X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=6f143dbb5b54f24342db1cc7c355d17558822b99;hb=fa9da54fb97cb2eacb1af7859024d90166bddb8f;hp=d8ed3eeba55acdb6635868e15c22f167f30fc949;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index d8ed3ee..6f143db 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -1,776 +1,1136 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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.schemes.*;
-
-import jalview.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.print.*;
-
-import java.util.*;
-
-import javax.swing.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class TreeCanvas extends JPanel implements MouseListener, Runnable,
- Printable
-{
- /** DOCUMENT ME!! */
- public static final String PLACEHOLDER = " * ";
- NJTree tree;
- JScrollPane scrollPane;
- AlignViewport av;
- Font font;
- int fontSize = 12;
- boolean fitToWindow = true;
- boolean showDistances = false;
- boolean showBootstrap = false;
- boolean markPlaceholders = 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();
-
- /**
- * Creates a new TreeCanvas object.
- *
- * @param av DOCUMENT ME!
- * @param tree DOCUMENT ME!
- * @param scroller DOCUMENT ME!
- * @param label DOCUMENT ME!
- */
- 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, av.alignment);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param sequence DOCUMENT ME!
- */
- 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, true);
-
- PaintRefresher.Refresh(this, av.alignment);
- repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param tree DOCUMENT ME!
- */
- public void setTree(NJTree tree)
- {
- this.tree = tree;
- tree.findHeight(tree.getTopNode());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- * @param node DOCUMENT ME!
- * @param chunk DOCUMENT ME!
- * @param scale DOCUMENT ME!
- * @param width DOCUMENT ME!
- * @param offx DOCUMENT ME!
- * @param offy DOCUMENT ME!
- */
- 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);
- }
-
- String name = (markPlaceholders && node.isPlaceholder())
- ? (PLACEHOLDER + node.getName()) : node.getName();
- FontMetrics fm = g.getFontMetrics(font);
- int charWidth = fm.stringWidth(name) + 3;
- int charHeight = fm.getHeight();
-
- Rectangle rect = new Rectangle(xend + 20, ypos - charHeight,
- charWidth, charHeight);
-
- nameHash.put((SequenceI) node.element(), rect);
-
- // Colour selected leaves differently
- 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(name, 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);
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param x DOCUMENT ME!
- * @param y DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- 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;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param pickBox DOCUMENT ME!
- */
- 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);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param pickBox DOCUMENT ME!
- * @param node DOCUMENT ME!
- * @param chunk DOCUMENT ME!
- * @param scale DOCUMENT ME!
- * @param width DOCUMENT ME!
- * @param offx DOCUMENT ME!
- * @param offy DOCUMENT ME!
- */
- 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, true);
- }
- }
- }
- }
- else
- {
- pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width,
- offx, offy);
- pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,
- offx, offy);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
- * @param c DOCUMENT ME!
- */
- 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);
- }
- }
-
- /**
- * DOCUMENT ME!
- */
- 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();
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param pg DOCUMENT ME!
- * @param pf DOCUMENT ME!
- * @param pi DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- *
- * @throws PrinterException DOCUMENT ME!
- */
- 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;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- */
- public void paintComponent(Graphics g)
- {
- super.paintComponent(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();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getFontSize()
- {
- return fontSize;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param fontSize DOCUMENT ME!
- */
- public void setFontSize(int fontSize)
- {
- this.fontSize = fontSize;
- repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g1 DOCUMENT ME!
- * @param width DOCUMENT ME!
- * @param height DOCUMENT ME!
- */
- 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());
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void mouseReleased(MouseEvent e)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void mouseEntered(MouseEvent e)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void mouseExited(MouseEvent e)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void mouseClicked(MouseEvent e)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- 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());
-
- Vector sequences = new Vector();
-
- for (int j = 0; j < l.size(); j++)
- {
- SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j)).element();
-
- if (!sequences.contains(s1))
- {
- sequences.addElement(s1);
- }
- }
-
- ColourSchemeI cs = ColourSchemeProperty.getColour(sequences,
- av.alignment.getWidth(),
- ColourSchemeProperty.getColourName(
- av.getGlobalColourScheme()));
-
- SequenceGroup sg = new SequenceGroup(sequences,
- "TreeGroup", cs, true, true, false, 0,
- av.alignment.getWidth());
-
- if (sg.cs != null)
- {
- ((ResidueColourScheme) sg.cs).setThreshold(25);
- }
-
- 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, av.alignment);
- repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
- */
- public void setShowDistances(boolean state)
- {
- this.showDistances = state;
- repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
- */
- public void setShowBootstrap(boolean state)
- {
- this.showBootstrap = state;
- repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
- */
- public void setMarkPlaceholders(boolean state)
- {
- this.markPlaceholders = 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