X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=7d457d4129bcac4ccda243d4e6823baddb0b3882;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=4a38767d0fb01f30d3df5c98c70be1d788ffeadb;hpb=811fb76382f3601b35dc08b8c0ceabed049c3326;p=jalview.git
diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 4a38767..7d457d4 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -1,19 +1,22 @@
/*
- * 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 2.8.2b1)
+ * Copyright (C) 2014 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;
@@ -64,9 +67,12 @@ 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 +91,7 @@ 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 +147,7 @@ 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)
{
@@ -192,13 +198,12 @@ 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);
@@ -222,7 +227,7 @@ 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);
@@ -388,11 +393,13 @@ public class TreeCanvas extends Panel implements MouseListener,
}
}
+ @Override
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
if (tree == null)
@@ -438,8 +445,7 @@ 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();
@@ -463,26 +469,29 @@ 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)
@@ -512,10 +521,12 @@ public class TreeCanvas extends Panel implements MouseListener,
}
}
+ @Override
public void mouseDragged(MouseEvent ect)
{
}
+ @Override
public void mouseMoved(MouseEvent evt)
{
av.setCurrentTree(tree);
@@ -537,6 +548,7 @@ public class TreeCanvas extends Panel implements MouseListener,
}
}
+ @Override
public void mousePressed(MouseEvent e)
{
av.setCurrentTree(tree);
@@ -568,8 +580,8 @@ 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();
colourGroups();
@@ -606,6 +618,9 @@ 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)
@@ -617,17 +632,20 @@ public class TreeCanvas extends Panel implements MouseListener,
}
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.getIgnoreGapsConsensus());
}
-
- 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);
@@ -639,16 +657,17 @@ public class TreeCanvas extends Panel implements MouseListener,
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);
}
+ ap.updateAnnotation();
}