int end;\r
TreeCanvas treeCanvas;\r
NJTree tree;\r
+ AlignViewport av;\r
\r
public NJTree getTree()\r
{\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
try\r
{\r
ex.printStackTrace();\r
}\r
\r
- initTreePanel(av, seqVector, type, pwtype, s, e, null);\r
+ initTreePanel(av, type, pwtype, null);\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
try\r
{\r
e.printStackTrace();\r
}\r
\r
- initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);\r
+ initTreePanel(av, type, pwtype, newtree);\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,\r
+ String type,\r
+ String pwtype,\r
+ NewickFile newTree)\r
{\r
\r
+ this.av = av;\r
this.type = type;\r
this.pwtype = pwtype;\r
\r
- start = s;\r
- end = e;\r
-\r
- seq = new Sequence[seqVector.size()];\r
- for(int i=0; i<seqVector.size(); i++)\r
- seq[i] = (SequenceI)seqVector.elementAt(i);\r
-\r
-\r
treeCanvas = new TreeCanvas(av, scrollPane);\r
scrollPane.add(treeCanvas);\r
\r
\r
public void run()\r
{\r
- if(newtree!=null)\r
- tree = new NJTree(seq, newtree);\r
+ if (newtree != null)\r
+ tree = new NJTree(av.alignment.getSequencesArray(),\r
+ newtree);\r
else\r
- tree = new NJTree(seq, type, pwtype, start, end);\r
+ {\r
+ int start, end;\r
+ SequenceI [] seqs;\r
+ CigarArray seqStrings = null;\r
+ // if (av.hasHiddenColumns)\r
+ {\r
+ // seqStrings = av.getSelectionAsString();\r
+ }\r
+\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
+ }\r
\r
tree.reCount(tree.getTopNode());\r
tree.findHeight(tree.getTopNode());\r
\r
treeCanvas.repaint();\r
\r
+ av.setCurrentTree(tree);\r
+\r
}\r
}\r
\r
}\r
\r
\r
+\r
+\r
BorderLayout borderLayout1 = new BorderLayout();\r
protected ScrollPane scrollPane = new ScrollPane();\r
MenuBar jMenuBar1 = new MenuBar();\r