/*\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
+ * 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.io.NewickFile;\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
\r
-public class TreePanel extends GTreePanel\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
{\r
SequenceI[] seq;\r
String type;\r
String pwtype;\r
- AlignViewport av;\r
+ AlignmentPanel ap;\r
int start;\r
int end;\r
TreeCanvas treeCanvas;\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, Vector seqVector, String type,\r
+ String pwtype, int s, int e)\r
+ {\r
+ super();\r
+ initTreePanel(av, seqVector, type, pwtype, s, e, null);\r
+ }\r
+\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, Vector seqVector, NewickFile newtree,\r
+ String type, String pwtype)\r
{\r
super();\r
+ initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);\r
+ }\r
+\r
+\r
+ void initTreePanel(AlignViewport av, Vector seqVector, String type,\r
+ String pwtype, int s, int e, NewickFile newTree)\r
+ {\r
\r
this.type = type;\r
this.pwtype = pwtype;\r
start = s;\r
end = e;\r
\r
- String longestName = "";\r
- seq = new Sequence [seqVector.size()];\r
- for (int i=0;i < seqVector.size();i++)\r
- {\r
- seq[i] = (Sequence) seqVector.elementAt(i);\r
- if(seq[i].getName().length()>longestName.length())\r
- longestName = seq[i].getName();\r
- }\r
-\r
- tree = new NJTree(seq, type, pwtype, start, end);\r
+ seq = new Sequence[seqVector.size()];\r
+ for(int i=0; i<seqVector.size(); i++)\r
+ seq[i] = (SequenceI)seqVector.elementAt(i);\r
\r
- treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
+ treeCanvas = new TreeCanvas(av, scrollPane);\r
scrollPane.add(treeCanvas);\r
\r
+\r
+ TreeLoader tl = new TreeLoader(newTree);\r
+ tl.start();\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
\r
- start = 0;\r
- end = seqVector.size();\r
+ class TreeLoader extends Thread\r
+ {\r
+ NewickFile newtree;\r
\r
- String longestName = "";\r
- seq = new Sequence [seqVector.size()];\r
- for (int i=0;i < seqVector.size();i++)\r
- {\r
- seq[i] = (Sequence) seqVector.elementAt(i);\r
- }\r
- // This constructor matches sequence names to treenodes and sets up the tree layouts.\r
- tree = new NJTree(seq, newtree);\r
- // Now have to calculate longest name based on the leaves\r
- Vector leaves = tree.findLeaves(tree.getTopNode(),new Vector());\r
+ public TreeLoader(NewickFile newtree)\r
+ {\r
+ this.newtree = newtree;\r
+ }\r
\r
- for (int i=0;i < leaves.size();i++)\r
- if (longestName.length()<((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName().length())\r
- longestName = TreeCanvas.PLACEHOLDER+((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName();\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
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
- treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
- treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
- treeCanvas.setShowDistances(newtree.HasDistances());\r
- distanceMenu.setState(newtree.HasDistances());\r
- bootstrapMenu.setState(newtree.HasBootstrap());\r
- if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree\r
- placeholdersMenu.setState(treeCanvas.markPlaceholders);\r
- scrollPane.add(treeCanvas);\r
+\r
+ treeCanvas.repaint();\r
\r
}\r
+ }\r
\r
-public String getText(String format) {\r
- return null;\r
-}\r
+ public String getText(String format)\r
+ {\r
+ return null;\r
+ }\r
\r
protected void fitToWindow_actionPerformed(ActionEvent e)\r
{\r
treeCanvas.fitToWindow = fitToWindow.getState();\r
- repaint();\r
+ treeCanvas.repaint();\r
}\r
\r
public void newickOutput_actionPerformed(ActionEvent actionEvent)\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, ap.alignFrame.applet);\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
+ jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);\r
}\r
\r
+ public java.awt.Font getTreeFont()\r
+ {\r
+ return treeCanvas.font;\r
+ }\r
\r
+ public void setTreeFont(java.awt.Font font)\r
+ {\r
+ treeCanvas.font = font;\r
+ treeCanvas.repaint();\r
+ }\r
\r
protected void fontSize_actionPerformed(ActionEvent e)\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
+ if( treeCanvas==null )\r
+ return;\r
+\r
+ new FontChooser(this);\r
}\r
\r
protected void distanceMenu_actionPerformed(ActionEvent e)\r
\r
protected void placeholdersMenu_actionPerformed(ActionEvent e)\r
{\r
- treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());\r
+ treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());\r
}\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff