/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
-
package jalview.appletgui;
import java.util.*;
import jalview.schemes.*;
import jalview.util.*;
-public class TreeCanvas
- extends Panel implements MouseListener, MouseMotionListener
+public class TreeCanvas extends Panel implements MouseListener,
+ MouseMotionListener
{
NJTree tree;
+
ScrollPane scrollPane;
+
AlignViewport av;
+
public static final String PLACEHOLDER = " * ";
+
Font font;
+
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;
- public TreeCanvas(AlignViewport av, ScrollPane scroller)
+ AlignmentPanel ap;
+ public TreeCanvas(AlignmentPanel ap, ScrollPane scroller)
{
- this.av = av;
+ this.ap = ap;
+ this.av = ap.av;
font = av.getFont();
scrollPane = scroller;
addMouseListener(this);
has_placeholders = true;
}
- if (longestName.length() < ( (Sequence) lf.element()).getName()
- .length())
+ if (longestName.length() < ((Sequence) lf.element()).getName()
+ .length())
{
- longestName = TreeCanvas.PLACEHOLDER +
- ( (Sequence) lf.element()).getName();
+ longestName = TreeCanvas.PLACEHOLDER
+ + ((Sequence) lf.element()).getName();
}
}
setMarkPlaceholders(has_placeholders);
}
- public void drawNode(Graphics g, SequenceNode node, float chunk, float scale,
- int width, int offx, int offy)
+ public void drawNode(Graphics g, SequenceNode node, float chunk,
+ float scale, int width, int offx, int offy)
{
if (node == null)
{
float height = node.height;
float dist = node.dist;
- int xstart = (int) ( (height - dist) * scale) + offx;
+ 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();
+ SequenceI seq = (SequenceI) ((SequenceNode) node).element();
if (av.getSequenceColour(seq) == Color.white)
{
if (showBootstrap)
{
int btstrap = node.getBootstrap();
- if (btstrap>-1)
- {
+ if (btstrap > -1)
+ {
if (showDistances)
{
nodeLabel = nodeLabel + " : ";
g.drawString(nodeLabel, xstart + 2, ypos - 2);
}
- String name = (markPlaceholders && node.isPlaceholder()) ?
- (PLACEHOLDER + node.getName()) : node.getName();
+ String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node
+ .getName()) : node.getName();
FontMetrics fm = g.getFontMetrics(font);
int charWidth = fm.stringWidth(name) + 3;
int charHeight = fm.getHeight();
Rectangle rect = new Rectangle(xend + 10, ypos - charHeight,
- charWidth, charHeight);
+ charWidth, charHeight);
- nameHash.put( (SequenceI) node.element(), rect);
+ nameHash.put((SequenceI) node.element(), rect);
// Colour selected leaves differently
SequenceGroup selected = av.getSelectionGroup();
- if (selected != null &&
- selected.getSequences(null).contains( (SequenceI) node.element()))
+ if (selected != null
+ && selected.getSequences(null).contains(
+ (SequenceI) node.element()))
{
g.setColor(Color.gray);
}
else
{
- drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx, offy);
- drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx, offy);
+ 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 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());
+ g.setColor(((SequenceNode) node).color.darker());
// Draw horizontal line
g.drawLine(xstart, ypos, xend, ypos);
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;
+ 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);
+ g.drawLine((int) (height * scale) + offx, ystart,
+ (int) (height * scale) + offx, yend);
String nodeLabel = "";
if (showBootstrap)
{
int btstrap = node.getBootstrap();
- if (btstrap>-1)
- {
+ if (btstrap > -1)
+ {
if (showDistances)
{
nodeLabel = nodeLabel + " : ";
Object ob = keys.nextElement();
Rectangle rect = (Rectangle) nameHash.get(ob);
- if (x >= rect.x && x <= (rect.x + rect.width) &&
- y >= rect.y && y <= (rect.y + rect.height))
+ if (x >= rect.x && x <= (rect.x + rect.width) && y >= rect.y
+ && y <= (rect.y + rect.height))
{
return ob;
}
Object ob = keys.nextElement();
Rectangle rect = (Rectangle) nodeHash.get(ob);
- if (x >= rect.x && x <= (rect.x + rect.width) &&
- y >= rect.y && y <= (rect.y + rect.height))
+ if (x >= rect.x && x <= (rect.x + rect.width) && y >= rect.y
+ && y <= (rect.y + rect.height))
{
return ob;
}
SequenceNode top = tree.getTopNode();
- float wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight()
- ;
+ float wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight();
if (top.count == 0)
{
- top.count = ( (SequenceNode) top.left()).count +
- ( (SequenceNode) top.right()).count;
+ top.count = ((SequenceNode) top.left()).count
+ + ((SequenceNode) top.right()).count;
}
float chunk = (float) (height - offy) / top.count;
}
public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
- float scale, int width, int offx, int offy)
+ float scale, int width, int offx, int offy)
{
if (node == null)
{
if (node.left() == null && node.right() == null)
{
float height = node.height;
- //float dist = node.dist;
+ // float dist = node.dist;
- //int xstart = (int) ( (height - dist) * scale) + offx;
+ // int xstart = (int) ( (height - dist) * scale) + offx;
int xend = (int) (height * scale) + offx;
int ypos = (int) (node.ycount * chunk) + offy;
}
else
{
- pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width, offx,
- offy);
- pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width, offx,
- offy);
+ pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width,
+ offx, offy);
+ pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,
+ offx, offy);
}
}
if (node.element() instanceof SequenceI)
{
- av.setSequenceColour( (SequenceI) node.element(), c);
+ av.setSequenceColour((SequenceI) node.element(), c);
}
}
else
{
node.color = c;
- setColor( (SequenceNode) node.left(), c);
- setColor( (SequenceNode) node.right(), c);
+ setColor((SequenceNode) node.left(), c);
+ setColor((SequenceNode) node.right(), c);
}
}
setSize(new Dimension(width, height));
g.setFont(font);
-
draw(g, width, height);
-
+ validate();
}
public void draw(Graphics g, int width, int height)
g.setColor(Color.white);
g.fillRect(0, 0, width, height);
- labelLength = g.getFontMetrics(font).stringWidth(longestName) + 20; //20 allows for scrollbar
+ labelLength = g.getFontMetrics(font).stringWidth(longestName) + 20; // 20
+ // allows
+ // for
+ // scrollbar
- float wscale = (float) (width - labelLength - offx * 2) / tree.getMaxHeight();
+ float wscale = (float) (width - labelLength - offx * 2)
+ / tree.getMaxHeight();
SequenceNode top = tree.getTopNode();
if (top.count == 0)
{
- top.count = ( (SequenceNode) top.left()).count +
- ( (SequenceNode) top.right()).count;
+ top.count = ((SequenceNode) top.left()).count
+ + ((SequenceNode) top.right()).count;
}
float chunk = (float) (height - offy) / top.count;
g.setColor(Color.gray);
}
- int x = (int) (threshold *
- (float) (getSize().width - labelLength - 2 * offx) + offx);
+ int x = (int) (threshold
+ * (float) (getSize().width - labelLength - 2 * offx) + offx);
g.drawLine(x, 0, x, getSize().height);
}
}
public void mouseReleased(MouseEvent e)
- {}
+ {
+ }
public void mouseEntered(MouseEvent e)
- {}
+ {
+ }
public void mouseExited(MouseEvent e)
- {}
+ {
+ }
public void mouseClicked(MouseEvent evt)
{
for (int i = 0; i < leaves.size(); i++)
{
- SequenceI seq =
- (SequenceI) ( (SequenceNode) leaves.elementAt(i)).element();
+ SequenceI seq = (SequenceI) ((SequenceNode) leaves.elementAt(i))
+ .element();
treeSelectionChanged(seq);
}
}
PaintRefresher.Refresh(this, av.getSequenceSetId());
repaint();
+ av.sendSelection();
}
}
public void mouseDragged(MouseEvent ect)
- {}
+ {
+ }
public void mouseMoved(MouseEvent evt)
{
if (ob instanceof SequenceI)
{
- treeSelectionChanged( (Sequence) ob);
+ treeSelectionChanged((Sequence) ob);
PaintRefresher.Refresh(this, av.getSequenceSetId());
repaint();
+ av.sendSelection();
return;
}
- else if (! (ob instanceof SequenceNode))
+ else if (!(ob instanceof SequenceNode))
{
// Find threshold
if (tree.getMaxHeight() != 0)
{
- threshold = (float) (x - offx) /
- (float) (getSize().width - labelLength - 2 * offx);
+ threshold = (float) (x - offx)
+ / (float) (getSize().width - labelLength - 2 * offx);
tree.getGroups().removeAllElements();
tree.groupNodes(tree.getTopNode(), threshold);
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());
+ Color col = new Color((int) (Math.random() * 255),
+ (int) (Math.random() * 255), (int) (Math.random() * 255));
+ setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter());
- Vector l = tree.findLeaves( (SequenceNode) tree.getGroups().elementAt(
- i), new Vector());
+ Vector l = tree.findLeaves(
+ (SequenceNode) tree.getGroups().elementAt(i), new Vector());
Vector sequences = new Vector();
for (int j = 0; j < l.size(); j++)
{
- SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element();
+ SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j))
+ .element();
if (!sequences.contains(s1))
{
sequences.addElement(s1);
if (av.getGlobalColourScheme() instanceof UserColourScheme)
{
cs = new UserColourScheme(
- ( (UserColourScheme) av.getGlobalColourScheme()).getColours());
+ ((UserColourScheme) av.getGlobalColourScheme())
+ .getColours());
}
else
{
- cs = ColourSchemeProperty.getColour(sequences,
- av.alignment.getWidth(),
- ColourSchemeProperty.
- getColourName(
- av.getGlobalColourScheme()));
+ cs = ColourSchemeProperty.getColour(sequences, av.alignment
+ .getWidth(), ColourSchemeProperty.getColourName(av
+ .getGlobalColourScheme()));
+ }
+ // cs is null if shading is an annotationColourGradient
+ if (cs!=null)
+ {
+ cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
+ av.getIgnoreGapsConsensus());
}
-
- cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
- av.getIgnoreGapsConsensus());
}
- SequenceGroup sg = new SequenceGroup(sequences, "",
- cs, true, true,
- false, 0,
- av.alignment.getWidth() - 1);
+ SequenceGroup sg = new SequenceGroup(sequences, "", cs, true, true,
+ false, 0, av.alignment.getWidth() - 1);
sg.setName("JTreeGroup:" + sg.hashCode());
sg.setIdColour(col);
if (av.getGlobalColourScheme() != null
- && av.getGlobalColourScheme().conservationApplied())
+ && av.getGlobalColourScheme().conservationApplied())
{
Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.getSequences(null),
- sg.getStartRes(),
- sg.getEndRes());
+ ResidueProperties.propHash, 3, sg.getSequences(null),
+ sg.getStartRes(), sg.getEndRes());
c.calculate();
c.verdict(false, av.ConsPercGaps);
av.alignment.addGroup(sg);
}
-
+ ap.updateAnnotation();
+
}
public void setShowDistances(boolean state)
git://source.jalview.org / jalview.git / blobdiff