From d7d3a412210d013e401a3825eaf425fa55ce8106 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Mon, 18 Sep 2006 13:25:27 +0000 Subject: [PATCH] click node to select sequences --- src/jalview/appletgui/TreeCanvas.java | 133 +++++++++++++++------ src/jalview/gui/TreeCanvas.java | 207 ++++++++++++++++++++------------- 2 files changed, 229 insertions(+), 111 deletions(-) diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java index a9be9bc..928d21f 100755 --- a/src/jalview/appletgui/TreeCanvas.java +++ b/src/jalview/appletgui/TreeCanvas.java @@ -30,7 +30,7 @@ import jalview.schemes.*; import jalview.util.*; public class TreeCanvas - extends Panel implements MouseListener + extends Panel implements MouseListener, MouseMotionListener { NJTree tree; ScrollPane scrollPane; @@ -50,25 +50,25 @@ public class TreeCanvas String longestName; int labelLength = -1; - //RubberbandRectangle rubberband; - - Vector listeners; - Hashtable nameHash = new Hashtable(); Hashtable nodeHash = new Hashtable(); + SequenceNode highlightNode; + + public TreeCanvas(AlignViewport av, ScrollPane scroller) { this.av = av; font = av.getFont(); scrollPane = scroller; addMouseListener(this); + addMouseMotionListener(this); setLayout(null); PaintRefresher.Register(this, av.alignment); } - public void TreeSelectionChanged(Sequence sequence) + public void treeSelectionChanged(SequenceI sequence) { SequenceGroup selected = av.getSelectionGroup(); if (selected == null) @@ -79,9 +79,6 @@ public class TreeCanvas selected.setEndRes(av.alignment.getWidth()-1); selected.addOrRemove(sequence, true); - - PaintRefresher.Refresh(this, av.alignment); - repaint(); } public void setTree(NJTree tree) @@ -214,7 +211,10 @@ public class TreeCanvas // Draw horizontal line g.drawLine(xstart, ypos, xend, ypos); - g.fillRect(xend - 2, ypos - 2, 4, 4); + 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; @@ -348,22 +348,39 @@ public class TreeCanvas } } - public void paint(Graphics g) + public void update(Graphics g) + { + paint(g); + } + + Image offscreen; + public void paint(Graphics g1) { if(tree==null) return; - g.setFont(font); - - - FontMetrics fm = g.getFontMetrics(font); - if (nameHash.size() == 0) { repaint(); } + FontMetrics fm = g1.getFontMetrics(font); + + int width = scrollPane.getSize().width; + int height = scrollPane.getSize().height; + if(!fitToWindow) + height = fm.getHeight() * nameHash.size(); + + + if(offscreen==null || offscreen.getWidth(this)!=width + || offscreen.getHeight(this)!=height) + offscreen = createImage(width, height); + + Graphics g = offscreen.getGraphics(); + + g.setFont(font); + if (fitToWindow || (!fitToWindow && scrollPane.getSize().height > fm.getHeight() * nameHash.size() + offy)) @@ -377,6 +394,7 @@ public class TreeCanvas draw(g, scrollPane.getSize().width, fm.getHeight() * nameHash.size()); } + g1.drawImage(offscreen, 0, 0, this); scrollPane.validate(); } @@ -431,8 +449,57 @@ public class TreeCanvas public void mouseExited(MouseEvent e) {} - public void mouseClicked(MouseEvent e) + public void mouseClicked(MouseEvent evt) + { + if (highlightNode != null) + { + 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); + } + } + + PaintRefresher.Refresh(this, av.alignment); + repaint(); + } + } + + public void mouseDragged(MouseEvent ect) + {} + + + public void mouseMoved(MouseEvent evt) { + av.setCurrentTree(tree); + + Object ob = findElement(evt.getX(), evt.getY()); + + if (ob instanceof SequenceNode) + { + highlightNode = (SequenceNode) ob; + repaint(); + } + else + { + if (highlightNode != null) + { + highlightNode = null; + repaint(); + } + } } public void mousePressed(MouseEvent e) @@ -446,19 +513,12 @@ public class TreeCanvas if (ob instanceof SequenceI) { - TreeSelectionChanged( (Sequence) ob); + treeSelectionChanged( (Sequence) ob); + PaintRefresher.Refresh(this, av.alignment); repaint(); return; - } - else if (ob instanceof SequenceNode) - { - SequenceNode tmpnode = (SequenceNode) ob; - tree.swapNodes(tmpnode); - tree.reCount(tree.getTopNode()); - tree.findHeight(tree.getTopNode()); - } - else + else if ( !(ob instanceof SequenceNode)) { // Find threshold @@ -474,7 +534,19 @@ public class TreeCanvas av.setSelectionGroup(null); av.alignment.deleteAllGroups(); - for (int i = 0; i < tree.getGroups().size(); i++) + colourGroups(); + + } + } + + PaintRefresher.Refresh(this, av.alignment); + repaint(); + + } + + void colourGroups() + { + for (int i = 0; i < tree.getGroups().size(); i++) { Color col = new Color( (int) (Math.random() * 255), @@ -538,11 +610,6 @@ public class TreeCanvas av.alignment.addGroup(sg); } - } - } - - PaintRefresher.Refresh(this, av.alignment); - repaint(); } diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index 154fe46..70aeb60 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -42,7 +42,7 @@ import javax.swing.*; * @version $Revision$ */ public class TreeCanvas extends JPanel implements MouseListener, Runnable, - Printable + Printable, MouseMotionListener { /** DOCUMENT ME!! */ public static final String PLACEHOLDER = " * "; @@ -61,10 +61,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, String longestName; int labelLength = -1; - //RubberbandRectangle rubberband; - Vector listeners; Hashtable nameHash = new Hashtable(); Hashtable nodeHash = new Hashtable(); + SequenceNode highlightNode; /** * Creates a new TreeCanvas object. @@ -80,6 +79,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, font = av.getFont(); scrollPane = scroller; addMouseListener(this); + addMouseMotionListener(this); PaintRefresher.Register(this, av.alignment); } @@ -89,7 +89,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * * @param sequence DOCUMENT ME! */ - public void TreeSelectionChanged(Sequence sequence) + public void treeSelectionChanged(SequenceI sequence) { SequenceGroup selected = av.getSelectionGroup(); @@ -101,9 +101,6 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, selected.setEndRes(av.alignment.getWidth()-1); selected.addOrRemove(sequence, true); - - PaintRefresher.Refresh(this, av.alignment); - repaint(); } /** @@ -258,7 +255,10 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, // Draw horizontal line g.drawLine(xstart, ypos, xend, ypos); - g.fillRect(xend - 2, ypos - 2, 4, 4); + 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; @@ -657,10 +657,60 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * * @param e DOCUMENT ME! */ - public void mouseClicked(MouseEvent e) + public void mouseClicked(MouseEvent evt) { + if(highlightNode!=null) + { + 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); + } + } + + PaintRefresher.Refresh(this, av.alignment); + repaint(); + } } + + + public void mouseMoved(MouseEvent evt) + { + av.setCurrentTree(tree); + + Object ob = findElement(evt.getX(), evt.getY()); + + if (ob instanceof SequenceNode) + { + highlightNode = (SequenceNode) ob; + repaint(); + } + else + { + if (highlightNode != null) + { + highlightNode = null; + repaint(); + } + } + } + + public void mouseDragged(MouseEvent ect) + {} + /** * DOCUMENT ME! * @@ -677,19 +727,12 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (ob instanceof SequenceI) { - TreeSelectionChanged((Sequence) ob); - repaint(); - - return; - } - else if (ob instanceof SequenceNode) - { - SequenceNode tmpnode = (SequenceNode) ob; - tree.swapNodes(tmpnode); - tree.reCount(tree.getTopNode()); - tree.findHeight(tree.getTopNode()); + treeSelectionChanged( (Sequence) ob); + PaintRefresher.Refresh(this, av.alignment); + repaint(); + return; } - else + else if( !(ob instanceof SequenceNode) ) { // Find threshold if (tree.getMaxHeight() != 0) @@ -704,76 +747,84 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, av.setSelectionGroup(null); av.alignment.deleteAllGroups(); - 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()); + colourGroups(); + } - Vector l = tree.findLeaves((SequenceNode) tree.getGroups() - .elementAt(i), - new Vector()); + PaintRefresher.Refresh(this, av.alignment); + repaint(); + } - 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); - } - } + 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()); - ColourSchemeI cs = null; + Vector l = tree.findLeaves( (SequenceNode) tree.getGroups() + .elementAt(i), + new Vector()); - 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()); - } + Vector sequences = new Vector(); + for (int j = 0; j < l.size(); j++) + { + SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element(); - SequenceGroup sg = new SequenceGroup(sequences, - "TreeGroup", cs, true, true, false, 0, - av.alignment.getWidth()-1); + if (!sequences.contains(s1)) + { + sequences.addElement(s1); + } + } + ColourSchemeI cs = null; - 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); - } + if (av.getGlobalColourScheme() != null) + { + if (av.getGlobalColourScheme() instanceof UserColourScheme) + { + cs = new UserColourScheme( + ( (UserColourScheme) av.getGlobalColourScheme()).getColours()); - av.alignment.addGroup(sg); - } - } + } + else + cs = ColourSchemeProperty.getColour(sequences, + av.alignment.getWidth(), + ColourSchemeProperty. + getColourName( + av.getGlobalColourScheme())); + + cs.setThreshold(av.getGlobalColourScheme().getThreshold(), + av.getIgnoreGapsConsensus()); } - PaintRefresher.Refresh(this, av.alignment); - repaint(); + 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); + } + + av.alignment.addGroup(sg); + } + } /** -- 1.7.10.2