/*\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.*;\r
import java.awt.event.*;\r
\r
import jalview.analysis.*;\r
import jalview.datamodel.*;\r
import jalview.io.*;\r
-import jalview.jbappletgui.*;\r
\r
public class TreePanel\r
- extends GTreePanel\r
+ extends Frame implements ActionListener, ItemListener\r
{\r
SequenceI[] seq;\r
String type;\r
String pwtype;\r
- AlignmentPanel ap;\r
int start;\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
- super();\r
- initTreePanel(av, seqVector, type, pwtype, s, e, null);\r
+ try\r
+ {\r
+ jbInit();\r
+ this.setMenuBar(jMenuBar1);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
\r
- // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default\r
- treeCanvas.setShowDistances(true);\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
- super();\r
- initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);\r
- }\r
+ try\r
+ {\r
+ jbInit();\r
+ this.setMenuBar(jMenuBar1);\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
\r
+ initTreePanel(av, type, pwtype, newtree);\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
- 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
- NJTree tree;\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.setShowBootstrap(newtree.HasBootstrap());\r
treeCanvas.setShowDistances(newtree.HasDistances());\r
}\r
\r
-\r
treeCanvas.repaint();\r
\r
+ av.setCurrentTree(tree);\r
+\r
}\r
}\r
\r
- public String getText(String format)\r
+ public void actionPerformed(ActionEvent evt)\r
{\r
- return null;\r
+ if (evt.getSource() == newickOutput)\r
+ {\r
+ newickOutput_actionPerformed();\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
- protected void fitToWindow_actionPerformed(ActionEvent e)\r
+ public void itemStateChanged(ItemEvent evt)\r
{\r
- treeCanvas.fitToWindow = fitToWindow.getState();\r
- repaint();\r
+ if (evt.getSource() == fitToWindow)\r
+ {\r
+ treeCanvas.fitToWindow = fitToWindow.getState();\r
+ }\r
+\r
+ else if (evt.getSource() == distanceMenu)\r
+ {\r
+ treeCanvas.setShowDistances(distanceMenu.getState());\r
+ }\r
+\r
+ else if (evt.getSource() == bootstrapMenu)\r
+ {\r
+ treeCanvas.setShowBootstrap(bootstrapMenu.getState());\r
+ }\r
+\r
+ else if (evt.getSource() == placeholdersMenu)\r
+ {\r
+ treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());\r
+ }\r
+\r
+ treeCanvas.repaint();\r
}\r
\r
- public void newickOutput_actionPerformed(ActionEvent actionEvent)\r
+ public void newickOutput_actionPerformed()\r
{\r
jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
String output = fout.print(false, true);\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame.applet);\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);\r
cap.setText(output);\r
java.awt.Frame frame = new java.awt.Frame();\r
frame.add(cap);\r
jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);\r
}\r
\r
- protected void fontSize_actionPerformed(ActionEvent e)\r
+ public java.awt.Font getTreeFont()\r
{\r
- /* if( treeCanvas==null )\r
- return;\r
-\r
- String size = fontSize.getLabel().substring( fontSize.getLabel().indexOf("-")+1);\r
-\r
- Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
- "Select font size",\r
- "Font size",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
- ,"Font Size - "+size);\r
- if(selection!=null)\r
- {\r
- fontSize.setText("Font Size - " + selection);\r
-\r
- int i = Integer.parseInt(selection.toString());\r
- treeCanvas.setFontSize(i);\r
- }\r
- scrollPane.setViewportView(treeCanvas);\r
- */\r
+ return treeCanvas.font;\r
}\r
\r
- protected void distanceMenu_actionPerformed(ActionEvent e)\r
+ public void setTreeFont(java.awt.Font font)\r
{\r
- treeCanvas.setShowDistances(distanceMenu.getState());\r
+ treeCanvas.font = font;\r
+ treeCanvas.repaint();\r
}\r
\r
- protected void bootstrapMenu_actionPerformed(ActionEvent e)\r
+ protected void fontSize_actionPerformed()\r
{\r
- treeCanvas.setShowBootstrap(bootstrapMenu.getState());\r
+ if (treeCanvas == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ new FontChooser(this);\r
}\r
\r
- protected void placeholdersMenu_actionPerformed(ActionEvent e)\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ protected ScrollPane scrollPane = new ScrollPane();\r
+ MenuBar jMenuBar1 = new MenuBar();\r
+ Menu jMenu2 = new Menu();\r
+ protected MenuItem fontSize = new MenuItem();\r
+ protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();\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()\r
+ throws Exception\r
{\r
- treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());\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
+ fileMenu.add(newickOutput);\r
+ fileMenu.add(inputData);\r
+ inputData.addActionListener(this);\r
}\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff