X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=81abf03de39d1da25e3b0d8ae81adf6b1a717ed7;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=7644673b87c183a8c0c77ea356a13a975cc2774d;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 7644673..81abf03 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -1,20 +1,20 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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;
@@ -86,13 +86,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
* Creates a new TreeCanvas object.
*
* @param av
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param tree
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param scroller
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param label
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public TreeCanvas(TreePanel tp, AlignmentPanel ap, JScrollPane scroller)
{
@@ -110,7 +110,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
* DOCUMENT ME!
*
* @param sequence
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void treeSelectionChanged(SequenceI sequence)
{
@@ -126,7 +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);
}
}
@@ -135,7 +135,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
* DOCUMENT ME!
*
* @param tree
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setTree(NJTree tree)
{
@@ -171,19 +171,19 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
* DOCUMENT ME!
*
* @param g
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param node
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param chunk
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param scale
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param width
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param offx
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param offy
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void drawNode(Graphics g, SequenceNode node, float chunk,
float scale, int width, int offx, int offy)
@@ -248,8 +248,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
}
String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node
- .getName())
- : node.getName();
+ .getName()) : node.getName();
int charWidth = fm.stringWidth(name) + 3;
int charHeight = font.getSize();
@@ -341,9 +340,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
* DOCUMENT ME!
*
* @param x
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param y
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
@@ -384,7 +383,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
* DOCUMENT ME!
*
* @param pickBox
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void pickNodes(Rectangle pickBox)
{
@@ -411,19 +410,19 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
* DOCUMENT ME!
*
* @param pickBox
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param node
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param chunk
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param scale
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param width
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param offx
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param offy
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
float scale, int width, int offx, int offy)
@@ -470,9 +469,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
* DOCUMENT ME!
*
* @param node
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param c
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setColor(SequenceNode node, Color c)
{
@@ -488,9 +487,12 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
if (node.element() instanceof SequenceI)
{
AlignmentPanel[] aps = getAssociatedPanels();
- for (int a = 0; a < aps.length; a++)
+ if (aps != null)
{
- aps[a].av.setSequenceColour((SequenceI) node.element(), c);
+ for (int a = 0; a < aps.length; a++)
+ {
+ aps[a].av.setSequenceColour((SequenceI) node.element(), c);
+ }
}
}
}
@@ -535,16 +537,16 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
* DOCUMENT ME!
*
* @param pg
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param pf
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param pi
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*
* @throws PrinterException
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public int print(Graphics pg, PageFormat pf, int pi)
throws PrinterException
@@ -598,7 +600,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
* DOCUMENT ME!
*
* @param g
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void paintComponent(Graphics g)
{
@@ -607,7 +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
{
@@ -627,9 +629,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
}
else
{
- setPreferredSize(new Dimension(scrollPane.getWidth(), fm
- .getHeight()
- * nameHash.size()));
+ setPreferredSize(new Dimension(scrollPane.getWidth(),
+ fm.getHeight() * nameHash.size()));
draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());
}
@@ -641,7 +642,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
* DOCUMENT ME!
*
* @param fontSize
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setFont(Font font)
{
@@ -653,11 +654,11 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
* DOCUMENT ME!
*
* @param g1
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param width
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param height
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void draw(Graphics g1, int width, int height)
{
@@ -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);
@@ -711,7 +715,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseReleased(MouseEvent e)
{
@@ -721,7 +725,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseEntered(MouseEvent e)
{
@@ -731,7 +735,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseExited(MouseEvent e)
{
@@ -741,7 +745,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseClicked(MouseEvent evt)
{
@@ -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();
}
@@ -815,7 +817,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mousePressed(MouseEvent e)
{
@@ -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();
}
@@ -865,14 +867,15 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
void colourGroups()
{
+ AlignmentPanel[] aps = getAssociatedPanels();
for (int i = 0; i < tree.getGroups().size(); i++)
{
- Color col = new Color((int) (Math.random() * 255), (int) (Math
- .random() * 255), (int) (Math.random() * 255));
+ Color col = new Color((int) (Math.random() * 255),
+ (int) (Math.random() * 255), (int) (Math.random() * 255));
setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter());
- Vector l = tree.findLeaves((SequenceNode) tree.getGroups().elementAt(
- i), new Vector());
+ Vector l = tree.findLeaves(
+ (SequenceNode) tree.getGroups().elementAt(i), new Vector());
Vector sequences = new Vector();
@@ -888,49 +891,58 @@ 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)
{
if (av.getGlobalColourScheme() instanceof UserColourScheme)
{
- cs = new UserColourScheme(((UserColourScheme) av
- .getGlobalColourScheme()).getColours());
+ cs = new UserColourScheme(
+ ((UserColourScheme) av.getGlobalColourScheme())
+ .getColours());
}
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);
- AlignmentPanel[] aps = getAssociatedPanels();
for (int a = 0; a < aps.length; a++)
{
if (aps[a].av.getGlobalColourScheme() != null
&& aps[a].av.getGlobalColourScheme().conservationApplied())
{
Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(null), sg
- .getStartRes(), sg.getEndRes());
+ ResidueProperties.propHash, 3, sg.getSequences(null),
+ 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
+ }
}
@@ -938,7 +950,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
* DOCUMENT ME!
*
* @param state
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setShowDistances(boolean state)
{
@@ -950,7 +962,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
* DOCUMENT ME!
*
* @param state
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setShowBootstrap(boolean state)
{
@@ -962,7 +974,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
* DOCUMENT ME!
*
* @param state
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setMarkPlaceholders(boolean state)
{