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package jalview.gui; |
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import java.awt.BasicStroke; |
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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.Graphics2D; |
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import java.awt.Point; |
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import java.awt.Rectangle; |
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import java.awt.RenderingHints; |
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import java.awt.Stroke; |
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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.awt.print.PageFormat; |
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import java.awt.print.Printable; |
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import java.awt.print.PrinterException; |
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import java.awt.print.PrinterJob; |
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import java.util.ArrayList; |
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import java.util.BitSet; |
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import java.util.Collections; |
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import java.util.HashMap; |
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import java.util.Hashtable; |
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import java.util.LinkedHashSet; |
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import java.util.List; |
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import java.util.Map; |
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import java.util.Map.Entry; |
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import java.util.Vector; |
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import org.jcolorbrewer.ColorBrewer; |
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import javax.swing.JPanel; |
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import javax.swing.JScrollPane; |
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import javax.swing.SwingUtilities; |
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import javax.swing.ToolTipManager; |
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import jalview.analysis.AlignmentUtils; |
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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.bin.Console; |
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import jalview.datamodel.AlignmentAnnotation; |
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import jalview.datamodel.Annotation; |
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import jalview.datamodel.BinaryNode; |
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import jalview.datamodel.ColumnSelection; |
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import jalview.datamodel.ContactMatrixI; |
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import jalview.datamodel.HiddenColumns; |
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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.gui.JalviewColourChooser.ColourChooserListener; |
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import jalview.schemes.ColourSchemeI; |
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import jalview.structure.SelectionSource; |
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import jalview.util.ColorUtils; |
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import jalview.util.Format; |
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import jalview.util.MessageManager; |
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import jalview.ws.datamodel.MappableContactMatrixI; |
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@author |
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@version |
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| 7% |
Uncovered Elements: 786 (845) |
Complexity: 210 |
Complexity Density: 0.38 |
|
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public class TreeCanvas extends JPanel implements MouseListener, Runnable, |
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Printable, MouseMotionListener, SelectionSource |
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{ |
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public static final String PLACEHOLDER = " * "; |
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93 |
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private static final int DASHED_LINE_Y_OFFSET = 6; |
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|
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TreeModel tree; |
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JScrollPane scrollPane; |
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TreePanel tp; |
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private AlignViewport av; |
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private AlignmentPanel ap; |
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Font font; |
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|
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FontMetrics fm; |
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|
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boolean fitToWindow = true; |
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boolean showDistances = false; |
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boolean showStructureProviderLabels = false; |
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|
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boolean showStructureProviderColouredLines = false; |
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boolean showBootstrap = false; |
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boolean markPlaceholders = false; |
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int offx = 20; |
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int offy; |
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private float threshold; |
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int labelLengthThreshold = 4; |
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String longestName; |
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int labelLength = -1; |
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Map<BinaryNode, Rectangle> nameHash = new Hashtable<>(); |
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Map<BinaryNode, Rectangle> nodeHash = new Hashtable<>(); |
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BinaryNode highlightNode; |
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boolean applyToAllViews = false; |
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private Map<BinaryNode, List<Rectangle>> labelBoundsMap = new HashMap<>(); |
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@param |
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@param |
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@param |
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@param |
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|
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| 100% |
Uncovered Elements: 0 (8) |
Complexity: 1 |
Complexity Density: 0.12 |
|
159 |
14 |
public TreeCanvas(TreePanel tp, AlignmentPanel ap, JScrollPane scroller)... |
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{ |
161 |
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this.tp = tp; |
162 |
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this.av = ap.av; |
163 |
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this.setAssociatedPanel(ap); |
164 |
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font = av.getFont(); |
165 |
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scrollPane = scroller; |
166 |
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addMouseListener(this); |
167 |
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addMouseMotionListener(this); |
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|
169 |
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ToolTipManager.sharedInstance().registerComponent(this); |
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} |
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| 0% |
Uncovered Elements: 22 (22) |
Complexity: 5 |
Complexity Density: 0.36 |
|
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0 |
public void clearSelectedLeaves()... |
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{ |
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Vector<BinaryNode> leaves = tp.getTree() |
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.findLeaves(tp.getTree().getTopNode()); |
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if (tp.isColumnWise()) |
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{ |
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markColumnsFor(getAssociatedPanels(), leaves, Color.white, true); |
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} |
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else |
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{ |
182 |
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for (AlignmentPanel ap : getAssociatedPanels()) |
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{ |
184 |
0 |
SequenceGroup selected = ap.av.getSelectionGroup(); |
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if (selected != null) |
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{ |
187 |
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{ |
188 |
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for (int i = 0; i < leaves.size(); i++) |
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{ |
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SequenceI seq = (SequenceI) leaves.elementAt(i).element(); |
191 |
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if (selected.contains(seq)) |
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{ |
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selected.addOrRemove(seq, false); |
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} |
195 |
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} |
196 |
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selected.recalcConservation(); |
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} |
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} |
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ap.av.sendSelection(); |
200 |
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} |
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} |
202 |
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PaintRefresher.Refresh(tp, av.getSequenceSetId()); |
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repaint(); |
204 |
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} |
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206 |
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207 |
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208 |
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209 |
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@param |
210 |
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211 |
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| 0% |
Uncovered Elements: 12 (12) |
Complexity: 3 |
Complexity Density: 0.38 |
|
212 |
0 |
public void treeSelectionChanged(SequenceI sequence)... |
213 |
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{ |
214 |
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AlignmentPanel[] aps = getAssociatedPanels(); |
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|
216 |
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for (int a = 0; a < aps.length; a++) |
217 |
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{ |
218 |
0 |
SequenceGroup selected = aps[a].av.getSelectionGroup(); |
219 |
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|
220 |
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if (selected == null) |
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{ |
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selected = new SequenceGroup(); |
223 |
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aps[a].av.setSelectionGroup(selected); |
224 |
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} |
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selected.setEndRes(aps[a].av.getAlignment().getWidth() - 1); |
227 |
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selected.addOrRemove(sequence, true); |
228 |
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} |
229 |
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} |
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@param |
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236 |
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| 69.7% |
Uncovered Elements: 10 (33) |
Complexity: 11 |
Complexity Density: 0.52 |
|
237 |
14 |
public void setTree(TreeModel tree)... |
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{ |
239 |
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this.tree = tree; |
240 |
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tree.findHeight(tree.getTopNode()); |
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243 |
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Vector<BinaryNode> leaves = tree.findLeaves(tree.getTopNode()); |
244 |
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boolean has_placeholders = false; |
245 |
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longestName = ""; |
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|
247 |
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AlignmentAnnotation aa = tp.getAssocAnnotation(); |
248 |
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ContactMatrixI cm = (aa != null) ? av.getContactMatrix(aa) : null; |
249 |
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if (cm != null && cm.hasCutHeight()) |
250 |
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{ |
251 |
0 |
threshold = (float) cm.getCutHeight(); |
252 |
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} |
253 |
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|
254 |
184 |
for (int i = 0; i < leaves.size(); i++) |
255 |
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{ |
256 |
170 |
BinaryNode lf = leaves.elementAt(i); |
257 |
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|
258 |
170 |
if (lf instanceof SequenceNode && ((SequenceNode) lf).isPlaceholder()) |
259 |
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{ |
260 |
0 |
has_placeholders = true; |
261 |
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} |
262 |
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|
263 |
170 |
if (longestName.length() < lf.getDisplayName().length()) |
264 |
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{ |
265 |
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longestName = TreeCanvas.PLACEHOLDER + lf.getDisplayName(); |
266 |
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} |
267 |
170 |
if (tp.isColumnWise() && cm != null) |
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{ |
269 |
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|
270 |
0 |
try |
271 |
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{ |
272 |
0 |
Color col = cm.getGroupColorForPosition(parseColumnNode(lf)); |
273 |
0 |
setColor(lf, col.brighter()); |
274 |
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} catch (NumberFormatException ex) |
275 |
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{ |
276 |
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} |
277 |
0 |
; |
278 |
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} |
279 |
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} |
280 |
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281 |
14 |
setMarkPlaceholders(has_placeholders); |
282 |
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} |
283 |
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285 |
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286 |
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287 |
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@param |
288 |
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289 |
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@param |
290 |
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291 |
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@param |
292 |
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293 |
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@param |
294 |
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295 |
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@param |
296 |
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297 |
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@param |
298 |
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299 |
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@param |
300 |
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301 |
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| 0% |
Uncovered Elements: 156 (156) |
Complexity: 38 |
Complexity Density: 0.37 |
|
302 |
0 |
public void drawNode(Graphics g, BinaryNode node, double chunk,... |
303 |
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double wscale, int width, int offx, int offy) |
304 |
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{ |
305 |
0 |
if (node == null) |
306 |
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{ |
307 |
0 |
return; |
308 |
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} |
309 |
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|
310 |
0 |
Vector<BinaryNode> leaves = tree.findLeaves(node); |
311 |
0 |
gatherLabelsTo(node, leaves); |
312 |
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|
313 |
0 |
if ((node.left() == null) && (node.right() == null)) |
314 |
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{ |
315 |
0 |
Color originalColor, translucentColor = Color.WHITE; |
316 |
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|
317 |
0 |
double height = node.height; |
318 |
0 |
double dist = node.dist; |
319 |
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|
320 |
0 |
int xstart = (int) ((height - dist) * wscale) + offx; |
321 |
0 |
int xend = (int) (height * wscale) + offx; |
322 |
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|
323 |
0 |
int ypos = (int) (node.ycount * chunk) + offy; |
324 |
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|
325 |
0 |
if (node.element() instanceof SequenceI) |
326 |
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{ |
327 |
0 |
SequenceI seq = (SequenceI) node.element(); |
328 |
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|
329 |
0 |
if (av.getSequenceColour(seq) == Color.white) |
330 |
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{ |
331 |
0 |
g.setColor(Color.black); |
332 |
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} |
333 |
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else |
334 |
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{ |
335 |
0 |
originalColor = av.getSequenceColour(seq); |
336 |
0 |
translucentColor = new Color(originalColor.getRed(), originalColor.getGreen(), originalColor.getBlue(), 128); |
337 |
0 |
g.setColor(Color.black); |
338 |
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} |
339 |
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} |
340 |
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else |
341 |
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{ |
342 |
0 |
g.setColor(Color.black); |
343 |
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} |
344 |
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345 |
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346 |
0 |
g.drawLine(xstart, ypos, xend, ypos); |
347 |
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348 |
0 |
String nodeLabel = ""; |
349 |
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350 |
0 |
if (showDistances && (node.dist > 0)) |
351 |
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{ |
352 |
0 |
nodeLabel = new Format("%g").form(node.dist); |
353 |
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} |
354 |
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|
355 |
0 |
if (showBootstrap && node.bootstrap > -1) |
356 |
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{ |
357 |
0 |
if (showDistances) |
358 |
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{ |
359 |
0 |
nodeLabel = nodeLabel + " : "; |
360 |
|
} |
361 |
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|
362 |
0 |
nodeLabel = nodeLabel + String.valueOf(node.bootstrap); |
363 |
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} |
364 |
0 |
if(node.hasLabel() && showStructureProviderColouredLines) { |
365 |
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|
366 |
0 |
drawLinesAndLabelsForSecondaryStructureProvider(g, node, xstart, xend, ypos, nodeLabel); |
367 |
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|
368 |
0 |
Rectangle labelBounds = new Rectangle(xstart, ypos, xend, ypos + DASHED_LINE_Y_OFFSET); |
369 |
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370 |
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371 |
0 |
labelBoundsMap.computeIfAbsent(node, k -> new ArrayList<>()).add(labelBounds); |
372 |
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|
373 |
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} |
374 |
0 |
else if (!nodeLabel.equals("")) |
375 |
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{ |
376 |
0 |
g.drawString(nodeLabel, xstart + 2, ypos - 2); |
377 |
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} |
378 |
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|
379 |
0 |
String name = (markPlaceholders && ((node instanceof SequenceNode |
380 |
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&& ((SequenceNode) node).isPlaceholder()))) |
381 |
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? (PLACEHOLDER + node.getDisplayName()) |
382 |
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: node.getDisplayName(); |
383 |
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|
384 |
0 |
int charWidth = fm.stringWidth(name) + 3; |
385 |
0 |
int charHeight = font.getSize(); |
386 |
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|
387 |
0 |
Rectangle rect = new Rectangle(xend + 10, ypos - charHeight / 2, |
388 |
|
charWidth, charHeight); |
389 |
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|
390 |
0 |
nameHash.put(node, rect); |
391 |
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|
392 |
0 |
g.setColor(translucentColor); |
393 |
0 |
g.fillRect(xend + 10, ypos - charHeight / 2, charWidth, charHeight); |
394 |
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|
395 |
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|
396 |
0 |
g.setColor(Color.black); |
397 |
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|
398 |
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|
399 |
0 |
boolean isSelected = false; |
400 |
0 |
if (tp.isColumnWise()) |
401 |
|
{ |
402 |
0 |
isSelected = isColumnForNodeSelected(node); |
403 |
|
} |
404 |
|
else |
405 |
|
{ |
406 |
0 |
SequenceGroup selected = av.getSelectionGroup(); |
407 |
|
|
408 |
0 |
if ((selected != null) |
409 |
|
&& selected.getSequences(null).contains(node.element())) |
410 |
|
{ |
411 |
0 |
isSelected = true; |
412 |
|
} |
413 |
|
} |
414 |
0 |
if (isSelected) |
415 |
|
{ |
416 |
0 |
g.setColor(Color.gray); |
417 |
|
|
418 |
0 |
g.fillRect(xend + 10, ypos - charHeight / 2, charWidth, charHeight); |
419 |
0 |
g.setColor(Color.white); |
420 |
|
} |
421 |
|
|
422 |
0 |
g.drawString(name, xend + 10, ypos + fm.getDescent()); |
423 |
0 |
g.setColor(Color.black); |
424 |
|
} |
425 |
|
else |
426 |
|
{ |
427 |
0 |
drawNode(g, (BinaryNode) node.left(), chunk, wscale, width, offx, |
428 |
|
offy); |
429 |
0 |
drawNode(g, (BinaryNode) node.right(), chunk, wscale, width, offx, |
430 |
|
offy); |
431 |
|
|
432 |
0 |
double height = node.height; |
433 |
0 |
double dist = node.dist; |
434 |
|
|
435 |
0 |
int xstart = (int) ((height - dist) * wscale) + offx; |
436 |
0 |
int xend = (int) (height * wscale) + offx; |
437 |
0 |
int ypos = (int) (node.ycount * chunk) + offy; |
438 |
|
|
439 |
|
|
440 |
|
|
441 |
|
|
442 |
0 |
g.setColor(Color.black); |
443 |
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|
444 |
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|
445 |
0 |
g.drawLine(xstart, ypos, xend, ypos); |
446 |
0 |
if (node == highlightNode) |
447 |
|
{ |
448 |
0 |
g.fillRect(xend - 3, ypos - 3, 6, 6); |
