+++ /dev/null
-/*
- * 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.
- *
- * 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 <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.gui;
-
-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, 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!
- */
- public TreeCanvas(TreePanel tp, AlignmentPanel ap, JScrollPane scroller)
- {
- this.tp = tp;
- this.av = ap.av;
- this.ap = 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++)
- {
- SequenceGroup selected = aps[a].av.getSelectionGroup();
-
- if (selected == null)
- {
- selected = new SequenceGroup();
- aps[a].av.setSelectionGroup(selected);
- }
-
- selected.setEndRes(aps[a].av.getAlignment().getWidth() - 1);
- selected.addOrRemove(sequence, true);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param tree
- * DOCUMENT ME!
- */
- public void setTree(NJTree tree)
- {
- this.tree = tree;
- tree.findHeight(tree.getTopNode());
-
- // Now have to calculate longest name based on the leaves
- Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
- boolean has_placeholders = false;
- longestName = "";
-
- for (int i = 0; i < leaves.size(); i++)
- {
- SequenceNode lf = (SequenceNode) leaves.elementAt(i);
-
- if (lf.isPlaceholder())
- {
- has_placeholders = true;
- }
-
- if (longestName.length() < ((Sequence) lf.element()).getName()
- .length())
- {
- longestName = TreeCanvas.PLACEHOLDER
- + ((Sequence) lf.element()).getName();
- }
- }
-
- setMarkPlaceholders(has_placeholders);
- }
-
- /**
- * 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 == null)
- {
- return;
- }
-
- 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 xend = (int) (height * scale) + offx;
-
- int ypos = (int) (node.ycount * chunk) + offy;
-
- if (node.element() instanceof SequenceI)
- {
- SequenceI seq = (SequenceI) 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 && node.bootstrap > -1)
- {
- if (showDistances)
- {
- nodeLabel = nodeLabel + " : ";
- }
-
- nodeLabel = nodeLabel + String.valueOf(node.bootstrap);
- }
-
- 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
- {
- 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(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);
-
- String nodeLabel = "";
-
- if (showDistances && (node.dist > 0))
- {
- nodeLabel = new Format("%-.2f").form(node.dist);
- }
-
- if (showBootstrap && node.bootstrap > -1)
- {
- if (showDistances)
- {
- nodeLabel = nodeLabel + " : ";
- }
-
- nodeLabel = nodeLabel + String.valueOf(node.bootstrap);
- }
-
- if (!nodeLabel.equals(""))
- {
- g.drawString(nodeLabel, xstart + 2, ypos - 2);
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param x
- * DOCUMENT ME!
- * @param y
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Object findElement(int x, int y)
- {
- Enumeration keys = nameHash.keys();
-
- 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;
- }
- }
-
- keys = nodeHash.keys();
-
- while (keys.hasMoreElements())
- {
- 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;
- }
- }
-
- return null;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param pickBox
- * DOCUMENT ME!
- */
- public void pickNodes(Rectangle pickBox)
- {
- int width = getWidth();
- int height = getHeight();
-
- SequenceNode top = tree.getTopNode();
-
- float wscale = (float) ((width * .8) - (offx * 2))
- / tree.getMaxHeight();
-
- if (top.count == 0)
- {
- top.count = ((SequenceNode) top.left()).count
- + ((SequenceNode) top.right()).count;
- }
-
- float chunk = (float) (height - (offy)) / top.count;
-
- pickNode(pickBox, top, chunk, wscale, width, offx, 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)
- {
- if (node == null)
- {
- return;
- }
-
- 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);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param node
- * DOCUMENT ME!
- * @param c
- * DOCUMENT ME!
- */
- public void setColor(SequenceNode node, Color c)
- {
- if (node == null)
- {
- return;
- }
-
- if ((node.left() == null) && (node.right() == null)) // TODO: internal node
- {
- node.color = c;
-
- if (node.element() instanceof SequenceI)
- {
- AlignmentPanel[] aps = getAssociatedPanels();
- if (aps != null)
- {
- 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);
- }
- }
-
- /**
- * DOCUMENT ME!
- */
- void startPrinting()
- {
- Thread thread = new Thread(this);
- thread.start();
- }
-
- // put printing in a thread to avoid painting problems
- @Override
- public void run()
- {
- PrinterJob printJob = PrinterJob.getPrinterJob();
- PageFormat pf = printJob.pageDialog(printJob.defaultPage());
-
- printJob.setPrintable(this, pf);
-
- if (printJob.printDialog())
- {
- try
- {
- printJob.print();
- } catch (Exception PrintException)
- {
- PrintException.printStackTrace();
- }
- }
- }
-
- /**
- * 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 (pwidth > getWidth())
- {
- pwidth = getWidth();
- }
-
- if (fitToWindow)
- {
- if (pheight > getHeight())
- {
- pheight = getHeight();
- }
-
- 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);
-
- 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)
- {
- g.drawString(MessageManager.getString("label.calculating_tree")
- + "....", 20, getHeight() / 2);
- }
- else
- {
- fm = g.getFontMetrics(font);
-
- if (nameHash.size() == 0)
- {
- repaint();
- }
-
- 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());
- }
-
- scrollPane.revalidate();
- }
- }
-
- /**
- * 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.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
-
- 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;
- }
-
- float chunk = (float) (height - (offy)) / top.count;
-
- 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);
- }
-
- int x = (int) ((threshold * (getWidth() - labelLength - (2 * offx))) + offx);
-
- g2.drawLine(x, 0, x, getHeight());
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void mouseReleased(MouseEvent e)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void mouseEntered(MouseEvent e)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void mouseExited(MouseEvent e)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void mouseClicked(MouseEvent evt)
- {
- if (highlightNode != null)
- {
- if (SwingUtilities.isRightMouseButton(evt))
- {
- Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_subtree_colour"),
- highlightNode.color);
- if (col != null)
- {
- 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) ((SequenceNode) leaves.elementAt(i))
- .element();
- treeSelectionChanged(seq);
- }
- av.sendSelection();
- }
-
- PaintRefresher.Refresh(tp, av.getSequenceSetId());
- repaint();
- }
- }
-
- @Override
- public void mouseMoved(MouseEvent evt)
- {
- av.setCurrentTree(tree);
-
- Object ob = findElement(evt.getX(), evt.getY());
-
- if (ob instanceof SequenceNode)
- {
- highlightNode = (SequenceNode) ob;
- this.setToolTipText("<html>"
- + MessageManager.getString("label.highlightnode"));
- repaint();
-
- }
- else
- {
- if (highlightNode != null)
- {
- highlightNode = null;
- setToolTipText(null);
- repaint();
- }
- }
- }
-
- @Override
- public void mouseDragged(MouseEvent ect)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void mousePressed(MouseEvent e)
- {
- av.setCurrentTree(tree);
-
- int x = e.getX();
- int y = e.getY();
-
- Object ob = findElement(x, y);
-
- if (ob instanceof SequenceI)
- {
- treeSelectionChanged((Sequence) ob);
- PaintRefresher.Refresh(tp, ap.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));
-
- tree.getGroups().removeAllElements();
- tree.groupNodes(tree.getTopNode(), threshold);
- setColor(tree.getTopNode(), Color.black);
-
- 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 (aps[a].av.getCodingComplement() != null)
- {
- aps[a].av.getCodingComplement().setSelectionGroup(null);
- aps[a].av.getCodingComplement().getAlignment()
- .deleteAllGroups();
- aps[a].av.getCodingComplement().clearSequenceColours();
- }
- }
- colourGroups();
- }
-
- PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
- repaint();
- }
-
- }
-
- 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());
-
- 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();
-
- if (!sequences.contains(s1))
- {
- sequences.addElement(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());
-
- }
- else
- {
- 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());
- }
- }
- 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
- && aps[a].av.getGlobalColourScheme().conservationApplied())
- {
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(null),
- sg.getStartRes(), sg.getEndRes());
-
- c.calculate();
- c.verdict(false, aps[a].av.getConsPercGaps());
- sg.cs.setConservation(c);
- }
-
- aps[a].av.getAlignment().addGroup(new SequenceGroup(sg));
- // TODO can we push all of the below into AlignViewportI?
- final AlignViewportI codingComplement = aps[a].av
- .getCodingComplement();
- if (codingComplement != null)
- {
- 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(s) 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
- final AlignViewportI codingComplement = aps[a].av
- .getCodingComplement();
- if (codingComplement != null)
- {
- ((AlignViewport) codingComplement).getAlignPanel()
- .updateAnnotation();
-
- }
-
- }
-
- }
-
- /**
- * 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)
- {
- return PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
- }
- else
- {
- return new AlignmentPanel[] { ap };
- }
- }
-}
git://source.jalview.org / jalview.git / blobdiff