X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=c6d87d703f19c80245b4afd371f82697eeabd673;hb=acfc0d246c770a0a1e9cea7cb7fc40cf11f03ca7;hp=3bb910807ca54f4ac22f8ff6d43574f0a1b6c3cc;hpb=7b3241c464d774516c4295a5023f4aef7939298e;p=jalview.git
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 3bb9108..c6d87d7 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -1,613 +1,751 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
*/
package jalview.gui;
-import jalview.analysis.*;
-
-import jalview.datamodel.*;
-
-import jalview.io.*;
-
-import jalview.jbgui.*;
-
-import org.jibble.epsgraphics.*;
+import java.beans.*;
+import java.io.*;
+import java.util.*;
+import javax.imageio.*;
import java.awt.*;
import java.awt.event.*;
import java.awt.image.*;
-
-import java.io.*;
-
-import java.util.*;
-
import javax.swing.*;
-import javax.imageio.*;
-
-import java.beans.PropertyChangeEvent;
+import org.jibble.epsgraphics.*;
+import jalview.analysis.*;
+import jalview.commands.OrderCommand;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.jbgui.*;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
public class TreePanel extends GTreePanel
{
- String type;
- String pwtype;
- TreeCanvas treeCanvas;
- NJTree tree;
- AlignViewport av;
-
- /**
- * Creates a new TreePanel object.
- *
- * @param av DOCUMENT ME!
- * @param seqVector DOCUMENT ME!
- * @param type DOCUMENT ME!
- * @param pwtype DOCUMENT ME!
- * @param s DOCUMENT ME!
- * @param e DOCUMENT ME!
- */
- public TreePanel(AlignmentPanel ap, String type, String pwtype)
+ String type;
+
+ String pwtype;
+
+ TreeCanvas treeCanvas;
+
+ NJTree tree;
+
+ AlignViewport av;
+
+ /**
+ * Creates a new TreePanel object.
+ *
+ * @param av
+ * DOCUMENT ME!
+ * @param seqVector
+ * DOCUMENT ME!
+ * @param type
+ * DOCUMENT ME!
+ * @param pwtype
+ * DOCUMENT ME!
+ * @param s
+ * DOCUMENT ME!
+ * @param e
+ * DOCUMENT ME!
+ */
+ public TreePanel(AlignmentPanel ap, String type, String pwtype)
+ {
+ super();
+ initTreePanel(ap, type, pwtype, null, null);
+
+ // We know this tree has distances. JBPNote TODO: prolly should add this as
+ // a userdefined default
+ // showDistances(true);
+ }
+
+ /**
+ * Creates a new TreePanel object.
+ *
+ * @param av
+ * DOCUMENT ME!
+ * @param seqVector
+ * DOCUMENT ME!
+ * @param newtree
+ * DOCUMENT ME!
+ * @param type
+ * DOCUMENT ME!
+ * @param pwtype
+ * DOCUMENT ME!
+ */
+ public TreePanel(AlignmentPanel ap, String type, String pwtype,
+ NewickFile newtree)
+ {
+ super();
+ initTreePanel(ap, type, pwtype, newtree, null);
+ }
+
+ public TreePanel(AlignmentPanel av, String type, String pwtype,
+ NewickFile newtree, AlignmentView inputData)
+ {
+ super();
+ initTreePanel(av, type, pwtype, newtree, inputData);
+ }
+
+ public AlignmentI getAlignment()
+ {
+ return treeCanvas.av.getAlignment();
+ }
+
+ public AlignViewport getViewPort()
+ {
+ return treeCanvas.av;
+ }
+
+ void initTreePanel(AlignmentPanel ap, String type, String pwtype,
+ NewickFile newTree, AlignmentView inputData)
+ {
+
+ av = ap.av;
+ this.type = type;
+ this.pwtype = pwtype;
+
+ treeCanvas = new TreeCanvas(this, ap, scrollPane);
+ scrollPane.setViewportView(treeCanvas);
+
+ PaintRefresher.Register(this, ap.av.getSequenceSetId());
+
+ buildAssociatedViewMenu();
+
+ av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
{
- super();
- initTreePanel(ap, type, pwtype, null, null);
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ if (evt.getPropertyName().equals("alignment"))
+ {
+ if (tree == null)
+ {
+ System.out.println("tree is null");
+ }
+ if (evt.getNewValue() == null)
+ {
+ System.out
+ .println("new alignment sequences vector value is null");
+ }
- // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
- // showDistances(true);
- }
+ tree.UpdatePlaceHolders((Vector) evt.getNewValue());
+ treeCanvas.nameHash.clear(); // reset the mapping between canvas
+ // rectangles and leafnodes
+ repaint();
+ }
+ }
+ });
- /**
- * Creates a new TreePanel object.
- *
- * @param av DOCUMENT ME!
- * @param seqVector DOCUMENT ME!
- * @param newtree DOCUMENT ME!
- * @param type DOCUMENT ME!
- * @param pwtype DOCUMENT ME!
- */
- public TreePanel(AlignmentPanel ap,
- String type,
- String pwtype,
- NewickFile newtree)
+ TreeLoader tl = new TreeLoader(newTree);
+ if (inputData != null)
{
- super();
- initTreePanel(ap, type, pwtype, newtree, null);
+ tl.odata = inputData;
}
+ tl.start();
- public TreePanel(AlignmentPanel av,
- String type,
- String pwtype,
- NewickFile newtree, AlignmentView inputData) {
- super();
- initTreePanel(av,type,pwtype,newtree,inputData);
- }
+ }
- public AlignmentI getAlignment()
- {
- return treeCanvas.av.getAlignment();
- }
- public AlignViewport getViewPort() {
- return treeCanvas.av;
- }
+ public void viewMenu_menuSelected()
+ {
+ buildAssociatedViewMenu();
+ }
- void initTreePanel(AlignmentPanel ap, String type, String pwtype,
- NewickFile newTree, AlignmentView inputData)
+ void buildAssociatedViewMenu()
+ {
+ AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
+ .getSequenceSetId());
+ if (aps.length == 1 && treeCanvas.ap == aps[0])
{
+ associateLeavesMenu.setVisible(false);
+ return;
+ }
- av = ap.av;
- this.type = type;
- this.pwtype = pwtype;
+ associateLeavesMenu.setVisible(true);
- buildAssociatedViewMenu();
+ if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
+ {
+ viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
+ }
- treeCanvas = new TreeCanvas(ap, scrollPane);
- scrollPane.setViewportView(treeCanvas);
+ associateLeavesMenu.removeAll();
- av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
+ JRadioButtonMenuItem item;
+ ButtonGroup buttonGroup = new ButtonGroup();
+ int i, iSize = aps.length;
+ final TreePanel thisTreePanel = this;
+ for (i = 0; i < iSize; i++)
+ {
+ final AlignmentPanel ap = aps[i];
+ item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
+ buttonGroup.add(item);
+ item.addActionListener(new ActionListener()
{
- public void propertyChange(PropertyChangeEvent evt)
+ public void actionPerformed(ActionEvent evt)
{
- if (evt.getPropertyName().equals("alignment"))
- {
- if(tree==null)
- System.out.println("tree is null");
- if(evt.getNewValue()==null)
- System.out.println("new alignment sequences vector value is null");
-
- tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
- treeCanvas.nameHash.clear(); // reset the mapping between canvas rectangles and leafnodes
- repaint();
- }
+ treeCanvas.applyToAllViews = false;
+ treeCanvas.ap = ap;
+ treeCanvas.av = ap.av;
+ PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
}
});
- TreeLoader tl = new TreeLoader(newTree);
- if (inputData!=null) {
- tl.odata=inputData;
- }
- tl.start();
-
+ associateLeavesMenu.add(item);
}
- void buildAssociatedViewMenu()
+ final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
+ buttonGroup.add(itemf);
+ itemf.setSelected(treeCanvas.applyToAllViews);
+ itemf.addActionListener(new ActionListener()
{
- AlignmentPanel [] aps = PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
- if(aps.length<2)
+ public void actionPerformed(ActionEvent evt)
{
- associateLeavesMenu.setVisible(false);
- return;
+ treeCanvas.applyToAllViews = itemf.isSelected();
}
- associateLeavesMenu.addSeparator();
+ });
+ associateLeavesMenu.add(itemf);
- JRadioButtonMenuItem item;
- ButtonGroup buttonGroup = new ButtonGroup();
- int i, iSize = aps.length;
- for(i=0; i>>This is a fix for the moment, until a better solution is found!!<<<
- // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
-
- // af.addSortByOrderMenuItem(ServiceName + " Ordering",
- // msaorder);
-
- Desktop.addInternalFrame(af, "Original Data for " + this.title,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
- }
- }
- }
+ if (true)
+ {
+ // make a new frame!
