-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 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\r
-{\r
- NJTree tree;\r
- ScrollPane scrollPane;\r
- AlignViewport av;\r
- public static final String PLACEHOLDER = " * ";\r
- Font font;\r
- int fontSize = 12;\r
-\r
- boolean fitToWindow = true;\r
- boolean showDistances = false;\r
- boolean showBootstrap = false;\r
- boolean markPlaceholders = false;\r
-\r
- int offx = 20;\r
- int offy = 20;\r
-\r
- float threshold;\r
-\r
- String longestName;\r
- int labelLength = -1;\r
-\r
- //RubberbandRectangle rubberband;\r
-\r
- Vector listeners;\r
-\r
- Hashtable nameHash = new Hashtable();\r
- Hashtable nodeHash = new Hashtable();\r
-\r
- public TreeCanvas(AlignViewport av, NJTree tree, ScrollPane scroller,\r
- String label)\r
- {\r
- this.av = av;\r
- this.tree = tree;\r
- scrollPane = scroller;\r
- addMouseListener(this);\r
- tree.findHeight(tree.getTopNode());\r
- longestName = label;\r
- setLayout(null);\r
-\r
- PaintRefresher.Register(this, av.alignment);\r
- }\r
-\r
- public void TreeSelectionChanged(Sequence 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
- PaintRefresher.Refresh(this, av.alignment);\r
- repaint();\r
- }\r
-\r
- public void setTree(NJTree tree)\r
- {\r
- this.tree = tree;\r
- tree.findHeight(tree.getTopNode());\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
- if ( ( (SequenceI) ( (SequenceNode) node).element()).getColor() ==\r
- Color.white)\r
- {\r
- g.setColor(Color.black);\r
- }\r
- else\r
- {\r
- g.setColor( ( (SequenceI) ( (SequenceNode) node).element()).getColor().\r
- 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("%5.2f").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, ypos - 10);\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 + 20, 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.sequences.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
- g.fillRect(xend - 2, ypos - 2, 4, 4);\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("%5.2f").form(node.dist), xstart, ypos - 5);\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 * 2) / 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
- ( (SequenceI) node.element()).setColor(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 paint(Graphics g)\r
- {\r
-\r
- font = new Font("Verdana", Font.PLAIN, fontSize);\r
- g.setFont(font);\r
-\r
- FontMetrics fm = g.getFontMetrics(font);\r
-\r
- if (nameHash.size() == 0)\r
- {\r
- repaint();\r
- }\r
-\r
- if (fitToWindow ||\r
- (!fitToWindow &&\r
- scrollPane.getSize().height > fm.getHeight() * nameHash.size() + offy))\r
- {\r
- draw(g, scrollPane.getSize().width, scrollPane.getSize().height);\r
- }\r
- else\r
- {\r
- setSize(new Dimension(scrollPane.getSize().width,\r
- fm.getHeight() * nameHash.size()));\r
- draw(g, scrollPane.getSize().width, fm.getHeight() * nameHash.size());\r
- }\r
-\r
- scrollPane.validate();\r
- }\r
-\r
- public int getFontSize()\r
- {\r
- return fontSize;\r
- }\r
-\r
- public void setFontSize(int fontSize)\r
- {\r
- this.fontSize = fontSize;\r
- repaint();\r
- }\r
-\r
- public void draw(Graphics g, int width, int height)\r
- {\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 * 2) / 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 e)\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
- repaint();\r
- return;\r
-\r
- }\r
- else if (ob instanceof SequenceNode)\r
- {\r
- SequenceNode tmpnode = (SequenceNode) ob;\r
- tree.swapNodes(tmpnode);\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
- }\r
- else\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
-\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
- sequences.addElement(s1);\r
- }\r
-\r
- ColourSchemeI cs = ColourSchemeProperty.getColour(sequences, av.alignment.getWidth(),\r
- ColourSchemeProperty.getColourName(av.getGlobalColourScheme()));\r
-\r
-\r
- SequenceGroup sg = new SequenceGroup(sequences, "TreeGroup",\r
- cs, true, true,\r
- false, 0, av.alignment.getWidth()-1);\r
-\r
-\r
- if ( av.getGlobalColourScheme()!=null\r
- && av.getGlobalColourScheme().conservationApplied())\r
- {\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.sequences, 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
- PaintRefresher.Refresh(this, av.alignment);\r
- repaint();\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 ($$Version-Rel$$)
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.analysis.Conservation;
+import jalview.analysis.NJTree;
+import jalview.api.AlignViewportI;
+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.Vector;
+
+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;
+
+ 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(NJTree tree)
+ {
+ this.tree = tree;
+ tree.findHeight(tree.getTopNode());
+
+ // Now have to calculate longest name based on the leaves
+ Vector<SequenceNode> leaves = tree.findLeaves(tree.getTopNode());
+ boolean has_placeholders = false;
+ longestName = "";
+
+ for (int i = 0; i < leaves.size(); i++)
+ {
+ SequenceNode lf = 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) 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.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, (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(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)
+ {
+ 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;
+
+ 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);
+ }
+ }
+
+ @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
+
+ float wscale = (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 * (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<SequenceNode> 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 SequenceNode)
+ {
+ highlightNode = (SequenceNode) 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);
+
+ tree.getGroups().removeAllElements();
+ tree.groupNodes(tree.getTopNode(), 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();
+
+ }
+ }
+
+ 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(tree.getGroups().elementAt(i), col.brighter());
+
+ Vector<SequenceNode> l = tree.findLeaves(tree.getGroups()
+ .elementAt(i));
+
+ Vector<SequenceI> sequences = new Vector<SequenceI>();
+ 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.getColour(sg, ColourSchemeProperty
+ .getColourName(av.getGlobalColourScheme()));
+ }
+ // cs is null if shading is an annotationColourGradient
+ if (cs != null)
+ {
+ cs.setThreshold(av.getGlobalColourScheme().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.cs = cs;
+
+ sg.setName("JTreeGroup:" + sg.hashCode());
+ sg.setIdColour(col);
+ if (av.getGlobalColourScheme() != null
+ && av.getGlobalColourScheme().conservationApplied())
+ {
+ Conservation c = new Conservation("Group", 3,
+ sg.getSequences(null), sg.getStartRes(), sg.getEndRes());
+
+ c.calculate();
+ c.verdict(false, av.getConsPercGaps());
+ cs.setConservation(c);
+
+ sg.cs = cs;
+
+ }
+
+ 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();
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff