start();\r
class TreeLoader extends Thread\r
{\r
NewickFile newtree;\r
-\r
+ jalview.datamodel.CigarArray odata=null;\r
public TreeLoader(NewickFile newtree)\r
{\r
this.newtree = newtree;\r
\r
public void run()\r
{\r
- if(newtree!=null)\r
- tree = new NJTree(seq, newtree);\r
+\r
+ if(newtree!=null) {\r
+\r
+ if (odata==null) {\r
+ tree = new NJTree(av.alignment.getSequencesArray(),\r
+ newtree);\r
+ } else {\r
+ tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);\r
+ }\r
+ if (!tree.hasOriginalSequenceData())\r
+ allowOriginalSeqData(false);\r
+ }\r
else\r
- tree = new NJTree(seq, type, pwtype, start, end);\r
+ {\r
+ int start, end;\r
+ SequenceI [] seqs;\r
+ CigarArray seqStrings = av.getViewAsCigars(av.getSelectionGroup()!=null);\r
+ if(av.getSelectionGroup()==null)\r
+ {\r
+ start = 0;\r
+ end = av.alignment.getWidth();\r
+ seqs = av.alignment.getSequencesArray();\r
+ }\r
+ else\r
+ {\r
+ start = av.getSelectionGroup().getStartRes();\r
+ end = av.getSelectionGroup().getEndRes()+1;\r
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
+ }\r
+\r
+ tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);\r
+ showDistances(true);\r
+ }\r
+\r
\r
tree.reCount(tree.getTopNode());\r
tree.findHeight(tree.getTopNode());\r
treeCanvas.setTree(tree);\r
-\r
treeCanvas.repaint();\r
+ av.setCurrentTree(tree);\r
\r
}\r
}\r
placeholdersMenu.setState(b);\r
treeCanvas.setMarkPlaceholders(b);\r
}\r
-\r
+ private void allowOriginalSeqData(boolean b) {\r
+ originalSeqData.setVisible(b);\r
+ }\r
\r
\r
\r
treeCanvas.startPrinting();\r
}\r
\r
+\r
+ public void originalSeqData_actionPerformed(ActionEvent e)\r
+ {\r
+ String originalData = tree.printOriginalSequenceData(av.getGapCharacter());\r
+ if (originalData!=null) {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ cap.setText(originalData);\r
+ Desktop.addInternalFrame(cap, "Original Data",\r
+ 400, 400);\r
+ } else {\r
+ System.err.println("IMPLEMENTATION BUG! originalSeqData is not available.");\r
+ }\r
+\r
+ }\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r