/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 jalview.analysis.*;
-
-import jalview.datamodel.*;
-
-import jalview.schemes.*;
-
-import jalview.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.print.*;
-
-import java.util.*;
-
-import javax.swing.*;
-
+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.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Vector;
+
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
+
+import jalview.analysis.Conservation;
+import jalview.analysis.TreeModel;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.schemes.ColourSchemeI;
+import jalview.structure.SelectionSource;
+import jalview.util.Format;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
- Printable, MouseMotionListener
+ Printable, MouseMotionListener, SelectionSource
{
- /** DOCUMENT ME!! */
- public static final String PLACEHOLDER = " * ";
- NJTree tree;
- JScrollPane scrollPane;
- 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;
-
- /**
- * Creates a new TreeCanvas object.
- *
- * @param av DOCUMENT ME!
- * @param tree DOCUMENT ME!
- * @param scroller DOCUMENT ME!
- * @param label DOCUMENT ME!
- */
- public TreeCanvas(AlignmentPanel ap, JScrollPane scroller)
- {
- this.av = ap.av;
- this.ap = ap;
- font = av.getFont();
- scrollPane = scroller;
- addMouseListener(this);
- addMouseMotionListener(this);
- PaintRefresher.Register(this, ap.av.getSequenceSetId());
- ToolTipManager.sharedInstance().registerComponent(this);
- }
+ /** DOCUMENT ME!! */
+ public static final String PLACEHOLDER = " * ";
+ TreeModel tree;
- /**
- * DOCUMENT ME!
- *
- * @param sequence DOCUMENT ME!
- */
- public void treeSelectionChanged(SequenceI sequence)
- {
- SequenceGroup selected = av.getSelectionGroup();
+ JScrollPane scrollPane;
- if (selected == null)
- {
- selected = new SequenceGroup();
- av.setSelectionGroup(selected);
- }
+ TreePanel tp;
- selected.setEndRes(av.alignment.getWidth()-1);
- selected.addOrRemove(sequence, true);
- }
+ private AlignViewport av;
- /**
- * DOCUMENT ME!
- *
- * @param tree DOCUMENT ME!
- */
- public void setTree(NJTree tree)
+ private AlignmentPanel ap;
+
+ Font font;
+
+ FontMetrics fm;
+
+ boolean fitToWindow = true;
+
+ boolean showDistances = false;
+
+ boolean showBootstrap = false;
+
+ boolean markPlaceholders = false;
+
+ int offx = 20;
+
+ int offy;
+
+ private float threshold;
+
+ String longestName;
+
+ int labelLength = -1;
+
+ Map<Object, Rectangle> nameHash = new Hashtable<>();
+
+ Map<SequenceNode, Rectangle> 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!
+ */
+ public TreeCanvas(TreePanel tp, AlignmentPanel ap, JScrollPane scroller)
+ {
+ this.tp = tp;
+ this.av = ap.av;
+ this.setAssociatedPanel(ap);
+ font = av.getFont();
+ scrollPane = scroller;
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ ToolTipManager.sharedInstance().registerComponent(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param sequence
+ * DOCUMENT ME!
+ */
+ public void treeSelectionChanged(SequenceI sequence)
+ {
+ AlignmentPanel[] aps = getAssociatedPanels();
+
+ for (int a = 0; a < aps.length; a++)
{
- this.tree = tree;
- tree.findHeight(tree.getTopNode());
+ SequenceGroup selected = aps[a].av.getSelectionGroup();
- // Now have to calculate longest name based on the leaves
- Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
- boolean has_placeholders = false;
- longestName = "";
+ if (selected == null)
+ {
+ selected = new SequenceGroup();
+ aps[a].av.setSelectionGroup(selected);
+ }
- for (int i = 0; i < leaves.size(); i++)
- {
- SequenceNode lf = (SequenceNode) leaves.elementAt(i);
+ selected.setEndRes(aps[a].av.getAlignment().getWidth() - 1);
+ selected.addOrRemove(sequence, true);
+ }
+ }
- if (lf.isPlaceholder())
- {
- has_placeholders = true;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param tree
+ * DOCUMENT ME!
+ */
+ public void setTree(TreeModel tree)
+ {
+ this.tree = tree;
+ tree.findHeight(tree.getTopNode());
+
+ // Now have to calculate longest name based on the leaves
+ Vector<SequenceNode> leaves = tree.findLeaves(tree.getTopNode());
+ boolean has_placeholders = false;
+ longestName = "";
+
+ for (int i = 0; i < leaves.size(); i++)
+ {
+ SequenceNode lf = leaves.elementAt(i);
- if (longestName.length() < ( (Sequence) lf.element()).getName()
+ if (lf.isPlaceholder())
+ {
+ has_placeholders = true;
+ }
+
+ if (longestName.length() < ((Sequence) lf.element()).getName()
.length())
- {
- longestName = TreeCanvas.PLACEHOLDER +
- ( (Sequence) lf.element()).getName();
- }
- }
+ {
+ longestName = TreeCanvas.PLACEHOLDER
+ + ((Sequence) lf.element()).getName();
+ }
+ }
- setMarkPlaceholders(has_placeholders);
+ setMarkPlaceholders(has_placeholders);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param node
+ * DOCUMENT ME!
