X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=6617277d2500901e3fa79eadbb595b87b3da0124;hb=4a3def9f59cefe629c9a33d87483283aee085928;hp=d4c88de7acb8c238b51d0079145034ce66379d4b;hpb=a7c9bef24b1d0fedd17c0ab0468864ca97c0b649;p=jalview.git
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index d4c88de..6617277 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -1,501 +1,1136 @@
-package jalview.gui;
-
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.util.*;
-import jalview.schemes.*;
-import javax.swing.*;
-import java.awt.*;
-import java.awt.event.*;
-import java.util.*;
-import java.awt.print.*;
-
-public class TreeCanvas extends JPanel implements MouseListener, Runnable, Printable
-{
- NJTree tree;
- JScrollPane scrollPane;
- AlignViewport av;
-
- Font font;
- int fontSize = 12;
-
- boolean fitToWindow = true;
- boolean showDistances = false;
- boolean showBootstrap = false;
-
- int offx = 20;
- int offy = 20;
-
- float threshold;
-
- String longestName;
- int labelLength=-1;
-
- //RubberbandRectangle rubberband;
-
- Vector listeners;
-
- Hashtable nameHash = new Hashtable();
- Hashtable nodeHash = new Hashtable();
-
- public TreeCanvas(AlignViewport av, NJTree tree, JScrollPane scroller, String label)
- {
- this.av = av;
- this.tree = tree;
- scrollPane = scroller;
- addMouseListener(this);
- tree.findHeight(tree.getTopNode());
- longestName = label;
-
- PaintRefresher.Register(this);
- }
- public void TreeSelectionChanged(Sequence sequence)
- {
- SequenceGroup selected = av.getSelectionGroup();
- if(selected == null)
- {
- selected = new SequenceGroup();
- av.setSelectionGroup(selected);
- }
-
- selected.setEndRes(av.alignment.getWidth());
- selected.addOrRemove(sequence);
-
-
- PaintRefresher.Refresh(this);
- repaint();
- }
-
-
-
- public void setTree(NJTree tree) {
- this.tree = tree;
- tree.findHeight(tree.getTopNode());
- }
-
- public void drawNode(Graphics g,SequenceNode node, float chunk, float scale, int width,int offx, int offy) {
- if (node == null) {
- return;
- }
-
- if (node.left() == null && node.right() == null) {
- // Drawing leaf node
-
- float height = node.height;
- float dist = node.dist;
-
- int xstart = (int)((height-dist)*scale) + offx;
- int xend = (int)(height*scale) + offx;
-
- int ypos = (int)(node.ycount * chunk) + offy;
-
- if (node.element() instanceof SequenceI)
- {
- if ( ( (SequenceI) ( (SequenceNode) node).element()).getColor() == Color.white)
- {
- g.setColor(Color.black);
- }
- else
- g.setColor( ( (SequenceI) ( (SequenceNode) node).element()).getColor().
- darker());
-
- }
- else
- g.setColor(Color.black);
-
-
- // Draw horizontal line
- g.drawLine(xstart,ypos,xend,ypos);
-
- String nodeLabel = "";
- if (showDistances && node.dist > 0) {
- nodeLabel = new Format("%5.2f").form(node.dist);
- }
- if (showBootstrap) {
- if (showDistances) {
- nodeLabel = nodeLabel + " : ";
- }
- nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
- }
- if (! nodeLabel.equals("")) {
- g.drawString(nodeLabel,xstart,ypos - 10);
- }
-
- // Colour selected leaves differently
- String name = node.getName();
- FontMetrics fm = g.getFontMetrics(font);
- int charWidth = fm.stringWidth(node.getName()) + 3;
- int charHeight = fm.getHeight();
-
- Rectangle rect = new Rectangle(xend+20,ypos-charHeight,
- charWidth,charHeight);
-
- nameHash.put((SequenceI)node.element(),rect);
-
- SequenceGroup selected = av.getSelectionGroup();
- if (selected!=null && selected.sequences.contains((SequenceI)node.element())) {
- g.setColor(Color.gray);
-
- g.fillRect(xend + 10, ypos - charHeight + 3,charWidth,charHeight);
- g.setColor(Color.white);
- }
- g.drawString(node.getName(),xend+10,ypos);
- g.setColor(Color.black);
- } else {
- drawNode(g,(SequenceNode)node.left(), chunk,scale,width,offx,offy);
- drawNode(g,(SequenceNode)node.right(),chunk,scale,width,offx,offy);
-
- float height = node.height;
- float dist = node.dist;
-
- int xstart = (int)((height-dist)*scale) + offx;
- int xend = (int)(height *scale) + offx;
- int ypos = (int)(node.ycount *chunk) + offy;
-
- g.setColor(((SequenceNode)node).color.darker());
-
- // Draw horizontal line
- g.drawLine(xstart,ypos,xend,ypos);
- g.fillRect(xend-2, ypos-2, 4,4);
-
- int ystart = (int)(((SequenceNode)node.left()) .ycount * chunk) + offy;
- int yend = (int)(((SequenceNode)node.right()).ycount * chunk) + offy;
-
- Rectangle pos = new Rectangle(xend-2,ypos-2,5,5);
- nodeHash.put(node,pos);
-
- g.drawLine((int)(height*scale) + offx, ystart,
- (int)(height*scale) + offx, yend);
-
- if (showDistances && node.dist > 0) {
- g.drawString(new Format("%5.2f").form(node.dist),xstart,ypos - 5);
- }
-
- }
- }
- public Object findElement(int x, int y) {
- Enumeration keys = nameHash.keys();
-
- while (keys.hasMoreElements()) {
- Object ob = keys.nextElement();
- Rectangle rect = (Rectangle)nameHash.get(ob);
-
- if (x >= rect.x && x <= (rect.x + rect.width) &&
- y >= rect.y && y <= (rect.y + rect.height)) {
- return ob;
- }
- }
- keys = nodeHash.keys();
-
- while (keys.hasMoreElements()) {
- Object ob = keys.nextElement();
- Rectangle rect = (Rectangle)nodeHash.get(ob);
-
- if (x >= rect.x && x <= (rect.x + rect.width) &&
- y >= rect.y && y <= (rect.y + rect.height)) {
- return ob;
- }
- }
- return null;
-
- }
-
- public void pickNodes(Rectangle pickBox) {
- int width = getWidth();
- int height = getHeight();
-
- SequenceNode top = tree.getTopNode();
-
- float wscale = (float)(width*.8-offx*2)/tree.getMaxHeight()
-;
- if (top.count == 0) {
- top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;
- }
- float chunk = (float)(height-offy*2)/top.count;
-
- pickNode(pickBox,top,chunk,wscale,width,offx,offy);
- }
-
- public void pickNode(Rectangle pickBox, SequenceNode node, float chunk, float scale, int width,int offx, int offy) {
- if (node == null) {
- return;
- }
-
- if (node.left() == null && node.right() == null) {
- float height = node.height;
- float dist = node.dist;
-
- int xstart = (int)((height-dist)*scale) + offx;
- int xend = (int)(height*scale) + offx;
-
- int ypos = (int)(node.ycount * chunk) + offy;
-
- if (pickBox.contains(new Point(xend,ypos))) {
- if (node.element() instanceof SequenceI) {
- SequenceI seq = (SequenceI)node.element();
- SequenceGroup sg = av.getSelectionGroup();
- if(sg!=null)
- sg.addOrRemove(seq);
- }
- }
- } else {
- pickNode(pickBox,(SequenceNode)node.left(), chunk,scale,width,offx,offy);
- pickNode(pickBox,(SequenceNode)node.right(),chunk,scale,width,offx,offy);
- }
- }
-
- public void setColor(SequenceNode node, Color c)
- {
- if (node == null)
- return;
-
- if (node.left() == null && node.right() == null)
- {
- node.color = c;
-
- if (node.element() instanceof SequenceI)
- ((SequenceI)node.element()).setColor(c);
- } else
- {
- node.color = c;
- setColor((SequenceNode)node.left(),c);
- setColor((SequenceNode)node.right(),c);
- }
- }
-
- void startPrinting()
- {
- Thread thread = new Thread(this);
- thread.start();
- }
-
- // put printing in a thread to avoid painting problems
- public void run()
- {
- PrinterJob printJob = PrinterJob.getPrinterJob();
- PageFormat pf = printJob.pageDialog(printJob.defaultPage());
-
- printJob.setPrintable(this, pf);
- if (printJob.printDialog())
- {
- try
- {
- printJob.print();
- }
- catch (Exception PrintException)
- {
- PrintException.printStackTrace();
- }
- }
- }
-
-
- public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
- {
-
- pg.setFont(font);
- pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
- int pwidth = (int) pf.getImageableWidth();
- int pheight = (int) pf.getImageableHeight();
-
- int noPages = getHeight() / pheight;
- if(pi>noPages)
- return Printable.NO_SUCH_PAGE;
-
-
- if (pwidth > getWidth())
- pwidth = getWidth();
-
- if(fitToWindow)
- {
- if (pheight > getHeight())
- pheight = getHeight();
-
- noPages = 0;
- }
- else
- {
-
- FontMetrics fm = pg.getFontMetrics(font);
- int height = fm.getHeight() * nameHash.size();
- pg.translate(0, -pi*pheight );
- pg.setClip(0,pi*pheight, pwidth,pi*pheight + pheight);
- // translate number of pages,
- // height is screen size as this is the
- // non overlapping text size
- pheight = height;
- }
-
- draw(pg, pwidth, pheight);
-
- return Printable.PAGE_EXISTS;
-
- }
-
- public void paintComponent(Graphics g)
- {
-
- font = new Font("Verdana",Font.PLAIN,fontSize);
- g.setFont(font);
-
- FontMetrics fm = g.getFontMetrics(font);
-
- if(nameHash.size()==0)
- repaint();
-
-
- if( fitToWindow || (!fitToWindow && scrollPane.getHeight() > fm.getHeight() * nameHash.size()+offy ) )
- {
- draw(g,scrollPane.getWidth(),scrollPane.getHeight());
- setPreferredSize(null);
- }
- else
- {
- setPreferredSize(new Dimension(scrollPane.getWidth(), fm.getHeight() * nameHash.size()));
- draw( g,scrollPane.getWidth(), fm.getHeight() * nameHash.size());
- }
-
- scrollPane.revalidate();
- }
- public int getFontSize() {
- return fontSize;
- }
- public void setFontSize(int fontSize) {
- this.fontSize = fontSize;
- repaint();
- }
- public void draw(Graphics g1, int width, int height) {
-
- Graphics2D g2 = (Graphics2D)g1;
- g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
- g2.setColor(Color.white);
- g2.fillRect(0,0,width,height);
-
-
- labelLength = g2.getFontMetrics(font).stringWidth(longestName)+ 20;//20 allows for scrollbar
-
- float wscale =(float)(width - labelLength -offx*2)/tree.getMaxHeight();
-
- SequenceNode top = tree.getTopNode();
-
- if (top.count == 0) {
- top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;
- }
- float chunk = (float)(height-offy*2)/top.count ;
-
- drawNode(g2,tree.getTopNode(),chunk,wscale,width,offx,offy);
-
- if (threshold != 0)
- {
- if(av.getCurrentTree() == tree)
- g2.setColor(Color.red);
- else
- g2.setColor(Color.gray);
-
- int x = (int)( threshold * (float)(getWidth()-labelLength - 2*offx) +offx ) ;
