*/\r
package jalview.gui;\r
\r
-import java.io.*;\r
-import java.util.*;\r
-import javax.imageio.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import java.awt.image.*;\r
-import javax.swing.*;\r
-\r
-import org.jibble.epsgraphics.*;\r
import jalview.analysis.*;\r
+\r
import jalview.datamodel.*;\r
+\r
import jalview.io.*;\r
+\r
import jalview.jbgui.*;\r
\r
-public class TreePanel\r
- extends GTreePanel\r
-{\r
- SequenceI[] seq;\r
- String type;\r
- String pwtype;\r
- int start;\r
- int end;\r
- TreeCanvas treeCanvas;\r
- NJTree tree;\r
\r
- public TreePanel(AlignViewport av, Vector seqVector, String type,\r
- String pwtype, int s, int e)\r
- {\r
- super();\r
+import java.awt.*;\r
+import java.awt.event.*;\r
\r
- this.type = type;\r
- this.pwtype = pwtype;\r
+import java.io.*;\r
+\r
+import java.util.*;\r
\r
- start = s;\r
- end = e;\r
+import java.beans.PropertyChangeEvent;\r
\r
- String longestName = "";\r
- seq = new Sequence[seqVector.size()];\r
\r
- for (int i = 0; i < seqVector.size(); i++)\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class TreePanel extends GTreePanel\r
+{\r
+ SequenceI[] seq;\r
+ String type;\r
+ String pwtype;\r
+ int start;\r
+ int end;\r
+ TreeCanvas treeCanvas;\r
+ NJTree tree;\r
+\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
- seq[i] = (Sequence) seqVector.elementAt(i);\r
+ super();\r
+ initTreePanel(av, seqVector, type, pwtype, s, e, null);\r
\r
- if (seq[i].getName().length() > longestName.length())\r
- {\r
- longestName = seq[i].getName();\r
- }\r
+ // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default\r
+ showDistances(true);\r
}\r
\r
- tree = new NJTree(seq, type, pwtype, start, end);\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
- treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
- treeCanvas.setShowDistances(true); // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default\r
- setViewStateFromTreeCanvas(treeCanvas);\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
- scrollPane.setViewportView(treeCanvas);\r
- }\r
+ public AlignmentI getAlignment()\r
+ {\r
+ return treeCanvas.av.getAlignment();\r
+ }\r
\r
- public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
- String type, String pwtype)\r
- {\r
- super();\r
\r
- // These are probably only arbitrary strings reflecting source of tree\r
- this.type = type;\r
- this.pwtype = pwtype;\r
+ void initTreePanel(AlignViewport av, Vector seqVector, String type,\r
+ String pwtype, int s, int e, NewickFile newTree)\r
+ {\r
\r
- start = 0;\r
- end = seqVector.size();\r
+ this.type = type;\r
+ this.pwtype = pwtype;\r
\r
- String longestName = "";\r
- seq = new Sequence[seqVector.size()];\r
+ start = s;\r
+ end = e;\r
\r
- for (int i = 0; i < seqVector.size(); i++)\r
- {\r
- seq[i] = (Sequence) seqVector.elementAt(i);\r
- }\r
+ seq = new Sequence[seqVector.size()];\r
+ seqVector.toArray(seq);\r
+\r
+\r
+ treeCanvas = new TreeCanvas(av, scrollPane);\r
+ scrollPane.setViewportView(treeCanvas);\r
+\r
+ av.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
+ {\r
+ public void propertyChange(PropertyChangeEvent evt)\r
+ {\r
+ if (evt.getPropertyName().equals("alignment"))\r
+ {\r
+ if(tree==null)\r
+ System.out.println("tree is null");\r
+ if(evt.getNewValue()==null)\r
+ System.out.println("new value is null");\r
+\r
+ tree.UpdatePlaceHolders( (Vector) evt.getNewValue());\r
+\r
+ repaint();\r
+ }\r
+ }\r
+ });\r
\r
- // This constructor matches sequence names to treenodes and sets up the tree layouts.\r
- tree = new NJTree(seq, newtree);\r
\r
- // Now have to calculate longest name based on the leaves\r
- Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());\r
- boolean has_placeholders = false;\r
+ TreeLoader tl = new TreeLoader(newTree);\r
+ tl.start();\r
\r
- for (int i = 0; i < leaves.size(); i++)\r
+ }\r
+\r
+ class TreeLoader extends Thread\r
{\r
- SequenceNode lf = (SequenceNode) leaves.elementAt(i);\r
+ NewickFile newtree;\r
\r
- if (lf.isPlaceholder())\r
+ public TreeLoader(NewickFile newtree)\r
{\r
- has_placeholders = true;\r
+ this.newtree = newtree;\r
+ if (newtree != null)\r
+ {\r
+ // Must be outside run(), as Jalview2XML tries to\r
+ // update distance/bootstrap visibility at the same time\r
+ showBootstrap(newtree.HasBootstrap());\r
+ showDistances(newtree.HasDistances());\r
+ showPlaceholders(true);\r
+ }\r
}\r
\r
- if (longestName.length() < ( (Sequence) lf.element()).getName()\r
- .length())\r
+ public void run()\r
{\r
- longestName = TreeCanvas.PLACEHOLDER +\r
- ( (Sequence) lf.element()).getName();\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
+\r
+ treeCanvas.repaint();\r
}\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
- scrollPane.setViewportView(treeCanvas);\r
- treeCanvas.setMarkPlaceholders(has_placeholders);\r
- setViewStateFromTreeCanvas(treeCanvas);\r
-\r
- // JBPNote TODO: preference for always marking placeholders in new associated tree\r
- }\r
-\r
- public NJTree getTree()\r
- {\r
- return tree;\r
- }\r
-\r
- private void setViewStateFromTreeCanvas(TreeCanvas tree)\r
- {\r
- // update view menu state from treeCanvas render state\r
- distanceMenu.setSelected(tree.showDistances);\r
- bootstrapMenu.setSelected(tree.showBootstrap);\r
- placeholdersMenu.setSelected(tree.markPlaceholders);\r
- }\r
-\r
- private void setTreeCanvasFromViewState(TreeCanvas tree)\r
- {\r
- // update view menu state from treeCanvas render state\r
- tree.showDistances = distanceMenu.isSelected();\r
- tree.showBootstrap = bootstrapMenu.isSelected();\r
- tree.markPlaceholders = placeholdersMenu.isSelected();\r
- }\r
-\r
- public void textbox_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
-\r
- StringBuffer buffer = new StringBuffer();\r
-\r
- if (type.equals("AV"))\r
+ public void showDistances(boolean b)\r
{\r
- buffer.append("Average distance tree using ");\r
+ treeCanvas.setShowDistances(b);\r
+ distanceMenu.setSelected(b);\r
}\r
- else\r
+\r
+ public void showBootstrap(boolean b)\r
{\r
- buffer.append("Neighbour joining tree using ");\r
+ treeCanvas.setShowBootstrap(b);\r
+ bootstrapMenu.setSelected(b);\r
}\r
\r
- if (pwtype.equals("BL"))\r
+ public void showPlaceholders(boolean b)\r
{\r
- buffer.append("BLOSUM62");\r
+ placeholdersMenu.setState(b);\r
+ treeCanvas.setMarkPlaceholders(b);\r
}\r
- else\r
+\r
+\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public NJTree getTree()\r
{\r
- buffer.append("PID");\r
+ return tree;\r
}\r
\r
- Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);\r
\r
- jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
- cap.setText(fout.print(false, true));\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void textbox_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
\r
- public void saveAsNewick_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
- getProperty(\r
- "LAST_DIRECTORY"));\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Save tree as newick file");\r
- chooser.setToolTipText("Save");\r
+ StringBuffer buffer = new StringBuffer();\r
\r
- int value = chooser.showSaveDialog(null);\r
+ if (type.equals("AV"))\r
+ {\r
+ buffer.append("Average distance tree using ");\r
+ }\r
+ else\r
+ {\r
+ buffer.append("Neighbour joining tree using ");\r
+ }\r
\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
+ if (pwtype.equals("BL"))\r
+ {\r
+ buffer.append("BLOSUM62");\r
+ }\r
+ else\r
+ {\r
+ buffer.append("PID");\r
+ }\r
+\r
+ Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);\r
\r
- try\r
- {\r
jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
- String output = fout.print(false, true); // distances only\r
- java.io.PrintWriter out = new java.io.PrintWriter(new java.io.\r
- FileWriter(\r
- choice));\r
- out.println(output);\r
- out.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
+ cap.setText(fout.print(false, true));\r
}\r
- }\r
-\r
- public void printMenu_actionPerformed(ActionEvent e)\r
- {\r
- //Putting in a thread avoids Swing painting problems\r
- treeCanvas.startPrinting();\r
- }\r
-\r
- public void fitToWindow_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.fitToWindow = fitToWindow.isSelected();\r
- repaint();\r
- }\r
-\r
- public void fontSize_actionPerformed(ActionEvent e)\r
- {\r
- if (treeCanvas == null)\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void saveAsNewick_actionPerformed(ActionEvent e)\r
{\r
- return;\r
- }\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"));\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Save tree as newick file");\r
+ chooser.setToolTipText("Save");\r
\r
- String size = fontSize.getText().substring(fontSize.getText().indexOf("-") +\r
- 1);\r
+ int value = chooser.showSaveDialog(null);\r
\r
- Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
- "Select font size", "Font size", JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- new String[]\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
{\r
- "1", "2", "4", "6", "8", "10", "12", "14", "16", "18", "20"\r
- }, "Font Size - " + size);\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
+\r
+ try\r
+ {\r
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
+ String output = fout.print(false, true); // distances only\r
+ java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(\r
+ choice));\r
+ out.println(output);\r
+ out.close();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
\r
- if (selection != null)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void printMenu_actionPerformed(ActionEvent e)\r
{\r
- fontSize.setText("Font Size - " + selection);\r
-\r
- int i = Integer.parseInt(selection.toString());\r
- treeCanvas.setFontSize(i);\r
+ //Putting in a thread avoids Swing painting problems\r
+ treeCanvas.startPrinting();\r
}\r
\r
- scrollPane.setViewportView(treeCanvas);\r
- }\r
-\r
- public void distanceMenu_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.setShowDistances(distanceMenu.isSelected());\r
- }\r
-\r
- public void bootstrapMenu_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void fitToWindow_actionPerformed(ActionEvent e)\r
+ {\r
+ treeCanvas.fitToWindow = fitToWindow.isSelected();\r
+ repaint();\r
+ }\r
\r
- public void placeholdersMenu_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void font_actionPerformed(ActionEvent e)\r
+ {\r
+ if (treeCanvas == null)\r
+ {\r
+ return;\r
+ }\r
\r
- public void epsTree_actionPerformed(ActionEvent e)\r
- {\r
- int width = treeCanvas.getWidth();\r
- int height = treeCanvas.getHeight();\r
+ new FontChooser(this);\r
+ }\r
\r
- try\r
+ public Font getTreeFont()\r
{\r
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
- jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[]\r
- {"eps"},\r
- new String[]\r
- {"Encapsulated Postscript"},\r
- "Encapsulated Postscript");\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle("Create EPS file from tree");\r
- chooser.setToolTipText("Save");\r
-\r
- int value = chooser.showSaveDialog(this);\r
-\r
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- return;\r
- }\r
-\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
+ return treeCanvas.font;\r
+ }\r
\r
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
- EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,\r
- height);\r
+ public void setTreeFont(Font font)\r
+ {\r
+ if(treeCanvas!=null)\r
+ treeCanvas.setFont(font);\r
+ }\r
\r
- treeCanvas.draw(pg, width, height);\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void distanceMenu_actionPerformed(ActionEvent e)\r
+ {\r
+ treeCanvas.setShowDistances(distanceMenu.isSelected());\r
+ }\r
\r
- pg.flush();\r
- pg.close();\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void bootstrapMenu_actionPerformed(ActionEvent e)\r
+ {\r
+ treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());\r
}\r
- catch (Exception ex)\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void placeholdersMenu_actionPerformed(ActionEvent e)\r
{\r
- ex.printStackTrace();\r
+ treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());\r
}\r
- }\r
\r
- public void pngTree_actionPerformed(ActionEvent e)\r
- {\r
- int width = treeCanvas.getWidth();\r
- int height = treeCanvas.getHeight();\r
\r
- try\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void epsTree_actionPerformed(ActionEvent e)\r
{\r
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
- jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[]\r
- {"png"},\r
- new String[]\r
- {"Portable network graphics"},\r
- "Portable network graphics");\r
-\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle("Create PNG image from tree");\r
- chooser.setToolTipText("Save");\r
+ makeTreeImage(jalview.util.ImageMaker.EPS);\r
+ }\r
\r
- int value = chooser.showSaveDialog(this);\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void pngTree_actionPerformed(ActionEvent e)\r
+ {\r
+ makeTreeImage(jalview.util.ImageMaker.PNG);\r
+ }\r
\r
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
+ void makeTreeImage(int type)\r
+ {\r
+ int width = treeCanvas.getWidth();\r
+ int height = treeCanvas.getHeight();\r
+\r
+ jalview.util.ImageMaker im;\r
+\r
+ if(type == jalview.util.ImageMaker.PNG)\r
+ im = new jalview.util.ImageMaker(this,\r
+ jalview.util.ImageMaker.PNG,\r
+ "Make PNG image from tree",\r
+ width, height,\r
+ null, null);\r
+ else\r
+ im = new jalview.util.ImageMaker(this,\r
+ jalview.util.ImageMaker.EPS,\r
+ "Make EPS file from tree",\r
+ width, height,\r
+ null, this.getTitle());\r
+\r
+ if(im.getGraphics()!=null)\r
{\r
- return;\r
+ treeCanvas.draw(im.getGraphics(), width, height);\r
+ im.writeImage();\r
}\r
-\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
-\r
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
-\r
- BufferedImage bi = new BufferedImage(width, height,\r
- BufferedImage.TYPE_INT_RGB);\r
- Graphics png = bi.getGraphics();\r
-\r
- treeCanvas.draw(png, width, height);\r
-\r
- ImageIO.write(bi, "png", out);\r
- out.close();\r
}\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff