/*\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
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
+import jalview.jbappletgui.*;\r
\r
-public class TreePanel extends GTreePanel\r
+public class TreePanel\r
+ extends GTreePanel\r
{\r
SequenceI[] seq;\r
String type;\r
return tree;\r
}\r
\r
- public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)\r
+ public TreePanel(AlignViewport av, Vector seqVector, String type,\r
+ String pwtype, int s, int e)\r
{\r
super();\r
\r
end = e;\r
\r
String longestName = "";\r
- seq = new Sequence [seqVector.size()];\r
- for (int i=0;i < seqVector.size();i++)\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
+ if (seq[i].getName().length() > longestName.length())\r
+ {\r
longestName = seq[i].getName();\r
+ }\r
}\r
\r
tree = new NJTree(seq, type, pwtype, start, end);\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
+ {\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
+ start = 0;\r
+ end = seqVector.size();\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
\r
- String longestName = "";\r
- seq = new Sequence [seqVector.size()];\r
- for (int i=0;i < seqVector.size();i++)\r
+ for (int i = 0; i < leaves.size(); i++)\r
+ {\r
+ if (longestName.length() <\r
+ ( (Sequence) ( (SequenceNode) leaves.elementAt(i)).element()).getName().\r
+ length())\r
{\r
- seq[i] = (Sequence) seqVector.elementAt(i);\r
+ longestName = TreeCanvas.PLACEHOLDER +\r
+ ( (Sequence) ( (SequenceNode) leaves.elementAt(i)).element()).\r
+ getName();\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
-\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
-\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\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
+\r
+ tree.reCount(tree.getTopNode());\r
+ tree.findHeight(tree.getTopNode());\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
+ {\r
+ placeholdersMenu.setState(treeCanvas.markPlaceholders);\r
}\r
+ scrollPane.add(treeCanvas);\r
\r
-public String getText(String format) {\r
- return null;\r
-}\r
+ }\r
+\r
+ public String getText(String format)\r
+ {\r
+ return null;\r
+ }\r
\r
protected void fitToWindow_actionPerformed(ActionEvent e)\r
{\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
-\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
+ 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
}\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