449 |
|
} |
450 |
|
else |
451 |
|
{ |
452 |
0 |
g.fillRect(xend - 2, ypos - 2, 4, 4); |
453 |
|
} |
454 |
|
|
455 |
0 |
int ystart = (node.left() == null ? 0 |
456 |
|
: (int) (node.left().ycount * chunk)) + offy; |
457 |
0 |
int yend = (node.right() == null ? 0 |
458 |
|
: (int) (node.right().ycount * chunk)) + offy; |
459 |
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|
460 |
0 |
Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5); |
461 |
0 |
nodeHash.put(node, pos); |
462 |
|
|
463 |
0 |
g.drawLine((int) (height * wscale) + offx, ystart, |
464 |
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(int) (height * wscale) + offx, yend); |
465 |
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|
466 |
0 |
String nodeLabel = ""; |
467 |
|
|
468 |
0 |
if (showDistances && (node.dist > 0)) |
469 |
|
{ |
470 |
0 |
nodeLabel = new Format("%g").form(node.dist); |
471 |
|
} |
472 |
|
|
473 |
0 |
if (showBootstrap && node.bootstrap > -1) |
474 |
|
{ |
475 |
0 |
if (showDistances) |
476 |
|
{ |
477 |
0 |
nodeLabel = nodeLabel + " : "; |
478 |
|
} |
479 |
|
|
480 |
0 |
nodeLabel = nodeLabel + String.valueOf(node.bootstrap); |
481 |
|
} |
482 |
|
|
483 |
|
|
484 |
|
|
485 |
|
|
486 |
|
|
487 |
0 |
boolean labelHandled = false; |
488 |
0 |
if(node.hasLabel()) { |
489 |
|
|
490 |
0 |
if (showStructureProviderColouredLines) |
491 |
|
{ |
492 |
0 |
drawLinesAndLabelsForSecondaryStructureProvider(g, node, xstart, xend, ypos, nodeLabel); |
493 |
|
|
494 |
0 |
Rectangle labelBounds = new Rectangle(xstart, ypos, xend, ypos + DASHED_LINE_Y_OFFSET); |
495 |
|
|
496 |
|
|
497 |
0 |
labelBoundsMap.computeIfAbsent(node, k -> new ArrayList<>()).add(labelBounds); |
498 |
0 |
labelHandled = true; |
499 |
|
|
500 |
|
} |
501 |
|
|
502 |
0 |
if (showStructureProviderLabels && node.count > 3) |
503 |
|
{ |
504 |
|
|
505 |
0 |
String label = node.getLabel(); |
506 |
|
|
507 |
0 |
if(label.length() > labelLengthThreshold) { |
508 |
|
|
509 |
|
|
510 |
|
} |
511 |
|
|
512 |
0 |
nodeLabel = label + " | " + nodeLabel; |
513 |
|
|
514 |
|
|
515 |
0 |
String[] lines = nodeLabel.split("\\|"); |
516 |
|
|
517 |
|
|
518 |
0 |
String longestLabelString = ""; |
519 |
0 |
int i = 0; |
520 |
0 |
for (i = 0; i < lines.length; i++) { |
521 |
0 |
g.drawString(lines[i].trim(), xstart + 2, ypos - 2 - (i * fm.getHeight())); |
522 |
0 |
if(longestLabelString.length() < lines[i].trim().length()) { |
523 |
0 |
longestLabelString = lines[i].trim(); |
524 |
|
} |
525 |
|
} |
526 |
|
|
527 |
0 |
int labelWidth = fm.stringWidth(longestLabelString); |
528 |
0 |
int labelHeight = fm.getHeight() * (i-1); |
529 |
|
|
530 |
|
|
531 |
0 |
int xLabelPos = xstart + 2; |
532 |
0 |
int yLabelPos = ypos - 2; |
533 |
0 |
Rectangle labelBounds = new Rectangle(xLabelPos, yLabelPos - labelHeight, labelWidth, labelHeight); |
534 |
|
|
535 |
|
|
536 |
0 |
labelBoundsMap.computeIfAbsent(node, k -> new ArrayList<>()).add(labelBounds); |
537 |
|
|
538 |
0 |
labelHandled = true; |
539 |
|
} |
540 |
|
} |
541 |
|
|
542 |
0 |
if (!nodeLabel.equals("") && !labelHandled) |
543 |
|
{ |
544 |
0 |
g.drawString(nodeLabel, xstart + 2, ypos - 2); |
545 |
|
} |
546 |
|
} |
547 |
|
} |
548 |
|
|
549 |
|
|
|
|
| 0% |
Uncovered Elements: 12 (12) |
Complexity: 1 |
Complexity Density: 0.08 |
|
550 |
0 |
private void drawLinesAndLabelsForSecondaryStructureProvider(Graphics g, BinaryNode node, ... |
551 |
|
int xstart, int xend, int ypos, String nodeLabel) { |
552 |
|
|
553 |
0 |
Graphics2D g2d = (Graphics2D) g.create(); |
554 |
|
|
555 |
|
|
556 |
|
|
557 |
|
|
558 |
|
|
559 |
|
|
560 |
|
|
561 |
|
|
562 |
|
|
563 |
|
|
564 |
|
|
565 |
0 |
g2d.setStroke(new BasicStroke( |
566 |
|
4.0f, |
567 |
|
BasicStroke.CAP_BUTT, |
568 |
|
BasicStroke.JOIN_ROUND |
569 |
|
)); |
570 |
|
|
571 |
0 |
String label = node.getLabel(); |
572 |
0 |
String[] lines = label.split("\\|"); |
573 |
|
|
574 |
0 |
int mid = lines.length / 2; |
575 |
|
|
576 |
|
|
577 |
0 |
int firstHalfLinesCount = mid; |
578 |
|
|
579 |
0 |
drawSecondaryStructureProviderLinesSection(g2d, |
580 |
|
lines, 0, mid, xstart, xend, |
581 |
|
ypos - DASHED_LINE_Y_OFFSET, |
582 |
|
true); |
583 |
0 |
drawVerticalLineAndLabel(g, xstart, ypos, firstHalfLinesCount, true, nodeLabel); |
584 |
|
|
585 |
|
|
586 |
0 |
int secondHalfLinesCount = lines.length - mid; |
587 |
0 |
drawSecondaryStructureProviderLinesSection(g2d, |
588 |
|
lines, mid, lines.length, xstart, xend, |
589 |
|
ypos, |
590 |
|
false); |
591 |
0 |
drawVerticalLineAndLabel(g, xstart, ypos, secondHalfLinesCount, false, nodeLabel); |
592 |
|
|
593 |
0 |
g2d.dispose(); |
594 |
|
} |
595 |
|
|
|
|
| 0% |
Uncovered Elements: 14 (14) |
Complexity: 5 |
Complexity Density: 0.62 |
|
596 |
0 |
private void drawSecondaryStructureProviderLinesSection(Graphics2D g2d, String[] lines, int start, int end, int xstart, int xend, int baseY, boolean above) {... |
597 |
|
|
598 |
0 |
