-/*
- * 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.appletgui;
-
-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.util.Format;
-import jalview.util.MappingUtils;
-import jalview.viewmodel.AlignmentViewport;
-
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Graphics;
-import javax.swing.JPanel;
-import java.awt.Point;
-import java.awt.Rectangle;
-import javax.swing.JScrollPane;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.MouseMotionListener;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Vector;
-
-public class TreeCanvas extends JPanel implements MouseListener,
- MouseMotionListener
-{
- NJTree tree;
-
- JScrollPane scrollPane;
-
- AlignViewport av;
-
- public static final String PLACEHOLDER = " * ";
-
- Font font;
-
- 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;
-
- AlignmentPanel ap;
-
- public TreeCanvas(AlignmentPanel ap, JScrollPane scroller)
- {
- this.ap = ap;
- this.av = ap.av;
- font = av.getFont();
- scrollPane = scroller;
- addMouseListener(this);
- addMouseMotionListener(this);
- setLayout(null);
-
- PaintRefresher.Register(this, av.getSequenceSetId());
- }
-
- public void treeSelectionChanged(SequenceI sequence)
- {
- SequenceGroup selected = av.getSelectionGroup();
- if (selected == null)
- {
- selected = new SequenceGroup();
- av.setSelectionGroup(selected);
- }
-
- selected.setEndRes(av.getAlignment().getWidth() - 1);
- selected.addOrRemove(sequence, true);
- }
-
- 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);
- }
-
- 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").formDouble(node.dist);
- }
- if (showBootstrap)
- {
- int btstrap = node.getBootstrap();
- if (btstrap > -1)
- {
- 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();
- FontMetrics fm = g.getFontMetrics(font);
- int charWidth = fm.stringWidth(name) + 3;
- int charHeight = fm.getHeight();
-
- Rectangle rect = new Rectangle(xend + 10, ypos - charHeight,
- 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 + 3, charWidth, charHeight);
- g.setColor(Color.white);
- }
- g.drawString(name, xend + 10, ypos);
- 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").formDouble(node.dist);
- }
-
- if (showBootstrap)
- {
- int btstrap = node.getBootstrap();
- if (btstrap > -1)
- {
- if (showDistances)
- {
- nodeLabel = nodeLabel + " : ";
- }
- nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
- }
- }
-
- if (!nodeLabel.equals(""))
- {
- g.drawString(nodeLabel, xstart + 2, ypos - 2);
- }
-
- }
- }
-
- 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;
-
- }
-
- public void pickNodes(Rectangle pickBox)
- {
- int width = getSize().width;
- int height = getSize().height;
-
- 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);
- }
-
- 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);
- }
- }
-
- public void setColor(SequenceNode node, Color c)
- {
- if (node == null)
- {
- return;
- }
-
- if (node.left() == null && node.right() == null)
- {
- node.color = c;
-
- 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);
- }
- }
-
- @Override
- public void update(Graphics g)
- {
- paint(g);
- }
-
- @Override
- public void paint(Graphics g)
- {
- if (tree == null)
- {
- return;
- }
-
- if (nameHash.size() == 0)
- {
- repaint();
- }
-
- int width = scrollPane.getSize().width;
- int height = scrollPane.getSize().height;
- if (!fitToWindow)
- {
- height = g.getFontMetrics(font).getHeight() * nameHash.size();
- }
-
- if (getSize().width > width)
- {
- setSize(new Dimension(width, height));
- scrollPane.validate();
- return;
- }
-
- setSize(new Dimension(width, height));
-
- g.setFont(font);
- draw(g, width, height);
- validate();
- }
-
- public void draw(Graphics g, int width, int height)
- {
- offy = font.getSize() + 10;
-
- g.setColor(Color.white);
- g.fillRect(0, 0, width, height);
-
- labelLength = g.getFontMetrics(font).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(g, tree.getTopNode(), chunk, wscale, width, offx, offy);
-
- if (threshold != 0)
- {
- if (av.getCurrentTree() == tree)
- {
- g.setColor(Color.red);
- }
- else
- {
- g.setColor(Color.gray);
- }
-
- int x = (int) (threshold * (getSize().width - labelLength - 2 * offx) + offx);
-
- g.drawLine(x, 0, x, getSize().height);
- }
-
- }
-
- @Override
- public void mouseReleased(MouseEvent e)
- {
- }
-
- @Override
- public void mouseEntered(MouseEvent e)
- {
- }
-
- @Override
- public void mouseExited(MouseEvent e)
- {
- }
-
- @Override
- public void mouseClicked(MouseEvent evt)
- {
- if (highlightNode != null)
- {
- 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);
- }
- }
-
- PaintRefresher.Refresh(this, av.getSequenceSetId());
- repaint();
- av.sendSelection();
- }
- }
-
- @Override
- public void mouseDragged(MouseEvent ect)
- {
- }
-
- @Override
- public void mouseMoved(MouseEvent evt)
- {
- av.setCurrentTree(tree);
-
- Object ob = findElement(evt.getX(), evt.getY());
-
- if (ob instanceof SequenceNode)
- {
- highlightNode = (SequenceNode) ob;
- repaint();
- }
- else
- {
- if (highlightNode != null)
- {
- highlightNode = null;
- repaint();
- }
- }
- }
-
- @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(this, av.getSequenceSetId());
- repaint();
- av.sendSelection();
- return;
- }
- else if (!(ob instanceof SequenceNode))
- {
- // Find threshold
-
- if (tree.getMaxHeight() != 0)
- {
- threshold = (float) (x - offx)
- / (float) (getSize().width - labelLength - 2 * offx);
-
- tree.getGroups().removeAllElements();
- tree.groupNodes(tree.getTopNode(), threshold);
- setColor(tree.getTopNode(), Color.black);
-
- av.setSelectionGroup(null);
- av.getAlignment().deleteAllGroups();
- av.clearSequenceColours();
- final AlignViewportI codingComplement = av.getCodingComplement();
- if (codingComplement != null)
- {
- codingComplement.setSelectionGroup(null);
- codingComplement.getAlignment().deleteAllGroups();
- codingComplement.clearSequenceColours();
- }
-
- colourGroups();
-
- }
- }
-
- PaintRefresher.Refresh(this, av.getSequenceSetId());
- repaint();
-
- }
-
- void colourGroups()
- {
- 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, "", 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());
- }
- }
- // TODO: cs used to be initialized with a sequence collection and
- // recalcConservation called automatically
- // instead we set it manually - recalc called after updateAnnotation
- sg.cs = cs;
-
- sg.setName("JTreeGroup:" + sg.hashCode());
- sg.setIdColour(col);
- if (av.getGlobalColourScheme() != null
- && av.getGlobalColourScheme().conservationApplied())
- {
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(null),
- sg.getStartRes(), sg.getEndRes());
-
- c.calculate();
- c.verdict(false, av.getConsPercGaps());
- cs.setConservation(c);
-
- sg.cs = cs;
-
- }
-
- av.getAlignment().addGroup(sg);
-
- // TODO this is duplicated with gui TreeCanvas - refactor
- 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())
- {
- // TODO why does gui require col.brighter() here??
- codingComplement.setSequenceColour(seq, col);
- }
- }
- }
-
- }
- ap.updateAnnotation();
- if (av.getCodingComplement() != null)
- {
- ((AlignmentViewport) av.getCodingComplement()).firePropertyChange(
- "alignment", null, ap.av.getAlignment().getSequences());
- }
- }
-
- public void setShowDistances(boolean state)
- {
- this.showDistances = state;
- repaint();
- }
-
- public void setShowBootstrap(boolean state)
- {
- this.showBootstrap = state;
- repaint();
- }
-
- public void setMarkPlaceholders(boolean state)
- {
- this.markPlaceholders = state;
- repaint();
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)\r
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ * The Jalview Authors are detailed in the 'AUTHORS' file.\r
+ */\r
+package jalview.appletgui;\r
+\r
+import jalview.analysis.Conservation;\r
+import jalview.analysis.NJTree;\r
+import jalview.api.AlignViewportI;\r
+import jalview.datamodel.Sequence;\r
+import jalview.datamodel.SequenceGroup;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.datamodel.SequenceNode;\r
+import jalview.schemes.ColourSchemeI;\r
+import jalview.schemes.ColourSchemeProperty;\r
+import jalview.schemes.ResidueProperties;\r
+import jalview.schemes.UserColourScheme;\r
+import jalview.util.Format;\r
+import jalview.util.MappingUtils;\r
+import jalview.viewmodel.AlignmentViewport;\r
+\r
+import java.awt.Color;\r
+import java.awt.Dimension;\r
+import java.awt.Font;\r
+import java.awt.FontMetrics;\r
+import java.awt.Graphics;\r
+import javax.swing.JPanel;\r
+import java.awt.Point;\r
+import java.awt.Rectangle;\r
+import javax.swing.JScrollPane;\r
+import java.awt.event.MouseEvent;\r
+import java.awt.event.MouseListener;\r
+import java.awt.event.MouseMotionListener;\r
+import java.util.Enumeration;\r
+import java.util.Hashtable;\r
+import java.util.Vector;\r
+\r
+public class TreeCanvas extends JPanel implements MouseListener,\r
+ MouseMotionListener\r
+{\r
+ NJTree tree;\r
+\r
+ JScrollPane scrollPane;\r
+\r
+ AlignViewport av;\r
+\r
+ public static final String PLACEHOLDER = " * ";\r
+\r
+ Font font;\r
+\r
+ boolean fitToWindow = true;\r
+\r
+ boolean showDistances = false;\r
+\r
+ boolean showBootstrap = false;\r
+\r
+ boolean markPlaceholders = false;\r
+\r
+ int offx = 20;\r
+\r
+ int offy;\r
+\r
+ float threshold;\r
+\r
+ String longestName;\r
+\r
+ int labelLength = -1;\r
+\r
+ Hashtable nameHash = new Hashtable();\r
+\r
+ Hashtable nodeHash = new Hashtable();\r
+\r
+ SequenceNode highlightNode;\r
+\r
+ AlignmentPanel ap;\r
+\r
+ public TreeCanvas(AlignmentPanel ap, JScrollPane scroller)\r
+ {\r
+ this.ap = ap;\r
+ this.av = ap.av;\r
+ font = av.getFont();\r
+ scrollPane = scroller;\r
+ addMouseListener(this);\r
+ addMouseMotionListener(this);\r
+ setLayout(null);\r
+\r
+ PaintRefresher.Register(this, av.getSequenceSetId());\r
+ }\r
+\r
+ public void treeSelectionChanged(SequenceI sequence)\r
+ {\r
+ SequenceGroup selected = av.getSelectionGroup();\r
+ if (selected == null)\r
+ {\r
+ selected = new SequenceGroup();\r
+ av.setSelectionGroup(selected);\r
+ }\r
+\r
+ selected.setEndRes(av.getAlignment().getWidth() - 1);\r
+ selected.addOrRemove(sequence, true);\r
+ }\r
+\r
+ public void setTree(NJTree tree)\r
+ {\r
+ this.tree = tree;\r
+ tree.findHeight(tree.getTopNode());\r
+\r
+ // Now have to calculate longest name based on the leaves\r
+ Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());\r
+ boolean has_placeholders = false;\r
+ longestName = "";\r
+\r
+ for (int i = 0; i < leaves.size(); i++)\r
+ {\r
+ SequenceNode lf = (SequenceNode) leaves.elementAt(i);\r
+\r
+ if (lf.isPlaceholder())\r
+ {\r
+ has_placeholders = true;\r
+ }\r
+\r
+ if (longestName.length() < ((Sequence) lf.element()).getName()\r
+ .length())\r
+ {\r
+ longestName = TreeCanvas.PLACEHOLDER\r
+ + ((Sequence) lf.element()).getName();\r
+ }\r
+ }\r
+\r
+ setMarkPlaceholders(has_placeholders);\r
+ }\r
+\r
+ public void drawNode(Graphics g, SequenceNode node, float chunk,\r
+ float scale, int width, int offx, int offy)\r
+ {\r
+ if (node == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (node.left() == null && node.right() == null)\r
+ {\r
+ // Drawing leaf node\r
+\r
+ float height = node.height;\r
+ float dist = node.dist;\r
+\r
+ int xstart = (int) ((height - dist) * scale) + offx;\r
+ int xend = (int) (height * scale) + offx;\r
+\r
+ int ypos = (int) (node.ycount * chunk) + offy;\r
+\r
+ if (node.element() instanceof SequenceI)\r
+ {\r
+ SequenceI seq = (SequenceI) node.element();\r
+\r
+ if (av.getSequenceColour(seq) == Color.white)\r
+ {\r
+ g.setColor(Color.black);\r
+ }\r
+ else\r
+ {\r
+ g.setColor(av.getSequenceColour(seq).darker());\r
+ }\r
+\r
+ }\r
+ else\r
+ {\r
+ g.setColor(Color.black);\r
+ }\r
+\r
+ // Draw horizontal line\r
+ g.drawLine(xstart, ypos, xend, ypos);\r
+\r
+ String nodeLabel = "";\r
+ if (showDistances && node.dist > 0)\r
+ {\r
+ nodeLabel = new Format("%-.2f").formDouble(node.dist);\r
+ }\r
+ if (showBootstrap)\r
+ {\r
+ int btstrap = node.getBootstrap();\r
+ if (btstrap > -1)\r
+ {\r
+ if (showDistances)\r
+ {\r
+ nodeLabel = nodeLabel + " : ";\r
+ }\r
+ nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());\r
+ }\r
+ }\r
+ if (!nodeLabel.equals(""))\r
+ {\r
+ g.drawString(nodeLabel, xstart + 2, ypos - 2);\r
+ }\r
+\r
+ String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node\r
+ .getName()) : node.getName();\r
+ FontMetrics fm = g.getFontMetrics(font);\r
+ int charWidth = fm.stringWidth(name) + 3;\r
+ int charHeight = fm.getHeight();\r
+\r
+ Rectangle rect = new Rectangle(xend + 10, ypos - charHeight,\r
+ charWidth, charHeight);\r
+\r
+ nameHash.put(node.element(), rect);\r
+\r
+ // Colour selected leaves differently\r
+ SequenceGroup selected = av.getSelectionGroup();\r
+ if (selected != null\r
+ && selected.getSequences(null).contains(node.element()))\r
+ {\r
+ g.setColor(Color.gray);\r
+\r
+ g.fillRect(xend + 10, ypos - charHeight + 3, charWidth, charHeight);\r
+ g.setColor(Color.white);\r
+ }\r
+ g.drawString(name, xend + 10, ypos);\r
+ g.setColor(Color.black);\r
+ }\r
+ else\r
+ {\r
+ drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx,\r
+ offy);\r
+ drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,\r
+ offy);\r
+\r
+ float height = node.height;\r
+ float dist = node.dist;\r
+\r
+ int xstart = (int) ((height - dist) * scale) + offx;\r
+ int xend = (int) (height * scale) + offx;\r
+ int ypos = (int) (node.ycount * chunk) + offy;\r
+\r
+ g.setColor(node.color.darker());\r
+\r
+ // Draw horizontal line\r
+ g.drawLine(xstart, ypos, xend, ypos);\r
+ if (node == highlightNode)\r
+ {\r
+ g.fillRect(xend - 3, ypos - 3, 6, 6);\r
+ }\r
+ else\r
+ {\r
+ g.fillRect(xend - 2, ypos - 2, 4, 4);\r
+ }\r
+\r
+ int ystart = (int) (((SequenceNode) node.left()).ycount * chunk)\r
+ + offy;\r
+ int yend = (int) (((SequenceNode) node.right()).ycount * chunk)\r
+ + offy;\r
+\r
+ Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);\r
+ nodeHash.put(node, pos);\r
+\r
+ g.drawLine((int) (height * scale) + offx, ystart,\r
+ (int) (height * scale) + offx, yend);\r
+\r
+ String nodeLabel = "";\r
+\r
+ if (showDistances && (node.dist > 0))\r
+ {\r
+ nodeLabel = new Format("%-.2f").formDouble(node.dist);\r
+ }\r
+\r
+ if (showBootstrap)\r
+ {\r
+ int btstrap = node.getBootstrap();\r
+ if (btstrap > -1)\r
+ {\r
+ if (showDistances)\r
+ {\r
+ nodeLabel = nodeLabel + " : ";\r
+ }\r
+ nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());\r
+ }\r
+ }\r
+\r
+ if (!nodeLabel.equals(""))\r
+ {\r
+ g.drawString(nodeLabel, xstart + 2, ypos - 2);\r
+ }\r
+\r
+ }\r
+ }\r
+\r
+ public Object findElement(int x, int y)\r
+ {\r
+ Enumeration keys = nameHash.keys();\r
+\r
+ while (keys.hasMoreElements())\r
+ {\r
+ Object ob = keys.nextElement();\r
+ Rectangle rect = (Rectangle) nameHash.get(ob);\r
+\r
+ if (x >= rect.x && x <= (rect.x + rect.width) && y >= rect.y\r
+ && y <= (rect.y + rect.height))\r
+ {\r
+ return ob;\r
+ }\r
+ }\r
+ keys = nodeHash.keys();\r
+\r
+ while (keys.hasMoreElements())\r
+ {\r
+ Object ob = keys.nextElement();\r
+ Rectangle rect = (Rectangle) nodeHash.get(ob);\r
+\r
+ if (x >= rect.x && x <= (rect.x + rect.width) && y >= rect.y\r
+ && y <= (rect.y + rect.height))\r
+ {\r
+ return ob;\r
+ }\r
+ }\r
+ return null;\r
+\r
+ }\r
+\r
+ public void pickNodes(Rectangle pickBox)\r
+ {\r
+ int width = getSize().width;\r
+ int height = getSize().height;\r
+\r
+ SequenceNode top = tree.getTopNode();\r
+\r
+ float wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight();\r
+ if (top.count == 0)\r
+ {\r
+ top.count = ((SequenceNode) top.left()).count\r
+ + ((SequenceNode) top.right()).count;\r
+ }\r
+ float chunk = (float) (height - offy) / top.count;\r
+\r
+ pickNode(pickBox, top, chunk, wscale, width, offx, offy);\r
+ }\r
+\r
+ public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,\r
+ float scale, int width, int offx, int offy)\r
+ {\r
+ if (node == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (node.left() == null && node.right() == null)\r
+ {\r
+ float height = node.height;\r
+ // float dist = node.dist;\r
+\r
+ // int xstart = (int) ( (height - dist) * scale) + offx;\r
+ int xend = (int) (height * scale) + offx;\r
+\r
+ int ypos = (int) (node.ycount * chunk) + offy;\r
+\r
+ if (pickBox.contains(new Point(xend, ypos)))\r
+ {\r
+ if (node.element() instanceof SequenceI)\r
+ {\r
+ SequenceI seq = (SequenceI) node.element();\r
+ SequenceGroup sg = av.getSelectionGroup();\r
+ if (sg != null)\r
+ {\r
+ sg.addOrRemove(seq, true);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width,\r
+ offx, offy);\r
+ pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,\r
+ offx, offy);\r
+ }\r
+ }\r
+\r
+ public void setColor(SequenceNode node, Color c)\r
+ {\r
+ if (node == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (node.left() == null && node.right() == null)\r
+ {\r
+ node.color = c;\r
+\r
+ if (node.element() instanceof SequenceI)\r
+ {\r
+ av.setSequenceColour((SequenceI) node.element(), c);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ node.color = c;\r
+ setColor((SequenceNode) node.left(), c);\r
+ setColor((SequenceNode) node.right(), c);\r
+ }\r
+ }\r
+\r
+ @Override\r
+ public void update(Graphics g)\r
+ {\r
+ paint(g);\r
+ }\r
+\r
+ @Override\r
+ public void paint(Graphics g)\r
+ {\r
+ if (tree == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (nameHash.size() == 0)\r
+ {\r
+ repaint();\r
+ }\r
+\r
+ int width = scrollPane.getSize().width;\r
+ int height = scrollPane.getSize().height;\r
+ if (!fitToWindow)\r
+ {\r
+ height = g.getFontMetrics(font).getHeight() * nameHash.size();\r
+ }\r
+\r
