X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=6f60792b45f11059185b669aef7731caebfb6420;hb=ddf3aca722d27da4bd2c58e9f0ab0909ba9639c0;hp=ed9677a56c1a8228695b276e6b33dbaa1cea92f2;hpb=577f505f54fe343e89f581461e780ea8308c20ec;p=jalview.git
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index ed9677a..6f60792 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -1,473 +1,881 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
package jalview.gui;
-
import jalview.analysis.*;
+
import jalview.datamodel.*;
-import jalview.util.*;
+
import jalview.schemes.*;
-import javax.swing.*;
+
+import jalview.util.*;
+
import java.awt.*;
import java.awt.event.*;
-import java.util.*;
import java.awt.print.*;
-public class TreeCanvas extends JPanel implements MouseListener, Runnable, Printable
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class TreeCanvas extends JPanel implements MouseListener, Runnable,
+ Printable, MouseMotionListener
{
- NJTree tree;
- JScrollPane scrollPane;
- AlignViewport av;
+ /** DOCUMENT ME!! */
+ public static final String PLACEHOLDER = " * ";
+ NJTree tree;
+ JScrollPane scrollPane;
+ 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;
+
+ /**
+ * Creates a new TreeCanvas object.
+ *
+ * @param av DOCUMENT ME!
+ * @param tree DOCUMENT ME!
+ * @param scroller DOCUMENT ME!
+ * @param label DOCUMENT ME!
+ */
+ public TreeCanvas(AlignmentPanel ap, JScrollPane scroller)
+ {
+ this.av = ap.av;
+ this.ap = ap;
+ font = av.getFont();
+ scrollPane = scroller;
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ PaintRefresher.Register(this, ap.av.getSequenceSetId());
+ ToolTipManager.sharedInstance().registerComponent(this);
+ }
- Font font;
- int fontSize = 12;
- boolean fitToWindow = true;
- boolean showDistances = false;
- boolean showBootstrap = false;
+ /**
+ * DOCUMENT ME!
+ *
+ * @param sequence DOCUMENT ME!
+ */
+ public void treeSelectionChanged(SequenceI sequence)
+ {
+ SequenceGroup selected = av.getSelectionGroup();
- int offx = 20;
- int offy = 20;
+ if (selected == null)
+ {
+ selected = new SequenceGroup();
+ av.setSelectionGroup(selected);
+ }
- int threshold;
+ selected.setEndRes(av.alignment.getWidth()-1);
+ selected.addOrRemove(sequence, true);
+ }
- String longestName;
- int labelLength=-1;
+ /**
+ * DOCUMENT ME!
+ *
+ * @param tree DOCUMENT ME!
+ */
+ public void setTree(NJTree tree)
+ {
+ this.tree = tree;
+ tree.findHeight(tree.getTopNode());
- //RubberbandRectangle rubberband;
+ // Now have to calculate longest name based on the leaves
+ Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
+ boolean has_placeholders = false;
+ longestName = "";
- Vector listeners;
+ for (int i = 0; i < leaves.size(); i++)
+ {
+ SequenceNode lf = (SequenceNode) leaves.elementAt(i);
- Hashtable nameHash = new Hashtable();
- Hashtable nodeHash = new Hashtable();
+ if (lf.isPlaceholder())
+ {
+ has_placeholders = true;
+ }
- public TreeCanvas(AlignViewport av, NJTree tree, JScrollPane scroller, String label)
- {
- this.av = av;
- this.tree = tree;
- scrollPane = scroller;
- addMouseListener(this);
- tree.findHeight(tree.getTopNode());
- longestName = label;
+ if (longestName.length() < ( (Sequence) lf.element()).getName()
+ .length())
+ {
+ longestName = TreeCanvas.PLACEHOLDER +
+ ( (Sequence) lf.element()).getName();
+ }
+ }
- PaintRefresher.Register(this);
- }
- public void TreeSelectionChanged(Sequence sequence)
- {
- SequenceGroup selected = av.getSelectionGroup();
- if(selected == null)
- {
- selected = new SequenceGroup();
- av.setSelectionGroup(selected);
+ setMarkPlaceholders(has_placeholders);
}
- selected.setEndRes(av.alignment.getWidth());
- selected.addOrRemove(sequence);
+ /**
+ * 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);
+ }
- PaintRefresher.Refresh(this);
- repaint();
- }
+ // Draw horizontal line
+ g.drawLine(xstart, ypos, xend, ypos);
+ String nodeLabel = "";
+ if (showDistances && (node.dist > 0))
+ {
+ nodeLabel = new Format("%-.2f").form(node.dist);
+ }
- public void setTree(NJTree tree) {
- this.tree = tree;
- tree.findHeight(tree.getTopNode());
- }
+ if (showBootstrap)
+ {
+ if (showDistances)
+ {
+ nodeLabel = nodeLabel + " : ";
+ }
- public void drawNode(Graphics g,SequenceNode node, float chunk, float scale, int width,int offx, int offy) {
- if (node == null) {
- return;
- }
+ nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
+ }
- if (node.left() == null && node.right() == null) {
- // Drawing leaf node
+ if (!nodeLabel.equals(""))
+ {
+ g.drawString(nodeLabel, xstart+2, ypos - 2);
+ }
- float height = node.height;
- float dist = node.dist;
+ String name = (markPlaceholders && node.isPlaceholder())
+ ? (PLACEHOLDER + node.getName()) : node.getName();
- int xstart = (int)((height-dist)*scale) + offx;
- int xend = (int)(height*scale) + offx;
+ int charWidth = fm.stringWidth(name) + 3;
+ int charHeight = font.getSize();
- int ypos = (int)(node.ycount * chunk) + offy;
+ Rectangle rect = new Rectangle(xend+10, ypos-charHeight/2,
+ charWidth, charHeight);
- 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());
+ nameHash.put((SequenceI) node.element(), rect);
- }
- else
- g.setColor(Color.black);
+ // Colour selected leaves differently
+ SequenceGroup selected = av.getSelectionGroup();
+ if ((selected != null) &&
+ selected.getSequences(false).contains((SequenceI) node.element()))
+ {
+ g.setColor(Color.gray);
- // Draw horizontal line
- g.drawLine(xstart,ypos,xend,ypos);
+ g.fillRect(xend + 10, ypos-charHeight/2, charWidth,
+ charHeight);
+ g.setColor(Color.white);
+ }
- String nodeLabel = "";
- if (showDistances && node.dist > 0) {
- nodeLabel = new Format("%5.2f").form(node.dist);
- }
- if (showBootstrap) {
- if (showDistances) {
- nodeLabel = nodeLabel + " : ";
+ g.drawString(name, xend + 10, ypos+fm.getDescent());
+ g.setColor(Color.black);
}
- nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
- }
- if (! nodeLabel.equals("")) {
- g.drawString(nodeLabel,xstart,ypos - 10);
- }
-
- // Colour selected leaves differently
- String name = node.getName();
- FontMetrics fm = g.getFontMetrics(font);
- int charWidth = fm.stringWidth(node.getName()) + 3;
- int charHeight = fm.getHeight();
+ 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);
+
+ if (showDistances && (node.dist > 0))
+ {
+ g.drawString(new Format("%-.2f").form(node.dist).trim(), xstart+2,
+ ypos - 2);
+ }
+ }
+ }
- Rectangle rect = new Rectangle(xend+20,ypos-charHeight,
- charWidth,charHeight);
+ /**
+ * DOCUMENT ME!
+ *
+ * @param x DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object findElement(int x, int y)
+ {
+ Enumeration keys = nameHash.keys();
- nameHash.put((SequenceI)node.element(),rect);
+ while (keys.hasMoreElements())
+ {
+ Object ob = keys.nextElement();
+ Rectangle rect = (Rectangle) nameHash.get(ob);
- SequenceGroup selected = av.getSelectionGroup();
- if (selected!=null && selected.sequences.contains((SequenceI)node.element())) {
- g.setColor(Color.gray);
+ if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&
+ (y <= (rect.y + rect.height)))
+ {
+ return ob;
+ }
+ }
- g.fillRect(xend + 10, ypos - charHeight + 3,charWidth,charHeight);
- g.setColor(Color.white);
- }
- g.drawString(node.getName(),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);
+ keys = nodeHash.keys();
- float height = node.height;
- float dist = node.dist;
+ while (keys.hasMoreElements())
+ {
+ Object ob = keys.nextElement();
+ Rectangle rect = (Rectangle) nodeHash.get(ob);
- int xstart = (int)((height-dist)*scale) + offx;
- int xend = (int)(height *scale) + offx;
- int ypos = (int)(node.ycount *chunk) + offy;
+ if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&
+ (y <= (rect.y + rect.height)))
+ {
+ return ob;
+ }
+ }
- g.setColor(((SequenceNode)node).color.darker());
+ return null;
+ }
- // Draw horizontal line
- g.drawLine(xstart,ypos,xend,ypos);
- g.fillRect(xend-2, ypos-2, 4,4);
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pickBox DOCUMENT ME!
+ */
+ public void pickNodes(Rectangle pickBox)
+ {
+ int width = getWidth();
+ int height = getHeight();
- int ystart = (int)(((SequenceNode)node.left()) .ycount * chunk) + offy;
- int yend = (int)(((SequenceNode)node.right()).ycount * chunk) + offy;
+ SequenceNode top = tree.getTopNode();
- Rectangle pos = new Rectangle(xend-2,ypos-2,5,5);
- nodeHash.put(node,pos);
+ float wscale = (float) ((width * .8) - (offx * 2)) / tree.getMaxHeight();
- g.drawLine((int)(height*scale) + offx, ystart,
- (int)(height*scale) + offx, yend);
+ if (top.count == 0)
+ {
+ top.count = ((SequenceNode) top.left()).count +
+ ((SequenceNode) top.right()).count;
+ }
- if (showDistances && node.dist > 0) {
- g.drawString(new Format("%5.2f").form(node.dist),xstart,ypos - 5);
- }
+ float chunk = (float) (height - (offy)) / top.count;
+ pickNode(pickBox, top, chunk, wscale, width, offx, offy);
}
- }
- public Object findElement(int x, int y) {
- Enumeration keys = nameHash.keys();
- while (keys.hasMoreElements()) {
- Object ob = keys.nextElement();
- Rectangle rect = (Rectangle)nameHash.get(ob);
+ /**
+ * 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 (x >= rect.x && x <= (rect.x + rect.width) &&
- y >= rect.y && y <= (rect.y + rect.height)) {
- return ob;
- }
- }
- keys = nodeHash.keys();
+ if ((node.left() == null) && (node.right() == null))
+ {
+ float height = node.height;
+ float dist = node.dist;
- while (keys.hasMoreElements()) {
- Object ob = keys.nextElement();
- Rectangle rect = (Rectangle)nodeHash.get(ob);
+ 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 (x >= rect.x && x <= (rect.x + rect.width) &&
- y >= rect.y && y <= (rect.y + rect.height)) {
- return ob;
+ 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);
+ }
}
- return null;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param c DOCUMENT ME!
+ */
+ public void setColor(SequenceNode node, Color c)
+ {
+ if (node == null)
+ {
+ return;
+ }
- public void pickNodes(Rectangle pickBox) {
- int width = getWidth();
- int height = getHeight();
+ if ((node.left() == null) && (node.right() == null))
+ {
+ node.color = c;
- SequenceNode top = tree.getTopNode();
+ 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);
+ }
+ }
- float wscale = (float)(width*.8-offx*2)/tree.getMaxHeight()
-;
- if (top.count == 0) {
- top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;
+ /**
+ * DOCUMENT ME!
+ */
+ void startPrinting()
+ {
+ Thread thread = new Thread(this);
+ thread.start();
}
- float chunk = (float)(height-offy*2)/top.count;
- pickNode(pickBox,top,chunk,wscale,width,offx,offy);
- }
+ // 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);
- public void pickNode(Rectangle pickBox, SequenceNode node, float chunk, float scale, int width,int offx, int offy) {
- if (node == null) {
- return;
+ if (printJob.printDialog())
+ {
+ try
+ {
+ printJob.print();
+ }
+ catch (Exception PrintException)
+ {
+ PrintException.printStackTrace();
+ }
+ }
}
- if (node.left() == null && node.right() == null) {
- float height = node.height;
- float dist = node.dist;
+ /**
+ * 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 xstart = (int)((height-dist)*scale) + offx;
- int xend = (int)(height*scale) + offx;
+ int pwidth = (int) pf.getImageableWidth();
+ int pheight = (int) pf.getImageableHeight();
- int ypos = (int)(node.ycount * chunk) + offy;
+ int noPages = getHeight() / pheight;
- 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);
+ if (pi > noPages)
+ {
+ return Printable.NO_SUCH_PAGE;
}
- }
- } 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 (pwidth > getWidth())
+ {
+ pwidth = getWidth();
+ }
- if (node.left() == null && node.right() == null)
- {
- node.color = c;
+ if (fitToWindow)
+ {
+ if (pheight > getHeight())
+ {
+ pheight = getHeight();
+ }
- if (node.element() instanceof SequenceI)
- ((SequenceI)node.element()).setColor(c);
- } else
- {
- node.color = c;
- setColor((SequenceNode)node.left(),c);
- setColor((SequenceNode)node.right(),c);
- }
- }
+ 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;
+ }
- void startPrinting()
- {
- Thread thread = new Thread(this);
- thread.start();
- }
+ draw(pg, pwidth, pheight);
- // 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();
- }
+ return Printable.PAGE_EXISTS;
}
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g DOCUMENT ME!