+ AlignFrame af = new AlignFrame(al,
+ (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void fitToWindow_actionPerformed(ActionEvent e)
- {
- treeCanvas.fitToWindow = fitToWindow.isSelected();
- repaint();
- }
+ // >>>This is a fix for the moment, until a better solution is
+ // found!!<<<
+ // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void font_actionPerformed(ActionEvent e)
- {
- if (treeCanvas == null)
- {
- return;
- }
+ // af.addSortByOrderMenuItem(ServiceName + " Ordering",
+ // msaorder);
- new FontChooser(this);
+ Desktop.addInternalFrame(af, "Original Data for " + this.title,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ }
}
-
- public Font getTreeFont()
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void fitToWindow_actionPerformed(ActionEvent e)
+ {
+ treeCanvas.fitToWindow = fitToWindow.isSelected();
+ repaint();
+ }
+
+ /**
+ * sort the associated alignment view by the current tree.
+ * @param e
+ */
+ public void sortByTree_actionPerformed(ActionEvent e)
+ {
+ AlignmentPanel ap = av.getAlignPanel();
+ SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByTree(av.getAlignment(), tree);
+
+ ap.alignFrame
+ .addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
+ av.alignment));
+
+ ap.paintAlignment(true);
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void font_actionPerformed(ActionEvent e)
+ {
+ if (treeCanvas == null)
{
- return treeCanvas.font;
+ return;
}
- public void setTreeFont(Font font)
+ new FontChooser(this);
+ }
+
+ public Font getTreeFont()
+ {
+ return treeCanvas.font;
+ }
+
+ public void setTreeFont(Font font)
+ {
+ if (treeCanvas != null)
{
- if(treeCanvas!=null)
treeCanvas.setFont(font);
}
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void distanceMenu_actionPerformed(ActionEvent e)
+ {
+ treeCanvas.setShowDistances(distanceMenu.isSelected());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void bootstrapMenu_actionPerformed(ActionEvent e)
+ {
+ treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void placeholdersMenu_actionPerformed(ActionEvent e)
+ {
+ treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void epsTree_actionPerformed(ActionEvent e)
+ {
+ boolean accurateText = true;
+
+ String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
+ "Prompt each time");
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void distanceMenu_actionPerformed(ActionEvent e)
+ // If we need to prompt, and if the GUI is visible then
+ // Prompt for EPS rendering style
+ if (renderStyle.equalsIgnoreCase("Prompt each time")
+ && !(System.getProperty("java.awt.headless") != null && System
+ .getProperty("java.awt.headless").equals("true")))
{
- treeCanvas.setShowDistances(distanceMenu.isSelected());
- }
+ EPSOptions eps = new EPSOptions();
+ renderStyle = eps.getValue();
+
+ if (renderStyle == null || eps.cancelled)
+ {
+ return;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void bootstrapMenu_actionPerformed(ActionEvent e)
- {
- treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
}
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void placeholdersMenu_actionPerformed(ActionEvent e)
+ if (renderStyle.equalsIgnoreCase("text"))
{
- treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
+ accurateText = false;
}
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void epsTree_actionPerformed(ActionEvent e)
+ int width = treeCanvas.getWidth();
+ int height = treeCanvas.getHeight();
+
+ try
{
- boolean accurateText = true;
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+ { "eps" }, new String[]
+ { "Encapsulated Postscript" }, "Encapsulated Postscript");
+ chooser.setFileView(new jalview.io.JalviewFileView());
+ chooser.setDialogTitle("Create EPS file from tree");
+ chooser.setToolTipText("Save");
- String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
- "Prompt each time");
+ int value = chooser.showSaveDialog(this);
- // If we need to prompt, and if the GUI is visible then
- // Prompt for EPS rendering style
- if (renderStyle.equalsIgnoreCase("Prompt each time")
- && !
