/*\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
+ * 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 jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-import jalview.util.*;\r
-import jalview.schemes.*;\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.util.*;\r
\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.schemes.*;\r
+import jalview.util.*;\r
\r
-public class TreeCanvas extends Panel implements MouseListener\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
+ public static final String PLACEHOLDER = " * ";\r
Font font;\r
- int fontSize = 12;\r
+ int fontSize = 12;\r
\r
boolean fitToWindow = true;\r
boolean showDistances = false;\r
float threshold;\r
\r
String longestName;\r
- int labelLength=-1;\r
+ int labelLength = -1;\r
\r
//RubberbandRectangle rubberband;\r
\r
- Vector listeners;\r
+ Vector listeners;\r
\r
Hashtable nameHash = new Hashtable();\r
Hashtable nodeHash = new Hashtable();\r
\r
- public TreeCanvas(AlignViewport av, NJTree tree, ScrollPane scroller, String label)\r
+ public TreeCanvas(AlignViewport av, NJTree tree, ScrollPane scroller,\r
+ String label)\r
{\r
this.av = av;\r
- this.tree = tree;\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);\r
+ PaintRefresher.Register(this, av.alignment);\r
}\r
+\r
public void TreeSelectionChanged(Sequence sequence)\r
- {\r
+ {\r
SequenceGroup selected = av.getSelectionGroup();\r
- if(selected == null)\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
+ selected.addOrRemove(sequence, true);\r
\r
-\r
- PaintRefresher.Refresh(this);\r
+System.out.println("called here");\r
+ PaintRefresher.Refresh(this, av.alignment);\r
repaint();\r
- }\r
-\r
-\r
+ }\r
\r
- public void setTree(NJTree tree) {\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, int width,int offx, int offy) {\r
- if (node == null) {\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
+ if (node.left() == null && node.right() == null)\r
+ {\r
// Drawing leaf node\r
\r
float height = node.height;\r
- float dist = node.dist;\r
+ float dist = node.dist;\r
\r
- int xstart = (int)((height-dist)*scale) + offx;\r
- int xend = (int)(height*scale) + offx;\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
+ 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
+ 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
- g.setColor(Color.black);\r
-\r
+ {\r
+ g.setColor(Color.black);\r
+ }\r
\r
// Draw horizontal line\r
- g.drawLine(xstart,ypos,xend,ypos);\r
+ g.drawLine(xstart, ypos, xend, ypos);\r
\r
String nodeLabel = "";\r
- if (showDistances && node.dist > 0) {\r
+ if (showDistances && node.dist > 0)\r
+ {\r
nodeLabel = new Format("%5.2f").form(node.dist);\r
}\r
- if (showBootstrap) {\r
- if (showDistances) {\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
- g.drawString(nodeLabel,xstart,ypos - 10);\r
+ if (!nodeLabel.equals(""))\r
+ {\r
+ g.drawString(nodeLabel, xstart, ypos - 10);\r
}\r
\r
- String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER+node.getName()) : node.getName();\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 charWidth = fm.stringWidth(name) + 3;\r
int charHeight = fm.getHeight();\r
\r
- Rectangle rect = new Rectangle(xend+20,ypos-charHeight,\r
- charWidth,charHeight);\r
+ Rectangle rect = new Rectangle(xend + 20, ypos - charHeight,\r
+ charWidth, charHeight);\r
\r
- nameHash.put((SequenceI)node.element(),rect);\r
+ nameHash.put( (SequenceI) node.element(), rect);\r
\r
// Colour selected leaves differently\r
SequenceGroup selected = av.getSelectionGroup();\r
- if (selected!=null && selected.sequences.contains((SequenceI)node.element())) {\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.fillRect(xend + 10, ypos - charHeight + 3, charWidth, charHeight);\r
g.setColor(Color.white);\r
}\r
- g.drawString(name,xend+10,ypos);\r
+ g.drawString(name, 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ if (showDistances && node.dist > 0)\r
+ {\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
+ public Object findElement(int x, int y)\r
+ {\r
+ Enumeration keys = nameHash.keys();\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
+ while (keys.hasMoreElements())\r
+ {\r
+ Object ob = keys.nextElement();\r
+ Rectangle rect = (Rectangle) nameHash.get(ob);\r
\r
- while (keys.hasMoreElements()) {\r
- Object ob = keys.nextElement();\r
- Rectangle rect = (Rectangle)nodeHash.get(ob);\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
- return 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
+ return null;\r
\r
}\r
\r
- public void pickNodes(Rectangle pickBox) {\r
- int width = getSize().width;\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
- top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;\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
+ float chunk = (float) (height - offy * 2) / top.count;\r
\r
- pickNode(pickBox,top,chunk,wscale,width,offx,offy);\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
+ 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
+ if (node.left() == null && node.right() == null)\r
+ {\r
float height = node.height;\r
- float dist = node.dist;\r
+ float dist = node.dist;\r
\r
- int xstart = (int)((height-dist)*scale) + offx;\r
- int xend = (int)(height*scale) + offx;\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
+ 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
+ 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
- sg.addOrRemove(seq);\r
+ if (sg != null)\r
+ {\r
+ sg.addOrRemove(seq, true);\r
+ }\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
+ 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
- ((SequenceI)node.element()).setColor(c);\r
- } else\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
+ setColor( (SequenceNode) node.left(), c);\r
+ setColor( (SequenceNode) node.right(), c);\r
}\r
}\r
\r
-\r
public void paint(Graphics g)\r
{\r
\r
- font = new Font("Verdana",Font.PLAIN,fontSize);\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
+ if (nameHash.size() == 0)\r
+ {\r
repaint();\r
+ }\r
\r
-\r
- if( fitToWindow || (!fitToWindow && scrollPane.getSize().height > fm.getHeight() * nameHash.size()+offy ) )\r
- {\r
- draw(g,scrollPane.getSize().width,scrollPane.getSize().height);\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, fm.getHeight() * nameHash.size()));\r
- draw( g,scrollPane.getSize().width, fm.getHeight() * nameHash.size());\r
- }\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
- 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 g, int width, int height) {\r
\r
- g.setColor(Color.white);\r
- g.fillRect(0,0,width,height);\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
- labelLength = g.getFontMetrics(font).stringWidth(longestName)+ 20;//20 allows for scrollbar\r
+ public void draw(Graphics g, int width, int height)\r
+ {\r
\r
- float wscale =(float)(width - labelLength -offx*2)/tree.getMaxHeight();\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, width, height);\r
\r
- SequenceNode top = tree.getTopNode();\r
+ labelLength = g.getFontMetrics(font).stringWidth(longestName) + 20; //20 allows for scrollbar\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
+ float wscale = (float) (width - labelLength - offx * 2) / tree.getMaxHeight();\r
\r
- drawNode(g,tree.getTopNode(),chunk,wscale,width,offx,offy);\r
+ SequenceNode top = tree.getTopNode();\r
\r
- if (threshold != 0)\r
- {\r
- if(av.getCurrentTree() == tree)\r
- g.setColor(Color.red);\r
- else\r
- g.setColor(Color.gray);\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
- int x = (int)( threshold * (float)(getSize().width-labelLength - 2*offx) +offx ) ;\r
+ drawNode(g, tree.getTopNode(), chunk, wscale, width, offx, offy);\r
\r
- g.drawLine(x,0,x,getSize().height);\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
- public void mouseEntered(MouseEvent e) { }\r
- public void mouseExited(MouseEvent e) { }\r
- public void mouseClicked(MouseEvent e) {\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
+ public void mousePressed(MouseEvent e)\r
+ {\r
+ av.setCurrentTree(tree);\r
\r
- av.setCurrentTree(tree);\r
+ int x = e.getX();\r
+ int y = e.getY();\r
\r
- int x = e.getX();\r
- int y = e.getY();\r
+ Object ob = findElement(x, y);\r
\r
- Object ob = findElement(x,y);\r
+ if (ob instanceof SequenceI)\r
+ {\r
+ TreeSelectionChanged( (Sequence) ob);\r
+ repaint();\r
+ return;\r
\r
- if (ob instanceof SequenceI)\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
- TreeSelectionChanged((Sequence)ob);\r
- repaint();\r
- return;\r
+ threshold = (float) (x - offx) /\r
+ (float) (getSize().width - labelLength - 2 * offx);\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
+ tree.getGroups().removeAllElements();\r
+ tree.groupNodes(tree.getTopNode(), threshold);\r
+ setColor(tree.getTopNode(), Color.black);\r
\r
- if (tree.getMaxHeight() != 0) {\r
- threshold = (float)(x - offx)/(float)(getSize().width-labelLength - 2*offx);\r
+ av.setSelectionGroup(null);\r
+ av.alignment.deleteAllGroups();\r
\r
- tree.getGroups().removeAllElements();\r
- tree.groupNodes(tree.getTopNode(),threshold);\r
- setColor(tree.getTopNode(),Color.black);\r
+ for (int i = 0; i < tree.getGroups().size(); i++)\r
+ {\r
\r
- av.setSelectionGroup(null);\r
- av.alignment.deleteAllGroups();\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
- for (int i=0; i < tree.getGroups().size(); i++)\r
- {\r
+ Vector l = tree.findLeaves( (SequenceNode) tree.getGroups().elementAt(\r
+ i), new Vector());\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
+ 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
- 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
+ ColourSchemeI cs = ColourSchemeProperty.getColour(sequences, av.alignment.getWidth(),\r
+ ColourSchemeProperty.getColourName(av.getGlobalColourScheme()));\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
+ SequenceGroup sg = new SequenceGroup(sequences, "TreeGroup",\r
+ cs, true, true,\r
+ false, 0, av.alignment.getWidth());\r
\r
- c.calculate();\r
- c.verdict(false, av.ConsPercGaps);\r
- ccs = new ConservationColourScheme(c, ccs.cs);\r
\r
- sg.cs = ccs;\r
+ if (av.getGlobalColourScheme().conservationApplied())\r
+ {\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.sequences, sg.getStartRes(),\r
+ sg.getEndRes());\r
\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
+ av.alignment.addGroup(sg);\r
\r
- }\r
- }\r
+ }\r
}\r
+ }\r
\r
- PaintRefresher.Refresh(this);\r
- repaint();\r
+ PaintRefresher.Refresh(this, av.alignment);\r
+ repaint();\r
\r
}\r
\r
- public void setShowDistances(boolean state) {\r
- this.showDistances = state;\r
- repaint();\r
- }\r
+ public void setShowDistances(boolean state)\r
+ {\r
+ this.showDistances = state;\r
+ repaint();\r
+ }\r
\r
- public void setShowBootstrap(boolean state) {\r
- this.showBootstrap = state;\r
- repaint();\r
- }\r
- public void setMarkPlaceholders(boolean state) {\r
- this.markPlaceholders = state;\r
- repaint();\r
- }\r
+ public void setShowBootstrap(boolean state)\r
+ {\r
+ this.showBootstrap = state;\r
+ repaint();\r
+ }\r
\r
-}\r
+ public void setMarkPlaceholders(boolean state)\r
+ {\r
+ this.markPlaceholders = state;\r
+ repaint();\r
+ }\r
\r
+}\r
git://source.jalview.org / jalview.git / blobdiff