/*\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) 2007 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
package jalview.appletgui;\r
\r
-import java.util.*;\r
-\r
-import java.awt.event.*;\r
import java.awt.*;\r
+import java.awt.event.*;\r
\r
import jalview.analysis.*;\r
import jalview.datamodel.*;\r
import jalview.io.*;\r
\r
-public class TreePanel extends Frame implements ActionListener, ItemListener\r
+public class TreePanel\r
+ extends Frame implements ActionListener, ItemListener\r
{\r
SequenceI[] seq;\r
String type;\r
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
TreeLoader tl = new TreeLoader(newTree);\r
tl.start();\r
\r
}\r
\r
- class TreeLoader extends Thread\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
+ {\r
+ System.out.println("Original Tree Data not available");\r
+ }\r
+ }\r
+\r
+ class TreeLoader\r
+ 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(seq, newtree);\r
+ if (newtree != null)\r
+ {\r
+ if (odata == null)\r
+ {\r
+ tree = new NJTree(av.alignment.getSequencesArray(),\r
+ newtree);\r
+ }\r
+ else\r
+ {\r
+ tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);\r
+ }\r
+\r
+ }\r
else\r
- tree = new NJTree(seq, type, pwtype, start, end);\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
treeCanvas.setTree(tree);\r
- if(newtree!=null)\r
+ if (newtree != null)\r
{\r
distanceMenu.setState(newtree.HasDistances());\r
bootstrapMenu.setState(newtree.HasBootstrap());\r
treeCanvas.setShowDistances(newtree.HasDistances());\r
}\r
\r
-\r
treeCanvas.repaint();\r
\r
+ av.setCurrentTree(tree);\r
+\r
}\r
}\r
\r
public void actionPerformed(ActionEvent evt)\r
{\r
- if(evt.getSource()==newickOutput)\r
+ if (evt.getSource() == newickOutput)\r
+ {\r
newickOutput_actionPerformed();\r
- else if(evt.getSource()==fontSize)\r
+ }\r
+ else if (evt.getSource() == fontSize)\r
+ {\r
fontSize_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == inputData)\r
+ {\r
+ showOriginalData();\r
+ }\r
}\r
\r
public void itemStateChanged(ItemEvent evt)\r
{\r
- if(evt.getSource()==fitToWindow)\r
+ if (evt.getSource() == fitToWindow)\r
+ {\r
treeCanvas.fitToWindow = fitToWindow.getState();\r
+ }\r
\r
- else if(evt.getSource()==distanceMenu)\r
+ else if (evt.getSource() == distanceMenu)\r
+ {\r
treeCanvas.setShowDistances(distanceMenu.getState());\r
+ }\r
\r
- else if(evt.getSource()==bootstrapMenu)\r
+ else if (evt.getSource() == bootstrapMenu)\r
+ {\r
treeCanvas.setShowBootstrap(bootstrapMenu.getState());\r
+ }\r
\r
- else if(evt.getSource()==placeholdersMenu)\r
+ else if (evt.getSource() == placeholdersMenu)\r
+ {\r
treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());\r
+ }\r
\r
treeCanvas.repaint();\r
}\r
\r
-\r
public void newickOutput_actionPerformed()\r
{\r
jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
\r
protected void fontSize_actionPerformed()\r
{\r
- if( treeCanvas==null )\r
- return;\r
+ if (treeCanvas == null)\r
+ {\r
+ return;\r
+ }\r
\r
new FontChooser(this);\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
- this.setBackground(Color.white);\r
- this.setFont(new java.awt.Font("Verdana", 0, 12));\r
- jMenu2.setLabel("View");\r
- fontSize.setLabel("Font...");\r
- fontSize.addActionListener(this);\r
- bootstrapMenu.setLabel("Show Bootstrap Values");\r
- bootstrapMenu.addItemListener(this);\r
- distanceMenu.setLabel("Show Distances");\r
- distanceMenu.addItemListener(this);\r
- placeholdersMenu.setLabel("Mark Unassociated Leaves");\r
- placeholdersMenu.addItemListener(this);\r
- fitToWindow.setState(true);\r
- fitToWindow.setLabel("Fit To Window");\r
- fitToWindow.addItemListener(this);\r
- fileMenu.setLabel("File");\r
- newickOutput.setLabel("Newick Format");\r
- newickOutput.addActionListener(this);\r
+ private void jbInit()\r
+ throws Exception\r
+ {\r
+ setLayout(borderLayout1);\r
+ this.setBackground(Color.white);\r
+ this.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ jMenu2.setLabel("View");\r
+ fontSize.setLabel("Font...");\r
+ fontSize.addActionListener(this);\r
+ bootstrapMenu.setLabel("Show Bootstrap Values");\r
+ bootstrapMenu.addItemListener(this);\r
+ distanceMenu.setLabel("Show Distances");\r
+ distanceMenu.addItemListener(this);\r
+ placeholdersMenu.setLabel("Mark Unassociated Leaves");\r
+ placeholdersMenu.addItemListener(this);\r
+ fitToWindow.setState(true);\r
+ fitToWindow.setLabel("Fit To Window");\r
+ fitToWindow.addItemListener(this);\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
- jMenuBar1.add(jMenu2);\r
- jMenu2.add(fitToWindow);\r
- jMenu2.add(fontSize);\r
- jMenu2.add(distanceMenu);\r
- jMenu2.add(bootstrapMenu);\r
- jMenu2.add(placeholdersMenu);\r
+ jMenuBar1.add(fileMenu);\r
+ jMenuBar1.add(jMenu2);\r
+ jMenu2.add(fitToWindow);\r
+ jMenu2.add(fontSize);\r
+ jMenu2.add(distanceMenu);\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