/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * 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.
- *
- * 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.util.*;
-
-public class TreeCanvas
- extends Panel implements MouseListener, MouseMotionListener
+import jalview.analysis.Conservation;
+import jalview.analysis.NJTree;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+import jalview.util.Format;
+import jalview.util.MappingUtils;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Panel;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.ScrollPane;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
+
+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);
av.setSelectionGroup(selected);
}
- selected.setEndRes(av.alignment.getWidth() - 1);
+ selected.setEndRes(av.getAlignment().getWidth() - 1);
selected.addOrRemove(sequence, true);
}
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) node.element();
if (av.getSequenceColour(seq) == Color.white)
{
}
if (showBootstrap)
{
- if (showDistances)
+ int btstrap = node.getBootstrap();
+ if (btstrap > -1)
{
- nodeLabel = nodeLabel + " : ";
+ if (showDistances)
+ {
+ nodeLabel = nodeLabel + " : ";
+ }
+ nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
}
- nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
}
if (!nodeLabel.equals(""))
{
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(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(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(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)
{
- if (showDistances)
+ int btstrap = node.getBootstrap();
+ if (btstrap > -1)
{
- nodeLabel = nodeLabel + " : ";
+ if (showDistances)
+ {
+ nodeLabel = nodeLabel + " : ";
+ }
+ nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
}
-
- nodeLabel = nodeLabel + String.valueOf(node.bootstrap);
}
if (!nodeLabel.equals(""))
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);
}
}
+ @Override
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
if (tree == null)
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 = (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 * (getSize().width - labelLength - 2 * offx) + offx);
g.drawLine(x, 0, x, getSize().height);
}
}
+ @Override
public void mouseReleased(MouseEvent e)
- {}
+ {
+ }
+ @Override
public void mouseEntered(MouseEvent e)
- {}
+ {
+ }
+ @Override
public void mouseExited(MouseEvent e)
- {}
+ {
+ }
+ @Override
public void mouseClicked(MouseEvent evt)
{
if (highlightNode != null)
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();
}
}
+ @Override
public void mouseDragged(MouseEvent ect)
- {}
+ {
+ }
+ @Override
public void mouseMoved(MouseEvent evt)
{
av.setCurrentTree(tree);
}
}
+ @Override
public void mousePressed(MouseEvent e)
{
av.setCurrentTree(tree);
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);
setColor(tree.getTopNode(), Color.black);
av.setSelectionGroup(null);
- av.alignment.deleteAllGroups();
- av.sequenceColours = null;
+ av.getAlignment().deleteAllGroups();
+ av.clearSequenceColours();
+ final AlignViewportI codingComplement = av.getCodingComplement();
+ if (codingComplement != null)
+ {
+ codingComplement.setSelectionGroup(null);
+ codingComplement.getAlignment().deleteAllGroups();
+ codingComplement.clearSequenceColours();
+ }
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());
+ 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);
ColourSchemeI cs = null;
+ SequenceGroup sg = new SequenceGroup(sequences, "", cs, true, true,
+ false, 0, av.getAlignment().getWidth() - 1);
+
if (av.getGlobalColourScheme() != null)
{
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(sg, ColourSchemeProperty
+ .getColourName(av.getGlobalColourScheme()));
+ }
+ // cs is null if shading is an annotationColourGradient
+ if (cs != null)
+ {
+ cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
+ av.isIgnoreGapsConsensus());
}
-
- cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
- av.getIgnoreGapsConsensus());
}
-
- SequenceGroup sg = new SequenceGroup(sequences, "",
- cs, true, true,
- false, 0,
- av.alignment.getWidth() - 1);
+ // TODO: cs used to be initialized with a sequence collection and
+ // recalcConservation called automatically
+ // instead we set it manually - recalc called after updateAnnotation
+ sg.cs = cs;
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);
+ c.verdict(false, av.getConsPercGaps());
cs.setConservation(c);
sg.cs = cs;
}
- av.alignment.addGroup(sg);
+ av.getAlignment().addGroup(sg);
- }
+ // TODO this is duplicated with gui TreeCanvas - refactor
+ av.getAlignment().addGroup(sg);
+ final AlignViewportI codingComplement = av.getCodingComplement();
+ if (codingComplement != null)
+ {
+ SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, av,
+ codingComplement);
+ if (mappedGroup.getSequences().size() > 0)
+ {
+ codingComplement.getAlignment().addGroup(mappedGroup);
+ for (SequenceI seq : mappedGroup.getSequences())
+ {
+ // TODO why does gui require col.brighter() here??
+ codingComplement.setSequenceColour(seq, col);
+ }
+ }
+ }
+ }
+ ap.updateAnnotation();
+ if (av.getCodingComplement() != null)
+ {
+ ((AlignmentViewport) av.getCodingComplement()).firePropertyChange(
+ "alignment", null, ap.av.getAlignment().getSequences());
+ }
}
public void setShowDistances(boolean state)
git://source.jalview.org / jalview.git / blobdiff