X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=f965ff4686b41d79f7209b7e2b36e76c61736447;hb=a7169b1c72607f3c9357195b4999869650a2a891;hp=af1d752897a78d10b230306775b536db3ce67e06;hpb=df9b85c1cf39894039018499fe802406cc37f209;p=jalview.git
diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index af1d752..f965ff4 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -1,567 +1,743 @@
-/*
- * 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.appletgui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.util.*;
-
-public class TreeCanvas
- extends Panel implements MouseListener
-{
- NJTree tree;
- ScrollPane scrollPane;
- AlignViewport av;
- public static final String PLACEHOLDER = " * ";
- Font font;
- boolean fitToWindow = true;
- boolean showDistances = false;
- boolean showBootstrap = false;
- boolean markPlaceholders = false;
-
- int offx = 20;
- int offy;
-
- float threshold;
-
- String longestName;
- int labelLength = -1;
-
- //RubberbandRectangle rubberband;
-
- Vector listeners;
-
- Hashtable nameHash = new Hashtable();
- Hashtable nodeHash = new Hashtable();
-
- public TreeCanvas(AlignViewport av, ScrollPane scroller)
- {
- this.av = av;
- font = av.getFont();
- scrollPane = scroller;
- addMouseListener(this);
- setLayout(null);
-
- PaintRefresher.Register(this, av.alignment);
- }
-
- public void TreeSelectionChanged(Sequence sequence)
- {
- SequenceGroup selected = av.getSelectionGroup();
- if (selected == null)
- {
- selected = new SequenceGroup();
- av.setSelectionGroup(selected);
- }
-
- selected.setEndRes(av.alignment.getWidth()-1);
- selected.addOrRemove(sequence, true);
-
- PaintRefresher.Refresh(this, av.alignment);
- repaint();
- }
-
- public void setTree(NJTree tree)
- {
- this.tree = tree;
- tree.findHeight(tree.getTopNode());
-
- // Now have to calculate longest name based on the leaves
- Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
- boolean has_placeholders = false;
- longestName = "";
-
- for (int i = 0; i < leaves.size(); i++)
- {
- SequenceNode lf = (SequenceNode) leaves.elementAt(i);
-
- if (lf.isPlaceholder())
- {
- has_placeholders = true;
- }
-
- if (longestName.length() < ( (Sequence) lf.element()).getName()
- .length())
- {
- longestName = TreeCanvas.PLACEHOLDER +
- ( (Sequence) lf.element()).getName();
- }
- }
-
- setMarkPlaceholders(has_placeholders);
- }
-
- 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("%-.2f").form(node.dist);
- }
- if (showBootstrap)
- {
- if (showDistances)
- {
- nodeLabel = nodeLabel + " : ";
- }
- nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
- }
- if (!nodeLabel.equals(""))
- {
- g.drawString(nodeLabel, xstart+2, ypos - 2);
- }
-
- 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 + 10, ypos - charHeight,
- charWidth, charHeight);
-
- nameHash.put( (SequenceI) node.element(), rect);
-
- // Colour selected leaves differently
- SequenceGroup selected = av.getSelectionGroup();
- if (selected != null &&
- selected.getSequences(false).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("%-.2f").form(node.dist), xstart+2, ypos - 2);
- }
-
- }
- }
-
- 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 = getSize().width;
- int height = getSize().height;
-
- 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) / 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, true);
- }
- }
- }
- }
- 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);
- }
- }
-
- public void paint(Graphics g)
- {
-
- if(tree==null)
- return;
-
- g.setFont(font);
-
-
- FontMetrics fm = g.getFontMetrics(font);
-
- if (nameHash.size() == 0)
- {
- repaint();
- }
-
- if (fitToWindow ||
- (!fitToWindow &&
- scrollPane.getSize().height > fm.getHeight() * nameHash.size() + offy))
- {
- draw(g, scrollPane.getSize().width, scrollPane.getSize().height);
- }
- else
- {
- setSize(new Dimension(scrollPane.getSize().width,
- fm.getHeight() * nameHash.size()));
- draw(g, scrollPane.getSize().width, fm.getHeight() * nameHash.size());
- }
-
- scrollPane.validate();
- }
-
-
- public void draw(Graphics g, int width, int height)
- {
- offy = font.getSize()+10;
-
- g.setColor(Color.white);
- g.fillRect(0, 0, width, height);
-
- labelLength = g.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) / top.count;
-
- drawNode(g, tree.getTopNode(), chunk, wscale, width, offx, offy);
-
- if (threshold != 0)
- {
- if (av.getCurrentTree() == tree)
- {
- g.setColor(Color.red);
- }
- else
- {
- g.setColor(Color.gray);
- }
-
- int x = (int) (threshold *
- (float) (getSize().width - labelLength - 2 * offx) + offx);
-
- g.drawLine(x, 0, x, getSize().height);
- }
-
- }
-
- 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) (getSize().width - 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 = null;
-
- if (av.getGlobalColourScheme() != null)
- {
- if (av.getGlobalColourScheme() instanceof UserColourScheme)
- {
- cs = new UserColourScheme(
- ( (UserColourScheme) av.getGlobalColourScheme()).getColours());
-
- }
- else
- cs = ColourSchemeProperty.getColour(sequences,
- av.alignment.getWidth(),
- ColourSchemeProperty.getColourName(
- av.getGlobalColourScheme()));
-
- cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
- av.getIgnoreGapsConsensus());
- }
-
- SequenceGroup sg = new SequenceGroup(sequences, "TreeGroup",
- cs, true, true,
- false, 0, av.alignment.getWidth()-1);
-
-
- if ( av.getGlobalColourScheme()!=null
- && av.getGlobalColourScheme().conservationApplied())
- {
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.getSequences(false),
- sg.getStartRes(),
- sg.getEndRes());
-
- c.calculate();
- c.verdict(false, av.ConsPercGaps);
- cs.setConservation(c);
-
- sg.cs = cs;
-
- }
-
- av.alignment.addGroup(sg);
-
- }
- }
- }
-
- PaintRefresher.Refresh(this, av.alignment);
- repaint();
-
- }
-
- public void setShowDistances(boolean state)
- {
- this.showDistances = state;
- repaint();
- }
-
- public void setShowBootstrap(boolean state)
- {
- this.showBootstrap = state;
- repaint();
- }
-
- 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.appletgui;
+
+import jalview.analysis.Conservation;
+import jalview.analysis.TreeModel;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.BinaryNode;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
+import jalview.util.Format;
+import jalview.util.MappingUtils;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Panel;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.ScrollPane;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+public class TreeCanvas extends Panel
+ implements MouseListener, MouseMotionListener
+{
+ TreeModel tree;
+
+ ScrollPane scrollPane;
+
+ AlignViewport av;
+
+ public static final String PLACEHOLDER = " * ";
+
+ Font font;
+
+ boolean fitToWindow = true;
+
+ boolean showDistances = false;
+
+ boolean showBootstrap = false;
+
+ boolean markPlaceholders = false;
+
+ int offx = 20;
+
+ int offy;
+
+ float threshold;
+
+ String longestName;
+
+ int labelLength = -1;
+
+ Hashtable nameHash = new Hashtable();
+
+ Hashtable nodeHash = new Hashtable();
+
+ BinaryNode highlightNode;
+
+ AlignmentPanel ap;
+
+ public TreeCanvas(AlignmentPanel ap, ScrollPane scroller)
+ {
+ this.ap = ap;
+ this.av = ap.av;
+ font = av.getFont();
+ scrollPane = scroller;
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ setLayout(null);
+
+ PaintRefresher.Register(this, av.getSequenceSetId());
+ }
+
+ public void treeSelectionChanged(SequenceI sequence)
+ {
+ SequenceGroup selected = av.getSelectionGroup();
+ if (selected == null)
+ {
+ selected = new SequenceGroup();
+ av.setSelectionGroup(selected);
+ }
+
+ selected.setEndRes(av.getAlignment().getWidth() - 1);
+ selected.addOrRemove(sequence, true);
+ }
+
+ public void setTree(TreeModel tree2)
+ {
+ this.tree = tree2;
+ tree2.findHeight(tree2.getTopNode());
+
+ // Now have to calculate longest name based on the leaves
+ Vector leaves = tree2.findLeaves(tree2.getTopNode());
+ boolean has_placeholders = false;
+ longestName = "";
+
+ for (int i = 0; i < leaves.size(); i++)
+ {
+ BinaryNode lf = leaves.elementAt(i);
+
+ if (lf instanceof SequenceNode && ((SequenceNode) lf).isPlaceholder())
+ {
+ has_placeholders = true;
+ }
+
+ if (longestName.length() < ((Sequence) lf.element()).getName()
+ .length())
+ {
+ longestName = TreeCanvas.PLACEHOLDER
+ + ((Sequence) lf.element()).getName();
+ }
+ }
+
+ setMarkPlaceholders(has_placeholders);
+ }
+
+ public void drawNode(Graphics g, BinaryNode node, float chunk,
+ double scale, int width, int offx, int offy)
+ {
+ if (node == null)
+ {
+ return;
+ }
+
+ if (node.left() == null && node.right() == null)
+ {
+ // Drawing leaf node
+
+ double height = node.height;
+ double 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)
+ {
+ SequenceI seq = (SequenceI) node.element();
+
+ if (av.getSequenceColour(seq) == Color.white)
+ {
+ g.setColor(Color.black);
+ }
+ else
+ {
+ g.setColor(av.getSequenceColour(seq).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("%-.2f").form(node.dist);
+ }
+ if (showBootstrap)
+ {
+ int btstrap = node.getBootstrap();
+ if (btstrap > -1)
+ {
+ if (showDistances)
+ {
+ nodeLabel = nodeLabel + " : ";
+ }
+ nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
+ }
+ }
+ if (!nodeLabel.equals(""))
+ {
+ g.drawString(nodeLabel, xstart + 2, ypos - 2);
+ }
+
+ String name = (markPlaceholders && node instanceof SequenceNode
+ && ((SequenceNode) 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 + 10, ypos - charHeight,
+ charWidth, charHeight);
+
+ nameHash.put(node.element(), rect);
+
+ // Colour selected leaves differently
+ SequenceGroup selected = av.getSelectionGroup();
+ if (selected != null
+ && selected.getSequences(null).contains(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, (BinaryNode) node.left(), chunk, scale, width, offx,
+ offy);
+ drawNode(g, (BinaryNode) node.right(), chunk, scale, width, offx,
+ offy);
+
+ double height = node.height;
+ double 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(node.color.darker());
+
+ // Draw horizontal line
+ g.drawLine(xstart, ypos, xend, ypos);
+ if (node == highlightNode)
+ {
+ g.fillRect(xend - 3, ypos - 3, 6, 6);
+ }
+ else
+ {
+ g.fillRect(xend - 2, ypos - 2, 4, 4);
+ }
+
+ int ystart = (int) (node.left() == null ? 0
+ : (((BinaryNode) node.left()).ycount * chunk)) + offy;
+ int yend = (int) (node.right() == null ? 0
+ : (((BinaryNode) 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);
+
+ String nodeLabel = "";
+
+ if (showDistances && (node.dist > 0))
+ {
+ nodeLabel = new Format("%-.2f").form(node.dist);
+ }
+
+ if (showBootstrap)
+ {
+ int btstrap = node.getBootstrap();
+ if (btstrap > -1)
+ {
+ if (showDistances)
+ {
+ nodeLabel = nodeLabel + " : ";
+ }
+ nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
+ }
+ }
+
+ if (!nodeLabel.equals(""))
+ {
+ g.drawString(nodeLabel, xstart + 2, ypos - 2);
+ }
+
+ }
+ }
+
+ 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 = getSize().width;
+ int height = getSize().height;
+
+ BinaryNode top = tree.getTopNode();
+
+ double wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight();
+ if (top.count == 0)
+ {
+ top.count = ((BinaryNode) top.left()).count
+ + ((BinaryNode) top.right()).count;
+ }
+ float chunk = (float) (height - offy) / top.count;
+
