X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=97cca4b34536c105a3a43e78c75ee3f2412ab71c;hb=d919b93d3c0a57e36c2a90a34a6788bca86bfe81;hp=a66f25173a968b96f39c3778bb00d443ca6ceef8;hpb=40460cd7a6f6d80c6a8c2f86c5bc55d941445975;p=jalview.git
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index a66f251..97cca4b 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -1,19 +1,20 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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.
- *
+ *
* 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
@@ -125,7 +126,7 @@ 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 +609,7 @@ 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 +667,12 @@ 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);
@@ -790,9 +794,7 @@ 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 +853,8 @@ 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 +891,8 @@ 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)
{
@@ -901,18 +905,18 @@ 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)
+ {
+ cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
+ av.getIgnoreGapsConsensus());
}
-
- 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++)
@@ -925,17 +929,19 @@ 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
}
}