-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 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
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-\r
-package jalview.appletgui;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-import jalview.util.*;\r
-\r
-public class TreeCanvas\r
- extends Panel implements MouseListener, MouseMotionListener\r
-{\r
- NJTree tree;\r
- ScrollPane scrollPane;\r
- AlignViewport av;\r
- public static final String PLACEHOLDER = " * ";\r
- Font font;\r
- boolean fitToWindow = true;\r
- boolean showDistances = false;\r
- boolean showBootstrap = false;\r
- boolean markPlaceholders = false;\r
-\r
- int offx = 20;\r
- int offy;\r
-\r
- float threshold;\r
-\r
- String longestName;\r
- int labelLength = -1;\r
-\r
- Hashtable nameHash = new Hashtable();\r
- Hashtable nodeHash = new Hashtable();\r
-\r
- SequenceNode highlightNode;\r
-\r
- public TreeCanvas(AlignViewport av, ScrollPane scroller)\r
- {\r
- this.av = av;\r
- font = av.getFont();\r
- scrollPane = scroller;\r
- addMouseListener(this);\r
- addMouseMotionListener(this);\r
- setLayout(null);\r
-\r
- PaintRefresher.Register(this, av.getSequenceSetId());\r
- }\r
-\r
- public void treeSelectionChanged(SequenceI sequence)\r
- {\r
- SequenceGroup selected = av.getSelectionGroup();\r
- if (selected == null)\r
- {\r
- selected = new SequenceGroup();\r
- av.setSelectionGroup(selected);\r
- }\r
-\r
- selected.setEndRes(av.alignment.getWidth() - 1);\r
- selected.addOrRemove(sequence, true);\r
- }\r
-\r
- public void setTree(NJTree tree)\r
- {\r
- this.tree = tree;\r
- tree.findHeight(tree.getTopNode());\r
-\r
- // Now have to calculate longest name based on the leaves\r
- Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());\r
- boolean has_placeholders = false;\r
- longestName = "";\r
-\r
- for (int i = 0; i < leaves.size(); i++)\r
- {\r
- SequenceNode lf = (SequenceNode) leaves.elementAt(i);\r
-\r
- if (lf.isPlaceholder())\r
- {\r
- has_placeholders = true;\r
- }\r
-\r
- if (longestName.length() < ( (Sequence) lf.element()).getName()\r
- .length())\r
- {\r
- longestName = TreeCanvas.PLACEHOLDER +\r
- ( (Sequence) lf.element()).getName();\r
- }\r
- }\r
-\r
- setMarkPlaceholders(has_placeholders);\r
- }\r
-\r
- public void drawNode(Graphics g, SequenceNode node, float chunk, float scale,\r
- int width, int offx, int offy)\r
- {\r
- if (node == null)\r
- {\r
- return;\r
- }\r
-\r
- if (node.left() == null && node.right() == null)\r
- {\r
- // Drawing leaf node\r
-\r
- float height = node.height;\r
- float dist = node.dist;\r
-\r
- int xstart = (int) ( (height - dist) * scale) + offx;\r
- int xend = (int) (height * scale) + offx;\r
-\r
- int ypos = (int) (node.ycount * chunk) + offy;\r
-\r
- if (node.element() instanceof SequenceI)\r
- {\r
- SequenceI seq = (SequenceI) ( (SequenceNode) node).element();\r
-\r
- if (av.getSequenceColour(seq) == Color.white)\r
- {\r
- g.setColor(Color.black);\r
- }\r
- else\r
- {\r
- g.setColor(av.getSequenceColour(seq).darker());\r
- }\r
-\r
- }\r
- else\r
- {\r
- g.setColor(Color.black);\r
- }\r
-\r
- // Draw horizontal line\r
- g.drawLine(xstart, ypos, xend, ypos);\r
-\r
- String nodeLabel = "";\r
- if (showDistances && node.dist > 0)\r
- {\r
- nodeLabel = new Format("%-.2f").form(node.dist);\r
- }\r
- if (showBootstrap)\r
- {\r
- if (showDistances)\r
- {\r
- nodeLabel = nodeLabel + " : ";\r
- }\r
- nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());\r
- }\r
- if (!nodeLabel.equals(""))\r
- {\r
- g.drawString(nodeLabel, xstart + 2, ypos - 2);\r
- }\r
-\r
- String name = (markPlaceholders && node.isPlaceholder()) ?\r
- (PLACEHOLDER + node.getName()) : node.getName();\r
- FontMetrics fm = g.getFontMetrics(font);\r
- int charWidth = fm.stringWidth(name) + 3;\r
- int charHeight = fm.getHeight();\r
-\r
- Rectangle rect = new Rectangle(xend + 10, ypos - charHeight,\r
- charWidth, charHeight);\r
-\r
- nameHash.put( (SequenceI) node.element(), rect);\r
-\r
- // Colour selected leaves differently\r
- SequenceGroup selected = av.getSelectionGroup();\r
- if (selected != null &&\r
- selected.getSequences(null).contains( (SequenceI) node.element()))\r
- {\r
- g.setColor(Color.gray);\r
-\r
- g.fillRect(xend + 10, ypos - charHeight + 3, charWidth, charHeight);\r
- g.setColor(Color.white);\r
- }\r
- g.drawString(name, xend + 10, ypos);\r
- g.setColor(Color.black);\r
- }\r
- else\r
- {\r
- drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx, offy);\r
- drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx, offy);\r
-\r
- float height = node.height;\r
- float dist = node.dist;\r
-\r
- int xstart = (int) ( (height - dist) * scale) + offx;\r
- int xend = (int) (height * scale) + offx;\r
- int ypos = (int) (node.ycount * chunk) + offy;\r
-\r
- g.setColor( ( (SequenceNode) node).color.darker());\r
-\r
- // Draw horizontal line\r
- g.drawLine(xstart, ypos, xend, ypos);\r
- if (node == highlightNode)\r
- {\r
- g.fillRect(xend - 3, ypos - 3, 6, 6);\r
- }\r
- else\r
- {\r
- g.fillRect(xend - 2, ypos - 2, 4, 4);\r
- }\r
-\r
- int ystart = (int) ( ( (SequenceNode) node.left()).ycount * chunk) + offy;\r
- int yend = (int) ( ( (SequenceNode) node.right()).ycount * chunk) + offy;\r
-\r
- Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);\r
- nodeHash.put(node, pos);\r
-\r
- g.drawLine( (int) (height * scale) + offx, ystart,\r
- (int) (height * scale) + offx, yend);\r
-\r
- if (showDistances && node.dist > 0)\r
- {\r
- g.drawString(new Format("%-.2f").form(node.dist), xstart + 2, ypos - 2);\r
- }\r
-\r
- }\r
- }\r
-\r
- public Object findElement(int x, int y)\r
- {\r
- Enumeration keys = nameHash.keys();\r
-\r
- while (keys.hasMoreElements())\r
- {\r
- Object ob = keys.nextElement();\r
- Rectangle rect = (Rectangle) nameHash.get(ob);\r
-\r
- if (x >= rect.x && x <= (rect.x + rect.width) &&\r
- y >= rect.y && y <= (rect.y + rect.height))\r
- {\r
- return ob;\r
- }\r
- }\r
- keys = nodeHash.keys();\r
-\r
- while (keys.hasMoreElements())\r
- {\r
- Object ob = keys.nextElement();\r
- Rectangle rect = (Rectangle) nodeHash.get(ob);\r
-\r
- if (x >= rect.x && x <= (rect.x + rect.width) &&\r
- y >= rect.y && y <= (rect.y + rect.height))\r
- {\r
- return ob;\r
- }\r
- }\r
- return null;\r
-\r
- }\r
-\r
- public void pickNodes(Rectangle pickBox)\r
- {\r
- int width = getSize().width;\r
- int height = getSize().height;\r
-\r
- SequenceNode top = tree.getTopNode();\r
-\r
- float wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight()\r
- ;\r
- if (top.count == 0)\r
- {\r
- top.count = ( (SequenceNode) top.left()).count +\r
- ( (SequenceNode) top.right()).count;\r
- }\r
- float chunk = (float) (height - offy) / top.count;\r
-\r
- pickNode(pickBox, top, chunk, wscale, width, offx, offy);\r
- }\r
-\r
- public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,\r
- float scale, int width, int offx, int offy)\r
- {\r
- if (node == null)\r
- {\r
- return;\r
- }\r
-\r
- if (node.left() == null && node.right() == null)\r
- {\r
- float height = node.height;\r
- //float dist = node.dist;\r
-\r
- //int xstart = (int) ( (height - dist) * scale) + offx;\r
- int xend = (int) (height * scale) + offx;\r
-\r
- int ypos = (int) (node.ycount * chunk) + offy;\r
-\r
- if (pickBox.contains(new Point(xend, ypos)))\r
- {\r
- if (node.element() instanceof SequenceI)\r
- {\r
- SequenceI seq = (SequenceI) node.element();\r
- SequenceGroup sg = av.getSelectionGroup();\r
- if (sg != null)\r
- {\r
- sg.addOrRemove(seq, true);\r
- }\r
- }\r
- }\r
- }\r
- else\r
- {\r
- pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width, offx,\r
- offy);\r
- pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width, offx,\r
- offy);\r
- }\r
- }\r
-\r
- public void setColor(SequenceNode node, Color c)\r
- {\r
- if (node == null)\r
- {\r
- return;\r
- }\r
-\r
- if (node.left() == null && node.right() == null)\r
- {\r
- node.color = c;\r
-\r
- if (node.element() instanceof SequenceI)\r
- {\r
- av.setSequenceColour( (SequenceI) node.element(), c);\r
- }\r
- }\r
- else\r
- {\r
- node.color = c;\r
- setColor( (SequenceNode) node.left(), c);\r
- setColor( (SequenceNode) node.right(), c);\r
- }\r
- }\r
-\r
- public void update(Graphics g)\r
- {\r
- paint(g);\r
- }\r
-\r
- public void paint(Graphics g)\r
- {\r
- if (tree == null)\r
- {\r
- return;\r
- }\r
-\r
- if (nameHash.size() == 0)\r
- {\r
- repaint();\r
- }\r
-\r
- int width = scrollPane.getSize().width;\r
- int height = scrollPane.getSize().height;\r
- if (!fitToWindow)\r
- {\r
- height = g.getFontMetrics(font).getHeight() * nameHash.size();\r
- }\r
-\r
- if (getSize().width > width)\r
- {\r
- setSize(new Dimension(width, height));\r
- scrollPane.validate();\r
- return;\r
- }\r
-\r
- setSize(new Dimension(width, height));\r
-\r
- g.setFont(font);\r
-\r
- draw(g, width, height);\r
-\r
- }\r
-\r
- public void draw(Graphics g, int width, int height)\r
- {\r
- offy = font.getSize() + 10;\r
-\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, width, height);\r
-\r
- labelLength = g.getFontMetrics(font).stringWidth(longestName) + 20; //20 allows for scrollbar\r
-\r
- float wscale = (float) (width - labelLength - offx * 2) / tree.getMaxHeight();\r
-\r
- SequenceNode top = tree.getTopNode();\r
-\r
- if (top.count == 0)\r
- {\r
- top.count = ( (SequenceNode) top.left()).count +\r
- ( (SequenceNode) top.right()).count;\r
- }\r
- float chunk = (float) (height - offy) / top.count;\r
-\r
- drawNode(g, tree.getTopNode(), chunk, wscale, width, offx, offy);\r
-\r
- if (threshold != 0)\r
- {\r
- if (av.getCurrentTree() == tree)\r
- {\r
- g.setColor(Color.red);\r
- }\r
- else\r
- {\r
- g.setColor(Color.gray);\r
- }\r
-\r
- int x = (int) (threshold *\r
- (float) (getSize().width - labelLength - 2 * offx) + offx);\r
-\r
- g.drawLine(x, 0, x, getSize().height);\r
- }\r
-\r
- }\r
-\r
- public void mouseReleased(MouseEvent e)\r
- {}\r
-\r
- public void mouseEntered(MouseEvent e)\r
- {}\r
-\r
- public void mouseExited(MouseEvent e)\r
- {}\r
-\r
- public void mouseClicked(MouseEvent evt)\r
- {\r
- if (highlightNode != null)\r
- {\r
- if (evt.getClickCount() > 1)\r
- {\r
- tree.swapNodes(highlightNode);\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
- }\r
- else\r
- {\r
- Vector leaves = new Vector();\r
- tree.findLeaves(highlightNode, leaves);\r
-\r
- for (int i = 0; i < leaves.size(); i++)\r
- {\r
- SequenceI seq =\r
- (SequenceI) ( (SequenceNode) leaves.elementAt(i)).element();\r
- treeSelectionChanged(seq);\r
- }\r
- }\r
-\r
- PaintRefresher.Refresh(this, av.getSequenceSetId());\r
- repaint();\r
- }\r
- }\r
-\r
- public void mouseDragged(MouseEvent ect)\r
- {}\r
-\r
- public void mouseMoved(MouseEvent evt)\r
- {\r
- av.setCurrentTree(tree);\r
-\r
- Object ob = findElement(evt.getX(), evt.getY());\r
-\r
- if (ob instanceof SequenceNode)\r
- {\r
- highlightNode = (SequenceNode) ob;\r
- repaint();\r
- }\r
- else\r
- {\r
- if (highlightNode != null)\r
- {\r
- highlightNode = null;\r
- repaint();\r
- }\r
- }\r
- }\r
-\r
- public void mousePressed(MouseEvent e)\r
- {\r
- av.setCurrentTree(tree);\r
-\r
- int x = e.getX();\r
- int y = e.getY();\r
-\r
- Object ob = findElement(x, y);\r
-\r
- if (ob instanceof SequenceI)\r
- {\r
- treeSelectionChanged( (Sequence) ob);\r
- PaintRefresher.Refresh(this, av.getSequenceSetId());\r
- repaint();\r
- return;\r
- }\r
- else if (! (ob instanceof SequenceNode))\r
- {\r
- // Find threshold\r
-\r
- if (tree.getMaxHeight() != 0)\r
- {\r
- threshold = (float) (x - offx) /\r
- (float) (getSize().width - labelLength - 2 * offx);\r
-\r
- tree.getGroups().removeAllElements();\r
- tree.groupNodes(tree.getTopNode(), threshold);\r
- setColor(tree.getTopNode(), Color.black);\r
-\r
- av.setSelectionGroup(null);\r
- av.alignment.deleteAllGroups();\r
- av.sequenceColours = null;\r
-\r
- colourGroups();\r
-\r
- }\r
- }\r
-\r
- PaintRefresher.Refresh(this, av.getSequenceSetId());\r
- repaint();\r
-\r
- }\r
-\r
- void colourGroups()\r
- {\r
- for (int i = 0; i < tree.getGroups().size(); i++)\r
- {\r
-\r
- Color col = new Color( (int) (Math.random() * 255),\r
- (int) (Math.random() * 255),\r
- (int) (Math.random() * 255));\r
- setColor( (SequenceNode) tree.getGroups().elementAt(i), col.brighter());\r
-\r
- Vector l = tree.findLeaves( (SequenceNode) tree.getGroups().elementAt(\r
- i), new Vector());\r
-\r
- Vector sequences = new Vector();\r
- for (int j = 0; j < l.size(); j++)\r
- {\r
- SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element();\r
- if (!sequences.contains(s1))\r
- {\r
- sequences.addElement(s1);\r
- }\r
- }\r
-\r
- ColourSchemeI cs = null;\r
-\r
- if (av.getGlobalColourScheme() != null)\r
- {\r
- if (av.getGlobalColourScheme() instanceof UserColourScheme)\r
- {\r
- cs = new UserColourScheme(\r
- ( (UserColourScheme) av.getGlobalColourScheme()).getColours());\r
-\r
- }\r
- else\r
- {\r
- cs = ColourSchemeProperty.getColour(sequences,\r
- av.alignment.getWidth(),\r
- ColourSchemeProperty.\r
- getColourName(\r
- av.getGlobalColourScheme()));\r
- }\r
-\r
- cs.setThreshold(av.getGlobalColourScheme().getThreshold(),\r
- av.getIgnoreGapsConsensus());\r
- }\r
-\r
- SequenceGroup sg = new SequenceGroup(sequences, "",\r
- cs, true, true,\r
- false, 0,\r
- av.alignment.getWidth() - 1);\r
-\r
- sg.setName("JTreeGroup:" + sg.hashCode());\r
-\r
- if (av.getGlobalColourScheme() != null\r
- && av.getGlobalColourScheme().conservationApplied())\r
- {\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.getSequences(null),\r
- sg.getStartRes(),\r
- sg.getEndRes());\r
-\r
- c.calculate();\r
- c.verdict(false, av.ConsPercGaps);\r
- cs.setConservation(c);\r
-\r
- sg.cs = cs;\r
-\r
- }\r
-\r
- av.alignment.addGroup(sg);\r
-\r
- }\r
-\r
- }\r
-\r
- public void setShowDistances(boolean state)\r
- {\r
- this.showDistances = state;\r
- repaint();\r
- }\r
-\r
- public void setShowBootstrap(boolean state)\r
- {\r
- this.showBootstrap = state;\r
- repaint();\r
- }\r
-\r
- public void setMarkPlaceholders(boolean state)\r
- {\r
- this.markPlaceholders = state;\r
- repaint();\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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, MouseMotionListener
+{
+ 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;
+
+ Hashtable nameHash = new Hashtable();
+ Hashtable nodeHash = new Hashtable();
+
+ SequenceNode highlightNode;
+
+ public TreeCanvas(AlignViewport av, ScrollPane scroller)
+ {
+ this.av = 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.alignment.getWidth() - 1);
+ selected.addOrRemove(sequence, true);
+ }
+
+ 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)
+ {
+ SequenceI seq = (SequenceI) ( (SequenceNode) 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)
+ {
+ 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(null).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);
+ if (node == highlightNode)
+ {
+ g.fillRect(xend - 3, ypos - 3, 6, 6);
+ }
+ else
+ {
+ 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);
+
+ 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.bootstrap);
+ }
+
+ 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;
+
+ 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)
+ {
+ av.setSequenceColour( (SequenceI) node.element(), c);
+ }
+ }
+ else
+ {
+ node.color = c;
+ setColor( (SequenceNode) node.left(), c);
+ setColor( (SequenceNode) node.right(), c);
+ }
+ }
+
+ public void update(Graphics g)
+ {
+ paint(g);
+ }
+
+ 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);
+
+ }
+
+ 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 evt)
+ {
+ if (highlightNode != null)
+ {
+ if (evt.getClickCount() > 1)
+ {
+ tree.swapNodes(highlightNode);
+ tree.reCount(tree.getTopNode());
+ tree.findHeight(tree.getTopNode());
+ }
+ else
+ {
+ Vector leaves = new Vector();
+ tree.findLeaves(highlightNode, leaves);
+
+ for (int i = 0; i < leaves.size(); i++)
+ {
+ SequenceI seq =
+ (SequenceI) ( (SequenceNode) leaves.elementAt(i)).element();
+ treeSelectionChanged(seq);
+ }
+ }
+
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ repaint();
+ }
+ }
+
+ public void mouseDragged(MouseEvent ect)
+ {}
+
+ public void mouseMoved(MouseEvent evt)
+ {
+ av.setCurrentTree(tree);
+
+ Object ob = findElement(evt.getX(), evt.getY());
+
+ if (ob instanceof SequenceNode)
+ {
+ highlightNode = (SequenceNode) ob;
+ repaint();
+ }
+ else
+ {
+ if (highlightNode != null)
+ {
+ highlightNode = null;
+ repaint();
+ }
+ }
+ }
+
+ 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();
+ return;
+ }
+ else if (! (ob instanceof SequenceNode))
+ {
+ // 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();
+ av.sequenceColours = null;
+
+ colourGroups();
+
+ }
+ }
+
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ repaint();
+
+ }
+
+ void colourGroups()
+ {
+ 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, "",
+ cs, true, true,
+ false, 0,
+ av.alignment.getWidth() - 1);
+
+ sg.setName("JTreeGroup:" + sg.hashCode());
+
+ if (av.getGlobalColourScheme() != null
+ && av.getGlobalColourScheme().conservationApplied())
+ {
+ Conservation c = new Conservation("Group",
+ ResidueProperties.propHash, 3,
+ sg.getSequences(null),
+ sg.getStartRes(),
+ sg.getEndRes());
+
+ c.calculate();
+ c.verdict(false, av.ConsPercGaps);
+ cs.setConservation(c);
+
+ sg.cs = cs;
+
+ }
+
+ av.alignment.addGroup(sg);
+
+ }
+
+ }
+
+ 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();
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff