/*\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
\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
\r
public void run()\r
{\r
- if (newtree != null)\r
- tree = new NJTree(av.alignment.getSequencesArray(),\r
- newtree);\r
- else\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
+ }\r
+ else\r
{\r
int start, end;\r
SequenceI [] seqs;\r
- CigarArray seqStrings = null;\r
- // if (av.hasHiddenColumns)\r
- {\r
- // seqStrings = av.getSelectionAsString();\r
- }\r
-\r
+ AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);\r
if(av.getSelectionGroup()==null)\r
{\r
start = 0;\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
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