- (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true")))
+ if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
{
- EPSOptions eps = new EPSOptions();
- renderStyle = eps.getValue();
+ return;
+ }
- if (renderStyle==null || eps.cancelled)
- return;
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+ .getSelectedFile().getParent());
+ FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+ EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
- }
+ pg.setAccurateTextMode(accurateText);
- if (renderStyle.equalsIgnoreCase("text"))
- {
- accurateText = false;
- }
+ treeCanvas.draw(pg, width, height);
- int width = treeCanvas.getWidth();
- int height = treeCanvas.getHeight();
+ pg.flush();
+ pg.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void pngTree_actionPerformed(ActionEvent e)
+ {
+ int width = treeCanvas.getWidth();
+ int height = treeCanvas.getHeight();
+
+ try
+ {
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+ { "png" }, new String[]
+ { "Portable network graphics" }, "Portable network graphics");
- try
- {
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
- "LAST_DIRECTORY"), new String[] { "eps" },
- new String[] { "Encapsulated Postscript" },
- "Encapsulated Postscript");
- chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Create EPS file from tree");
- chooser.setToolTipText("Save");
+ chooser.setFileView(new jalview.io.JalviewFileView());
+ chooser.setDialogTitle("Create PNG image from tree");
+ chooser.setToolTipText("Save");
- int value = chooser.showSaveDialog(this);
+ int value = chooser.showSaveDialog(this);
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
- {
- return;
- }
+ if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ {
+ return;
+ }
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- chooser.getSelectedFile().getParent());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+ .getSelectedFile().getParent());
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
- EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
- height);
+ FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
- pg.setAccurateTextMode(accurateText);
+ BufferedImage bi = new BufferedImage(width, height,
+ BufferedImage.TYPE_INT_RGB);
+ Graphics png = bi.getGraphics();
- treeCanvas.draw(pg, width, height);
+ treeCanvas.draw(png, width, height);
- pg.flush();
- pg.close();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void pngTree_actionPerformed(ActionEvent e)
+ ImageIO.write(bi, "png", out);
+ out.close();
+ } catch (Exception ex)
{
- int width = treeCanvas.getWidth();
- int height = treeCanvas.getHeight();
-
- try
+ ex.printStackTrace();
+ }
+ }
+ /**
+ * change node labels to the annotation referred to by labelClass
+ * TODO: promote to a datamodel modification that can be undone
+ * TODO: make argument one case of a generic transformation function ie { undoStep = apply(Tree, TransformFunction)};
+ * @param labelClass
+ */
+ public void changeNames(final String labelClass)
+ {
+ tree.applyToNodes(new NodeTransformI() {
+
+ public void transform(BinaryNode node)
+ {
+ if (node instanceof SequenceNode && !((SequenceNode) node).isPlaceholder() && !((SequenceNode) node).isDummy())
{
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
- "LAST_DIRECTORY"), new String[] { "png" },
- new String[] { "Portable network graphics" },
- "Portable network graphics");
-
- chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Create PNG image from tree");
- chooser.setToolTipText("Save");
-
- int value = chooser.showSaveDialog(this);
-
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ String newname=null;
+ SequenceI sq = (SequenceI) ((SequenceNode) node).element();
+ if (sq!=null)
+ {
+ // search dbrefs, features and annotation
+ DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(sq.getDBRef(), new String[] {labelClass.toUpperCase()});
+ if (refs!=null)
{
- return;
+ for (int i=0; i