-
- g2.drawLine(x,0,x,getHeight());
- }
-
- }
-
- public void mouseReleased(MouseEvent e) { }
- public void mouseEntered(MouseEvent e) { }
- public void mouseExited(MouseEvent e) { }
- public void mouseClicked(MouseEvent e) {
- }
-
- public void mousePressed(MouseEvent e) {
-
- av.setCurrentTree(tree);
-
- int x = e.getX();
- int y = e.getY();
-
- Object ob = findElement(x,y);
-
- if (ob instanceof SequenceI)
- {
- TreeSelectionChanged((Sequence)ob);
- repaint();
- return;
-
- } else if (ob instanceof SequenceNode) {
- SequenceNode tmpnode = (SequenceNode)ob;
- tree.swapNodes(tmpnode);
- tree.reCount(tree.getTopNode());
- tree.findHeight(tree.getTopNode());
- } else {
- // Find threshold
-
- if (tree.getMaxHeight() != 0) {
- threshold = (float)(x - offx)/(float)(getWidth()-labelLength - 2*offx);
-
- tree.getGroups().removeAllElements();
- tree.groupNodes(tree.getTopNode(),threshold);
- setColor(tree.getTopNode(),Color.black);
-
- av.setSelectionGroup(null);
- av.alignment.deleteAllGroups();
-
- for (int i=0; i < tree.getGroups().size(); i++)
- {
-
- Color col = new Color((int)(Math.random()*255),
- (int)(Math.random()*255),
- (int)(Math.random()*255));
- setColor((SequenceNode)tree.getGroups().elementAt(i),col.brighter());
-
- Vector l = tree.findLeaves((SequenceNode)tree.getGroups().elementAt(i),new Vector());
- SequenceGroup sg = null;
- for (int j = 0; j < l.size(); j++)
- {
- SequenceNode sn = (SequenceNode) l.elementAt(j);
- if(sg==null)
- sg = new SequenceGroup("TreeGroup", av.getGlobalColourScheme(), true, true,false,0,av.alignment.getWidth());
-
- sg.addSequence( (Sequence) sn.element());
- }
-
- if (av.getGlobalColourScheme() instanceof ConservationColourScheme)
- {
- ConservationColourScheme ccs = (ConservationColourScheme) av.getGlobalColourScheme();
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.sequences, sg.getStartRes(),
- sg.getEndRes());
-
- c.calculate();
- c.verdict(false, av.ConsPercGaps);
- ccs = new ConservationColourScheme(c, ccs.cs);
-
- sg.cs = ccs;
-
- }
-
-
-
- av.alignment.addGroup(sg);
-
- }
- }
- }
-
- PaintRefresher.Refresh(this);
- repaint();
-
- }
-
- public void setShowDistances(boolean state) {
- this.showDistances = state;
- repaint();
- }
-
- public void setShowBootstrap(boolean state) {
- this.showBootstrap = state;
- repaint();
- }
-
-}
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.RenderingHints;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.print.PageFormat;
+import java.awt.print.Printable;
+import java.awt.print.PrinterException;
+import java.awt.print.PrinterJob;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Vector;
+
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
+
+import jalview.analysis.Conservation;
+import jalview.analysis.TreeModel;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.schemes.ColourSchemeI;
+import jalview.structure.SelectionSource;
+import jalview.util.Format;
+import jalview.util.MessageManager;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class TreeCanvas extends JPanel implements MouseListener, Runnable,
+ Printable, MouseMotionListener, SelectionSource
+{
+ /** DOCUMENT ME!! */
+ public static final String PLACEHOLDER = " * ";
+
+ TreeModel tree;
+
+ JScrollPane scrollPane;
+
+ TreePanel tp;
+
+ private AlignViewport av;
+
+ private AlignmentPanel ap;
+
+ Font font;
+
+ FontMetrics fm;
+
+ boolean fitToWindow = true;
+
+ boolean showDistances = false;
+
+ boolean showBootstrap = false;
+
+ boolean markPlaceholders = false;
+
+ int offx = 20;
+
+ int offy;
+
+ private float threshold;
+
+ String longestName;
+
+ int labelLength = -1;
+
+ Map