+ if (getSize().width > width)\r
+ {\r
+ setSize(new Dimension(width, height));\r
+ scrollPane.validate();\r
+ return;\r
+ }\r
+\r
+ setSize(new Dimension(width, height));\r
+\r
+ g.setFont(font);\r
+ draw(g, width, height);\r
+ validate();\r
+ }\r
+\r
+ public void draw(Graphics g, int width, int height)\r
+ {\r
+ offy = font.getSize() + 10;\r
+\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, width, height);\r
+\r
+ labelLength = g.getFontMetrics(font).stringWidth(longestName) + 20; // 20\r
+ // allows\r
+ // for\r
+ // scrollbar\r
+\r
+ float wscale = (width - labelLength - offx * 2) / tree.getMaxHeight();\r
+\r
+ SequenceNode top = tree.getTopNode();\r
+\r
+ if (top.count == 0)\r
+ {\r
+ top.count = ((SequenceNode) top.left()).count\r
+ + ((SequenceNode) top.right()).count;\r
+ }\r
+ float chunk = (float) (height - offy) / top.count;\r
+\r
+ drawNode(g, tree.getTopNode(), chunk, wscale, width, offx, offy);\r
+\r
+ if (threshold != 0)\r
+ {\r
+ if (av.getCurrentTree() == tree)\r
+ {\r
+ g.setColor(Color.red);\r
+ }\r
+ else\r
+ {\r
+ g.setColor(Color.gray);\r
+ }\r
+\r
+ int x = (int) (threshold * (getSize().width - labelLength - 2 * offx) + offx);\r
+\r
+ g.drawLine(x, 0, x, getSize().height);\r
+ }\r
+\r
+ }\r
+\r
+ @Override\r
+ public void mouseReleased(MouseEvent e)\r
+ {\r
+ }\r
+\r
+ @Override\r
+ public void mouseEntered(MouseEvent e)\r
+ {\r
+ }\r
+\r
+ @Override\r
+ public void mouseExited(MouseEvent e)\r
+ {\r
+ }\r
+\r
+ @Override\r
+ public void mouseClicked(MouseEvent evt)\r
+ {\r
+ if (highlightNode != null)\r
+ {\r
+ if (evt.getClickCount() > 1)\r
+ {\r
+ tree.swapNodes(highlightNode);\r
+ tree.reCount(tree.getTopNode());\r
+ tree.findHeight(tree.getTopNode());\r
+ }\r
+ else\r
+ {\r
+ Vector leaves = new Vector();\r
+ tree.findLeaves(highlightNode, leaves);\r
+\r
+ for (int i = 0; i < leaves.size(); i++)\r
+ {\r
+ SequenceI seq = (SequenceI) ((SequenceNode) leaves.elementAt(i))\r
+ .element();\r
+ treeSelectionChanged(seq);\r
+ }\r
+ }\r
+\r
+ PaintRefresher.Refresh(this, av.getSequenceSetId());\r
+ repaint();\r
+ av.sendSelection();\r
+ }\r
+ }\r
+\r
+ @Override\r
+ public void mouseDragged(MouseEvent ect)\r
+ {\r
+ }\r
+\r
+ @Override\r
+ public void mouseMoved(MouseEvent evt)\r
+ {\r
+ av.setCurrentTree(tree);\r
+\r
+ Object ob = findElement(evt.getX(), evt.getY());\r
+\r
+ if (ob instanceof SequenceNode)\r
+ {\r
+ highlightNode = (SequenceNode) ob;\r
+ repaint();\r
+ }\r
+ else\r
+ {\r
+ if (highlightNode != null)\r
+ {\r
+ highlightNode = null;\r
+ repaint();\r
+ }\r
+ }\r
+ }\r
+\r
+ @Override\r
+ public void mousePressed(MouseEvent e)\r
+ {\r
+ av.setCurrentTree(tree);\r
+\r
+ int x = e.getX();\r
+ int y = e.getY();\r
+\r
+ Object ob = findElement(x, y);\r
+\r
+ if (ob instanceof SequenceI)\r
+ {\r
+ treeSelectionChanged((Sequence) ob);\r
+ PaintRefresher.Refresh(this, av.getSequenceSetId());\r
+ repaint();\r
+ av.sendSelection();\r
+ return;\r
+ }\r
+ else if (!(ob instanceof SequenceNode))\r
+ {\r
+ // Find threshold\r
+\r
+ if (tree.getMaxHeight() != 0)\r
+ {\r
+ threshold = (float) (x - offx)\r
+ / (float) (getSize().width - labelLength - 2 * offx);\r
+\r
+ tree.getGroups().removeAllElements();\r
+ tree.groupNodes(tree.getTopNode(), threshold);\r
+ setColor(tree.getTopNode(), Color.black);\r
+\r
+ av.setSelectionGroup(null);\r
+ av.getAlignment().deleteAllGroups();\r
+ av.clearSequenceColours();\r
+ final AlignViewportI codingComplement = av.getCodingComplement();\r
+ if (codingComplement != null)\r
+ {\r