+ * @param chunk
+ * DOCUMENT ME!
+ * @param wscale
+ * DOCUMENT ME!
+ * @param width
+ * DOCUMENT ME!
+ * @param offx
+ * DOCUMENT ME!
+ * @param offy
+ * DOCUMENT ME!
+ */
+ public void drawNode(Graphics g, SequenceNode node, float chunk,
+ double wscale, int width, int offx, int offy)
+ {
+ if (node == null)
+ {
+ return;
}
- /**
- * 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)
+ if ((node.left() == null) && (node.right() == null))
{
- if (node == null)
- {
- return;
- }
+ // Drawing leaf node
+ double height = node.height;
+ double dist = node.dist;
+
+ int xstart = (int) ((height - dist) * wscale) + offx;
+ int xend = (int) (height * wscale) + offx;
+
+ int ypos = (int) (node.ycount * chunk) + offy;
- if ((node.left() == null) && (node.right() == null))
+ if (node.element() instanceof SequenceI)
+ {
+ SequenceI seq = (SequenceI) node.element();
+
+ if (av.getSequenceColour(seq) == Color.white)
{
- // Drawing leaf node
- float height = node.height;
- float dist = node.dist;
-
- 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();
-
- if (av.getSequenceColour(seq) == Color.white)
- {
- g.setColor(Color.black);
- }
- else
- {
- g.setColor(av.getSequenceColour(seq).darker());
- }
- }
- else
- {
- g.setColor(Color.black);
- }
-
- // Draw horizontal line
- g.drawLine(xstart, ypos, xend, ypos);
-
- String nodeLabel = "";
-
- if (showDistances && (node.dist > 0))
- {
- nodeLabel = new Format("%-.2f").form(node.dist);
- }
-
- if (showBootstrap)
- {
- if (showDistances)
- {
- nodeLabel = nodeLabel + " : ";
- }
-
- nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
- }
-
- if (!nodeLabel.equals(""))
- {
- g.drawString(nodeLabel, xstart+2, ypos - 2);
- }
-
- 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);
-
- nameHash.put((SequenceI) node.element(), rect);
-
- // Colour selected leaves differently
- SequenceGroup selected = av.getSelectionGroup();
-
- if ((selected != null) &&
- selected.getSequences(false).contains((SequenceI) node.element()))
- {
- g.setColor(Color.gray);
-
- g.fillRect(xend + 10, ypos-charHeight/2, charWidth,
- charHeight);
- g.setColor(Color.white);
- }
-
- g.drawString(name, xend + 10, ypos+fm.getDescent());
- g.setColor(Color.black);
+ g.setColor(Color.black);
}
else
{
- drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx,
- offy);
- drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,
- offy);
-
- float height = node.height;
- float dist = node.dist;
-
- 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());
-
- // Draw horizontal line
- g.drawLine(xstart, ypos, xend, ypos);
- if (node == highlightNode)
- g.fillRect(xend - 3, ypos - 3, 6, 6);
- else
- 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;
-
- 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);
-
- if (showDistances && (node.dist > 0))
- {
- g.drawString(new Format("%-.2f").form(node.dist).trim(), xstart+2,
- ypos - 2);
- }
+ g.setColor(av.getSequenceColour(seq).darker());
}
- }
+ }
+ else
+ {
+ g.setColor(Color.black);
+ }
- /**
- * DOCUMENT ME!
- *
- * @param x DOCUMENT ME!
- * @param y DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Object findElement(int x, int y)
- {
- Enumeration keys = nameHash.keys();
+ // Draw horizontal line
+ g.drawLine(xstart, ypos, xend, ypos);
- while (keys.hasMoreElements())
- {
- 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)))
- {
- return ob;
- }
- }
+ String nodeLabel = "";
- keys = nodeHash.keys();
+ if (showDistances && (node.dist > 0))
+ {
+ nodeLabel = new Format("%g").form(node.dist);
+ }
- while (keys.hasMoreElements())
+ if (showBootstrap && node.bootstrap > -1)
+ {
+ if (showDistances)
{
- 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)))
- {
- return ob;
- }
+ nodeLabel = nodeLabel + " : ";
}
- return null;
- }
+ nodeLabel = nodeLabel + String.valueOf(node.bootstrap);
+ }
- /**
- * DOCUMENT ME!
- *
- * @param pickBox DOCUMENT ME!
- */
- public void pickNodes(Rectangle pickBox)
+ if (!nodeLabel.equals(""))
+ {
+ g.drawString(nodeLabel, xstart + 2, ypos - 2);
+ }
+
+ 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);
+
+ nameHash.put(node.element(), rect);
+
+ // Colour selected leaves differently
+ SequenceGroup selected = av.getSelectionGroup();
+
+ if ((selected != null)
+ && selected.getSequences(null).contains(node.element()))
+ {
+ g.setColor(Color.gray);
+
+ g.fillRect(xend + 10, ypos - charHeight / 2, charWidth, charHeight);
+ g.setColor(Color.white);
+ }
+
+ g.drawString(name, xend + 10, ypos + fm.getDescent());
+ g.setColor(Color.black);
+ }
+ else
{
- int width = getWidth();
- int height = getHeight();
+ drawNode(g, (SequenceNode) node.left(), chunk, wscale, width, offx,
+ offy);
+ drawNode(g, (SequenceNode) node.right(), chunk, wscale, width, offx,
+ offy);
+
+ double height = node.height;
+ double dist = node.dist;
+
+ int xstart = (int) ((height - dist) * wscale) + offx;
+ int xend = (int) (height * wscale) + offx;
+ int ypos = (int) (node.ycount * chunk) + offy;
+
+ g.setColor(node.color.darker());
+
+ // Draw horizontal line
+ g.drawLine(xstart, ypos, xend, ypos);
+ if (node == highlightNode)
+ {
+ g.fillRect(xend - 3, ypos - 3, 6, 6);
+ }
+ else
+ {
+ g.fillRect(xend - 2, ypos - 2, 4, 4);
+ }
+
+ int ystart = (node.left() == null ? 0
+ : (int) (((SequenceNode) node.left()).ycount * chunk)) + offy;
+ int yend = (node.right() == null ? 0
+ : (int) (((SequenceNode) node.right()).ycount * chunk))
+ + offy;
- SequenceNode top = tree.getTopNode();
+ Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
+ nodeHash.put(node, pos);
- float wscale = (float) ((width * .8) - (offx * 2)) / tree.getMaxHeight();
+ g.drawLine((int) (height * wscale) + offx, ystart,
+ (int) (height * wscale) + offx, yend);
- if (top.count == 0)
+ String nodeLabel = "";
+
+ if (showDistances && (node.dist > 0))
+ {
+ nodeLabel = new Format("%g").form(node.dist);
+ }
+
+ if (showBootstrap && node.bootstrap > -1)
+ {
+ if (showDistances)
{
- top.count = ((SequenceNode) top.left()).count +
- ((SequenceNode) top.right()).count;
+ nodeLabel = nodeLabel + " : ";
}
- float chunk = (float) (height - (offy)) / top.count;
+ nodeLabel = nodeLabel + String.valueOf(node.bootstrap);
+ }
- pickNode(pickBox, top, chunk, wscale, width, offx, offy);
+ if (!nodeLabel.equals(""))
+ {
+ g.drawString(nodeLabel, xstart + 2, ypos - 2);
+ }
}
+ }
- /**
- * 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)
+ /**
+ * DOCUMENT ME!
+ *
+ * @param x
+ * DOCUMENT ME!
+ * @param y
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Object findElement(int x, int y)
+ {
+ for (Entry<Object, Rectangle> entry : nameHash.entrySet())
{
- if (node == null)
- {
- return;
- }
+ Rectangle rect = entry.getValue();
- if ((node.left() == null) && (node.right() == null))
- {
- float height = node.height;
- float dist = node.dist;
-
- int xstart = (int) ((height - dist) * scale) + offx;
- int xend = (int) (height * scale) + offx;
-
- int ypos = (int) (node.ycount * chunk) + offy;
-
- if (pickBox.contains(new Point(xend, ypos)))
- {
- if (node.element() instanceof SequenceI)
- {
- SequenceI seq = (SequenceI) node.element();
- SequenceGroup sg = av.getSelectionGroup();
-
- if (sg != null)
- {
- sg.addOrRemove(seq, true);
- }
- }
- }
- }
- else
- {
- pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width,
- offx, offy);
- pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,
- offx, offy);
- }
+ if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y)
+ && (y <= (rect.y + rect.height)))
+ {
+ return entry.getKey();
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
- * @param c DOCUMENT ME!
- */
- public void setColor(SequenceNode node, Color c)
+ for (Entry<SequenceNode, Rectangle> entry : nodeHash.entrySet())
{
- if (node == null)
- {
- return;
- }
-
- if ((node.left() == null) && (node.right() == null))
- {
- node.color = c;
+ Rectangle rect = entry.getValue();
- if (node.element() instanceof SequenceI)
- {
- av.setSequenceColour((SequenceI) node.element(), c);
- }
- }
- else
- {
- node.color = c;
- setColor((SequenceNode) node.left(), c);
- setColor((SequenceNode) node.right(), c);
- }
+ if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y)
+ && (y <= (rect.y + rect.height)))
+ {
+ return entry.getKey();
+ }
}
- /**
- * DOCUMENT ME!
- */
- void startPrinting()
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pickBox
+ * DOCUMENT ME!
+ */
+ public void pickNodes(Rectangle pickBox)
+ {
+ int width = getWidth();
+ int height = getHeight();
+
+ SequenceNode top = tree.getTopNode();
+
+ double wscale = ((width * .8) - (offx * 2)) / tree.getMaxHeight();
+
+ if (top.count == 0)
{
- Thread thread = new Thread(this);
- thread.start();
+ top.count = ((SequenceNode) top.left()).count
+ + ((SequenceNode) top.right()).count;
}
- // put printing in a thread to avoid painting problems
- public void run()
- {
- PrinterJob printJob = PrinterJob.getPrinterJob();
- PageFormat pf = printJob.pageDialog(printJob.defaultPage());
+ float chunk = (float) (height - (offy)) / top.count;
- printJob.setPrintable(this, pf);
+ pickNode(pickBox, top, chunk, wscale, width, offx, offy);
+ }
- if (printJob.printDialog())
- {
- try
- {
- printJob.print();
- }
- catch (Exception PrintException)
- {
- PrintException.printStackTrace();
- }
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pickBox
+ * DOCUMENT ME!
+ * @param node
+ * DOCUMENT ME!
+ * @param chunk
+ * DOCUMENT ME!
+ * @param wscale
+ * DOCUMENT ME!
+ * @param width
+ * DOCUMENT ME!
+ * @param offx
+ * DOCUMENT ME!
+ * @param offy
+ * DOCUMENT ME!
+ */
+ public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
+ double wscale, int width, int offx, int offy)
+ {
+ if (node == null)
+ {
+ return;
}
- /**
- * DOCUMENT ME!
- *
- * @param pg DOCUMENT ME!
- * @param pf DOCUMENT ME!
- * @param pi DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- *
- * @throws PrinterException DOCUMENT ME!
- */
- public int print(Graphics pg, PageFormat pf, int pi)
- throws PrinterException
+ if ((node.left() == null) && (node.right() == null))
{
- pg.setFont(font);
- pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
-
- int pwidth = (int) pf.getImageableWidth();
- int pheight = (int) pf.getImageableHeight();
+ double height = node.height;
+ // double dist = node.dist;
+ // int xstart = (int) ((height - dist) * wscale) + offx;
+ int xend = (int) (height * wscale) + offx;
- int noPages = getHeight() / pheight;
+ int ypos = (int) (node.ycount * chunk) + offy;
- if (pi > noPages)
+ if (pickBox.contains(new Point(xend, ypos)))
+ {
+ if (node.element() instanceof SequenceI)
{
- return Printable.NO_SUCH_PAGE;
- }
+ SequenceI seq = (SequenceI) node.element();
+ SequenceGroup sg = av.getSelectionGroup();
- if (pwidth > getWidth())
- {
- pwidth = getWidth();
+ if (sg != null)
+ {
+ sg.addOrRemove(seq, true);
+ }
}
+ }
+ }
+ else
+ {
+ pickNode(pickBox, (SequenceNode) node.left(), chunk, wscale, width,
+ offx, offy);
+ pickNode(pickBox, (SequenceNode) node.right(), chunk, wscale, width,
+ offx, offy);
+ }
+ }
- if (fitToWindow)
- {
- if (pheight > getHeight())
- {
- pheight = getHeight();
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node
+ * DOCUMENT ME!
+ * @param c
+ * DOCUMENT ME!
+ */
+ public void setColor(SequenceNode node, Color c)
+ {
+ if (node == null)
+ {
+ return;
+ }
- noPages = 0;
- }
- else
+ node.color = c;
+ if (node.element() instanceof SequenceI)
+ {
+ final SequenceI seq = (SequenceI) node.element();
+ AlignmentPanel[] aps = getAssociatedPanels();
+ if (aps != null)
+ {
+ for (int a = 0; a < aps.length; a++)
{
- FontMetrics fm = pg.getFontMetrics(font);
- int height = fm.getHeight() * nameHash.size();
- pg.translate(0, -pi * pheight);
- pg.setClip(0, pi * pheight, pwidth, (pi * pheight) + pheight);
-
- // translate number of pages,
- // height is screen size as this is the
- // non overlapping text size
- pheight = height;
+ aps[a].av.setSequenceColour(seq, c);
}
+ }
+ }
+ setColor((SequenceNode) node.left(), c);
+ setColor((SequenceNode) node.right(), c);
+ }
- draw(pg, pwidth, pheight);
+ /**
+ * DOCUMENT ME!
+ */
+ void startPrinting()
+ {
+ Thread thread = new Thread(this);
+ thread.start();
+ }
- return Printable.PAGE_EXISTS;
+ // put printing in a thread to avoid painting problems
+ @Override
+ public void run()
+ {
+ PrinterJob printJob = PrinterJob.getPrinterJob();
+ PageFormat defaultPage = printJob.defaultPage();
+ PageFormat pf = printJob.pageDialog(defaultPage);
+
+ if (defaultPage == pf)
+ {
+ /*
+ * user cancelled
+ */
+ return;
}
- /**
- * DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- */
- public void paintComponent(Graphics g)
+ printJob.setPrintable(this, pf);
+
+ if (printJob.printDialog())
{
- super.paintComponent(g);
- g.setFont(font);
+ try
+ {
+ printJob.print();
+ } catch (Exception PrintException)
+ {
+ PrintException.printStackTrace();
+ }
+ }
+ }
- if(tree==null)
- {
- g.drawString("Calculating tree....", 20, getHeight()/2);
- }
- else
- {
- fm = g.getFontMetrics(font);
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pg
+ * DOCUMENT ME!
+ * @param pf
+ * DOCUMENT ME!
+ * @param pi
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws PrinterException
+ * DOCUMENT ME!
+ */
+ @Override
+ public int print(Graphics pg, PageFormat pf, int pi)
+ throws PrinterException
+ {
+ pg.setFont(font);
+ pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
+
+ int pwidth = (int) pf.getImageableWidth();
+ int pheight = (int) pf.getImageableHeight();
+
+ int noPages = getHeight() / pheight;
+
+ if (pi > noPages)
+ {
+ return Printable.NO_SUCH_PAGE;
+ }
- if (nameHash.size() == 0)
- {
- repaint();
- }
+ if (pwidth > getWidth())
+ {
+ pwidth = getWidth();
+ }
- 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()));
- draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());
- }
+ if (fitToWindow)
+ {
+ if (pheight > getHeight())
+ {
+ pheight = getHeight();
+ }
- scrollPane.revalidate();
- }
+ noPages = 0;
+ }
+ else
+ {
+ FontMetrics fm = pg.getFontMetrics(font);
+ int height = fm.getHeight() * nameHash.size();
+ pg.translate(0, -pi * pheight);
+ pg.setClip(0, pi * pheight, pwidth, (pi * pheight) + pheight);
+
+ // translate number of pages,
+ // height is screen size as this is the
+ // non overlapping text size
+ pheight = height;
}
+ draw(pg, pwidth, pheight);
- /**
- * DOCUMENT ME!
- *
- * @param fontSize DOCUMENT ME!
- */
- public void setFont(Font font)
+ return Printable.PAGE_EXISTS;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ */
+ @Override
+ public void paintComponent(Graphics g)
+ {
+ super.paintComponent(g);
+ g.setFont(font);
+
+ if (tree == null)
{
- this.font = font;
+ g.drawString(
+ MessageManager.getString("label.calculating_tree") + "....",
+ 20, getHeight() / 2);
+ }
+ else
+ {
+ fm = g.getFontMetrics(font);
+
+ int nameCount = nameHash.size();
+ if (nameCount == 0)
+ {
repaint();
+ }
+
+ if (fitToWindow || (!fitToWindow && (scrollPane
+ .getHeight() > ((fm.getHeight() * nameCount) + offy))))
+ {
+ draw(g, scrollPane.getWidth(), scrollPane.getHeight());
+ setPreferredSize(null);
+ }
+ else
+ {
+ setPreferredSize(new Dimension(scrollPane.getWidth(),
+ fm.getHeight() * nameCount));
+ draw(g, scrollPane.getWidth(), fm.getHeight() * nameCount);
+ }
+
+ scrollPane.revalidate();
}
+ }
- /**
- * 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,
+ /**
+ * DOCUMENT ME!
+ *
+ * @param fontSize
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setFont(Font font)
+ {
+ this.font = font;
+ repaint();
+ }
+
+ /**
+ * 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);
- g2.setColor(Color.white);
- g2.fillRect(0, 0, width, height);
+ g2.setColor(Color.white);
+ g2.fillRect(0, 0, width, height);
+ g2.setFont(font);
- g2.setFont(font);
+ if (longestName == null || tree == null)
+ {
+ g2.drawString("Calculating tree.", 20, 20);
+ }
+ offy = font.getSize() + 10;
- offy = font.getSize()+10;
+ fm = g2.getFontMetrics(font);
- fm = g2.getFontMetrics(font);
+ labelLength = fm.stringWidth(longestName) + 20; // 20 allows for scrollbar
- labelLength = fm.stringWidth(longestName) + 20; //20 allows for scrollbar
+ double wscale = (width - labelLength - (offx * 2))
+ / tree.getMaxHeight();
- float wscale = (float) (width - labelLength - (offx * 2)) / tree.getMaxHeight();
+ SequenceNode top = tree.getTopNode();
- SequenceNode top = tree.getTopNode();
+ if (top.count == 0)
+ {
+ top.count = ((SequenceNode) top.left()).count
+ + ((SequenceNode) top.right()).count;
+ }
- if (top.count == 0)
- {
- top.count = ((SequenceNode) top.left()).count +
- ((SequenceNode) top.right()).count;
- }
+ float chunk = (float) (height - (offy)) / top.count;
- float chunk = (float) (height - (offy)) / top.count;
+ drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy);
- drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy);
+ if (threshold != 0)
+ {
+ if (av.getCurrentTree() == tree)
+ {
+ g2.setColor(Color.red);
+ }
+ else
+ {
+ g2.setColor(Color.gray);
+ }
- if (threshold != 0)
- {
- if (av.getCurrentTree() == tree)
- {
- g2.setColor(Color.red);
- }
- else
- {
- g2.setColor(Color.gray);
- }
-
- int x = (int) ((threshold * (float) (getWidth() - labelLength -
- (2 * offx))) + offx);
-
- g2.drawLine(x, 0, x, getHeight());
- }
+ int x = (int) ((threshold * (getWidth() - labelLength - (2 * offx)))
+ + offx);
+
+ g2.drawLine(x, 0, x, getHeight());
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ /**
+ * Empty method to satisfy the MouseListener interface
+ *
+ * @param e
+ */
+ @Override
+ public void mouseReleased(MouseEvent e)
+ {
+ /*
+ * isPopupTrigger is set on mouseReleased on Windows
*/
- public void mouseReleased(MouseEvent e)
+ if (e.isPopupTrigger())
{
+ chooseSubtreeColour();
+ e.consume(); // prevent mouseClicked happening
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void mouseEntered(MouseEvent e)
+ /**
+ * Empty method to satisfy the MouseListener interface
+ *
+ * @param e
+ */
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ }
+
+ /**
+ * Empty method to satisfy the MouseListener interface
+ *
+ * @param e
+ */
+ @Override
+ public void mouseExited(MouseEvent e)
+ {
+ }
+
+ /**
+ * Handles a mouse click on a tree node (clicks elsewhere are handled in
+ * mousePressed). Click selects the sub-tree, double-click swaps leaf nodes
+ * order, right-click opens a dialogue to choose colour for the sub-tree.
+ *
+ * @param e
+ */
+ @Override
+ public void mouseClicked(MouseEvent evt)
+ {
+ if (highlightNode == null)
{
+ return;
}
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void mouseExited(MouseEvent e)
+ if (evt.getClickCount() > 1)
{
+ tree.swapNodes(highlightNode);
+ tree.reCount(tree.getTopNode());
+ tree.findHeight(tree.getTopNode());
}
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void mouseClicked(MouseEvent evt)
+ else
{
- if(highlightNode!=null)
- {
- if (SwingUtilities.isRightMouseButton(evt))
- {
- Color col = JColorChooser.showDialog(this, "Select Sub-Tree Colour",
- highlightNode.color);
+ Vector<SequenceNode> leaves = tree.findLeaves(highlightNode);
- setColor(highlightNode, col);
- }
- else
- if(evt.getClickCount()>1)
- {
- tree.swapNodes(highlightNode);
- tree.reCount(tree.getTopNode());
- tree.findHeight(tree.getTopNode());
- }
- else
- {
- Vector leaves = new Vector();
- tree.findLeaves(highlightNode, leaves);
+ for (int i = 0; i < leaves.size(); i++)
+ {
+ SequenceI seq = (SequenceI) leaves.elementAt(i).element();
+ treeSelectionChanged(seq);
+ }
+ av.sendSelection();
+ }
- for (int i = 0; i < leaves.size(); i++)
- {
- SequenceI seq =
- (SequenceI) ( (SequenceNode) leaves.elementAt(i)).element();
- treeSelectionChanged(seq);
- }
- }
+ PaintRefresher.Refresh(tp, av.getSequenceSetId());
+ repaint();
+ }
- PaintRefresher.Refresh(this, av.getSequenceSetId());
+ /**
+ * Offer the user the option to choose a colour for the highlighted node and
+ * its children; this colour is also applied to the corresponding sequence ids
+ * in the alignment
+ */
+ void chooseSubtreeColour()
+ {
+ String ttl = MessageManager.getString("label.select_subtree_colour");
+ ColourChooserListener listener = new ColourChooserListener()
+ {
+ @Override
+ public void colourSelected(Color c)
+ {
+ setColor(highlightNode, c);
+ PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
repaint();
}
- }
+ };
+ JalviewColourChooser.showColourChooser(this, ttl, highlightNode.color,
+ listener);
+ }
+ @Override
+ public void mouseMoved(MouseEvent evt)
+ {
+ av.setCurrentTree(tree);
+ Object ob = findElement(evt.getX(), evt.getY());
- public void mouseMoved(MouseEvent evt)
+ if (ob instanceof SequenceNode)
{
- av.setCurrentTree(tree);
-
- Object ob = findElement(evt.getX(), evt.getY());
+ highlightNode = (SequenceNode) ob;
+ this.setToolTipText(
+ "<html>" + MessageManager.getString("label.highlightnode"));
+ repaint();
- if (ob instanceof SequenceNode)
+ }
+ else
+ {
+ if (highlightNode != null)
{
- highlightNode = (SequenceNode) ob;
- this.setToolTipText(
- "<html>Left click to select leaves"
- + "<br>Double-click to invert leaves"
- + "<br>Right click to change colour");
+ highlightNode = null;
+ setToolTipText(null);
repaint();
-
- }
- else
- {
- if (highlightNode != null)
- {
- highlightNode = null;
- setToolTipText(null);
- repaint();
- }
}
+ }
}
- public void mouseDragged(MouseEvent ect)
- {}
+ @Override
+ public void mouseDragged(MouseEvent ect)
+ {
+ }
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ /**
+ * Handles a mouse press on a sequence name or the tree background canvas
+ * (click on a node is handled in mouseClicked). The action is to create
+ * groups by partitioning the tree at the mouse position. Colours for the
+ * groups (and sequence names) are generated randomly.
+ *
+ * @param e
+ */
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ av.setCurrentTree(tree);
+
+ /*
+ * isPopupTrigger is set for mousePressed (Mac)
+ * or mouseReleased (Windows)
*/
- public void mousePressed(MouseEvent e)
+ if (e.isPopupTrigger())
{
- av.setCurrentTree(tree);
+ if (highlightNode != null)
+ {
+ chooseSubtreeColour();
+ }
+ return;
+ }
- int x = e.getX();
- int y = e.getY();
+ /*
+ * defer right-click handling on Windows to
+ * mouseClicked; note isRightMouseButton
+ * also matches Cmd-click on Mac which should do
+ * nothing here
+ */
+ if (SwingUtilities.isRightMouseButton(e))
+ {
+ return;
+ }
- Object ob = findElement(x, y);
+ int x = e.getX();
+ int y = e.getY();
- if (ob instanceof SequenceI)
- {
- treeSelectionChanged( (Sequence) ob);
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
- repaint();
- return;
- }
- else if( !(ob instanceof SequenceNode) )
- {
- // Find threshold
- if (tree.getMaxHeight() != 0)
- {
- threshold = (float) (x - offx) / (float) (getWidth() -
- labelLength - (2 * offx));
+ Object ob = findElement(x, y);
- tree.getGroups().removeAllElements();
- tree.groupNodes(tree.getTopNode(), threshold);
- setColor(tree.getTopNode(), Color.black);
+ if (ob instanceof SequenceI)
+ {
+ treeSelectionChanged((Sequence) ob);
+ PaintRefresher.Refresh(tp,
+ getAssociatedPanel().av.getSequenceSetId());
+ repaint();
+ av.sendSelection();
+ return;
+ }
+ else if (!(ob instanceof SequenceNode))
+ {
+ // Find threshold
+ if (tree.getMaxHeight() != 0)
+ {
+ threshold = (float) (x - offx)
+ / (float) (getWidth() - labelLength - (2 * offx));
- av.setSelectionGroup(null);
- av.alignment.deleteAllGroups();
- av.sequenceColours=null;
+ List<SequenceNode> groups = tree.groupNodes(threshold);
+ setColor(tree.getTopNode(), Color.black);
- colourGroups();
- }
+ AlignmentPanel[] aps = getAssociatedPanels();
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
- repaint();
+ // 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 (aps[a].av.getCodingComplement() != null)
+ {
+ aps[a].av.getCodingComplement().setSelectionGroup(null);
+ aps[a].av.getCodingComplement().getAlignment()
+ .deleteAllGroups();
+ aps[a].av.getCodingComplement().clearSequenceColours();
+ }
+ aps[a].av.setUpdateStructures(true);
}
+ colourGroups(groups);
+ /*
+ * clear partition (don't show vertical line) if
+ * it is to the right of all nodes
+ */
+ if (groups.isEmpty())
+ {
+ threshold = 0f;
+ }
+ }
+ PaintRefresher.Refresh(tp,
+ getAssociatedPanel().av.getSequenceSetId());
+ repaint();
}
- void colourGroups()
+ }
+
+ void colourGroups(List<SequenceNode> groups)
+ {
+ AlignmentPanel[] aps = getAssociatedPanels();
+ for (int i = 0; i < groups.size(); i++)
{
- 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(groups.get(i), col.brighter());
- Vector l = tree.findLeaves( (SequenceNode) tree.getGroups()
- .elementAt(i),
- new Vector());
+ Vector<SequenceNode> l = tree.findLeaves(groups.get(i));
- Vector sequences = new Vector();
+ Vector<SequenceI> sequences = new Vector<>();
- for (int j = 0; j < l.size(); j++)
- {
- SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element();
+ for (int j = 0; j < l.size(); j++)
+ {
+ SequenceI s1 = (SequenceI) l.elementAt(j).element();
- if (!sequences.contains(s1))
- {
- sequences.addElement(s1);
- }
+ if (!sequences.contains(s1))
+ {
+ sequences.addElement(s1);
}
+ }
- ColourSchemeI cs = null;
-
- if (av.getGlobalColourScheme() != null)
- {
- if (av.getGlobalColourScheme() instanceof UserColourScheme)
- {
- cs = new UserColourScheme(
- ( (UserColourScheme) av.getGlobalColourScheme()).getColours());
+ ColourSchemeI cs = null;
+ SequenceGroup _sg = new SequenceGroup(sequences, null, cs, true, true,
+ false, 0, av.getAlignment().getWidth() - 1);
- }
- else
- cs = ColourSchemeProperty.getColour(sequences,
- av.alignment.getWidth(),
- ColourSchemeProperty.
- getColourName(
- av.getGlobalColourScheme()));
-
- cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
- av.getIgnoreGapsConsensus());
- }
+ _sg.setName("JTreeGroup:" + _sg.hashCode());
+ _sg.setIdColour(col);
- SequenceGroup sg = new SequenceGroup(sequences,
- "TreeGroup", cs, true, true, false,
- 0,
- av.alignment.getWidth() - 1);
+ for (int a = 0; a < aps.length; a++)
+ {
+ SequenceGroup sg = new SequenceGroup(_sg);
+ AlignViewport viewport = aps[a].av;
- if (av.getGlobalColourScheme() != null
- && av.getGlobalColourScheme().conservationApplied())
+ // Propagate group colours in each view
+ if (viewport.getGlobalColourScheme() != null)
{
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.getSequences(false),
- sg.getStartRes(), sg.getEndRes());
-
- c.calculate();
- c.verdict(false, av.ConsPercGaps);
- sg.cs.setConservation(c);
- }
+ cs = viewport.getGlobalColourScheme().getInstance(viewport, sg);
+ sg.setColourScheme(cs);
+ sg.getGroupColourScheme().setThreshold(
+ viewport.getResidueShading().getThreshold(),
+ viewport.isIgnoreGapsConsensus());
- av.alignment.addGroup(sg);
+ if (viewport.getResidueShading().conservationApplied())
+ {
+ Conservation c = new Conservation("Group",
+ sg.getSequences(null), sg.getStartRes(),
+ sg.getEndRes());
+ c.calculate();
+ c.verdict(false, viewport.getConsPercGaps());
+ sg.cs.setConservation(c);
+ }
+ }
+ // indicate that associated structure views will need an update
+ viewport.setUpdateStructures(true);
+ // propagate structure view update and sequence group to complement view
+ viewport.addSequenceGroup(sg);
}
-
}
- /**
- * DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
- */
- public void setShowDistances(boolean state)
+ // notify the panel(s) to redo any group specific stuff
+ // also updates structure views if necessary
+ for (int a = 0; a < aps.length; a++)
{
- this.showDistances = state;
- repaint();
+ aps[a].updateAnnotation();
+ final AlignViewportI codingComplement = aps[a].av
+ .getCodingComplement();
+ if (codingComplement != null)
+ {
+ ((AlignViewport) codingComplement).getAlignPanel()
+ .updateAnnotation();
+ }
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
- */
- public void setShowBootstrap(boolean state)
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ public void setShowDistances(boolean state)
+ {
+ this.showDistances = state;
+ repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ public void setShowBootstrap(boolean state)
+ {
+ this.showBootstrap = state;
+ repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ public void setMarkPlaceholders(boolean state)
+ {
+ this.markPlaceholders = state;
+ repaint();
+ }
+
+ AlignmentPanel[] getAssociatedPanels()
+ {
+ if (applyToAllViews)
{
- this.showBootstrap = state;
- repaint();
+ return PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
}
-
- /**
- * DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
- */
- public void setMarkPlaceholders(boolean state)
+ else
{
- this.markPlaceholders = state;
- repaint();
+ return new AlignmentPanel[] { getAssociatedPanel() };
}
+ }
+
+ public AlignmentPanel getAssociatedPanel()
+ {
+ return ap;
+ }
+
+ public void setAssociatedPanel(AlignmentPanel ap)
+ {
+ this.ap = ap;
+ }
+
+ public AlignViewport getViewport()
+ {
+ return av;
+ }
+
+ public void setViewport(AlignViewport av)
+ {
+ this.av = av;
+ }
+
+ public float getThreshold()
+ {
+ return threshold;
+ }
+
+ public void setThreshold(float threshold)
+ {
+ this.threshold = threshold;
+ }
+
+ public boolean isApplyToAllViews()
+ {
+ return this.applyToAllViews;
+ }
+
+ public void setApplyToAllViews(boolean applyToAllViews)
+ {
+ this.applyToAllViews = applyToAllViews;
+ }
}
git://source.jalview.org / jalview.git / blobdiff