X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=47b85d17a08519313983cdcea9a4fd7cc0f53f8b;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=d1c6c614b6813fccbb3b0e74303f8dd93499df96;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index d1c6c61..47b85d1 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -1,31 +1,55 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * 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.
- *
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * 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.*;
+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
@@ -64,9 +88,12 @@ public class TreeCanvas extends Panel implements MouseListener,
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);
@@ -85,7 +112,7 @@ public class TreeCanvas extends Panel implements MouseListener,
av.setSelectionGroup(selected);
}
- selected.setEndRes(av.alignment.getWidth() - 1);
+ selected.setEndRes(av.getAlignment().getWidth() - 1);
selected.addOrRemove(sequence, true);
}
@@ -141,7 +168,7 @@ public class TreeCanvas extends Panel implements MouseListener,
if (node.element() instanceof SequenceI)
{
- SequenceI seq = (SequenceI) ((SequenceNode) node).element();
+ SequenceI seq = (SequenceI) node.element();
if (av.getSequenceColour(seq) == Color.white)
{
@@ -184,8 +211,7 @@ public class TreeCanvas extends Panel implements MouseListener,
}
String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node
- .getName())
- : node.getName();
+ .getName()) : node.getName();
FontMetrics fm = g.getFontMetrics(font);
int charWidth = fm.stringWidth(name) + 3;
int charHeight = fm.getHeight();
@@ -193,13 +219,12 @@ public class TreeCanvas extends Panel implements MouseListener,
Rectangle rect = new Rectangle(xend + 10, ypos - 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()))
+ && selected.getSequences(null).contains(node.element()))
{
g.setColor(Color.gray);
@@ -223,7 +248,7 @@ public class TreeCanvas extends Panel implements MouseListener,
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);
@@ -389,11 +414,13 @@ public class TreeCanvas extends Panel implements MouseListener,
}
}
+ @Override
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
if (tree == null)
@@ -439,8 +466,7 @@ public class TreeCanvas extends Panel implements MouseListener,
// for
// scrollbar
- float wscale = (float) (width - labelLength - offx * 2)
- / tree.getMaxHeight();
+ float wscale = (width - labelLength - offx * 2) / tree.getMaxHeight();
SequenceNode top = tree.getTopNode();
@@ -464,26 +490,29 @@ public class TreeCanvas extends Panel implements MouseListener,
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)
@@ -509,13 +538,16 @@ public class TreeCanvas extends Panel implements MouseListener,
PaintRefresher.Refresh(this, av.getSequenceSetId());
repaint();
+ av.sendSelection();
}
}
+ @Override
public void mouseDragged(MouseEvent ect)
{
}
+ @Override
public void mouseMoved(MouseEvent evt)
{
av.setCurrentTree(tree);
@@ -537,6 +569,7 @@ public class TreeCanvas extends Panel implements MouseListener,
}
}
+ @Override
public void mousePressed(MouseEvent e)
{
av.setCurrentTree(tree);
@@ -551,6 +584,7 @@ public class TreeCanvas extends Panel implements MouseListener,
treeSelectionChanged((Sequence) ob);
PaintRefresher.Refresh(this, av.getSequenceSetId());
repaint();
+ av.sendSelection();
return;
}
else if (!(ob instanceof SequenceNode))
@@ -567,8 +601,15 @@ public class TreeCanvas extends Panel implements MouseListener,
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();
@@ -585,12 +626,12 @@ public class TreeCanvas extends Panel implements MouseListener,
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));
+ 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++)
@@ -605,27 +646,34 @@ public class TreeCanvas extends Panel implements MouseListener,
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());
+ cs = new UserColourScheme(
+ ((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);
@@ -633,21 +681,44 @@ public class TreeCanvas extends Panel implements MouseListener,
&& 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)