X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=c5650f5a973013c65c436c11991d76b7bd60a390;hb=aced09c4feeaf3406269442c14e54abeeb4cad81;hp=42a09aaad6cc717b8987712fad24de0ac01d5ffb;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 42a09aa..c5650f5 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/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
- * 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.gui;
@@ -125,7 +128,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
aps[a].av.setSelectionGroup(selected);
}
- selected.setEndRes(aps[a].av.alignment.getWidth() - 1);
+ selected.setEndRes(aps[a].av.getAlignment().getWidth() - 1);
selected.addOrRemove(sequence, true);
}
}
@@ -608,7 +611,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
if (tree == null)
{
- g.drawString("Calculating tree....", 20, getHeight() / 2);
+ g.drawString(MessageManager.getString("label.calculating_tree")
+ + "....", 20, getHeight() / 2);
}
else
{
@@ -666,9 +670,12 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
RenderingHints.VALUE_ANTIALIAS_ON);
g2.setColor(Color.white);
g2.fillRect(0, 0, width, height);
-
g2.setFont(font);
+ if (longestName == null || tree == null)
+ {
+ g2.drawString("Calculating tree.", 20, 20);
+ }
offy = font.getSize() + 10;
fm = g2.getFontMetrics(font);
@@ -750,7 +757,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
if (SwingUtilities.isRightMouseButton(evt))
{
Color col = JColorChooser.showDialog(this,
- "Select Sub-Tree Colour", highlightNode.color);
+ MessageManager.getString("label.select_subtree_colour"), highlightNode.color);
if (col != null)
{
setColor(highlightNode, col);
@@ -790,9 +797,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
if (ob instanceof SequenceNode)
{
highlightNode = (SequenceNode) ob;
- this.setToolTipText("Left click to select leaves"
- + "
Double-click to invert leaves"
- + "
Right click to change colour");
+ this.setToolTipText(""
+ + MessageManager.getString("label.highlightnode"));
repaint();
}
@@ -851,8 +857,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
for (int a = 0; a < aps.length; a++)
{
aps[a].av.setSelectionGroup(null);
- aps[a].av.alignment.deleteAllGroups();
- aps[a].av.sequenceColours = null;
+ aps[a].av.getAlignment().deleteAllGroups();
+ aps[a].av.clearSequenceColours();
}
colourGroups();
}
@@ -889,6 +895,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
}
ColourSchemeI cs = null;
+ SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true,
+ false, 0, av.getAlignment().getWidth() - 1);
if (av.getGlobalColourScheme() != null)
{
@@ -901,21 +909,18 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
}
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)
+ if (cs != null)
{
cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
av.getIgnoreGapsConsensus());
}
}
-
- SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true,
- false, 0, av.alignment.getWidth() - 1);
-
+ sg.cs = cs;
+ // sg.recalcConservation();
sg.setName("JTreeGroup:" + sg.hashCode());
sg.setIdColour(col);
for (int a = 0; a < aps.length; a++)
@@ -928,18 +933,19 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
sg.getStartRes(), sg.getEndRes());
c.calculate();
- c.verdict(false, aps[a].av.ConsPercGaps);
+ c.verdict(false, aps[a].av.getConsPercGaps());
sg.cs.setConservation(c);
}
- aps[a].av.alignment.addGroup(sg);
+ aps[a].av.getAlignment().addGroup(new SequenceGroup(sg));
}
}
// notify the panel to redo any group specific stuff.
for (int a = 0; a < aps.length; a++)
{
aps[a].updateAnnotation();
- // TODO: JAL-868 - need to ensure view colour change message is broadcast to any Jmols listening in
+ // TODO: JAL-868 - need to ensure view colour change message is broadcast
+ // to any Jmols listening in
}
}