+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 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
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
+\r
package jalview.appletgui;\r
\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
-import jalview.jbappletgui.GTreePanel;\r
-import java.awt.event.*;\r
import java.util.*;\r
-import jalview.io.NewickFile;\r
\r
+import java.awt.event.*;\r
+import java.awt.*;\r
+\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
\r
-public class TreePanel extends GTreePanel\r
+public class TreePanel extends Frame implements ActionListener, ItemListener\r
{\r
SequenceI[] seq;\r
String type;\r
String pwtype;\r
- AlignViewport av;\r
int start;\r
int end;\r
TreeCanvas treeCanvas;\r
NJTree tree;\r
+ AlignViewport av;\r
\r
public NJTree getTree()\r
{\r
return tree;\r
}\r
\r
- public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)\r
+ /**\r
+ * Creates a new TreePanel object.\r
+ *\r
+ * @param av DOCUMENT ME!\r
+ * @param seqVector DOCUMENT ME!\r
+ * @param type DOCUMENT ME!\r
+ * @param pwtype DOCUMENT ME!\r
+ * @param s DOCUMENT ME!\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public TreePanel(AlignViewport av, String type, String pwtype)\r
{\r
- super();\r
-\r
- this.type = type;\r
- this.pwtype = pwtype;\r
+ try\r
+ {\r
+ jbInit();\r
+ this.setMenuBar(jMenuBar1);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
\r
- start = s;\r
- end = e;\r
+ initTreePanel(av, type, pwtype, null);\r
+ }\r
\r
- String longestName = "";\r
- seq = new Sequence [seqVector.size()];\r
- for (int i=0;i < seqVector.size();i++)\r
+ /**\r
+ * Creates a new TreePanel object.\r
+ *\r
+ * @param av DOCUMENT ME!\r
+ * @param seqVector DOCUMENT ME!\r
+ * @param newtree DOCUMENT ME!\r
+ * @param type DOCUMENT ME!\r
+ * @param pwtype DOCUMENT ME!\r
+ */\r
+ public TreePanel(AlignViewport av,\r
+ String type,\r
+ String pwtype,\r
+ NewickFile newtree)\r
+ {\r
+ try\r
+ {\r
+ jbInit();\r
+ this.setMenuBar(jMenuBar1);\r
+ }\r
+ catch (Exception e)\r
{\r
- seq[i] = (Sequence) seqVector.elementAt(i);\r
- if(seq[i].getName().length()>longestName.length())\r
- longestName = seq[i].getName();\r
+ e.printStackTrace();\r
}\r
\r
- tree = new NJTree(seq, type, pwtype, start, end);\r
+ initTreePanel(av, type, pwtype, newtree);\r
+ }\r
+\r
+\r
+ void initTreePanel(AlignViewport av,\r
+ String type,\r
+ String pwtype,\r
+ NewickFile newTree)\r
+ {\r
\r
- treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
+ this.av = av;\r
+ this.type = type;\r
+ this.pwtype = pwtype;\r
\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
+ treeCanvas = new TreeCanvas(av, scrollPane);\r
scrollPane.add(treeCanvas);\r
\r
- }\r
\r
-public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
- String type, String pwtype)\r
-{\r
- super();\r
- // These are probably only arbitrary strings reflecting source of tree\r
- this.type = type;\r
- this.pwtype = pwtype;\r
+ TreeLoader tl = new TreeLoader(newTree);\r
+ tl.start();\r
\r
- start = 0;\r
- end = seqVector.size();\r
+ }\r
\r
- String longestName = "";\r
- seq = new Sequence [seqVector.size()];\r
- for (int i=0;i < seqVector.size();i++)\r
+ class TreeLoader extends Thread\r
{\r
- seq[i] = (Sequence) seqVector.elementAt(i);\r
- if(seq[i].getName().length()>longestName.length())\r
- longestName = seq[i].getName();\r
- }\r
- // This constructor matches sequence names to treenodes and sets up the tree layouts.\r
- tree = new NJTree(seq, newtree);\r
+ NewickFile newtree;\r
\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
+ public TreeLoader(NewickFile newtree)\r
+ {\r
+ this.newtree = newtree;\r
+ }\r
\r
- treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
- treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
- bootstrapMenu.setState(newtree.HasBootstrap());\r
- treeCanvas.setShowDistances(newtree.HasDistances());\r
- distanceMenu.setState(newtree.HasDistances());\r
- scrollPane.add(treeCanvas);\r
+ public void run()\r
+ {\r
+ if (newtree != null)\r
+ tree = new NJTree(av.alignment.getSequencesArray(),\r
+ newtree);\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
+ 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
+ {\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
+\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ if(evt.getSource()==newickOutput)\r
+ newickOutput_actionPerformed();\r
+ else if(evt.getSource()==fontSize)\r
+ fontSize_actionPerformed();\r
+ }\r
\r
+ public void itemStateChanged(ItemEvent evt)\r
+ {\r
+ if(evt.getSource()==fitToWindow)\r
+ treeCanvas.fitToWindow = fitToWindow.getState();\r
\r
+ else if(evt.getSource()==distanceMenu)\r
+ treeCanvas.setShowDistances(distanceMenu.getState());\r
\r
-public String getText(String format) {\r
- return null;\r
-}\r
+ else if(evt.getSource()==bootstrapMenu)\r
+ treeCanvas.setShowBootstrap(bootstrapMenu.getState());\r
\r
- protected void fitToWindow_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.fitToWindow = fitToWindow.getState();\r
- repaint();\r
+ else if(evt.getSource()==placeholdersMenu)\r
+ treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());\r
+\r
+ treeCanvas.repaint();\r
}\r
\r
- public void newickOutput_actionPerformed(ActionEvent actionEvent)\r
+\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);\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, 500,500);\r
+ jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);\r
}\r
\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
+ return;\r
+\r
+ new FontChooser(this);\r
+ }\r
+\r
+\r
+\r
+\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
+\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
+\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
}\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff