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package jalview.appletgui; |
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import jalview.analysis.Conservation; |
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import jalview.analysis.TreeModel; |
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import jalview.api.AlignViewportI; |
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import jalview.datamodel.BinaryNode; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceGroup; |
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import jalview.datamodel.SequenceI; |
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import jalview.datamodel.SequenceNode; |
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import jalview.schemes.ColourSchemeI; |
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import jalview.schemes.ColourSchemeProperty; |
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import jalview.schemes.UserColourScheme; |
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import jalview.util.Format; |
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import jalview.util.MappingUtils; |
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import jalview.viewmodel.AlignmentViewport; |
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import java.awt.Color; |
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import java.awt.Dimension; |
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import java.awt.Font; |
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import java.awt.FontMetrics; |
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import java.awt.Graphics; |
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import java.awt.Panel; |
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import java.awt.Point; |
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import java.awt.Rectangle; |
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import java.awt.ScrollPane; |
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import java.awt.event.MouseEvent; |
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import java.awt.event.MouseListener; |
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import java.awt.event.MouseMotionListener; |
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import java.util.Enumeration; |
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import java.util.Hashtable; |
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import java.util.List; |
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import java.util.Vector; |
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| 0% |
Uncovered Elements: 403 (403) |
Complexity: 99 |
Complexity Density: 0.38 |
|
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public class TreeCanvas extends Panel |
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implements MouseListener, MouseMotionListener |
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{ |
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TreeModel tree; |
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ScrollPane scrollPane; |
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AlignViewport av; |
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|
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public static final String PLACEHOLDER = " * "; |
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|
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Font font; |
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|
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boolean fitToWindow = true; |
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boolean showDistances = false; |
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|
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boolean showBootstrap = false; |
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|
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boolean markPlaceholders = false; |
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|
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int offx = 20; |
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|
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int offy; |
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|
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float threshold; |
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|
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String longestName; |
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|
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int labelLength = -1; |
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|
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Hashtable nameHash = new Hashtable(); |
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Hashtable nodeHash = new Hashtable(); |
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|
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BinaryNode highlightNode; |
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|
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AlignmentPanel ap; |
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| 0% |
Uncovered Elements: 8 (8) |
Complexity: 1 |
Complexity Density: 0.12 |
|
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0 |
public TreeCanvas(AlignmentPanel ap, ScrollPane scroller)... |
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{ |
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this.ap = ap; |
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this.av = ap.av; |
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font = av.getFont(); |
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0 |
scrollPane = scroller; |
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addMouseListener(this); |
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addMouseMotionListener(this); |
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setLayout(null); |
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|
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PaintRefresher.Register(this, av.getSequenceSetId()); |
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} |
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| 0% |
Uncovered Elements: 8 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
107 |
0 |
public void treeSelectionChanged(SequenceI sequence)... |
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{ |
109 |
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SequenceGroup selected = av.getSelectionGroup(); |
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if (selected == null) |
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{ |
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selected = new SequenceGroup(); |
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av.setSelectionGroup(selected); |
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} |
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|
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selected.setEndRes(av.getAlignment().getWidth() - 1); |
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0 |
selected.addOrRemove(sequence, true); |
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} |
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| 0% |
Uncovered Elements: 18 (18) |
Complexity: 5 |
Complexity Density: 0.42 |
|
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public void setTree(TreeModel tree2)... |
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{ |
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this.tree = tree2; |
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tree2.findHeight(tree2.getTopNode()); |
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|
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|
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Vector<BinaryNode> leaves = tree2.findLeaves(tree2.getTopNode()); |
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boolean has_placeholders = false; |
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longestName = ""; |
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|
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for (int i = 0; i < leaves.size(); i++) |
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{ |
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BinaryNode lf = leaves.elementAt(i); |
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|
134 |
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if (lf instanceof SequenceNode && ((SequenceNode) lf).isPlaceholder()) |
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{ |
136 |
0 |
has_placeholders = true; |
137 |
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} |
138 |
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|
139 |
0 |
if (longestName.length() < ((Sequence) lf.element()).getName() |
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.length()) |
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{ |
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longestName = TreeCanvas.PLACEHOLDER |
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+ ((Sequence) lf.element()).getName(); |
144 |
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} |
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} |
146 |
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|
147 |
0 |
setMarkPlaceholders(has_placeholders); |
148 |
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} |
149 |
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| 0% |
Uncovered Elements: 105 (105) |
Complexity: 26 |
Complexity Density: 0.39 |
|
150 |
0 |
public void drawNode(Graphics g, BinaryNode node, float chunk,... |
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double scale, int width, int offx, int offy) |
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{ |
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0 |
if (node == null) |
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{ |
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return; |
156 |
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} |
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|
158 |
0 |
if (node.left() == null && node.right() == null) |
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{ |
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double height = node.height; |
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double dist = node.dist; |
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int xstart = (int) ((height - dist) * scale) + offx; |
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int xend = (int) (height * scale) + offx; |
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|
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int ypos = (int) (node.ycount * chunk) + offy; |
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|
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if (node.element() instanceof SequenceI) |
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{ |
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SequenceI seq = (SequenceI) node.element(); |
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|
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if (av.getSequenceColour(seq) == Color.white) |
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{ |
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g.setColor(Color.black); |
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} |
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else |
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{ |
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g.setColor(av.getSequenceColour(seq).darker()); |
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} |
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} |
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else |
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{ |
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g.setColor(Color.black); |
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} |
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g.drawLine(xstart, ypos, xend, ypos); |
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String nodeLabel = ""; |
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if (showDistances && node.dist > 0) |
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{ |
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nodeLabel = new Format("%-.2f").form(node.dist); |
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} |
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if (showBootstrap) |
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{ |
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int btstrap = node.getBootstrap(); |
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0 |
if (btstrap > -1) |
201 |
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{ |
202 |
0 |
if (showDistances) |
203 |
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{ |
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0 |
nodeLabel = nodeLabel + " : "; |
205 |
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} |
206 |
0 |
nodeLabel = nodeLabel + String.valueOf(node.getBootstrap()); |
207 |
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} |
208 |
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} |
209 |
0 |
if (!nodeLabel.equals("")) |
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{ |
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0 |
g.drawString(nodeLabel, xstart + 2, ypos - 2); |
212 |
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} |
213 |
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|
214 |
0 |
String name = (markPlaceholders && node instanceof SequenceNode |
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&& ((SequenceNode) node).isPlaceholder()) |
216 |
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? (PLACEHOLDER + node.getName()) |
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: node.getName(); |
218 |
0 |
FontMetrics fm = g.getFontMetrics(font); |
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0 |
int charWidth = fm.stringWidth(name) + 3; |
220 |
0 |
int charHeight = fm.getHeight(); |
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|
222 |
0 |
Rectangle rect = new Rectangle(xend + 10, ypos - charHeight, |
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charWidth, charHeight); |
224 |
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|
225 |
0 |
nameHash.put(node.element(), rect); |
226 |
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|
227 |
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|
228 |
0 |
SequenceGroup selected = av.getSelectionGroup(); |
229 |
0 |
if (selected != null |
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&& selected.getSequences(null).contains(node.element())) |
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{ |
232 |
0 |
g.setColor(Color.gray); |
233 |
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|
234 |
0 |
g.fillRect(xend + 10, ypos - charHeight + 3, charWidth, charHeight); |
235 |
0 |
g.setColor(Color.white); |
236 |
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} |
237 |
0 |
g.drawString(name, xend + 10, ypos); |
238 |
0 |
g.setColor(Color.black); |
239 |
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} |
240 |
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else |
241 |
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{ |
242 |
0 |
drawNode(g, (BinaryNode) node.left(), chunk, scale, width, offx, |
243 |
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offy); |
244 |
0 |
drawNode(g, (BinaryNode) node.right(), chunk, scale, width, offx, |
245 |
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offy); |
246 |
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|
247 |
0 |
double height = node.height; |
248 |
0 |
double dist = node.dist; |
249 |
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|
250 |
0 |
int xstart = (int) ((height - dist) * scale) + offx; |
251 |
0 |
int xend = (int) (height * scale) + offx; |
252 |
0 |
int ypos = (int) (node.ycount * chunk) + offy; |
253 |
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|
254 |
0 |
g.setColor(node.color.darker()); |
255 |
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|
256 |
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|
257 |
0 |
g.drawLine(xstart, ypos, xend, ypos); |
258 |
0 |
if (node == highlightNode) |
259 |
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{ |
260 |
0 |
g.fillRect(xend - 3, ypos - 3, 6, 6); |
261 |
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} |
262 |
|
else |
263 |
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{ |
264 |
0 |
g.fillRect(xend - 2, ypos - 2, 4, 4); |
265 |
|
} |
266 |
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|
267 |
0 |
int ystart = (int) (node.left() == null ? 0 |
268 |
|
: (((BinaryNode) node.left()).ycount * chunk)) + offy; |
269 |
0 |
int yend = (int) (node.right() == null ? 0 |
270 |
|
: (((BinaryNode) node.right()).ycount * chunk)) + offy; |
271 |
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|
272 |
0 |
Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5); |
273 |
0 |
nodeHash.put(node, pos); |
274 |
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|
275 |
0 |
g.drawLine((int) (height * scale) + offx, ystart, |
276 |
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(int) (height * scale) + offx, yend); |
277 |
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|
278 |
0 |
String nodeLabel = ""; |
279 |
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|
280 |
0 |
if (showDistances && (node.dist > 0)) |
281 |
|
{ |
282 |
0 |
nodeLabel = new Format("%-.2f").form(node.dist); |
283 |
|
} |
284 |
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|
285 |
0 |
if (showBootstrap) |
286 |
|
{ |
287 |
0 |
int btstrap = node.getBootstrap(); |
288 |
0 |
if (btstrap > -1) |
289 |
|
{ |
290 |
0 |
if (showDistances) |
291 |
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{ |
292 |
0 |
nodeLabel = nodeLabel + " : "; |
293 |
|
} |
294 |
0 |
nodeLabel = nodeLabel + String.valueOf(node.getBootstrap()); |
295 |
|
} |
296 |
|
} |
297 |
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|
298 |
0 |
if (!nodeLabel.equals("")) |
299 |
|
{ |
300 |
0 |
g.drawString(nodeLabel, xstart + 2, ypos - 2); |
301 |
|
} |
302 |
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|
303 |
|
} |
304 |
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} |
305 |
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|
|
|
| 0% |
Uncovered Elements: 21 (21) |
Complexity: 11 |
Complexity Density: 0.85 |
|
306 |
0 |
public Object findElement(int x, int y)... |
307 |
|
{ |
308 |
0 |
Enumeration keys = nameHash.keys(); |
309 |
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|
310 |
0 |
while (keys.hasMoreElements()) |
311 |
|
{ |
312 |
0 |
Object ob = keys.nextElement(); |
313 |
0 |
Rectangle rect = (Rectangle) nameHash.get(ob); |
314 |
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|
315 |
0 |
if (x >= rect.x && x <= (rect.x + rect.width) && y >= rect.y |
316 |
|
&& y <= (rect.y + rect.height)) |
317 |
|
{ |
318 |
0 |
return ob; |
319 |
|
} |
320 |
|
} |
321 |
0 |
keys = nodeHash.keys(); |
322 |
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|
323 |
0 |
while (keys.hasMoreElements()) |
324 |
|
{ |
325 |
0 |
Object ob = keys.nextElement(); |
326 |
0 |
Rectangle rect = (Rectangle) nodeHash.get(ob); |
327 |
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|
328 |
0 |
if (x >= rect.x && x <= (rect.x + rect.width) && y >= rect.y |
329 |
|
&& y <= (rect.y + rect.height)) |
330 |
|
{ |
331 |
0 |
return ob; |
332 |
|
} |
333 |
|
} |
334 |
0 |
return null; |
335 |
|
|
336 |
|
} |
337 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 2 |
Complexity Density: 0.25 |
|
338 |
0 |
public void pickNodes(Rectangle pickBox)... |
339 |
|
{ |
340 |
0 |
int width = getSize().width; |
341 |
0 |
int height = getSize().height; |
342 |
|
|
343 |
0 |
BinaryNode top = tree.getTopNode(); |
344 |
|
|
345 |
0 |
double wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight(); |
346 |
0 |
if (top.count == 0) |
347 |
|
{ |
348 |
0 |
top.count = ((BinaryNode) top.left()).count |
349 |
|
+ ((BinaryNode) top.right()).count; |
350 |
|
} |
351 |
0 |
float chunk = (float) (height - offy) / top.count; |
352 |
|
|
353 |
0 |
pickNode(pickBox, top, chunk, wscale, width, offx, offy); |
354 |
|
} |
355 |
|
|
|
|
| 0% |
Uncovered Elements: 24 (24) |
Complexity: 7 |
Complexity Density: 0.5 |
|
356 |
0 |
public void pickNode(Rectangle pickBox, BinaryNode node, float chunk,... |
357 |
|
double scale, int width, int offx, int offy) |
358 |
|
{ |
359 |
0 |
if (node == null) |
360 |
|
{ |
361 |
0 |
return; |
362 |
|
} |
363 |
|
|
364 |
0 |
if (node.left() == null && node.right() == null) |
365 |
|
{ |
366 |
0 |
double height = node.height; |
367 |
|
|
368 |
|
|
369 |
|
|
370 |
0 |
int xend = (int) (height * scale) + offx; |
371 |
|
|
372 |
0 |
int ypos = (int) (node.ycount * chunk) + offy; |
373 |
|
|
374 |
0 |
if (pickBox.contains(new Point(xend, ypos))) |
375 |
|
{ |
376 |
0 |
if (node.element() instanceof SequenceI) |
377 |
|
{ |
378 |
0 |
SequenceI seq = (SequenceI) node.element(); |
379 |
0 |
SequenceGroup sg = av.getSelectionGroup(); |
380 |
0 |
if (sg != null) |
381 |
|
{ |
382 |
0 |
sg.addOrRemove(seq, true); |
383 |
|
} |
384 |
|
} |
385 |
|
} |
386 |
|
} |
387 |
|
else |
388 |
|
{ |
389 |
0 |
pickNode(pickBox, (BinaryNode) node.left(), chunk, scale, width, offx, |
390 |
|
offy); |
391 |
0 |
pickNode(pickBox, (BinaryNode) node.right(), chunk, scale, width, |
392 |
|
offx, offy); |
393 |
|
} |
394 |
|
} |
395 |
|
|
|
|
| 0% |
Uncovered Elements: 15 (15) |
Complexity: 5 |
Complexity Density: 0.56 |
|
396 |
0 |
public void setColor(BinaryNode node, Color c)... |
397 |
|
{ |
398 |
0 |
if (node == null) |
399 |
|
{ |
400 |
0 |
return; |
401 |
|
} |
402 |
|
|
403 |
0 |
if (node.left() == null && node.right() == null) |
404 |
|
{ |
405 |
0 |
node.color = c; |
406 |
|
|
407 |
0 |
if (node.element() instanceof SequenceI) |
408 |
|
{ |
409 |
0 |
av.setSequenceColour((SequenceI) node.element(), c); |
410 |
|
} |
411 |
|
} |
412 |
|
else |
413 |
|
{ |
414 |
0 |
node.color = c; |
415 |
0 |
setColor((BinaryNode) node.left(), c); |
416 |
0 |
setColor((BinaryNode) node.right(), c); |
417 |
|
} |
418 |
|
} |
419 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
420 |
0 |
@Override... |
421 |
|
public void update(Graphics g) |
422 |
|
{ |
423 |
0 |
paint(g); |
424 |
|
} |
425 |
|
|
|
|
| 0% |
Uncovered Elements: 24 (24) |
Complexity: 5 |
Complexity Density: 0.31 |
|
426 |
0 |
@Override... |
427 |
|
public void paint(Graphics g) |
428 |
|
{ |
429 |
0 |
if (tree == null) |
430 |
|
{ |
431 |
0 |
return; |
432 |
|
} |
433 |
|
|
434 |
0 |
if (nameHash.size() == 0) |
435 |
|
{ |
436 |
0 |
repaint(); |
437 |
|
} |
438 |
|
|
439 |
0 |
int width = scrollPane.getSize().width; |
440 |
0 |
int height = scrollPane.getSize().height; |
441 |
0 |
if (!fitToWindow) |
442 |
|
{ |
443 |
0 |
height = g.getFontMetrics(font).getHeight() * nameHash.size(); |
444 |
|
} |
445 |
|
|
446 |
0 |
if (getSize().width > width) |
447 |
|
{ |
448 |
0 |
setSize(new Dimension(width, height)); |
449 |
0 |
scrollPane.validate(); |
450 |
0 |
return; |
451 |
|
} |
452 |
|
|
453 |
0 |
setSize(new Dimension(width, height)); |
454 |
|
|
455 |
0 |
g.setFont(font); |
456 |
0 |
draw(g, width, height); |
457 |
0 |
validate(); |
458 |
|
} |
459 |
|
|
|
|
| 0% |
Uncovered Elements: 22 (22) |
Complexity: 4 |
Complexity Density: 0.25 |
|
460 |
0 |
public void draw(Graphics g, int width, int height)... |
461 |
|
{ |
462 |
0 |
offy = font.getSize() + 10; |
463 |
|
|
464 |
0 |
g.setColor(Color.white); |
465 |
0 |
g.fillRect(0, 0, width, height); |
466 |
|
|
467 |
0 |
labelLength = g.getFontMetrics(font).stringWidth(longestName) + 20; |
468 |
|
|
469 |
|
|
470 |
|
|
471 |
|
|
472 |
0 |
double wscale = (width - labelLength - offx * 2) / tree.getMaxHeight(); |
473 |
|
|
474 |
0 |
BinaryNode top = tree.getTopNode(); |
475 |
|
|
476 |
0 |
if (top.count == 0) |
477 |
|
{ |
478 |
0 |
top.count = ((BinaryNode) top.left()).count |
479 |
|
+ ((BinaryNode) top.right()).count; |
480 |
|
} |
481 |
0 |
float chunk = (float) (height - offy) / top.count; |
482 |
|
|
483 |
0 |
drawNode(g, tree.getTopNode(), chunk, wscale, width, offx, offy); |
484 |
|
|
485 |
0 |
if (threshold != 0) |
486 |
|
{ |
487 |
0 |
if (av.getCurrentTree() == tree) |
488 |
|
{ |
489 |
0 |
g.setColor(Color.red); |
490 |
|
} |
491 |
|
else |
492 |
|
{ |
493 |
0 |
g.setColor(Color.gray); |
494 |
|
} |
495 |
|
|
496 |
0 |
int x = (int) (threshold * (getSize().width - labelLength - 2 * offx) |
497 |
|
+ offx); |
498 |
|
|
499 |
0 |
g.drawLine(x, 0, x, getSize().height); |
500 |
|
} |
501 |
|
|
502 |
|
} |
503 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
504 |
0 |
@Override... |
505 |
|
public void mouseReleased(MouseEvent e) |
506 |
|
{ |
507 |
|
} |
508 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
509 |
0 |
@Override... |
510 |
|
public void mouseEntered(MouseEvent e) |
511 |
|
{ |
512 |
|
} |
513 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
514 |
0 |
@Override... |
515 |
|
public void mouseExited(MouseEvent e) |
516 |
|
{ |
517 |
|
} |
518 |
|
|
|
|
| 0% |
Uncovered Elements: 18 (18) |
Complexity: 4 |
Complexity Density: 0.33 |
|
519 |
0 |
@Override... |
520 |
|
public void mouseClicked(MouseEvent evt) |
521 |
|
{ |
522 |
0 |
if (highlightNode != null) |
523 |
|
{ |
524 |
0 |
if (evt.getClickCount() > 1) |
525 |
|
{ |
526 |
0 |
tree.swapNodes(highlightNode); |
527 |
0 |
tree.reCount(tree.getTopNode()); |
528 |
0 |
tree.findHeight(tree.getTopNode()); |
529 |
|
} |
530 |
|
else |
531 |
|
{ |
532 |
0 |
Vector<BinaryNode> leaves = tree.findLeaves(highlightNode); |
533 |
|
|
534 |
0 |
for (int i = 0; i < leaves.size(); i++) |
535 |
|
{ |
536 |
0 |
SequenceI seq = (SequenceI) leaves.elementAt(i).element(); |
537 |
0 |
treeSelectionChanged(seq); |
538 |
|
} |
539 |
|
} |
540 |
|
|
541 |
0 |
PaintRefresher.Refresh(this, av.getSequenceSetId()); |
542 |
0 |
repaint(); |
543 |
0 |
av.sendSelection(); |
544 |
|
} |
545 |
|
} |
546 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
547 |
0 |
@Override... |
548 |
|
public void mouseDragged(MouseEvent ect) |
549 |
|
{ |
550 |
|
} |
551 |
|
|
|
|
| 0% |
Uncovered Elements: 12 (12) |
Complexity: 3 |
Complexity Density: 0.38 |
|
552 |
0 |
@Override... |
553 |
|
public void mouseMoved(MouseEvent evt) |
554 |
|
{ |
555 |
0 |
av.setCurrentTree(tree); |
556 |
|
|
557 |
0 |
Object ob = findElement(evt.getX(), evt.getY()); |
558 |
|
|
559 |
0 |
if (ob instanceof BinaryNode) |
560 |
|
{ |
561 |
0 |
highlightNode = (BinaryNode) ob; |
562 |
0 |
repaint(); |
563 |
|
} |
564 |
|
else |
565 |
|
{ |
566 |
0 |
if (highlightNode != null) |
567 |
|
{ |
568 |
0 |
highlightNode = null; |
569 |
0 |
repaint(); |
570 |
|
} |
571 |
|
} |
572 |
|
} |
573 |
|
|
|
|
| 0% |
Uncovered Elements: 34 (34) |
Complexity: 5 |
Complexity Density: 0.19 |
|
574 |
0 |
@Override... |
575 |
|
public void mousePressed(MouseEvent e) |
576 |
|
{ |
577 |
0 |
av.setCurrentTree(tree); |
578 |
|
|
579 |
0 |
int x = e.getX(); |
580 |
0 |
int y = e.getY(); |
581 |
|
|
582 |
0 |
Object ob = findElement(x, y); |
583 |
|
|
584 |
0 |
if (ob instanceof SequenceI) |
585 |
|
{ |
586 |
0 |
treeSelectionChanged((Sequence) ob); |
587 |
0 |
PaintRefresher.Refresh(this, av.getSequenceSetId()); |
588 |
0 |
repaint(); |
589 |
0 |
av.sendSelection(); |
590 |
0 |
return; |
591 |
|
} |
592 |
0 |
else if (!(ob instanceof SequenceNode)) |
593 |
|
{ |
594 |
|
|
595 |
|
|
596 |
0 |
if (tree.getMaxHeight() != 0) |
597 |
|
{ |
598 |
0 |
threshold = (float) (x - offx) |
599 |
|
/ (float) (getSize().width - labelLength - 2 * offx); |
600 |
|
|
601 |
0 |
List<BinaryNode> groups = tree.groupNodes(threshold); |
602 |
0 |
setColor(tree.getTopNode(), Color.black); |
603 |
|
|
604 |
0 |
av.setSelectionGroup(null); |
605 |
0 |
av.getAlignment().deleteAllGroups(); |
606 |
0 |
av.clearSequenceColours(); |
607 |
0 |
final AlignViewportI codingComplement = av.getCodingComplement(); |
608 |
0 |
if (codingComplement != null) |
609 |
|
{ |
610 |
0 |
codingComplement.setSelectionGroup(null); |
611 |
0 |
codingComplement.getAlignment().deleteAllGroups(); |
612 |
0 |
codingComplement.clearSequenceColours(); |
613 |
|
} |
614 |
|
|
615 |
0 |
colourGroups(groups); |
616 |
|
|
617 |
|
} |
618 |
|
} |
619 |
|
|
620 |
0 |
PaintRefresher.Refresh(this, av.getSequenceSetId()); |
621 |
0 |
repaint(); |
622 |
|
|
623 |
|
} |
624 |
|
|
|
|
| 0% |
Uncovered Elements: 55 (55) |
Complexity: 11 |
Complexity Density: 0.3 |
|
625 |
0 |
void colourGroups(List<BinaryNode> groups)... |
626 |
|
{ |
627 |
0 |
for (int i = 0; i < groups.size(); i++) |
628 |
|
{ |
629 |
|
|
630 |
0 |
Color col = new Color((int) (Math.random() * 255), |
631 |
|
(int) (Math.random() * 255), (int) (Math.random() * 255)); |
632 |
0 |
setColor(groups.get(i), col.brighter()); |
633 |
|
|
634 |
0 |
Vector<BinaryNode> l = tree.findLeaves(groups.get(i)); |
635 |
|
|
636 |
0 |
Vector<SequenceI> sequences = new Vector<>(); |
637 |
0 |
for (int j = 0; j < l.size(); j++) |
638 |
|
{ |
639 |
0 |
SequenceI s1 = (SequenceI) l.elementAt(j).element(); |
640 |
0 |
if (!sequences.contains(s1)) |
641 |
|
{ |
642 |
0 |
sequences.addElement(s1); |
643 |
|
} |
644 |
|
} |
645 |
|
|
646 |
0 |
ColourSchemeI cs = null; |
647 |
|
|
648 |
0 |
SequenceGroup sg = new SequenceGroup(sequences, "", cs, true, true, |
649 |
|
false, 0, av.getAlignment().getWidth() - 1); |
650 |
|
|
651 |
0 |
if (av.getGlobalColourScheme() != null) |
652 |
|
{ |
653 |
0 |
if (av.getGlobalColourScheme() instanceof UserColourScheme) |
654 |
|
{ |
655 |
0 |
cs = new UserColourScheme( |
656 |
|
((UserColourScheme) av.getGlobalColourScheme()) |
657 |
|
.getColours()); |
658 |
|
|
659 |
|
} |
660 |
|
else |
661 |
|
{ |
662 |
0 |
cs = ColourSchemeProperty.getColourScheme(av, sg, |
663 |
|
ColourSchemeProperty |
664 |
|
.getColourName(av.getGlobalColourScheme())); |
665 |
|
} |
666 |
|
|
667 |
|
|
668 |
|
|
669 |
|
|
670 |
|
|
671 |
|
|
672 |
|
} |
673 |
|
|
674 |
|
|
675 |
|
|
676 |
0 |
sg.setColourScheme(cs); |
677 |
0 |
sg.getGroupColourScheme().setThreshold( |
678 |
|
av.getResidueShading().getThreshold(), |
679 |
|
av.isIgnoreGapsConsensus()); |
680 |
|
|
681 |
0 |
sg.setName("JTreeGroup:" + sg.hashCode()); |
682 |
0 |
sg.setIdColour(col); |
683 |
0 |
if (av.getGlobalColourScheme() != null |
684 |
|
&& av.getResidueShading().conservationApplied()) |
685 |
|
{ |
686 |
0 |
Conservation c = new Conservation("Group", sg.getSequences(null), |
687 |
|
sg.getStartRes(), sg.getEndRes()); |
688 |
|
|
689 |
0 |
c.calculate(); |
690 |
0 |
c.verdict(false, av.getConsPercGaps()); |
691 |
|
|
692 |
0 |
sg.setColourScheme(cs); |
693 |
0 |
sg.getGroupColourScheme().setConservation(c); |
694 |
|
} |
695 |
|
|
696 |
0 |
av.getAlignment().addGroup(sg); |
697 |
|
|
698 |
|
|
699 |
0 |
av.getAlignment().addGroup(sg); |
700 |
0 |
final AlignViewportI codingComplement = av.getCodingComplement(); |
701 |
0 |
if (codingComplement != null) |
702 |
|
{ |
703 |
0 |
SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, av, |
704 |
|
codingComplement); |
705 |
0 |
if (mappedGroup.getSequences().size() > 0) |
706 |
|
{ |
707 |
0 |
codingComplement.getAlignment().addGroup(mappedGroup); |
708 |
0 |
for (SequenceI seq : mappedGroup.getSequences()) |
709 |
|
{ |
710 |
|
|
711 |
0 |
codingComplement.setSequenceColour(seq, col); |
712 |
|
} |
713 |
|
} |
714 |
|
} |
715 |
|
|
716 |
|
} |
717 |
0 |
ap.updateAnnotation(); |
718 |
0 |
if (av.getCodingComplement() != null) |
719 |
|
{ |
720 |
0 |
((AlignmentViewport) av.getCodingComplement()).firePropertyChange( |
721 |
|
"alignment", null, ap.av.getAlignment().getSequences()); |
722 |
|
} |
723 |
|
} |
724 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
725 |
0 |
public void setShowDistances(boolean state)... |
726 |
|
{ |
727 |
0 |
this.showDistances = state; |
728 |
0 |
repaint(); |
729 |
|
} |
730 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
731 |
0 |
public void setShowBootstrap(boolean state)... |
732 |
|
{ |
733 |
0 |
this.showBootstrap = state; |
734 |
0 |
repaint(); |
735 |
|
} |
736 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
737 |
0 |
public void setMarkPlaceholders(boolean state)... |
738 |
|
{ |
739 |
0 |
this.markPlaceholders = state; |
740 |
0 |
repaint(); |
741 |
|
} |
742 |
|
|
743 |
|
} |