-package jalview.gui;\r
-\r
-\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-import jalview.util.*;\r
-import jalview.schemes.*;\r
-import javax.swing.*;\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import java.util.*;\r
-import java.awt.print.*;\r
-\r
-public class TreeCanvas extends JPanel implements MouseListener, Runnable, Printable\r
-{\r
- NJTree tree;\r
- JScrollPane scrollPane;\r
- AlignViewport av;\r
-\r
- Font font;\r
- int fontSize = 12;\r
-\r
- boolean fitToWindow = true;\r
- boolean showDistances = false;\r
- boolean showBootstrap = 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, JScrollPane scroller, 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
-\r
- PaintRefresher.Register(this);\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());\r
- selected.addOrRemove(sequence);\r
-\r
-\r
- PaintRefresher.Refresh(this);\r
- repaint();\r
- }\r
-\r
-\r
-\r
- public void setTree(NJTree tree) {\r
- this.tree = tree;\r
- tree.findHeight(tree.getTopNode());\r
- }\r
-\r
- public void drawNode(Graphics g,SequenceNode node, float chunk, float scale, int width,int offx, int offy) {\r
- if (node == null) {\r
- return;\r
- }\r
-\r
- if (node.left() == null && node.right() == null) {\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() == Color.white)\r
- {\r
- g.setColor(Color.black);\r
- }\r
- else\r
- g.setColor( ( (SequenceI) ( (SequenceNode) node).element()).getColor().\r
- darker());\r
-\r
- }\r
- else\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
- nodeLabel = new Format("%5.2f").form(node.dist);\r
- }\r
- if (showBootstrap) {\r
- if (showDistances) {\r
- nodeLabel = nodeLabel + " : ";\r
- }\r
- nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());\r
- }\r
- if (! nodeLabel.equals("")) {\r
- g.drawString(nodeLabel,xstart,ypos - 10);\r
- }\r
-\r
- // Colour selected leaves differently\r
- String name = node.getName();\r
- FontMetrics fm = g.getFontMetrics(font);\r
- int charWidth = fm.stringWidth(node.getName()) + 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
- SequenceGroup selected = av.getSelectionGroup();\r
- if (selected!=null && selected.sequences.contains((SequenceI)node.element())) {\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(node.getName(),xend+10,ypos);\r
- g.setColor(Color.black);\r
- } else {\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
- g.drawString(new Format("%5.2f").form(node.dist),xstart,ypos - 5);\r
- }\r
-\r
- }\r
- }\r
- public Object findElement(int x, int y) {\r
- Enumeration keys = nameHash.keys();\r
-\r
- while (keys.hasMoreElements()) {\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
- return ob;\r
- }\r
- }\r
- keys = nodeHash.keys();\r
-\r
- while (keys.hasMoreElements()) {\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
- return ob;\r
- }\r
- }\r
- return null;\r
-\r
- }\r
-\r
- public void pickNodes(Rectangle pickBox) {\r
- int width = getWidth();\r
- int height = getHeight();\r
-\r
- SequenceNode top = tree.getTopNode();\r
-\r
- float wscale = (float)(width*.8-offx*2)/tree.getMaxHeight()\r
-;\r
- if (top.count == 0) {\r
- top.count = ((SequenceNode)top.left()).count + ((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, float scale, int width,int offx, int offy) {\r
- if (node == null) {\r
- return;\r
- }\r
-\r
- if (node.left() == null && node.right() == null) {\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
- if (node.element() instanceof SequenceI) {\r
- SequenceI seq = (SequenceI)node.element();\r
- SequenceGroup sg = av.getSelectionGroup();\r
- if(sg!=null)\r
- sg.addOrRemove(seq);\r
- }\r
- }\r
- } else {\r
- pickNode(pickBox,(SequenceNode)node.left(), chunk,scale,width,offx,offy);\r
- pickNode(pickBox,(SequenceNode)node.right(),chunk,scale,width,offx,offy);\r
- }\r
- }\r
-\r
- public void setColor(SequenceNode node, Color c)\r
- {\r
- if (node == null)\r
- return;\r
-\r
- if (node.left() == null && node.right() == null)\r
- {\r
- node.color = c;\r
-\r
- if (node.element() instanceof SequenceI)\r
- ((SequenceI)node.element()).setColor(c);\r
- } else\r
- {\r
- node.color = c;\r
- setColor((SequenceNode)node.left(),c);\r
- setColor((SequenceNode)node.right(),c);\r
- }\r
- }\r
-\r
- void startPrinting()\r
- {\r
- Thread thread = new Thread(this);\r
- thread.start();\r
- }\r
-\r
- // put printing in a thread to avoid painting problems\r
- public void run()\r
- {\r
- PrinterJob printJob = PrinterJob.getPrinterJob();\r
- PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
-\r
- printJob.setPrintable(this, pf);\r
- if (printJob.printDialog())\r
- {\r
- try\r
- {\r
- printJob.print();\r
- }\r
- catch (Exception PrintException)\r
- {\r
- PrintException.printStackTrace();\r
- }\r
- }\r
- }\r
-\r
-\r
- public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException\r
- {\r
-\r
- pg.setFont(font);\r
- pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());\r
- int pwidth = (int) pf.getImageableWidth();\r
- int pheight = (int) pf.getImageableHeight();\r
-\r
- int noPages = getHeight() / pheight;\r
- if(pi>noPages)\r
- return Printable.NO_SUCH_PAGE;\r
-\r
-\r
- if (pwidth > getWidth())\r
- pwidth = getWidth();\r
-\r
- if(fitToWindow)\r
- {\r
- if (pheight > getHeight())\r
- pheight = getHeight();\r
-\r
- noPages = 0;\r
- }\r
- else\r
- {\r
-\r
- FontMetrics fm = pg.getFontMetrics(font);\r
- int height = fm.getHeight() * nameHash.size();\r
- pg.translate(0, -pi*pheight );\r
- pg.setClip(0,pi*pheight, pwidth,pi*pheight + pheight);\r
- // translate number of pages,\r
- // height is screen size as this is the\r
- // non overlapping text size\r
- pheight = height;\r
- }\r
-\r
- draw(pg, pwidth, pheight);\r
-\r
- return Printable.PAGE_EXISTS;\r
-\r
- }\r
-\r
- public void paintComponent(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
- repaint();\r
-\r
-\r
- if( fitToWindow || (!fitToWindow && scrollPane.getHeight() > fm.getHeight() * nameHash.size()+offy ) )\r
- {\r
- draw(g,scrollPane.getWidth(),scrollPane.getHeight());\r
- setPreferredSize(null);\r
- }\r
- else\r
- {\r
- setPreferredSize(new Dimension(scrollPane.getWidth(), fm.getHeight() * nameHash.size()));\r
- draw( g,scrollPane.getWidth(), fm.getHeight() * nameHash.size());\r
- }\r
-\r
- scrollPane.revalidate();\r
- }\r
- public int getFontSize() {\r
- return fontSize;\r
- }\r
- public void setFontSize(int fontSize) {\r
- this.fontSize = fontSize;\r
- repaint();\r
- }\r
- public void draw(Graphics g1, int width, int height) {\r
-\r
- Graphics2D g2 = (Graphics2D)g1;\r
- g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);\r
- g2.setColor(Color.white);\r
- g2.fillRect(0,0,width,height);\r
-\r
-\r
- labelLength = g2.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
- top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;\r
- }\r
- float chunk = (float)(height-offy*2)/top.count ;\r
-\r
- drawNode(g2,tree.getTopNode(),chunk,wscale,width,offx,offy);\r
-\r
- if (threshold != 0)\r
- {\r
- if(av.getCurrentTree() == tree)\r
- g2.setColor(Color.red);\r
- else\r
- g2.setColor(Color.gray);\r
-\r
- int x = (int)( threshold * (float)(getWidth()-labelLength - 2*offx) +offx ) ;\r
-\r
- g2.drawLine(x,0,x,getHeight());\r
- }\r
-\r
- }\r
-\r
- public void mouseReleased(MouseEvent e) { }\r
- public void mouseEntered(MouseEvent e) { }\r
- public void mouseExited(MouseEvent e) { }\r
- public void mouseClicked(MouseEvent e) {\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
- } else if (ob instanceof SequenceNode) {\r
- SequenceNode tmpnode = (SequenceNode)ob;\r
- tree.swapNodes(tmpnode);\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
- } else {\r
- // Find threshold\r
-\r
- if (tree.getMaxHeight() != 0) {\r
- threshold = (float)(x - offx)/(float)(getWidth()-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(i),new Vector());\r
- SequenceGroup sg = null;\r
- for (int j = 0; j < l.size(); j++)\r
- {\r
- SequenceNode sn = (SequenceNode) l.elementAt(j);\r
- if(sg==null)\r
- sg = new SequenceGroup("TreeGroup", av.getGlobalColourScheme(), true, true,false,0,av.alignment.getWidth());\r
-\r
- sg.addSequence( (Sequence) sn.element());\r
- }\r
-\r
- if (av.getGlobalColourScheme() instanceof ConservationColourScheme)\r
- {\r
- ConservationColourScheme ccs = (ConservationColourScheme) av.getGlobalColourScheme();\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
- ccs = new ConservationColourScheme(c, ccs.cs);\r
-\r
- sg.cs = ccs;\r
-\r
- }\r
-\r
-\r
-\r
- av.alignment.addGroup(sg);\r
-\r
- }\r
- }\r
- }\r
-\r
- PaintRefresher.Refresh(this);\r
- repaint();\r
-\r
- }\r
-\r
- public void setShowDistances(boolean state) {\r
- this.showDistances = state;\r
- repaint();\r
- }\r
-\r
- public void setShowBootstrap(boolean state) {\r
- this.showBootstrap = state;\r
- repaint();\r
- }\r
-\r
-}\r
-\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.gui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.print.*;
+import javax.swing.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import jalview.util.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class TreeCanvas extends JPanel implements MouseListener, Runnable,
+ Printable, MouseMotionListener
+{
+ /** DOCUMENT ME!! */
+ public static final String PLACEHOLDER = " * ";
+
+ NJTree tree;
+
+ JScrollPane scrollPane;
+
+ TreePanel tp;
+
+ AlignViewport av;
+
+ AlignmentPanel ap;
+
+ Font font;
+
+ FontMetrics fm;
+
+ 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;
+
+ boolean applyToAllViews = false;
+
+ /**
+ * Creates a new TreeCanvas object.
+ *
+ * @param av
+ * DOCUMENT ME!
+ * @param tree
+ * DOCUMENT ME!
+ * @param scroller
+ * DOCUMENT ME!
+ * @param label
+ * DOCUMENT ME!
+ */
+ public TreeCanvas(TreePanel tp, AlignmentPanel ap, JScrollPane scroller)
+ {
+ this.tp = tp;
+ this.av = ap.av;
+ this.ap = ap;
+ font = av.getFont();
+ scrollPane = scroller;
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ ToolTipManager.sharedInstance().registerComponent(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param sequence
+ * DOCUMENT ME!
+ */
+ public void treeSelectionChanged(SequenceI sequence)
+ {
+ AlignmentPanel[] aps = getAssociatedPanels();
+
+ for (int a = 0; a < aps.length; a++)
+ {
+ SequenceGroup selected = aps[a].av.getSelectionGroup();
+
+ if (selected == null)
+ {
+ selected = new SequenceGroup();
+ aps[a].av.setSelectionGroup(selected);
+ }
+
+ selected.setEndRes(aps[a].av.alignment.getWidth() - 1);
+ selected.addOrRemove(sequence, true);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param tree
+ * DOCUMENT ME!
+ */
+ 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);
+ }
+
+ /**
+ * 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)
+ {
+ 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 && node.bootstrap > -1)
+ {
+ if (showDistances)
+ {
+ nodeLabel = nodeLabel + " : ";
+ }
+
+ nodeLabel = nodeLabel + String.valueOf(node.bootstrap);
+ }
+
+ if (!nodeLabel.equals(""))
+ {
+ g.drawString(nodeLabel, xstart + 2, ypos - 2);
+ }
+
+ String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node
+ .getName()) : node.getName();
+
+ int charWidth = fm.stringWidth(name) + 3;
+ int charHeight = font.getSize();
+
+ Rectangle rect = new Rectangle(xend + 10, ypos - charHeight / 2,
+ 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 / 2, charWidth, charHeight);
+ g.setColor(Color.white);
+ }
+
+ g.drawString(name, xend + 10, ypos + fm.getDescent());
+ 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 && node.bootstrap > -1)
+ {
+ if (showDistances)
+ {
+ nodeLabel = nodeLabel + " : ";
+ }
+
+ nodeLabel = nodeLabel + String.valueOf(node.bootstrap);
+ }
+
+ if (!nodeLabel.equals(""))
+ {
+ g.drawString(nodeLabel, xstart + 2, ypos - 2);
+ }
+ }
+ }
+
+ /**
+ * 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)) / 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)) // TODO: internal node
+ {
+ node.color = c;
+
+ if (node.element() instanceof SequenceI)
+ {
+ AlignmentPanel[] aps = getAssociatedPanels();
+ if (aps != null)
+ {
+ for (int a = 0; a < aps.length; a++)
+ {
+ aps[a].av.setSequenceColour((SequenceI) node.element(), 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);
+ g.setFont(font);
+
+ if (tree == null)
+ {
+ g.drawString("Calculating tree....", 20, getHeight() / 2);
+ }
+ else
+ {
+ 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!
+ *
+ * @param fontSize
+ * DOCUMENT ME!
+ */
+ public void setFont(Font font)
+ {
+ this.font = font;
+ 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);
+
+ g2.setFont(font);
+
+ offy = font.getSize() + 10;
+
+ fm = g2.getFontMetrics(font);
+
+ labelLength = fm.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(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 evt)
+ {
+ if (highlightNode != null)
+ {
+ if (SwingUtilities.isRightMouseButton(evt))
+ {
+ Color col = JColorChooser.showDialog(this,
+ "Select Sub-Tree Colour", highlightNode.color);
+ if (col != null)
+ {
+ setColor(highlightNode, col);
+ }
+ }
+ else 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);
+ }
+ av.sendSelection();
+ }
+
+ PaintRefresher.Refresh(tp, av.getSequenceSetId());
+ repaint();
+ }
+ }
+
+ public void mouseMoved(MouseEvent evt)
+ {
+ av.setCurrentTree(tree);
+
+ Object ob = findElement(evt.getX(), evt.getY());
+
+ if (ob instanceof SequenceNode)
+ {
+ highlightNode = (SequenceNode) ob;
+ this.setToolTipText("<html>Left click to select leaves"
+ + "<br>Double-click to invert leaves"
+ + "<br>Right click to change colour");
+ repaint();
+
+ }
+ else
+ {
+ if (highlightNode != null)
+ {
+ highlightNode = null;
+ setToolTipText(null);
+ repaint();
+ }
+ }
+ }
+
+ public void mouseDragged(MouseEvent ect)
+ {
+ }
+
+ /**
+ * 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);
+ PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
+ repaint();
+ av.sendSelection();
+ return;
+ }
+ else if (!(ob instanceof SequenceNode))
+ {
+ // 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);
+
+ AlignmentPanel[] aps = getAssociatedPanels();
+
+ for (int a = 0; a < aps.length; a++)
+ {
+ aps[a].av.setSelectionGroup(null);
+ aps[a].av.alignment.deleteAllGroups();
+ aps[a].av.sequenceColours = null;
+ }
+ colourGroups();
+ }
+
+ PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
+ repaint();
+ }
+
+ }
+
+ void colourGroups()
+ {
+ AlignmentPanel[] aps = getAssociatedPanels();
+ 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 is null if shading is an annotationColourGradient
+ if (cs!=null)
+ {
+ cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
+ av.getIgnoreGapsConsensus());
+ }
+ }
+
+ SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true,
+ false, 0, av.alignment.getWidth() - 1);
+
+ sg.setName("JTreeGroup:" + sg.hashCode());
+ sg.setIdColour(col);
+ for (int a = 0; a < aps.length; a++)
+ {
+ if (aps[a].av.getGlobalColourScheme() != null
+ && aps[a].av.getGlobalColourScheme().conservationApplied())
+ {
+ Conservation c = new Conservation("Group",
+ ResidueProperties.propHash, 3, sg.getSequences(null),
+ sg.getStartRes(), sg.getEndRes());
+
+ c.calculate();
+ c.verdict(false, aps[a].av.ConsPercGaps);
+ sg.cs.setConservation(c);
+ }
+
+ aps[a].av.alignment.addGroup(sg);
+ }
+ }
+ // notify the panel to redo any group specific stuff.
+ for (int a = 0; a < aps.length; a++)
+ {
+ aps[a].updateAnnotation();
+ // TODO: JAL-868 - need to ensure view colour change message is broadcast to any Jmols listening in
+ }
+
+ }
+
+ /**
+ * 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();
+ }
+
+ AlignmentPanel[] getAssociatedPanels()
+ {
+ if (applyToAllViews)
+ {
+ return PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
+ }
+ else
+ {
+ return new AlignmentPanel[]
+ { ap };
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff