/*\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
import jalview.util.*;\r
\r
public class TreeCanvas\r
- extends Panel implements MouseListener\r
+ extends Panel implements MouseListener, MouseMotionListener\r
{\r
NJTree tree;\r
ScrollPane scrollPane;\r
AlignViewport av;\r
public static final String PLACEHOLDER = " * ";\r
Font font;\r
- int fontSize = 12;\r
-\r
boolean fitToWindow = true;\r
boolean showDistances = false;\r
boolean showBootstrap = false;\r
boolean markPlaceholders = false;\r
\r
int offx = 20;\r
- int offy = 20;\r
+ int offy;\r
\r
float threshold;\r
\r
String longestName;\r
int labelLength = -1;\r
\r
- //RubberbandRectangle rubberband;\r
-\r
- Vector listeners;\r
-\r
Hashtable nameHash = new Hashtable();\r
Hashtable nodeHash = new Hashtable();\r
\r
- public TreeCanvas(AlignViewport av, NJTree tree, ScrollPane scroller,\r
- String label)\r
+ SequenceNode highlightNode;\r
+\r
+\r
+ public TreeCanvas(AlignViewport av, ScrollPane scroller)\r
{\r
this.av = av;\r
- this.tree = tree;\r
+ font = av.getFont();\r
scrollPane = scroller;\r
addMouseListener(this);\r
- tree.findHeight(tree.getTopNode());\r
- longestName = label;\r
+ addMouseMotionListener(this);\r
setLayout(null);\r
\r
- PaintRefresher.Register(this);\r
+ PaintRefresher.Register(this, av.getSequenceSetId());\r
}\r
\r
- public void TreeSelectionChanged(Sequence sequence)\r
+ public void treeSelectionChanged(SequenceI sequence)\r
{\r
SequenceGroup selected = av.getSelectionGroup();\r
if (selected == null)\r
av.setSelectionGroup(selected);\r
}\r
\r
- selected.setEndRes(av.alignment.getWidth());\r
- selected.addOrRemove(sequence);\r
-\r
- PaintRefresher.Refresh(this);\r
- repaint();\r
+ selected.setEndRes(av.alignment.getWidth()-1);\r
+ selected.addOrRemove(sequence, true);\r
}\r
\r
public void setTree(NJTree tree)\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
public void drawNode(Graphics g, SequenceNode node, float chunk, float scale,\r
\r
if (node.element() instanceof SequenceI)\r
{\r
- if ( ( (SequenceI) ( (SequenceNode) node).element()).getColor() ==\r
- 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
}\r
String nodeLabel = "";\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
if (showBootstrap)\r
{\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
int charWidth = fm.stringWidth(name) + 3;\r
int charHeight = fm.getHeight();\r
\r
- Rectangle rect = new Rectangle(xend + 20, ypos - charHeight,\r
+ Rectangle rect = new Rectangle(xend + 10, ypos - charHeight,\r
charWidth, charHeight);\r
\r
nameHash.put( (SequenceI) node.element(), rect);\r
// Colour selected leaves differently\r
SequenceGroup selected = av.getSelectionGroup();\r
if (selected != null &&\r
- selected.sequences.contains( (SequenceI) node.element()))\r
+ selected.getSequences(null).contains( (SequenceI) node.element()))\r
{\r
g.setColor(Color.gray);\r
\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) + offy;\r
int yend = (int) ( ( (SequenceNode) node.right()).ycount * chunk) + offy;\r
\r
if (showDistances && node.dist > 0)\r
{\r
- g.drawString(new Format("%5.2f").form(node.dist), xstart, ypos - 5);\r
+ g.drawString(new Format("%-.2f").form(node.dist), xstart+2, ypos - 2);\r
}\r
\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) / top.count;\r
\r
pickNode(pickBox, top, chunk, wscale, width, offx, offy);\r
}\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 xstart = (int) ( (height - dist) * scale) + offx;\r
int xend = (int) (height * scale) + offx;\r
\r
int ypos = (int) (node.ycount * chunk) + offy;\r
SequenceGroup sg = av.getSelectionGroup();\r
if (sg != null)\r
{\r
- sg.addOrRemove(seq);\r
+ sg.addOrRemove(seq, true);\r
}\r
}\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
}\r
}\r
\r
- public void paint(Graphics g)\r
+ public void update(Graphics g)\r
{\r
+ paint(g);\r
+ }\r
\r
- font = new Font("Verdana", Font.PLAIN, fontSize);\r
- g.setFont(font);\r
-\r
- FontMetrics fm = g.getFontMetrics(font);\r
+ public void paint(Graphics g)\r
+ {\r
+ if(tree==null)\r
+ return;\r
\r
if (nameHash.size() == 0)\r
{\r
repaint();\r
}\r
\r
- if (fitToWindow ||\r
- (!fitToWindow &&\r
- scrollPane.getSize().height > fm.getHeight() * nameHash.size() + offy))\r
+ int width = scrollPane.getSize().width;\r
+ int height = scrollPane.getSize().height;\r
+ if(!fitToWindow)\r
{\r
- draw(g, scrollPane.getSize().width, scrollPane.getSize().height);\r
+ height = g.getFontMetrics(font).getHeight() * nameHash.size();\r
}\r
- else\r
+\r
+ if(getSize().width>width)\r
{\r
- setSize(new Dimension(scrollPane.getSize().width,\r
- fm.getHeight() * nameHash.size()));\r
- draw(g, scrollPane.getSize().width, fm.getHeight() * nameHash.size());\r
+ setSize(new Dimension(width,height));\r
+ scrollPane.validate();\r
+ return;\r
}\r
\r
- scrollPane.validate();\r
- }\r
+ setSize(new Dimension(width,height));\r
\r
- public int getFontSize()\r
- {\r
- return fontSize;\r
- }\r
\r
- public void setFontSize(int fontSize)\r
- {\r
- this.fontSize = fontSize;\r
- repaint();\r
+ g.setFont(font);\r
+\r
+ draw(g, width, height);\r
+\r
}\r
\r
+\r
public void draw(Graphics g, int width, int height)\r
{\r
+ offy = font.getSize()+10;\r
\r
g.setColor(Color.white);\r
g.fillRect(0, 0, width, height);\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) / top.count;\r
\r
drawNode(g, tree.getTopNode(), chunk, wscale, width, offx, offy);\r
\r
public void mouseExited(MouseEvent e)\r
{}\r
\r
- public void mouseClicked(MouseEvent e)\r
+ public void mouseClicked(MouseEvent evt)\r
+ {\r
+ if (highlightNode != null)\r
+ {\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
+ public void mouseDragged(MouseEvent ect)\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
+ repaint();\r
+ }\r
+ else\r
+ {\r
+ if (highlightNode != null)\r
+ {\r
+ highlightNode = null;\r
+ repaint();\r
+ }\r
+ }\r
}\r
\r
public void mousePressed(MouseEvent e)\r
{\r
-\r
av.setCurrentTree(tree);\r
\r
int x = e.getX();\r
\r
if (ob instanceof SequenceI)\r
{\r
- TreeSelectionChanged( (Sequence) ob);\r
+ treeSelectionChanged( (Sequence) ob);\r
+ PaintRefresher.Refresh(this, av.getSequenceSetId());\r
repaint();\r
return;\r
-\r
}\r
- else if (ob instanceof SequenceNode)\r
- {\r
- SequenceNode tmpnode = (SequenceNode) ob;\r
- tree.swapNodes(tmpnode);\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
- }\r
- else\r
+ else if ( !(ob instanceof SequenceNode))\r
{\r
// Find threshold\r
\r
\r
av.setSelectionGroup(null);\r
av.alignment.deleteAllGroups();\r
+ av.sequenceColours=null;\r
\r
- for (int i = 0; i < tree.getGroups().size(); i++)\r
+ colourGroups();\r
+\r
+ }\r
+ }\r
+\r
+ PaintRefresher.Refresh(this, av.getSequenceSetId());\r
+ repaint();\r
+\r
+ }\r
+\r
+ void colourGroups()\r
+ {\r
+ for (int i = 0; i < tree.getGroups().size(); i++)\r
{\r
\r
Color col = new Color( (int) (Math.random() * 255),\r
\r
Vector l = tree.findLeaves( (SequenceNode) tree.getGroups().elementAt(\r
i), new Vector());\r
- SequenceGroup sg = null;\r
+\r
+ Vector sequences = new Vector();\r
for (int j = 0; j < l.size(); j++)\r
{\r
- SequenceNode sn = (SequenceNode) l.elementAt(j);\r
- if (sg == null)\r
+ SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element();\r
+ if(!sequences.contains(s1))\r
+ sequences.addElement(s1);\r
+ }\r
+\r
+ ColourSchemeI cs = null;\r
+\r
+ if (av.getGlobalColourScheme() != null)\r
+ {\r
+ if (av.getGlobalColourScheme() instanceof UserColourScheme)\r
{\r
- sg = new SequenceGroup("TreeGroup", av.getGlobalColourScheme(), true, true, false,\r
- 0, av.alignment.getWidth());\r
- }\r
+ cs = new UserColourScheme(\r
+ ( (UserColourScheme) av.getGlobalColourScheme()).getColours());\r
\r
- sg.addSequence( (Sequence) sn.element());\r
+ }\r
+ else\r
+ cs = ColourSchemeProperty.getColour(sequences,\r
+ av.alignment.getWidth(),\r
+ ColourSchemeProperty.getColourName(\r
+ av.getGlobalColourScheme()));\r
+\r
+ cs.setThreshold(av.getGlobalColourScheme().getThreshold(),\r
+ av.getIgnoreGapsConsensus());\r
}\r
\r
- if (av.getGlobalColourScheme() instanceof ConservationColourScheme)\r
- {\r
- ConservationColourScheme ccs = (ConservationColourScheme) av.\r
- getGlobalColourScheme();\r
+ SequenceGroup sg = new SequenceGroup(sequences, "",\r
+ cs, true, true,\r
+ false, 0, av.alignment.getWidth()-1);\r
+\r
+ sg.setName("JTreeGroup:"+sg.hashCode());\r
+\r
+\r
+ if ( av.getGlobalColourScheme()!=null\r
+ && av.getGlobalColourScheme().conservationApplied())\r
+ {\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.sequences, sg.getStartRes(),\r
+ sg.getSequences(null),\r
+ sg.getStartRes(),\r
sg.getEndRes());\r
\r
c.calculate();\r
c.verdict(false, av.ConsPercGaps);\r
- ccs = new ConservationColourScheme(c, ccs.cs);\r
+ cs.setConservation(c);\r
\r
- sg.cs = ccs;\r
+ sg.cs = cs;\r
\r
}\r
\r
av.alignment.addGroup(sg);\r
\r
}\r
- }\r
- }\r
-\r
- PaintRefresher.Refresh(this);\r
- repaint();\r
\r
}\r
\r
git://source.jalview.org / jalview.git / blobdiff