import javax.imageio.*;\r
\r
import javax.swing.*;\r
+import java.beans.PropertyChangeEvent;\r
\r
\r
/**\r
* @param e DOCUMENT ME!\r
*/\r
public TreePanel(AlignViewport av, Vector seqVector, String type,\r
- String pwtype, int s, int e)\r
+ String pwtype, int s, int e)\r
{\r
- super();\r
+ super();\r
+ initTreePanel(av, seqVector, type, pwtype, s, e, null);\r
\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
-\r
- for (int i = 0; i < seqVector.size(); i++)\r
- {\r
- seq[i] = (Sequence) seqVector.elementAt(i);\r
-\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
-\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
+ // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default\r
+ showDistances(true);\r
}\r
\r
/**\r
* @param pwtype DOCUMENT ME!\r
*/\r
public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
- String type, String pwtype)\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
- super();\r
\r
- // These are probably only arbitrary strings reflecting source of tree\r
- this.type = type;\r
- this.pwtype = pwtype;\r
+ this.type = type;\r
+ this.pwtype = pwtype;\r
+\r
+ start = s;\r
+ end = e;\r
\r
- start = 0;\r
- end = seqVector.size();\r
+ seq = new Sequence[seqVector.size()];\r
+ seqVector.toArray(seq);\r
\r
- String longestName = "";\r
- seq = new Sequence[seqVector.size()];\r
\r
- for (int i = 0; i < seqVector.size(); i++)\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
- seq[i] = (Sequence) seqVector.elementAt(i);\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
- SequenceNode lf = (SequenceNode) leaves.elementAt(i);\r
+ }\r
\r
- if (lf.isPlaceholder())\r
- {\r
- has_placeholders = true;\r
- }\r
+ class TreeLoader extends Thread\r
+ {\r
+ NewickFile newtree;\r
\r
- if (longestName.length() < ((Sequence) lf.element()).getName()\r
- .length())\r
- {\r
- longestName = TreeCanvas.PLACEHOLDER +\r
- ((Sequence) lf.element()).getName();\r
- }\r
+ public TreeLoader(NewickFile newtree)\r
+ {\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
}\r
+ }\r
+\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
\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
+ treeCanvas.repaint();\r
\r
- // JBPNote TODO: preference for always marking placeholders in new associated tree\r
+ }\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public NJTree getTree()\r
+ public void showDistances(boolean b)\r
{\r
- return tree;\r
+ treeCanvas.setShowDistances(b);\r
+ distanceMenu.setSelected(b);\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param tree DOCUMENT ME!\r
- */\r
- private void setViewStateFromTreeCanvas(TreeCanvas tree)\r
+ public void showBootstrap(boolean b)\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
+ treeCanvas.setShowBootstrap(b);\r
+ bootstrapMenu.setSelected(b);\r
}\r
\r
+ public void showPlaceholders(boolean b)\r
+ {\r
+ placeholdersMenu.setState(b);\r
+ treeCanvas.setMarkPlaceholders(b);\r
+ }\r
+\r
+\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
- * @param tree DOCUMENT ME!\r
+ * @return DOCUMENT ME!\r
*/\r
- private void setTreeCanvasFromViewState(TreeCanvas tree)\r
+ public NJTree getTree()\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
+ return tree;\r
}\r
\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- public void fontSize_actionPerformed(ActionEvent e)\r
+ public void font_actionPerformed(ActionEvent e)\r
{\r
if (treeCanvas == null)\r
{\r
return;\r
}\r
\r
- String size = fontSize.getText().substring(fontSize.getText().indexOf("-") +\r
- 1);\r
-\r
- Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
- "Select font size", "Font size", JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- new String[]\r
- {\r
- "1", "2", "4", "6", "8", "10", "12", "14", "16", "18", "20"\r
- }, "Font Size - " + size);\r
-\r
- if (selection != null)\r
- {\r
- fontSize.setText("Font Size - " + selection);\r
+ new FontChooser(this);\r
+ }\r
\r
- int i = Integer.parseInt(selection.toString());\r
- treeCanvas.setFontSize(i);\r
- }\r
+ public Font getTreeFont()\r
+ {\r
+ return treeCanvas.font;\r
+ }\r
\r
- scrollPane.setViewportView(treeCanvas);\r
+ public void setTreeFont(Font font)\r
+ {\r
+ if(treeCanvas!=null)\r
+ treeCanvas.setFont(font);\r
}\r
\r
/**\r
*/\r
public void epsTree_actionPerformed(ActionEvent e)\r
{\r
+ boolean accurateText = true;\r
+\r
+ String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",\r
+ "Prompt each time");\r
+\r
+ // If we need to prompt, and if the GUI is visible then\r
+ // Prompt for EPS rendering style\r
+ if (renderStyle.equalsIgnoreCase("Prompt each time")\r
+ && !\r
+ (System.getProperty("java.awt.headless") != null\r
+ && System.getProperty("java.awt.headless").equals("true")))\r
+ {\r
+ EPSOptions eps = new EPSOptions();\r
+ renderStyle = eps.getValue();\r
+\r
+ if (renderStyle==null || eps.cancelled)\r
+ return;\r
+\r
+\r
+ }\r
+\r
+ if (renderStyle.equalsIgnoreCase("text"))\r
+ {\r
+ accurateText = false;\r
+ }\r
+\r
int width = treeCanvas.getWidth();\r
int height = treeCanvas.getHeight();\r
\r
}\r
\r
jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
+ chooser.getSelectedFile().getParent());\r
\r
FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,\r
- height);\r
+ height);\r
+\r
+ pg.setAccurateTextMode(accurateText);\r
\r
treeCanvas.draw(pg, width, height);\r
\r
git://source.jalview.org / jalview.git / blobdiff