+ pickNode(pickBox, top, chunk, wscale, width, offx, offy);
+ }
+
+ public void pickNode(Rectangle pickBox, BinaryNode node, float chunk,
+ double scale, int width, int offx, int offy)
+ {
+ if (node == null)
+ {
+ return;
+ }
+
+ if (node.left() == null && node.right() == null)
+ {
+ double 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, (BinaryNode) node.left(), chunk, scale, width, offx,
+ offy);
+ pickNode(pickBox, (BinaryNode) node.right(), chunk, scale, width,
+ offx, offy);
+ }
+ }
+
+ public void setColor(BinaryNode node, Color c)
+ {
+ if (node == null)
+ {
+ return;
+ }
+
+ if (node.left() == null && node.right() == null)
+ {
+ node.color = c;
+
+ if (node.element() instanceof SequenceI)
+ {
+ av.setSequenceColour((SequenceI) node.element(), c);
+ }
+ }
+ else
+ {
+ node.color = c;
+ setColor((BinaryNode) node.left(), c);
+ setColor((BinaryNode) node.right(), c);
+ }
+ }
+
+ @Override
+ public void update(Graphics g)
+ {
+ paint(g);
+ }
+
+ @Override
+ public void paint(Graphics g)
+ {
+ if (tree == null)
+ {
+ return;
+ }
+
+ if (nameHash.size() == 0)
+ {
+ repaint();
+ }
+
+ int width = scrollPane.getSize().width;
+ int height = scrollPane.getSize().height;
+ if (!fitToWindow)
+ {
+ height = g.getFontMetrics(font).getHeight() * nameHash.size();
+ }
+
+ if (getSize().width > width)
+ {
+ setSize(new Dimension(width, height));
+ scrollPane.validate();
+ return;
+ }
+
+ setSize(new Dimension(width, height));
+
+ g.setFont(font);
+ draw(g, width, height);
+ validate();
+ }
+
+ public void draw(Graphics g, int width, int height)
+ {
+ offy = font.getSize() + 10;
+
+ g.setColor(Color.white);
+ g.fillRect(0, 0, width, height);
+
+ labelLength = g.getFontMetrics(font).stringWidth(longestName) + 20; // 20
+ // allows
+ // for
+ // scrollbar
+
+ double wscale = (width - labelLength - offx * 2) / tree.getMaxHeight();
+
+ BinaryNode top = tree.getTopNode();
+
+ if (top.count == 0)
+ {
+ top.count = ((BinaryNode) top.left()).count
+ + ((BinaryNode) top.right()).count;
+ }
+ float chunk = (float) (height - offy) / top.count;
+
+ drawNode(g, tree.getTopNode(), chunk, wscale, width, offx, offy);
+
+ if (threshold != 0)
+ {
+ if (av.getCurrentTree() == tree)
+ {
+ g.setColor(Color.red);
+ }
+ else
+ {
+ g.setColor(Color.gray);
+ }
+
+ int x = (int) (threshold * (getSize().width - labelLength - 2 * offx)
+ + offx);
+
+ g.drawLine(x, 0, x, getSize().height);
+ }
+
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent e)
+ {
+ }
+
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ }
+
+ @Override
+ public void mouseExited(MouseEvent e)
+ {
+ }
+
+ @Override
+ public void mouseClicked(MouseEvent evt)
+ {
+ if (highlightNode != null)
+ {
+ if (evt.getClickCount() > 1)
+ {
+ tree.swapNodes(highlightNode);
+ tree.reCount(tree.getTopNode());
+ tree.findHeight(tree.getTopNode());
+ }
+ else
+ {
+ Vector leaves = tree.findLeaves(highlightNode);
+
+ for (int i = 0; i < leaves.size(); i++)
+ {
+ SequenceI seq = (SequenceI) leaves.elementAt(i).element();
+ treeSelectionChanged(seq);
+ }
+ }
+
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ repaint();
+ av.sendSelection();
+ }
+ }
+
+ @Override
+ public void mouseDragged(MouseEvent ect)
+ {
+ }
+
+ @Override
+ public void mouseMoved(MouseEvent evt)
+ {
+ av.setCurrentTree(tree);
+
+ Object ob = findElement(evt.getX(), evt.getY());
+
+ if (ob instanceof BinaryNode)
+ {
+ highlightNode = (BinaryNode) ob;
+ repaint();
+ }
+ else
+ {
+ if (highlightNode != null)
+ {
+ highlightNode = null;
+ repaint();
+ }
+ }
+ }
+
+ @Override
+ 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);
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ repaint();
+ av.sendSelection();
+ return;
+ }
+ else if (!(ob instanceof SequenceNode))
+ {