+ codingComplement.setSelectionGroup(null);\r
+ codingComplement.getAlignment().deleteAllGroups();\r
+ codingComplement.clearSequenceColours();\r
+ }\r
+\r
+ colourGroups();\r
+\r
+ }\r
+ }\r
+\r
+ PaintRefresher.Refresh(this, av.getSequenceSetId());\r
+ repaint();\r
+\r
+ }\r
+\r
+ void colourGroups()\r
+ {\r
+ for (int i = 0; i < tree.getGroups().size(); i++)\r
+ {\r
+\r
+ Color col = new Color((int) (Math.random() * 255),\r
+ (int) (Math.random() * 255), (int) (Math.random() * 255));\r
+ setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter());\r
+\r
+ Vector l = tree.findLeaves(\r
+ (SequenceNode) tree.getGroups().elementAt(i), new Vector());\r
+\r
+ Vector sequences = new Vector();\r
+ for (int j = 0; j < l.size(); j++)\r
+ {\r
+ SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j))\r
+ .element();\r
+ if (!sequences.contains(s1))\r
+ {\r
+ sequences.addElement(s1);\r
+ }\r
+ }\r
+\r
+ ColourSchemeI cs = null;\r
+\r
+ SequenceGroup sg = new SequenceGroup(sequences, "", cs, true, true,\r
+ false, 0, av.getAlignment().getWidth() - 1);\r
+\r
+ if (av.getGlobalColourScheme() != null)\r
+ {\r
+ if (av.getGlobalColourScheme() instanceof UserColourScheme)\r
+ {\r
+ cs = new UserColourScheme(\r
+ ((UserColourScheme) av.getGlobalColourScheme())\r
+ .getColours());\r
+\r
+ }\r
+ else\r
+ {\r
+ cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty\r
+ .getColourName(av.getGlobalColourScheme()));\r
+ }\r
+ // cs is null if shading is an annotationColourGradient\r
+ if (cs != null)\r
+ {\r
+ cs.setThreshold(av.getGlobalColourScheme().getThreshold(),\r
+ av.isIgnoreGapsConsensus());\r
+ }\r
+ }\r
+ // TODO: cs used to be initialized with a sequence collection and\r
+ // recalcConservation called automatically\r
+ // instead we set it manually - recalc called after updateAnnotation\r
+ sg.cs = cs;\r
+\r
+ sg.setName("JTreeGroup:" + sg.hashCode());\r
+ sg.setIdColour(col);\r
+ if (av.getGlobalColourScheme() != null\r
+ && av.getGlobalColourScheme().conservationApplied())\r
+ {\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3, sg.getSequences(null),\r
+ sg.getStartRes(), sg.getEndRes());\r
+\r
+ c.calculate();\r
+ c.verdict(false, av.getConsPercGaps());\r
+ cs.setConservation(c);\r
+\r
+ sg.cs = cs;\r
+\r
+ }\r
+\r
+ av.getAlignment().addGroup(sg);\r
+\r
+ // TODO this is duplicated with gui TreeCanvas - refactor\r
+ av.getAlignment().addGroup(sg);\r
+ final AlignViewportI codingComplement = av.getCodingComplement();\r
+ if (codingComplement != null)\r
+ {\r
+ SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, av,\r
+ codingComplement);\r
+ if (mappedGroup.getSequences().size() > 0)\r
+ {\r
+ codingComplement.getAlignment().addGroup(mappedGroup);\r
+ for (SequenceI seq : mappedGroup.getSequences())\r
+ {\r
+ // TODO why does gui require col.brighter() here??\r
+ codingComplement.setSequenceColour(seq, col);\r
+ }\r
+ }\r
+ }\r
+\r
+ }\r
+ ap.updateAnnotation();\r
+ if (av.getCodingComplement() != null)\r
+ {\r
+ ((AlignmentViewport) av.getCodingComplement()).firePropertyChange(\r
+ "alignment", null, ap.av.getAlignment().getSequences());\r
+ }\r
+ }\r
+\r
+ public void setShowDistances(boolean state)\r
+ {\r
+ this.showDistances = state;\r
+ repaint();\r
+ }\r
+\r
+ public void setShowBootstrap(boolean state)\r
+ {\r
+ this.showBootstrap = state;\r
+ repaint();\r
+ }\r
+\r
+ public void setMarkPlaceholders(boolean state)\r
+ {\r
+ this.markPlaceholders = state;\r
+ repaint();\r
+ }\r
+\r
+}\r
git://source.jalview.org / jalviewjs.git / blobdiff