/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 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
* @version $Revision$\r
*/\r
public class TreeCanvas extends JPanel implements MouseListener, Runnable,\r
- Printable\r
+ Printable, MouseMotionListener\r
{\r
/** DOCUMENT ME!! */\r
public static final String PLACEHOLDER = " * ";\r
NJTree tree;\r
JScrollPane scrollPane;\r
AlignViewport av;\r
+ AlignmentPanel ap;\r
Font font;\r
- int fontSize = 12;\r
+ FontMetrics fm;\r
boolean fitToWindow = true;\r
boolean showDistances = false;\r
boolean showBootstrap = false;\r
boolean markPlaceholders = false;\r
int offx = 20;\r
- int offy = 20;\r
+ int offy;\r
float threshold;\r
String longestName;\r
int labelLength = -1;\r
\r
- //RubberbandRectangle rubberband;\r
- Vector listeners;\r
Hashtable nameHash = new Hashtable();\r
Hashtable nodeHash = new Hashtable();\r
+ SequenceNode highlightNode;\r
\r
/**\r
* Creates a new TreeCanvas object.\r
* @param scroller DOCUMENT ME!\r
* @param label DOCUMENT ME!\r
*/\r
- public TreeCanvas(AlignViewport av, NJTree tree, JScrollPane scroller,\r
- String label)\r
+ public TreeCanvas(AlignmentPanel ap, JScrollPane scroller)\r
{\r
- this.av = av;\r
- this.tree = tree;\r
+ this.av = ap.av;\r
+ this.ap = ap;\r
+ font = av.getFont();\r
scrollPane = scroller;\r
addMouseListener(this);\r
- tree.findHeight(tree.getTopNode());\r
- longestName = label;\r
-\r
- PaintRefresher.Register(this, av.alignment);\r
+ addMouseMotionListener(this);\r
+ PaintRefresher.Register(this, ap.av.getSequenceSetId());\r
+ ToolTipManager.sharedInstance().registerComponent(this);\r
}\r
\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
* @param sequence DOCUMENT ME!\r
*/\r
- public void TreeSelectionChanged(Sequence sequence)\r
+ public void treeSelectionChanged(SequenceI sequence)\r
{\r
SequenceGroup selected = av.getSelectionGroup();\r
\r
av.setSelectionGroup(selected);\r
}\r
\r
- selected.setEndRes(av.alignment.getWidth());\r
+ selected.setEndRes(av.alignment.getWidth()-1);\r
selected.addOrRemove(sequence, true);\r
-\r
- PaintRefresher.Refresh(this, av.alignment);\r
- repaint();\r
}\r
\r
/**\r
{\r
this.tree = tree;\r
tree.findHeight(tree.getTopNode());\r
+\r
+ // Now have to calculate longest name based on the leaves\r
+ Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());\r
+ boolean has_placeholders = false;\r
+ longestName = "";\r
+\r
+ for (int i = 0; i < leaves.size(); i++)\r
+ {\r
+ SequenceNode lf = (SequenceNode) leaves.elementAt(i);\r
+\r
+ if (lf.isPlaceholder())\r
+ {\r
+ has_placeholders = true;\r
+ }\r
+\r
+ if (longestName.length() < ( (Sequence) lf.element()).getName()\r
+ .length())\r
+ {\r
+ longestName = TreeCanvas.PLACEHOLDER +\r
+ ( (Sequence) lf.element()).getName();\r
+ }\r
+ }\r
+\r
+ setMarkPlaceholders(has_placeholders);\r
}\r
\r
/**\r
\r
if (node.element() instanceof SequenceI)\r
{\r
- if (((SequenceI) ((SequenceNode) node).element()).getColor() == Color.white)\r
+ SequenceI seq = (SequenceI)((SequenceNode) node).element();\r
+\r
+ if (av.getSequenceColour(seq) == Color.white)\r
{\r
g.setColor(Color.black);\r
}\r
else\r
{\r
- g.setColor(((SequenceI) ((SequenceNode) node).element()).getColor()\r
- .darker());\r
+ g.setColor(av.getSequenceColour(seq).darker());\r
}\r
}\r
else\r
\r
if (showDistances && (node.dist > 0))\r
{\r
- nodeLabel = new Format("%5.2f").form(node.dist);\r
+ nodeLabel = new Format("%-.2f").form(node.dist);\r
}\r
\r
if (showBootstrap)\r
\r
if (!nodeLabel.equals(""))\r
{\r
- g.drawString(nodeLabel, xstart, ypos - 10);\r
+ g.drawString(nodeLabel, xstart+2, ypos - 2);\r
}\r
\r
String name = (markPlaceholders && node.isPlaceholder())\r
? (PLACEHOLDER + node.getName()) : node.getName();\r
- FontMetrics fm = g.getFontMetrics(font);\r
+\r
int charWidth = fm.stringWidth(name) + 3;\r
- int charHeight = fm.getHeight();\r
+ int charHeight = font.getSize();\r
\r
- Rectangle rect = new Rectangle(xend + 20, ypos - charHeight,\r
+ Rectangle rect = new Rectangle(xend+10, ypos-charHeight/2,\r
charWidth, charHeight);\r
\r
nameHash.put((SequenceI) node.element(), rect);\r
SequenceGroup selected = av.getSelectionGroup();\r
\r
if ((selected != null) &&\r
- selected.sequences.contains((SequenceI) node.element()))\r
+ selected.getSequences(false).contains((SequenceI) node.element()))\r
{\r
g.setColor(Color.gray);\r
\r
- g.fillRect(xend + 10, ypos - charHeight + 3, charWidth,\r
+ g.fillRect(xend + 10, ypos-charHeight/2, charWidth,\r
charHeight);\r
g.setColor(Color.white);\r
}\r
\r
- g.drawString(name, xend + 10, ypos);\r
+ g.drawString(name, xend + 10, ypos+fm.getDescent());\r
g.setColor(Color.black);\r
}\r
else\r
\r
// Draw horizontal line\r
g.drawLine(xstart, ypos, xend, ypos);\r
- g.fillRect(xend - 2, ypos - 2, 4, 4);\r
+ if (node == highlightNode)\r
+ g.fillRect(xend - 3, ypos - 3, 6, 6);\r
+ else\r
+ g.fillRect(xend - 2, ypos - 2, 4, 4);\r
\r
int ystart = (int) (((SequenceNode) node.left()).ycount * chunk) +\r
offy;\r
\r
if (showDistances && (node.dist > 0))\r
{\r
- g.drawString(new Format("%5.2f").form(node.dist), xstart,\r
- ypos - 5);\r
+ g.drawString(new Format("%-.2f").form(node.dist).trim(), xstart+2,\r
+ ypos - 2);\r
}\r
}\r
}\r
((SequenceNode) top.right()).count;\r
}\r
\r
- float chunk = (float) (height - (offy * 2)) / top.count;\r
+ float chunk = (float) (height - (offy)) / top.count;\r
\r
pickNode(pickBox, top, chunk, wscale, width, offx, offy);\r
}\r
\r
if (node.element() instanceof SequenceI)\r
{\r
- ((SequenceI) node.element()).setColor(c);\r
+ av.setSequenceColour((SequenceI) node.element(), c);\r
}\r
}\r
else\r
public void paintComponent(Graphics g)\r
{\r
super.paintComponent(g);\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(tree==null)\r
{\r
- repaint();\r
+ g.drawString("Calculating tree....", 20, getHeight()/2);\r
}\r
-\r
- if (fitToWindow ||\r
- (!fitToWindow &&\r
- (scrollPane.getHeight() > ((fm.getHeight() * nameHash.size()) +\r
- offy))))\r
+ else\r
{\r
+ fm = g.getFontMetrics(font);\r
+\r
+ if (nameHash.size() == 0)\r
+ {\r
+ repaint();\r
+ }\r
+\r
+ if (fitToWindow ||\r
+ (!fitToWindow &&\r
+ (scrollPane.getHeight() > ( (fm.getHeight() * nameHash.size()) +\r
+ offy))))\r
+ {\r
draw(g, scrollPane.getWidth(), scrollPane.getHeight());\r
setPreferredSize(null);\r
- }\r
- else\r
- {\r
+ }\r
+ else\r
+ {\r
setPreferredSize(new Dimension(scrollPane.getWidth(),\r
- fm.getHeight() * nameHash.size()));\r
+ fm.getHeight() * nameHash.size()));\r
draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());\r
- }\r
+ }\r
\r
- scrollPane.revalidate();\r
+ scrollPane.revalidate();\r
+ }\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getFontSize()\r
- {\r
- return fontSize;\r
- }\r
\r
/**\r
* DOCUMENT ME!\r
*\r
* @param fontSize DOCUMENT ME!\r
*/\r
- public void setFontSize(int fontSize)\r
+ public void setFont(Font font)\r
{\r
- this.fontSize = fontSize;\r
+ this.font = font;\r
repaint();\r
}\r
\r
g2.setColor(Color.white);\r
g2.fillRect(0, 0, width, height);\r
\r
- labelLength = g2.getFontMetrics(font).stringWidth(longestName) + 20; //20 allows for scrollbar\r
+ g2.setFont(font);\r
+\r
+ offy = font.getSize()+10;\r
+\r
+ fm = g2.getFontMetrics(font);\r
+\r
+ labelLength = fm.stringWidth(longestName) + 20; //20 allows for scrollbar\r
\r
float wscale = (float) (width - labelLength - (offx * 2)) / tree.getMaxHeight();\r
\r
((SequenceNode) top.right()).count;\r
}\r
\r
- float chunk = (float) (height - (offy * 2)) / top.count;\r
+ float chunk = (float) (height - (offy)) / top.count;\r
\r
drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy);\r
\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- public void mouseClicked(MouseEvent e)\r
+ public void mouseClicked(MouseEvent evt)\r
{\r
+ if(highlightNode!=null)\r
+ {\r
+ if (SwingUtilities.isRightMouseButton(evt))\r
+ {\r
+ Color col = JColorChooser.showDialog(this, "Select Background Colour",\r
+ highlightNode.color);\r
+\r
+ setColor(highlightNode, col);\r
+ }\r
+ else\r
+ if(evt.getClickCount()>1)\r
+ {\r
+ tree.swapNodes(highlightNode);\r
+ tree.reCount(tree.getTopNode());\r
+ tree.findHeight(tree.getTopNode());\r
+ }\r
+ else\r
+ {\r
+ Vector leaves = new Vector();\r
+ tree.findLeaves(highlightNode, leaves);\r
+\r
+ for (int i = 0; i < leaves.size(); i++)\r
+ {\r
+ SequenceI seq =\r
+ (SequenceI) ( (SequenceNode) leaves.elementAt(i)).element();\r
+ treeSelectionChanged(seq);\r
+ }\r
+ }\r
+\r
+ PaintRefresher.Refresh(this, av.getSequenceSetId());\r
+ repaint();\r
+ }\r
}\r
\r
+\r
+\r
+ public void mouseMoved(MouseEvent evt)\r
+ {\r
+ av.setCurrentTree(tree);\r
+\r
+ Object ob = findElement(evt.getX(), evt.getY());\r
+\r
+ if (ob instanceof SequenceNode)\r
+ {\r
+ highlightNode = (SequenceNode) ob;\r
+ this.setToolTipText(\r
+ "<html>Left click to select leaves"\r
+ + "<br>Double-click to invert leaves"\r
+ + "<br>Right click to change colour");\r
+ repaint();\r
+\r
+ }\r
+ else\r
+ {\r
+ if (highlightNode != null)\r
+ {\r
+ highlightNode = null;\r
+ setToolTipText(null);\r
+ repaint();\r
+ }\r
+ }\r
+ }\r
+\r
+ public void mouseDragged(MouseEvent ect)\r
+ {}\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
\r
if (ob instanceof SequenceI)\r
{\r
- TreeSelectionChanged((Sequence) ob);\r
- repaint();\r
-\r
- return;\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
+ treeSelectionChanged( (Sequence) ob);\r
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
+ repaint();\r
+ return;\r
}\r
- else\r
+ else if( !(ob instanceof SequenceNode) )\r
{\r
// Find threshold\r
if (tree.getMaxHeight() != 0)\r
\r
av.setSelectionGroup(null);\r
av.alignment.deleteAllGroups();\r
+ av.sequenceColours.clear();\r
\r
- for (int i = 0; i < tree.getGroups().size(); i++)\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),\r
- col.brighter());\r
+ colourGroups();\r
+ }\r
\r
- Vector l = tree.findLeaves((SequenceNode) tree.getGroups()\r
- .elementAt(i),\r
- new Vector());\r
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
+ repaint();\r
+ }\r
\r
- Vector sequences = new Vector();\r
\r
- for (int j = 0; j < l.size(); j++)\r
- {\r
- SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j)).element();\r
+ }\r
\r
- if (!sequences.contains(s1))\r
- {\r
- sequences.addElement(s1);\r
- }\r
- }\r
+ void colourGroups()\r
+ {\r
+ for (int i = 0; i < tree.getGroups().size(); i++)\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),\r
+ col.brighter());\r
\r
- ColourSchemeI cs = ColourSchemeProperty.getColour(sequences,\r
- av.alignment.getWidth(),\r
- ColourSchemeProperty.getColourName(\r
- av.getGlobalColourScheme()));\r
+ Vector l = tree.findLeaves( (SequenceNode) tree.getGroups()\r
+ .elementAt(i),\r
+ new Vector());\r
\r
- SequenceGroup sg = new SequenceGroup(sequences,\r
- "TreeGroup", cs, true, true, false, 0,\r
- av.alignment.getWidth());\r
+ Vector sequences = new Vector();\r
\r
- if (sg.cs != null)\r
- {\r
- sg.cs.setThreshold(25, av.getIgnoreGapsConsensus());\r
- }\r
+ for (int j = 0; j < l.size(); j++)\r
+ {\r
+ SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element();\r
\r
- if (av.getGlobalColourScheme().conservationApplied())\r
- {\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3, sg.sequences,\r
- sg.getStartRes(), sg.getEndRes());\r
+ if (!sequences.contains(s1))\r
+ {\r
+ sequences.addElement(s1);\r
+ }\r
+ }\r
\r
- c.calculate();\r
- c.verdict(false, av.ConsPercGaps);\r
- sg.cs.setConservation(c);\r
- }\r
+ ColourSchemeI cs = null;\r
\r
- av.alignment.addGroup(sg);\r
- }\r
- }\r
+ if (av.getGlobalColourScheme() != null)\r
+ {\r
+ if (av.getGlobalColourScheme() instanceof UserColourScheme)\r
+ {\r
+ cs = new UserColourScheme(\r
+ ( (UserColourScheme) av.getGlobalColourScheme()).getColours());\r
+\r
+ }\r
+ else\r
+ cs = ColourSchemeProperty.getColour(sequences,\r
+ av.alignment.getWidth(),\r
+ ColourSchemeProperty.\r
+ getColourName(\r
+ av.getGlobalColourScheme()));\r
+\r
+ cs.setThreshold(av.getGlobalColourScheme().getThreshold(),\r
+ av.getIgnoreGapsConsensus());\r
}\r
\r
- PaintRefresher.Refresh(this, av.alignment);\r
- repaint();\r
+ SequenceGroup sg = new SequenceGroup(sequences,\r
+ "TreeGroup", cs, true, true, false,\r
+ 0,\r
+ av.alignment.getWidth() - 1);\r
+\r
+ if (av.getGlobalColourScheme() != null\r
+ && av.getGlobalColourScheme().conservationApplied())\r
+ {\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.getSequences(false),\r
+ sg.getStartRes(), sg.getEndRes());\r
+\r
+ c.calculate();\r
+ c.verdict(false, av.ConsPercGaps);\r
+ sg.cs.setConservation(c);\r
+ }\r
+\r
+ av.alignment.addGroup(sg);\r
+ }\r
+\r
}\r
\r
/**\r
git://source.jalview.org / jalview.git / blobdiff