import java.util.*;\r
\r
import java.awt.event.*;\r
+import java.awt.*;\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
+public class TreePanel extends Frame\r
{\r
SequenceI[] seq;\r
String type;\r
return tree;\r
}\r
\r
- public TreePanel(AlignmentPanel ap, Vector seqVector, String type,\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
+ try\r
+ {\r
+ jbInit();\r
+ this.setMenuBar(jMenuBar1);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\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
+ try\r
+ {\r
+ jbInit();\r
+ this.setMenuBar(jMenuBar1);\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
+\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.ap = ap;\r
this.type = type;\r
this.pwtype = pwtype;\r
\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
- {\r
- longestName = seq[i].getName();\r
- }\r
- }\r
-\r
- tree = new NJTree(seq, type, pwtype, start, end);\r
+ for(int i=0; i<seqVector.size(); i++)\r
+ seq[i] = (SequenceI)seqVector.elementAt(i);\r
\r
- treeCanvas = new TreeCanvas(ap.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
\r
- public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
- String type, String pwtype)\r
+ class TreeLoader extends Thread\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
+ NewickFile newtree;\r
\r
- String longestName = "";\r
- seq = new Sequence[seqVector.size()];\r
- for (int i = 0; i < seqVector.size(); i++)\r
+ public TreeLoader(NewickFile newtree)\r
{\r
- seq[i] = (Sequence) seqVector.elementAt(i);\r
+ this.newtree = newtree;\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
+ public void run()\r
{\r
- if (longestName.length() <\r
- ( (Sequence) ( (SequenceNode) leaves.elementAt(i)).element()).getName().\r
- length())\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
- longestName = TreeCanvas.PLACEHOLDER +\r
- ( (Sequence) ( (SequenceNode) leaves.elementAt(i)).element()).\r
- getName();\r
+ distanceMenu.setState(newtree.HasDistances());\r
+ bootstrapMenu.setState(newtree.HasBootstrap());\r
+ treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
+ treeCanvas.setShowDistances(newtree.HasDistances());\r
}\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
+ treeCanvas.repaint();\r
\r
+ }\r
}\r
\r
public String getText(String format)\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
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
+ return treeCanvas.font;\r
+ }\r
\r
- String size = fontSize.getLabel().substring( fontSize.getLabel().indexOf("-")+1);\r
+ public void setTreeFont(java.awt.Font font)\r
+ {\r
+ treeCanvas.font = font;\r
+ treeCanvas.repaint();\r
+ }\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
+ protected void fontSize_actionPerformed(ActionEvent e)\r
+ {\r
+ if( treeCanvas==null )\r
+ return;\r
\r
- int i = Integer.parseInt(selection.toString());\r
- treeCanvas.setFontSize(i);\r
- }\r
- scrollPane.setViewportView(treeCanvas);\r
- */\r
+ new FontChooser(this);\r
}\r
\r
protected void distanceMenu_actionPerformed(ActionEvent e)\r
treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());\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(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ fontSize_actionPerformed(e);\r
+ }\r
+ });\r
+ bootstrapMenu.setLabel("Show Bootstrap Values");\r
+ bootstrapMenu.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ bootstrapMenu_actionPerformed(null);\r
+ }\r
+ });\r
+ distanceMenu.setLabel("Show Distances");\r
+ distanceMenu.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ distanceMenu_actionPerformed(null);\r
+ }\r
+ });\r
+ placeholdersMenu.setLabel("Mark Unassociated Leaves");\r
+ placeholdersMenu.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ placeholdersMenu_actionPerformed(null);\r
+ }\r
+ });\r
+ fitToWindow.setState(true);\r
+ fitToWindow.setLabel("Fit To Window");\r
+ fitToWindow.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ fitToWindow_actionPerformed(null);\r
+ }\r
+ });\r
+ fileMenu.setLabel("File");\r
+ newickOutput.setLabel("Newick Format");\r
+ newickOutput.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent actionEvent) {\r
+ newickOutput_actionPerformed(actionEvent);\r
+ }\r
+ });\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