/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 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
\r
import javax.imageio.*;\r
\r
-import javax.swing.*;\r
import java.beans.PropertyChangeEvent;\r
\r
\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
+ AlignViewport av;\r
\r
/**\r
* Creates a new TreePanel object.\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
+ public TreePanel(AlignmentPanel ap, String type, String pwtype)\r
{\r
super();\r
- initTreePanel(av, seqVector, type, pwtype, s, e, null);\r
+ initTreePanel(ap, type, pwtype, null);\r
\r
// We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default\r
- treeCanvas.setShowDistances(true);\r
+ // showDistances(true);\r
}\r
\r
/**\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
+ public TreePanel(AlignmentPanel ap,\r
+ String type,\r
+ String pwtype,\r
+ NewickFile newtree)\r
{\r
super();\r
- initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);\r
+ initTreePanel(ap, type, pwtype, newtree);\r
}\r
\r
+ public AlignmentI getAlignment()\r
+ {\r
+ return treeCanvas.av.getAlignment();\r
+ }\r
\r
- void initTreePanel(AlignViewport av, Vector seqVector, String type,\r
- String pwtype, int s, int e, NewickFile newTree)\r
+\r
+ void initTreePanel(AlignmentPanel ap, String type, String pwtype,\r
+ NewickFile newTree)\r
{\r
\r
+ av = ap.av;\r
this.type = type;\r
this.pwtype = pwtype;\r
\r
- start = s;\r
- end = e;\r
-\r
- seq = new Sequence[seqVector.size()];\r
- seqVector.toArray(seq);\r
-\r
-\r
- treeCanvas = new TreeCanvas(av, scrollPane);\r
+ treeCanvas = new TreeCanvas(ap, scrollPane);\r
scrollPane.setViewportView(treeCanvas);\r
\r
av.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
}\r
});\r
\r
+ this.av = av;\r
+\r
\r
TreeLoader tl = new TreeLoader(newTree);\r
tl.start();\r
class TreeLoader extends Thread\r
{\r
NewickFile newtree;\r
-\r
+ jalview.datamodel.AlignmentView odata=null;\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
if(newtree!=null)\r
{\r
- treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
- treeCanvas.setShowDistances(newtree.HasDistances());\r
+ if (odata==null) {\r
+ tree = new NJTree(av.alignment.getSequencesArray(),\r
+ newtree);\r
+ } else {\r
+ tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);\r
+ }\r
+ if (!tree.hasOriginalSequenceData())\r
+ allowOriginalSeqData(false);\r
+ }\r
+ else\r
+ {\r
+ int start, end;\r
+ SequenceI [] seqs;\r
+ AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);\r
+ if(av.getSelectionGroup()==null)\r
+ {\r
+ start = 0;\r
+ end = av.alignment.getWidth();\r
+ seqs = av.alignment.getSequencesArray();\r
+ }\r
+ else\r
+ {\r
+ start = av.getSelectionGroup().getStartRes();\r
+ end = av.getSelectionGroup().getEndRes()+1;\r
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
+ }\r
+\r
+ tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);\r
+ showDistances(true);\r
}\r
\r
- setViewStateFromTreeCanvas(treeCanvas);\r
\r
+ tree.reCount(tree.getTopNode());\r
+ tree.findHeight(tree.getTopNode());\r
+ treeCanvas.setTree(tree);\r
treeCanvas.repaint();\r
+ av.setCurrentTree(tree);\r
\r
}\r
}\r
\r
+ public void showDistances(boolean b)\r
+ {\r
+ treeCanvas.setShowDistances(b);\r
+ distanceMenu.setSelected(b);\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public NJTree getTree()\r
+ public void showBootstrap(boolean b)\r
{\r
- return tree;\r
+ treeCanvas.setShowBootstrap(b);\r
+ bootstrapMenu.setSelected(b);\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param tree DOCUMENT ME!\r
- */\r
- private void setViewStateFromTreeCanvas(TreeCanvas tree)\r
+ public void showPlaceholders(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
+ placeholdersMenu.setState(b);\r
+ treeCanvas.setMarkPlaceholders(b);\r
+ }\r
+\r
+ private void allowOriginalSeqData(boolean b) {\r
+ originalSeqData.setVisible(b);\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
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
+ cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));\r
}\r
\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
+ String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());\r
java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(\r
choice));\r
out.println(output);\r
treeCanvas.startPrinting();\r
}\r
\r
+\r
+ public void originalSeqData_actionPerformed(ActionEvent e)\r
+ {\r
+ if (!tree.hasOriginalSequenceData())\r
+ {\r
+ jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");\r
+ return;\r
+ }\r
+ // decide if av alignment is sufficiently different to original data to warrant a new window to be created\r
+ // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)\r
+ // or create a selection box around columns in alignment view\r
+ // test Alignment(SeqCigar[])\r
+ Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.\r
+ getGapCharacter());\r
+\r
+\r
+ if (alAndColsel != null && alAndColsel[0]!=null)\r
+ {\r
+ // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);\r
+\r
+ Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);\r
+ Alignment dataset = av.getAlignment().getDataset();\r
+ if (dataset != null)\r
+ {\r
+ al.setDataset(dataset);\r
+ }\r
+\r
+ if (true)\r
+ {\r
+ // make a new frame!\r
+ AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],\r
+ AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT\r
+);\r
+\r
+ //>>>This is a fix for the moment, until a better solution is found!!<<<\r
+ // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());\r
+\r
+ // af.addSortByOrderMenuItem(ServiceName + " Ordering",\r
+ // msaorder);\r
+\r
+ Desktop.addInternalFrame(af, "Original Data for " + this.title,\r
+ AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT);\r
+ }\r
+ }\r
+ }\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
git://source.jalview.org / jalview.git / blobdiff