+ */
+ public void paintComponent(Graphics g)
+ {
+ super.paintComponent(g);
+ g.setFont(font);
- public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
- {
- font = new Font("Verdana",Font.PLAIN,fontSize);
- pg.setFont(font);
- FontMetrics fm = pg.getFontMetrics(font);
+ if(tree==null)
+ {
+ g.drawString("Calculating tree....", 20, getHeight()/2);
+ }
+ else
+ {
+ fm = g.getFontMetrics(font);
- pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
+ if (nameHash.size() == 0)
+ {
+ repaint();
+ }
- int pwidth = (int) pf.getImageableWidth();
- int pheight = (int) pf.getImageableHeight();
+ 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());
+ }
- // adjust pheight to row height
- pheight -= (pheight%fm.getHeight());
- pg.setClip(0,0, pwidth, pheight);
+ scrollPane.revalidate();
+ }
+ }
- int noPages = (fm.getHeight() * nameHash.size()) / pheight;
- if(pi>noPages)
- return Printable.NO_SUCH_PAGE;
+ /**
+ * DOCUMENT ME!
+ *
+ * @param fontSize DOCUMENT ME!
+ */
+ public void setFont(Font font)
+ {
+ this.font = font;
+ repaint();
+ }
- pg.translate(0, -pheight*pi );
- draw(pg, pwidth, fm.getHeight() * nameHash.size());
+ /**
+ * 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);
- return Printable.PAGE_EXISTS;
+ g2.setFont(font);
- }
+ offy = font.getSize()+10;
- public void paintComponent(Graphics g)
- {
+ fm = g2.getFontMetrics(font);
- font = new Font("Verdana",Font.PLAIN,fontSize);
- g.setFont(font);
+ labelLength = fm.stringWidth(longestName) + 20; //20 allows for scrollbar
- FontMetrics fm = g.getFontMetrics(font);
+ float wscale = (float) (width - labelLength - (offx * 2)) / tree.getMaxHeight();
- if(nameHash.size()==0)
- repaint();
+ SequenceNode top = tree.getTopNode();
+ if (top.count == 0)
+ {
+ top.count = ((SequenceNode) top.left()).count +
+ ((SequenceNode) top.right()).count;
+ }
- 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());
- }
+ float chunk = (float) (height - (offy)) / top.count;
+ drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy);
- if (threshold != 0)
- {
- g.setColor(Color.red);
- g.drawLine(threshold,0,threshold,getHeight());
- }
+ if (threshold != 0)
+ {
+ if (av.getCurrentTree() == tree)
+ {
+ g2.setColor(Color.red);
+ }
+ else
+ {
+ g2.setColor(Color.gray);
+ }
- scrollPane.revalidate();
- }
- public int getFontSize() {
- return fontSize;
+ int x = (int) ((threshold * (float) (getWidth() - labelLength -
+ (2 * offx))) + offx);
+
+ g2.drawLine(x, 0, x, getHeight());
+ }
}
- public void setFontSize(int fontSize) {
- this.fontSize = fontSize;
- repaint();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseReleased(MouseEvent e)
+ {
}
- public void draw(Graphics g, int width, int height) {
- g.setColor(Color.white);
- g.fillRect(0,0,width,height);
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseEntered(MouseEvent e)
+ {
+ }
- labelLength = g.getFontMetrics(font).stringWidth(longestName)+ 20;//20 allows for scrollbar
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseExited(MouseEvent e)
+ {
+ }
- float wscale =(float)(width - labelLength -offx*2)/tree.getMaxHeight();
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseClicked(MouseEvent evt)
+ {
+ if(highlightNode!=null)
+ {
+ if (SwingUtilities.isRightMouseButton(evt))
+ {
+ Color col = JColorChooser.showDialog(this, "Select Background Colour",
+ highlightNode.color);
- SequenceNode top = tree.getTopNode();
+ 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);
+ }
+ }
- if (top.count == 0) {
- top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ repaint();
}
- float chunk = (float)(height-offy*2)/top.count ;
+ }
- drawNode(g,tree.getTopNode(),chunk,wscale,width,offx,offy);
- }
- 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) {
- int x = e.getX();
- int y = e.getY();
+ public void mouseMoved(MouseEvent evt)
+ {
+ av.setCurrentTree(tree);
- Object ob = findElement(x,y);
+ Object ob = findElement(evt.getX(), evt.getY());
- if (ob instanceof SequenceI)
+ if (ob instanceof SequenceNode)
+ {
+ highlightNode = (SequenceNode) ob;
+ this.setToolTipText(
+ "Left click to select leaves"
+ + "
Double-click to invert leaves"
+ + "
Right click to change colour");
+ repaint();
+
+ }
+ else
{
- TreeSelectionChanged((Sequence)ob);
+ if (highlightNode != null)
+ {
+ highlightNode = null;
+ setToolTipText(null);
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
+ public void mouseDragged(MouseEvent ect)
+ {}
- if (tree.getMaxHeight() != 0) {
- float fthreshold = (float)(x - offx)/(float)(getWidth()-labelLength - 2*offx);
- this.threshold = x;
- tree.getGroups().removeAllElements();
- tree.groupNodes(tree.getTopNode(),fthreshold);
- setColor(tree.getTopNode(),Color.black);
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mousePressed(MouseEvent e)
+ {
+ av.setCurrentTree(tree);
+
+ int x = e.getX();
+ int y = e.getY();
- av.setSelectionGroup(null);
- av.alignment.deleteAllGroups();
+ Object ob = findElement(x, y);
- for (int i=0; i < tree.getGroups().size(); i++)
- {
+ if (ob instanceof SequenceI)
+ {
+ treeSelectionChanged( (Sequence) ob);
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
+ repaint();
+ 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);
+
+ av.setSelectionGroup(null);
+ av.alignment.deleteAllGroups();
+ av.sequenceColours=null;
+
+ colourGroups();
+ }
- Color col = new Color((int)(Math.random()*255),
- (int)(Math.random()*255),
- (int)(Math.random()*255));
- setColor((SequenceNode)tree.getGroups().elementAt(i),col.brighter());
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
+ repaint();
+ }
- Vector l = tree.findLeaves((SequenceNode)tree.getGroups().elementAt(i),new Vector());
- SequenceGroup sg = null;
- for (int j = 0; j < l.size(); j++)
- {
- SequenceNode sn = (SequenceNode) l.elementAt(j);
- if(sg==null)
- sg = new SequenceGroup("TreeGroup", av.getGlobalColourScheme(), true, true,false,0,av.alignment.getWidth());
- sg.addSequence( (Sequence) sn.element());
- }
+ }
- if (av.getGlobalColourScheme() instanceof ConservationColourScheme)
- {
- ConservationColourScheme ccs = (ConservationColourScheme) av.getGlobalColourScheme();
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.sequences, sg.getStartRes(),
- sg.getEndRes());
+ 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());
- c.calculate();
- c.verdict(false, 100);
- ccs = new ConservationColourScheme(c, ccs.cs);
+ Vector l = tree.findLeaves( (SequenceNode) tree.getGroups()
+ .elementAt(i),
+ new Vector());
- sg.cs = ccs;
+ 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;
- av.alignment.addGroup(sg);
+ 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);
+ sg.cs.setConservation(c);
+ }
- PaintRefresher.Refresh(this);
- repaint();
+ av.alignment.addGroup(sg);
+ }
- }
+ }
- public void setShowDistances(boolean state) {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state DOCUMENT ME!
+ */
+ public void setShowDistances(boolean state)
+ {
this.showDistances = state;
repaint();
}
- public void setShowBootstrap(boolean state) {
- this.showBootstrap = 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();
+ }
}
-