/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * 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
+ * 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.
- *
- * 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 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
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * 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!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class TreeCanvas
- extends JPanel implements MouseListener, Runnable,
- Printable, MouseMotionListener
+public class TreeCanvas extends JPanel implements MouseListener, Runnable,
+ Printable, MouseMotionListener, SelectionSource
{
/** DOCUMENT ME!! */
public static final String PLACEHOLDER = " * ";
+
NJTree tree;
+
JScrollPane scrollPane;
+
TreePanel tp;
+
AlignViewport av;
+
AlignmentPanel ap;
+
Font font;
+
FontMetrics fm;
+
boolean fitToWindow = true;
+
boolean showDistances = false;
+
boolean showBootstrap = false;
+
boolean markPlaceholders = false;
+
int offx = 20;
+
int offy;
+
float threshold;
+
String longestName;
+
int labelLength = -1;
Hashtable nameHash = new Hashtable();
+
Hashtable nodeHash = new Hashtable();
+
SequenceNode highlightNode;
boolean applyToAllViews = false;
/**
* Creates a new TreeCanvas object.
- *
- * @param av DOCUMENT ME!
- * @param tree DOCUMENT ME!
- * @param scroller DOCUMENT ME!
- * @param label DOCUMENT ME!
+ *
+ * @param av
+ * DOCUMENT ME!
+ * @param tree
+ * DOCUMENT ME!
+ * @param scroller
+ * DOCUMENT ME!
+ * @param label
+ * DOCUMENT ME!
*/
- public TreeCanvas(TreePanel tp,
- AlignmentPanel ap,
- JScrollPane scroller)
+ public TreeCanvas(TreePanel tp, AlignmentPanel ap, JScrollPane scroller)
{
this.tp = tp;
this.av = ap.av;
/**
* DOCUMENT ME!
- *
- * @param sequence DOCUMENT ME!
+ *
+ * @param sequence
+ * DOCUMENT ME!
*/
public void treeSelectionChanged(SequenceI sequence)
{
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);
}
}
/**
* DOCUMENT ME!
- *
- * @param tree DOCUMENT ME!
+ *
+ * @param tree
+ * DOCUMENT ME!
*/
public void setTree(NJTree tree)
{
has_placeholders = true;
}
- if (longestName.length() < ( (Sequence) lf.element()).getName()
- .length())
+ if (longestName.length() < ((Sequence) lf.element()).getName()
+ .length())
{
- longestName = TreeCanvas.PLACEHOLDER +
- ( (Sequence) lf.element()).getName();
+ longestName = TreeCanvas.PLACEHOLDER
+ + ((Sequence) lf.element()).getName();
}
}
/**
* DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- * @param node DOCUMENT ME!
- * @param chunk DOCUMENT ME!
- * @param scale DOCUMENT ME!
- * @param width DOCUMENT ME!
- * @param offx DOCUMENT ME!
- * @param offy DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param node
+ * DOCUMENT ME!
+ * @param chunk
+ * DOCUMENT ME!
+ * @param scale
+ * DOCUMENT ME!
+ * @param width
+ * DOCUMENT ME!
+ * @param offx
+ * DOCUMENT ME!
+ * @param offy
+ * DOCUMENT ME!
*/
public void drawNode(Graphics g, SequenceNode node, float chunk,
- float scale, int width, int offx, int offy)
+ float scale, int width, int offx, int offy)
{
if (node == null)
{
return;
}
- if ( (node.left() == null) && (node.right() == null))
+ if ((node.left() == null) && (node.right() == null))
{
// Drawing leaf node
float height = node.height;
float dist = node.dist;
- int xstart = (int) ( (height - dist) * scale) + offx;
+ int xstart = (int) ((height - dist) * scale) + offx;
int xend = (int) (height * scale) + offx;
int ypos = (int) (node.ycount * chunk) + offy;
if (node.element() instanceof SequenceI)
{
- SequenceI seq = (SequenceI) ( (SequenceNode) node).element();
+ SequenceI seq = (SequenceI) node.element();
if (av.getSequenceColour(seq) == Color.white)
{
nodeLabel = new Format("%-.2f").form(node.dist);
}
- if (showBootstrap && node.bootstrap>-1)
+ if (showBootstrap && node.bootstrap > -1)
{
if (showDistances)
{
g.drawString(nodeLabel, xstart + 2, ypos - 2);
}
- String name = (markPlaceholders && node.isPlaceholder())
- ? (PLACEHOLDER + node.getName()) : node.getName();
+ String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node
+ .getName()) : node.getName();
int charWidth = fm.stringWidth(name) + 3;
int charHeight = font.getSize();
Rectangle rect = new Rectangle(xend + 10, ypos - charHeight / 2,
- charWidth, 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) &&
- selected.getSequences(null).contains( (SequenceI) node.element()))
+ if ((selected != null)
+ && selected.getSequences(null).contains(node.element()))
{
g.setColor(Color.gray);
- g.fillRect(xend + 10, ypos - charHeight / 2, charWidth,
- charHeight);
+ g.fillRect(xend + 10, ypos - charHeight / 2, charWidth, charHeight);
g.setColor(Color.white);
}
else
{
drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx,
- offy);
+ offy);
drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,
- offy);
+ offy);
float height = node.height;
float dist = node.dist;
- int xstart = (int) ( (height - dist) * scale) + offx;
+ int xstart = (int) ((height - dist) * scale) + offx;
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);
g.fillRect(xend - 2, ypos - 2, 4, 4);
}
- int ystart = (int) ( ( (SequenceNode) node.left()).ycount * chunk) +
- offy;
- int yend = (int) ( ( (SequenceNode) node.right()).ycount * chunk) +
- offy;
+ int ystart = (int) (((SequenceNode) node.left()).ycount * chunk)
+ + offy;
+ int yend = (int) (((SequenceNode) node.right()).ycount * chunk)
+ + offy;
Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
nodeHash.put(node, pos);
- g.drawLine( (int) (height * scale) + offx, ystart,
- (int) (height * scale) + offx, yend);
+ g.drawLine((int) (height * scale) + offx, ystart,
+ (int) (height * scale) + offx, yend);
String nodeLabel = "";
nodeLabel = new Format("%-.2f").form(node.dist);
}
- if (showBootstrap && node.bootstrap>-1)
+ if (showBootstrap && node.bootstrap > -1)
{
if (showDistances)
{
/**
* DOCUMENT ME!
- *
- * @param x DOCUMENT ME!
- * @param y DOCUMENT ME!
- *
+ *
+ * @param x
+ * DOCUMENT ME!
+ * @param y
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public Object findElement(int x, int y)
Object ob = keys.nextElement();
Rectangle rect = (Rectangle) nameHash.get(ob);
- if ( (x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&
- (y <= (rect.y + rect.height)))
+ if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y)
+ && (y <= (rect.y + rect.height)))
{
return ob;
}
Object ob = keys.nextElement();
Rectangle rect = (Rectangle) nodeHash.get(ob);
- if ( (x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&
- (y <= (rect.y + rect.height)))
+ if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y)
+ && (y <= (rect.y + rect.height)))
{
return ob;
}
/**
* DOCUMENT ME!
- *
- * @param pickBox DOCUMENT ME!
+ *
+ * @param pickBox
+ * DOCUMENT ME!
*/
public void pickNodes(Rectangle pickBox)
{
SequenceNode top = tree.getTopNode();
- float wscale = (float) ( (width * .8) - (offx * 2)) / tree.getMaxHeight();
+ float wscale = (float) ((width * .8) - (offx * 2))
+ / tree.getMaxHeight();
if (top.count == 0)
{
- top.count = ( (SequenceNode) top.left()).count +
- ( (SequenceNode) top.right()).count;
+ top.count = ((SequenceNode) top.left()).count
+ + ((SequenceNode) top.right()).count;
}
float chunk = (float) (height - (offy)) / top.count;
/**
* DOCUMENT ME!
- *
- * @param pickBox DOCUMENT ME!
- * @param node DOCUMENT ME!
- * @param chunk DOCUMENT ME!
- * @param scale DOCUMENT ME!
- * @param width DOCUMENT ME!
- * @param offx DOCUMENT ME!
- * @param offy DOCUMENT ME!
+ *
+ * @param pickBox
+ * DOCUMENT ME!
+ * @param node
+ * DOCUMENT ME!
+ * @param chunk
+ * DOCUMENT ME!
+ * @param scale
+ * DOCUMENT ME!
+ * @param width
+ * DOCUMENT ME!
+ * @param offx
+ * DOCUMENT ME!
+ * @param offy
+ * DOCUMENT ME!
*/
public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
- float scale, int width, int offx, int offy)
+ float scale, int width, int offx, int offy)
{
if (node == null)
{
return;
}
- if ( (node.left() == null) && (node.right() == null))
+ if ((node.left() == null) && (node.right() == null))
{
float height = node.height;
float dist = node.dist;
- int xstart = (int) ( (height - dist) * scale) + offx;
+ int xstart = (int) ((height - dist) * scale) + offx;
int xend = (int) (height * scale) + offx;
int ypos = (int) (node.ycount * chunk) + offy;
else
{
pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width,
- offx, offy);
+ offx, offy);
pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,
- offx, offy);
+ offx, offy);
}
}
/**
* DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
- * @param c DOCUMENT ME!
+ *
+ * @param node
+ * DOCUMENT ME!
+ * @param c
+ * DOCUMENT ME!
*/
public void setColor(SequenceNode node, Color c)
{
return;
}
- if ( (node.left() == null) && (node.right() == null)) // TODO: internal node
+ if ((node.left() == null) && (node.right() == null)) // TODO: internal node
{
node.color = c;
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++)
+ {
+ final SequenceI seq = (SequenceI) node.element();
+ aps[a].av.setSequenceColour(seq, c);
+ }
}
}
}
else
{
node.color = c;
- setColor( (SequenceNode) node.left(), c);
- setColor( (SequenceNode) node.right(), c);
+ setColor((SequenceNode) node.left(), c);
+ setColor((SequenceNode) node.right(), c);
}
}
try
{
printJob.print();
- }
- catch (Exception PrintException)
+ } catch (Exception PrintException)
{
PrintException.printStackTrace();
}
/**
* DOCUMENT ME!
- *
- * @param pg DOCUMENT ME!
- * @param pf DOCUMENT ME!
- * @param pi DOCUMENT ME!
- *
+ *
+ * @param pg
+ * DOCUMENT ME!
+ * @param pf
+ * DOCUMENT ME!
+ * @param pi
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
- *
- * @throws PrinterException DOCUMENT ME!
+ *
+ * @throws PrinterException
+ * DOCUMENT ME!
*/
public int print(Graphics pg, PageFormat pf, int pi)
- throws PrinterException
+ throws PrinterException
{
pg.setFont(font);
- pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
+ pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
int pwidth = (int) pf.getImageableWidth();
int pheight = (int) pf.getImageableHeight();
/**
* DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
*/
public void paintComponent(Graphics g)
{
if (tree == null)
{
- g.drawString("Calculating tree....", 20, getHeight() / 2);
+ g.drawString(MessageManager.getString("label.calculating_tree")
+ + "....", 20, getHeight() / 2);
}
else
{
repaint();
}
- if (fitToWindow ||
- (!fitToWindow &&
- (scrollPane.getHeight() > ( (fm.getHeight() * nameHash.size()) +
- offy))))
+ if (fitToWindow
+ || (!fitToWindow && (scrollPane.getHeight() > ((fm
+ .getHeight() * nameHash.size()) + offy))))
{
draw(g, scrollPane.getWidth(), scrollPane.getHeight());
setPreferredSize(null);
else
{
setPreferredSize(new Dimension(scrollPane.getWidth(),
- fm.getHeight() * nameHash.size()));
+ fm.getHeight() * nameHash.size()));
draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());
}
/**
* DOCUMENT ME!
- *
- * @param fontSize DOCUMENT ME!
+ *
+ * @param fontSize
+ * DOCUMENT ME!
*/
public void setFont(Font font)
{
/**
* DOCUMENT ME!
- *
- * @param g1 DOCUMENT ME!
- * @param width DOCUMENT ME!
- * @param height DOCUMENT ME!
+ *
+ * @param g1
+ * DOCUMENT ME!
+ * @param width
+ * DOCUMENT ME!
+ * @param height
+ * DOCUMENT ME!
*/
public void draw(Graphics g1, int width, int height)
{
Graphics2D g2 = (Graphics2D) g1;
g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
+ 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);
- labelLength = fm.stringWidth(longestName) + 20; //20 allows for scrollbar
+ 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();
if (top.count == 0)
{
- top.count = ( (SequenceNode) top.left()).count +
- ( (SequenceNode) top.right()).count;
+ top.count = ((SequenceNode) top.left()).count
+ + ((SequenceNode) top.right()).count;
}
float chunk = (float) (height - (offy)) / top.count;
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());
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void mouseReleased(MouseEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void mouseEntered(MouseEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void mouseExited(MouseEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void mouseClicked(MouseEvent evt)
{
{
if (SwingUtilities.isRightMouseButton(evt))
{
- Color col = JColorChooser.showDialog(this, "Select Sub-Tree Colour",
- highlightNode.color);
- if (col!=null)
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_subtree_colour"),
+ highlightNode.color);
+ if (col != null)
{
setColor(highlightNode, col);
}
}
- else
- if (evt.getClickCount() > 1)
+ else if (evt.getClickCount() > 1)
{
tree.swapNodes(highlightNode);
tree.reCount(tree.getTopNode());
for (int i = 0; i < leaves.size(); i++)
{
- SequenceI seq =
- (SequenceI) ( (SequenceNode) leaves.elementAt(i)).element();
+ SequenceI seq = (SequenceI) ((SequenceNode) leaves.elementAt(i))
+ .element();
treeSelectionChanged(seq);
}
+ av.sendSelection();
}
PaintRefresher.Refresh(tp, av.getSequenceSetId());
if (ob instanceof SequenceNode)
{
highlightNode = (SequenceNode) ob;
- this.setToolTipText(
- "<html>Left click to select leaves"
- + "<br>Double-click to invert leaves"
- + "<br>Right click to change colour");
+ this.setToolTipText("<html>"
+ + MessageManager.getString("label.highlightnode"));
repaint();
}
}
public void mouseDragged(MouseEvent ect)
- {}
+ {
+ }
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void mousePressed(MouseEvent e)
{
if (ob instanceof SequenceI)
{
- treeSelectionChanged( (Sequence) ob);
+ treeSelectionChanged((Sequence) ob);
PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
repaint();
+ av.sendSelection();
return;
}
- else if (! (ob instanceof SequenceNode))
+ else if (!(ob instanceof SequenceNode))
{
// Find threshold
if (tree.getMaxHeight() != 0)
{
- threshold = (float) (x - offx) / (float) (getWidth() -
- labelLength - (2 * offx));
+ threshold = (float) (x - offx)
+ / (float) (getWidth() - labelLength - (2 * offx));
tree.getGroups().removeAllElements();
tree.groupNodes(tree.getTopNode(), threshold);
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.alignment.deleteAllGroups();
- aps[a].av.sequenceColours = 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();
}
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));
- setColor( (SequenceNode) tree.getGroups().elementAt(i),
- col.brighter());
+ 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();
for (int j = 0; j < l.size(); j++)
{
- SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element();
+ SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j))
+ .element();
if (!sequences.contains(s1))
{
}
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());
+ ((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.isIgnoreGapsConsensus());
}
-
- 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())
+ && 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));
+ }
+
+ // 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++)
+ {
+ aps[a].updateAnnotation();
+ // TODO: JAL-868 - need to ensure view colour change message is broadcast
+ // to any Jmols listening in
+ }
+
+ if (av.getCodingComplement() != null)
+ {
+ ((AlignViewport) av.getCodingComplement()).getAlignPanel()
+ .updateAnnotation();
+ /*
+ * idPanel. repaint ()
+ */
+ }
}
/**
* DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
*/
public void setShowDistances(boolean state)
{
/**
* DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
*/
public void setShowBootstrap(boolean state)
{
/**
* DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
*/
public void setMarkPlaceholders(boolean state)
{
}
else
{
- return new AlignmentPanel[]
- {
- ap};
+ return new AlignmentPanel[] { ap };
}
}
}
git://source.jalview.org / jalview.git / blobdiff