/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\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
}\r
\r
+ void showOriginalData()\r
+ {\r
+ // decide if av alignment is sufficiently different to original data to warrant a new window to be created\r
+ // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)\r
+ // or create a selection box around columns in alignment view\r
+ // test Alignment(SeqCigar[])\r
+ if(tree.seqData!=null)\r
+ {\r
+ Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.\r
+ getGapCharacter());\r
+\r
+ if (alAndColsel != null && alAndColsel[0] != null)\r
+ {\r
+ Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);\r
+ AlignFrame af = new AlignFrame(al,\r
+ av.applet,\r
+ "Original Data for Tree",\r
+ false);\r
+\r
+ af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1]);\r
+ }\r
+ }\r
+ else\r
+ System.out.println("Original Tree Data not available");\r
+ }\r
+\r
class TreeLoader extends Thread\r
{\r
NewickFile newtree;\r
+ jalview.datamodel.AlignmentView odata=null;\r
\r
public TreeLoader(NewickFile newtree)\r
{\r
public void run()\r
{\r
if(newtree!=null)\r
- tree = new NJTree(seq, newtree);\r
- else\r
- tree = new NJTree(seq, type, pwtype, start, end);\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
+ }\r
+ else\r
+ {\r
+ int start, end;\r
+ SequenceI [] seqs;\r
+ AlignmentView seqStrings = av.getAlignmentView(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
+ }\r
\r
tree.reCount(tree.getTopNode());\r
tree.findHeight(tree.getTopNode());\r
newickOutput_actionPerformed();\r
else if(evt.getSource()==fontSize)\r
fontSize_actionPerformed();\r
+ else if(evt.getSource()==inputData)\r
+ showOriginalData();\r
}\r
\r
public void itemStateChanged(ItemEvent evt)\r
}\r
\r
\r
+\r
+\r
BorderLayout borderLayout1 = new BorderLayout();\r
protected ScrollPane scrollPane = new ScrollPane();\r
MenuBar jMenuBar1 = new MenuBar();\r
protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();\r
Menu fileMenu = new Menu();\r
MenuItem newickOutput = new MenuItem();\r
+ MenuItem inputData = new MenuItem();\r
\r
private void jbInit() throws Exception {\r
setLayout(borderLayout1);\r
fileMenu.setLabel("File");\r
newickOutput.setLabel("Newick Format");\r
newickOutput.addActionListener(this);\r
+ inputData.setLabel("Input Data...");\r
\r
add(scrollPane, BorderLayout.CENTER);\r
jMenuBar1.add(fileMenu);\r
jMenu2.add(bootstrapMenu);\r
jMenu2.add(placeholdersMenu);\r
fileMenu.add(newickOutput);\r
+ fileMenu.add(inputData);\r
+ inputData.addActionListener(this);\r
}\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff