X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=6ee75bd8a723586cc61e54a590ed8e0b1018b08f;hb=584c1b0136786968958e22e52b6ce51bd24511e5;hp=2ab7bf7f25ed7307986e098d610b91872ee60579;hpb=b65330720abd1329eac5fddbed9516b8302abe52;p=jalview.git
diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 2ab7bf7..6ee75bd 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -1,36 +1,60 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.*;
-
-public class TreeCanvas extends Panel implements MouseListener,
- MouseMotionListener
+import jalview.analysis.Conservation;
+import jalview.analysis.TreeModel;
+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.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.List;
+import java.util.Vector;
+
+public class TreeCanvas extends Panel
+ implements MouseListener, MouseMotionListener
{
- NJTree tree;
+ TreeModel tree;
ScrollPane scrollPane;
@@ -64,7 +88,8 @@ public class TreeCanvas extends Panel implements MouseListener,
SequenceNode highlightNode;
- AlignmentPanel ap;
+ AlignmentPanel ap;
+
public TreeCanvas(AlignmentPanel ap, ScrollPane scroller)
{
this.ap = ap;
@@ -87,23 +112,23 @@ 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);
}
- public void setTree(NJTree tree)
+ public void setTree(TreeModel tree2)
{
- this.tree = tree;
- tree.findHeight(tree.getTopNode());
+ this.tree = tree2;
+ tree2.findHeight(tree2.getTopNode());
// Now have to calculate longest name based on the leaves
- Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
+ Vector leaves = tree2.findLeaves(tree2.getTopNode());
boolean has_placeholders = false;
longestName = "";
for (int i = 0; i < leaves.size(); i++)
{
- SequenceNode lf = (SequenceNode) leaves.elementAt(i);
+ SequenceNode lf = leaves.elementAt(i);
if (lf.isPlaceholder())
{
@@ -122,7 +147,7 @@ public class TreeCanvas extends Panel implements MouseListener,
}
public void drawNode(Graphics g, SequenceNode node, float chunk,
- float scale, int width, int offx, int offy)
+ double scale, int width, int offx, int offy)
{
if (node == null)
{
@@ -133,8 +158,8 @@ public class TreeCanvas extends Panel implements MouseListener,
{
// Drawing leaf node
- float height = node.height;
- float dist = node.dist;
+ double height = node.height;
+ double dist = node.dist;
int xstart = (int) ((height - dist) * scale) + offx;
int xend = (int) (height * scale) + offx;
@@ -143,7 +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)
{
@@ -185,8 +210,9 @@ public class TreeCanvas extends Panel implements MouseListener,
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();
@@ -194,13 +220,12 @@ 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);
@@ -217,14 +242,14 @@ public class TreeCanvas extends Panel implements MouseListener,
drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,
offy);
- float height = node.height;
- float dist = node.dist;
+ double height = node.height;
+ double dist = node.dist;
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);
@@ -237,10 +262,10 @@ public class TreeCanvas extends Panel implements MouseListener,
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) (node.left() == null ? 0
+ : (((SequenceNode) node.left()).ycount * chunk)) + offy;
+ int yend = (int) (node.right() == null ? 0
+ : (((SequenceNode) node.right()).ycount * chunk)) + offy;
Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
nodeHash.put(node, pos);
@@ -315,7 +340,7 @@ public class TreeCanvas extends Panel implements MouseListener,
SequenceNode top = tree.getTopNode();
- float wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight();
+ double wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight();
if (top.count == 0)
{
top.count = ((SequenceNode) top.left()).count
@@ -327,7 +352,7 @@ public class TreeCanvas extends Panel implements MouseListener,
}
public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
- float scale, int width, int offx, int offy)
+ double scale, int width, int offx, int offy)
{
if (node == null)
{
@@ -336,7 +361,7 @@ public class TreeCanvas extends Panel implements MouseListener,
if (node.left() == null && node.right() == null)
{
- float height = node.height;
+ double height = node.height;
// float dist = node.dist;
// int xstart = (int) ( (height - dist) * scale) + offx;
@@ -390,11 +415,13 @@ public class TreeCanvas extends Panel implements MouseListener,
}
}
+ @Override
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
if (tree == null)
@@ -440,8 +467,7 @@ public class TreeCanvas extends Panel implements MouseListener,
// for
// scrollbar
- float wscale = (float) (width - labelLength - offx * 2)
- / tree.getMaxHeight();
+ double wscale = (width - labelLength - offx * 2) / tree.getMaxHeight();
SequenceNode top = tree.getTopNode();
@@ -465,26 +491,30 @@ 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)
@@ -497,13 +527,11 @@ public class TreeCanvas extends Panel implements MouseListener,
}
else
{
- Vector leaves = new Vector();
- tree.findLeaves(highlightNode, leaves);
+ Vector leaves = tree.findLeaves(highlightNode);
for (int i = 0; i < leaves.size(); i++)
{
- SequenceI seq = (SequenceI) ((SequenceNode) leaves.elementAt(i))
- .element();
+ SequenceI seq = (SequenceI) leaves.elementAt(i).element();
treeSelectionChanged(seq);
}
}
@@ -514,10 +542,12 @@ public class TreeCanvas extends Panel implements MouseListener,
}
}
+ @Override
public void mouseDragged(MouseEvent ect)
{
}
+ @Override
public void mouseMoved(MouseEvent evt)
{
av.setCurrentTree(tree);
@@ -539,6 +569,7 @@ public class TreeCanvas extends Panel implements MouseListener,
}
}
+ @Override
public void mousePressed(MouseEvent e)
{
av.setCurrentTree(tree);
@@ -565,15 +596,21 @@ public class TreeCanvas extends Panel implements MouseListener,
threshold = (float) (x - offx)
/ (float) (getSize().width - labelLength - 2 * offx);
- tree.getGroups().removeAllElements();
- tree.groupNodes(tree.getTopNode(), threshold);
+ List groups = tree.groupNodes(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();
+ colourGroups(groups);
}
}
@@ -583,23 +620,21 @@ public class TreeCanvas extends Panel implements MouseListener,
}
- void colourGroups()
+ void colourGroups(List groups)
{
- for (int i = 0; i < tree.getGroups().size(); i++)
+ for (int i = 0; i < groups.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());
+ setColor(groups.get(i), col.brighter());
- Vector l = tree.findLeaves(
- (SequenceNode) tree.getGroups().elementAt(i), new Vector());
+ Vector l = tree.findLeaves(groups.get(i));
- Vector sequences = 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) l.elementAt(j).element();
if (!sequences.contains(s1))
{
sequences.addElement(s1);
@@ -608,6 +643,9 @@ 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)
@@ -619,43 +657,66 @@ public class TreeCanvas extends Panel implements MouseListener,
}
else
{
- cs = ColourSchemeProperty.getColour(sequences, av.alignment
- .getWidth(), ColourSchemeProperty.getColourName(av
- .getGlobalColourScheme()));
+ cs = ColourSchemeProperty.getColourScheme(sg, ColourSchemeProperty
+ .getColourName(av.getGlobalColourScheme()));
}
// cs is null if shading is an annotationColourGradient
- if (cs!=null)
- {
- cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
- av.getIgnoreGapsConsensus());
- }
+ // if (cs != null)
+ // {
+ // cs.setThreshold(av.getViewportColourScheme().getThreshold(),
+ // av.isIgnoreGapsConsensus());
+ // }
}
-
- 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.setColourScheme(cs);
+ sg.getGroupColourScheme().setThreshold(
+ av.getResidueShading().getThreshold(),
+ av.isIgnoreGapsConsensus());
sg.setName("JTreeGroup:" + sg.hashCode());
sg.setIdColour(col);
if (av.getGlobalColourScheme() != null
- && av.getGlobalColourScheme().conservationApplied())
+ && av.getResidueShading().conservationApplied())
{
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(null),
+ Conservation c = new Conservation("Group", sg.getSequences(null),
sg.getStartRes(), sg.getEndRes());
c.calculate();
c.verdict(false, av.getConsPercGaps());
- cs.setConservation(c);
-
- sg.cs = cs;
+ sg.setColourScheme(cs);
+ sg.getGroupColourScheme().setConservation(c);
}
- 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)