+ // Find threshold
+
+ if (tree.getMaxHeight() != 0)
+ {
+ threshold = (float) (x - offx)
+ / (float) (getSize().width - labelLength - 2 * offx);
+
+ List groups = tree.groupNodes(threshold);
+ setColor(tree.getTopNode(), Color.black);
+
+ av.setSelectionGroup(null);
+ av.getAlignment().deleteAllGroups();
+ av.clearSequenceColours();
+ final AlignViewportI codingComplement = av.getCodingComplement();
+ if (codingComplement != null)
+ {
+ codingComplement.setSelectionGroup(null);
+ codingComplement.getAlignment().deleteAllGroups();
+ codingComplement.clearSequenceColours();
+ }
+
+ colourGroups(groups);
+
+ }
+ }
+
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ repaint();
+
+ }
+
+ void colourGroups(List groups)
+ {
+ for (int i = 0; i < groups.size(); i++)
+ {
+
+ Color col = new Color((int) (Math.random() * 255),
+ (int) (Math.random() * 255), (int) (Math.random() * 255));
+ setColor(groups.get(i), col.brighter());
+
+ Vector l = tree.findLeaves(groups.get(i));
+
+ Vector sequences = new Vector<>();
+ for (int j = 0; j < l.size(); j++)
+ {
+ SequenceI s1 = (SequenceI) l.elementAt(j).element();
+ if (!sequences.contains(s1))
+ {
+ sequences.addElement(s1);
+ }
+ }
+
+ ColourSchemeI cs = null;
+
+ SequenceGroup sg = new SequenceGroup(sequences, "", cs, true, true,
+ false, 0, av.getAlignment().getWidth() - 1);
+
+ if (av.getGlobalColourScheme() != null)
+ {
+ if (av.getGlobalColourScheme() instanceof UserColourScheme)
+ {
+ cs = new UserColourScheme(
+ ((UserColourScheme) av.getGlobalColourScheme())
+ .getColours());
+
+ }
+ else
+ {
+ cs = ColourSchemeProperty.getColourScheme(av, sg,
+ ColourSchemeProperty
+ .getColourName(av.getGlobalColourScheme()));
+ }
+ // cs is null if shading is an annotationColourGradient
+ // if (cs != null)
+ // {
+ // cs.setThreshold(av.getViewportColourScheme().getThreshold(),
+ // av.isIgnoreGapsConsensus());
+ // }
+ }
+ // TODO: cs used to be initialized with a sequence collection and
+ // recalcConservation called automatically
+ // instead we set it manually - recalc called after updateAnnotation
+ sg.setColourScheme(cs);
+ sg.getGroupColourScheme().setThreshold(
+ av.getResidueShading().getThreshold(),
+ av.isIgnoreGapsConsensus());
+
+ sg.setName("JTreeGroup:" + sg.hashCode());
+ sg.setIdColour(col);
+ if (av.getGlobalColourScheme() != null
+ && av.getResidueShading().conservationApplied())
+ {
+ Conservation c = new Conservation("Group", sg.getSequences(null),
+ sg.getStartRes(), sg.getEndRes());
+
+ c.calculate();
+ c.verdict(false, av.getConsPercGaps());
+
+ sg.setColourScheme(cs);
+ sg.getGroupColourScheme().setConservation(c);
+ }
+
+ av.getAlignment().addGroup(sg);
+
+ // TODO this is duplicated with gui TreeCanvas - refactor
+ av.getAlignment().addGroup(sg);
+ final AlignViewportI codingComplement = av.getCodingComplement();
+ if (codingComplement != null)
+ {
+ SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, av,
+ codingComplement);
+ if (mappedGroup.getSequences().size() > 0)
+ {
+ codingComplement.getAlignment().addGroup(mappedGroup);
+ for (SequenceI seq : mappedGroup.getSequences())
+ {
+ // TODO why does gui require col.brighter() here??
+ codingComplement.setSequenceColour(seq, col);
+ }
+ }
+ }
+
+ }
+ ap.updateAnnotation();
+ if (av.getCodingComplement() != null)
+ {
+ ((AlignmentViewport) av.getCodingComplement()).firePropertyChange(
+ "alignment", null, ap.av.getAlignment().getSequences());
+ }
+ }
+
+ public void setShowDistances(boolean state)
+ {
+ this.showDistances = state;
+ repaint();
+ }
+
+ public void setShowBootstrap(boolean state)
+ {
+ this.showBootstrap = state;
+ repaint();
+ }
+
+ public void setMarkPlaceholders(boolean state)
+ {
+ this.markPlaceholders = state;
+ repaint();
+ }
+
+}