X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=f590c2ec41c4233621e425d9b53eae5560d2fd91;hb=9876fdccf311378e690c1f9e18db52675d427b89;hp=81abf03de39d1da25e3b0d8ae81adf6b1a717ed7;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 81abf03..f590c2e 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -1,34 +1,66 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.print.*;
-import javax.swing.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.util.*;
+import jalview.analysis.Conservation;
+import jalview.analysis.NJTree;
+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.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.SelectionSource;
+import jalview.util.Format;
+import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.RenderingHints;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.print.PageFormat;
+import java.awt.print.Printable;
+import java.awt.print.PrinterException;
+import java.awt.print.PrinterJob;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
+
+import javax.swing.JColorChooser;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
/**
* DOCUMENT ME!
@@ -37,7 +69,7 @@ import jalview.util.*;
* @version $Revision$
*/
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
- Printable, MouseMotionListener
+ Printable, MouseMotionListener, SelectionSource
{
/** DOCUMENT ME!! */
public static final String PLACEHOLDER = " * ";
@@ -206,7 +238,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
if (node.element() instanceof SequenceI)
{
- SequenceI seq = (SequenceI) ((SequenceNode) node).element();
+ SequenceI seq = (SequenceI) node.element();
if (av.getSequenceColour(seq) == Color.white)
{
@@ -256,14 +288,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
Rectangle rect = new Rectangle(xend + 10, ypos - charHeight / 2,
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);
@@ -288,7 +319,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
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);
@@ -491,7 +522,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
{
for (int a = 0; a < aps.length; a++)
{
- aps[a].av.setSequenceColour((SequenceI) node.element(), c);
+ final SequenceI seq = (SequenceI) node.element();
+ aps[a].av.setSequenceColour(seq, c);
}
}
}
@@ -609,7 +641,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
if (tree == null)
{
- g.drawString(MessageManager.getString("label.calculating_tree") + "....", 20, getHeight() / 2);
+ g.drawString(MessageManager.getString("label.calculating_tree")
+ + "....", 20, getHeight() / 2);
}
else
{
@@ -669,9 +702,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
g2.fillRect(0, 0, width, height);
g2.setFont(font);
- if (longestName==null || tree ==null)
+ if (longestName == null || tree == null)
{
- g2.drawString("Calculating tree.",20,20);
+ g2.drawString("Calculating tree.", 20, 20);
}
offy = font.getSize() + 10;
@@ -679,8 +712,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
labelLength = fm.stringWidth(longestName) + 20; // 20 allows for scrollbar
- float wscale = (float) (width - labelLength - (offx * 2))
- / tree.getMaxHeight();
+ float wscale = (width - labelLength - (offx * 2)) / tree.getMaxHeight();
SequenceNode top = tree.getTopNode();
@@ -705,7 +737,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
g2.setColor(Color.gray);
}
- int x = (int) ((threshold * (float) (getWidth() - labelLength - (2 * offx))) + offx);
+ int x = (int) ((threshold * (getWidth() - labelLength - (2 * offx))) + offx);
g2.drawLine(x, 0, x, getHeight());
}
@@ -754,7 +786,8 @@ 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);
@@ -794,7 +827,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
if (ob instanceof SequenceNode)
{
highlightNode = (SequenceNode) ob;
- this.setToolTipText("" + MessageManager.getString("label.highlightnode"));
+ this.setToolTipText(""
+ + MessageManager.getString("label.highlightnode"));
repaint();
}
@@ -850,12 +884,20 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
AlignmentPanel[] aps = getAssociatedPanels();
+ // TODO push calls below into a single AlignViewportI method?
+ // see also AlignViewController.deleteGroups
for (int a = 0; a < aps.length; a++)
{
aps[a].av.setSelectionGroup(null);
aps[a].av.getAlignment().deleteAllGroups();
aps[a].av.clearSequenceColours();
}
+ if (av.getCodingComplement() != null)
+ {
+ av.getCodingComplement().setSelectionGroup(null);
+ av.getCodingComplement().getAlignment().deleteAllGroups();
+ av.getCodingComplement().clearSequenceColours();
+ }
colourGroups();
}
@@ -912,13 +954,14 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
if (cs != null)
{
cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
- av.getIgnoreGapsConsensus());
+ av.isIgnoreGapsConsensus());
}
}
sg.cs = cs;
// sg.recalcConservation();
sg.setName("JTreeGroup:" + sg.hashCode());
sg.setIdColour(col);
+
for (int a = 0; a < aps.length; a++)
{
if (aps[a].av.getGlobalColourScheme() != null
@@ -935,7 +978,25 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
aps[a].av.getAlignment().addGroup(new SequenceGroup(sg));
}
+
+ // TODO can we push all of the below into AlignViewportI?
+ 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())
+ {
+ codingComplement.setSequenceColour(seq, col.brighter());
+ }
+ }
+ }
}
+
// notify the panel to redo any group specific stuff.
for (int a = 0; a < aps.length; a++)
{
@@ -944,6 +1005,14 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
// to any Jmols listening in
}
+ if (av.getCodingComplement() != null)
+ {
+ ((AlignViewport) av.getCodingComplement()).getAlignPanel()
+ .updateAnnotation();
+ /*
+ * idPanel. repaint ()
+ */
+ }
}
/**
@@ -990,8 +1059,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
}
else
{
- return new AlignmentPanel[]
- { ap };
+ return new AlignmentPanel[] { ap };
}
}
}