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JAL-1643 jarred up the quaqua native libraries and added nativelib
[jalview.git]
/
src
/
jalview
/
appletgui
/
TreeCanvas.java
diff --git
a/src/jalview/appletgui/TreeCanvas.java
b/src/jalview/appletgui/TreeCanvas.java
index
2ab7bf7
..
745520b
100755
(executable)
--- a/
src/jalview/appletgui/TreeCanvas.java
+++ b/
src/jalview/appletgui/TreeCanvas.java
@@
-1,19
+1,22
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * 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 2.8.2)
+ * 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
*
* 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.
*
* 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
*/
package jalview.appletgui;
@@
-64,7
+67,8
@@
public class TreeCanvas extends Panel implements MouseListener,
SequenceNode highlightNode;
SequenceNode highlightNode;
- AlignmentPanel ap;
+ AlignmentPanel ap;
+
public TreeCanvas(AlignmentPanel ap, ScrollPane scroller)
{
this.ap = ap;
public TreeCanvas(AlignmentPanel ap, ScrollPane scroller)
{
this.ap = ap;
@@
-87,7
+91,7
@@
public class TreeCanvas extends Panel implements MouseListener,
av.setSelectionGroup(selected);
}
av.setSelectionGroup(selected);
}
- selected.setEndRes(av.alignment.getWidth() - 1);
+ selected.setEndRes(av.getAlignment().getWidth() - 1);
selected.addOrRemove(sequence, true);
}
selected.addOrRemove(sequence, true);
}
@@
-143,7
+147,7
@@
public class TreeCanvas extends Panel implements MouseListener,
if (node.element() instanceof SequenceI)
{
if (node.element() instanceof SequenceI)
{
- SequenceI seq = (SequenceI) ((SequenceNode) node).element();
+ SequenceI seq = (SequenceI) node.element();
if (av.getSequenceColour(seq) == Color.white)
{
if (av.getSequenceColour(seq) == Color.white)
{
@@
-194,13
+198,12
@@
public class TreeCanvas extends Panel implements MouseListener,
Rectangle rect = new Rectangle(xend + 10, ypos - charHeight,
charWidth, charHeight);
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
// 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);
{
g.setColor(Color.gray);
@@
-224,7
+227,7
@@
public class TreeCanvas extends Panel implements MouseListener,
int xend = (int) (height * scale) + offx;
int ypos = (int) (node.ycount * chunk) + offy;
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);
// Draw horizontal line
g.drawLine(xstart, ypos, xend, ypos);
@@
-390,11
+393,13
@@
public class TreeCanvas extends Panel implements MouseListener,
}
}
}
}
+ @Override
public void update(Graphics g)
{
paint(g);
}
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
if (tree == null)
public void paint(Graphics g)
{
if (tree == null)
@@
-440,8
+445,7
@@
public class TreeCanvas extends Panel implements MouseListener,
// for
// scrollbar
// for
// scrollbar
- float wscale = (float) (width - labelLength - offx * 2)
- / tree.getMaxHeight();
+ float wscale = (width - labelLength - offx * 2) / tree.getMaxHeight();
SequenceNode top = tree.getTopNode();
SequenceNode top = tree.getTopNode();
@@
-465,26
+469,29
@@
public class TreeCanvas extends Panel implements MouseListener,
g.setColor(Color.gray);
}
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);
}
}
g.drawLine(x, 0, x, getSize().height);
}
}
+ @Override
public void mouseReleased(MouseEvent e)
{
}
public void mouseReleased(MouseEvent e)
{
}
+ @Override
public void mouseEntered(MouseEvent e)
{
}
public void mouseEntered(MouseEvent e)
{
}
+ @Override
public void mouseExited(MouseEvent e)
{
}
public void mouseExited(MouseEvent e)
{
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
if (highlightNode != null)
public void mouseClicked(MouseEvent evt)
{
if (highlightNode != null)
@@
-514,10
+521,12
@@
public class TreeCanvas extends Panel implements MouseListener,
}
}
}
}
+ @Override
public void mouseDragged(MouseEvent ect)
{
}
public void mouseDragged(MouseEvent ect)
{
}
+ @Override
public void mouseMoved(MouseEvent evt)
{
av.setCurrentTree(tree);
public void mouseMoved(MouseEvent evt)
{
av.setCurrentTree(tree);
@@
-539,6
+548,7
@@
public class TreeCanvas extends Panel implements MouseListener,
}
}
}
}
+ @Override
public void mousePressed(MouseEvent e)
{
av.setCurrentTree(tree);
public void mousePressed(MouseEvent e)
{
av.setCurrentTree(tree);
@@
-570,8
+580,8
@@
public class TreeCanvas extends Panel implements MouseListener,
setColor(tree.getTopNode(), Color.black);
av.setSelectionGroup(null);
setColor(tree.getTopNode(), Color.black);
av.setSelectionGroup(null);
- av.alignment.deleteAllGroups();
- av.sequenceColours = null;
+ av.getAlignment().deleteAllGroups();
+ av.clearSequenceColours();
colourGroups();
colourGroups();
@@
-608,6
+618,9
@@
public class TreeCanvas extends Panel implements MouseListener,
ColourSchemeI cs = null;
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)
if (av.getGlobalColourScheme() != null)
{
if (av.getGlobalColourScheme() instanceof UserColourScheme)
@@
-619,20
+632,20
@@
public class TreeCanvas extends Panel implements MouseListener,
}
else
{
}
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
}
// cs is null if shading is an annotationColourGradient
- if (cs!=null)
+ 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);
sg.setName("JTreeGroup:" + sg.hashCode());
sg.setIdColour(col);
@@
-651,11
+664,11
@@
public class TreeCanvas extends Panel implements MouseListener,
}
}
- av.alignment.addGroup(sg);
+ av.getAlignment().addGroup(sg);
}
ap.updateAnnotation();
}
ap.updateAnnotation();
-
+
}
public void setShowDistances(boolean state)
}
public void setShowDistances(boolean state)