for (int i = start, j=0; i < end; i++, j++) { |
599 |
0 |
int adjustedY = above |
600 |
|
? baseY - ((i - start) * DASHED_LINE_Y_OFFSET) |
601 |
|
: baseY +((i - start) * DASHED_LINE_Y_OFFSET); |
602 |
|
|
603 |
|
|
604 |
0 |
Map<String, Color> secondaryStructureProviderColorMap = tp.getSecondaryStructureProviderColorMap(); |
605 |
0 |
Color providerColor = secondaryStructureProviderColorMap.getOrDefault(lines[i].toUpperCase().trim(), Color.BLACK); |
606 |
0 |
g2d.setColor(providerColor); |
607 |
0 |
if(i==start && !above) { |
608 |
0 |
g2d.drawLine(xstart, adjustedY, xend-3, adjustedY); |
609 |
|
} |
610 |
|
else |
611 |
|
{ |
612 |
0 |
g2d.drawLine(xstart, adjustedY, xend, adjustedY); |
613 |
|
} |
614 |
|
} |
615 |
|
} |
616 |
|
|
|
|
| 0% |
Uncovered Elements: 9 (9) |
Complexity: 4 |
Complexity Density: 0.8 |
|
617 |
0 |
private void drawVerticalLineAndLabel(Graphics g, int xstart, int ypos, ... |
618 |
|
int linesCount, boolean above, String nodeLabel) { |
619 |
|
|
620 |
0 |
int adjustment = (linesCount * DASHED_LINE_Y_OFFSET) + (DASHED_LINE_Y_OFFSET / 3); |
621 |
0 |
int adjustedY = ypos + (above ? -adjustment : adjustment - DASHED_LINE_Y_OFFSET); |
622 |
|
|
623 |
|
|
624 |
0 |
g.drawLine(xstart, ypos, xstart, adjustedY); |
625 |
|
|
626 |
|
|
627 |
0 |
if(above && !nodeLabel.equals("")) |
628 |
0 |
g.drawString(nodeLabel, xstart + 2, adjustedY - 2); |
629 |
|
} |
630 |
|
|
631 |
|
|
632 |
|
|
633 |
|
|
634 |
|
|
635 |
|
@param |
636 |
|
|
637 |
|
@param |
638 |
|
|
639 |
|
|
640 |
|
@return |
641 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 9 |
Complexity Density: 1 |
|
642 |
0 |
public Object findElement(int x, int y)... |
643 |
|
{ |
644 |
0 |
for (Entry<BinaryNode, Rectangle> entry : nameHash.entrySet()) |
645 |
|
{ |
646 |
0 |
Rectangle rect = entry.getValue(); |
647 |
|
|
648 |
0 |
if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) |
649 |
|
&& (y <= (rect.y + rect.height))) |
650 |
|
{ |
651 |
0 |
return entry.getKey().element(); |
652 |
|
} |
653 |
|
} |
654 |
|
|
655 |
0 |
for (Entry<BinaryNode, Rectangle> entry : nodeHash.entrySet()) |
656 |
|
{ |
657 |
0 |
Rectangle rect = entry.getValue(); |
658 |
|
|
659 |
0 |
if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) |
660 |
|
&& (y <= (rect.y + rect.height))) |
661 |
|
{ |
662 |
0 |
return entry.getKey(); |
663 |
|
} |
664 |
|
} |
665 |
|
|
666 |
0 |
return null; |
667 |
|
} |
668 |
|
|
669 |
|
|
670 |
|
|
671 |
|
|
672 |
|
@param |
673 |
|
|
674 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 2 |
Complexity Density: 0.25 |
|
675 |
0 |
public void pickNodes(Rectangle pickBox)... |
676 |
|
{ |
677 |
0 |
int width = getWidth(); |
678 |
0 |
int height = getHeight(); |
679 |
|
|
680 |
0 |
BinaryNode top = tree.getTopNode(); |
681 |
|
|
682 |
0 |
double wscale = ((width * .8) - (offx * 2)) / tree.getMaxHeight(); |
683 |
|
|
684 |
0 |
if (top.count == 0) |
685 |
|
{ |
686 |
0 |
top.count = ((BinaryNode) top.left()).count |
687 |
|
+ ((BinaryNode) top.right()).count; |
688 |
|
} |
689 |
|
|
690 |
0 |
float chunk = (float) (height - (offy)) / top.count; |
691 |
|
|
692 |
0 |
pickNode(pickBox, top, chunk, wscale, width, offx, offy); |
693 |
|
} |
694 |
|
|
695 |
|
|
696 |
|
|
697 |
|
|
698 |
|
@param |
699 |
|
|
700 |
|
@param |
701 |
|
|
702 |
|
@param |
703 |
|
|
704 |
|
@param |
705 |
|
|
706 |
|
@param |
707 |
|
|
708 |
|
@param |
709 |
|
|
710 |
|
@param |
711 |
|
|
712 |
|
|
|
|
| 0% |
Uncovered Elements: 24 (24) |
Complexity: 7 |
Complexity Density: 0.5 |
|
713 |
0 |
public void pickNode(Rectangle pickBox, BinaryNode node, float chunk,... |
714 |
|
double wscale, int width, int offx, int offy) |
715 |
|
{ |
716 |
0 |
if (node == null) |
717 |
|
{ |
718 |
0 |
return; |
719 |
|
} |
720 |
|
|
721 |
0 |
if ((node.left() == null) && (node.right() == null)) |
722 |
|
{ |
723 |
0 |
double height = node.height; |
724 |
|
|
725 |
|
|
726 |
0 |
int xend = (int) (height * wscale) + offx; |
727 |
|
|
728 |
0 |
int ypos = (int) (node.ycount * chunk) + offy; |
729 |
|
|
730 |
0 |
if (pickBox.contains(new Point(xend, ypos))) |
731 |
|
{ |
732 |
0 |
if (node.element() instanceof SequenceI) |
733 |
|
{ |
734 |
0 |
SequenceI seq = (SequenceI) node.element(); |
735 |
0 |
SequenceGroup sg = av.getSelectionGroup(); |
736 |
|
|
737 |
0 |
if (sg != null) |
738 |
|
{ |
739 |
0 |
sg.addOrRemove(seq, true); |
740 |
|
} |
741 |
|
} |
742 |
|
} |
743 |
|
} |
744 |
|
else |
745 |
|
{ |
746 |
0 |
pickNode(pickBox, (BinaryNode) node.left(), chunk, wscale, width, |
747 |
|
offx, offy); |
748 |
0 |
pickNode(pickBox, (BinaryNode) node.right(), chunk, wscale, width, |
749 |
|
offx, offy); |
750 |
|
} |
751 |
|
} |
752 |
|
|
753 |
|
|
754 |
|
|
755 |
|
|
756 |
|
@param |
757 |
|
|
758 |
|
@param |
759 |
|
|
760 |
|
|
|
|
| 0% |
Uncovered Elements: 19 (19) |
Complexity: 5 |
Complexity Density: 0.45 |
|
761 |
0 |
public void setColor(BinaryNode node, Color c)... |
762 |
|
{ |
763 |
0 |
if (node == null) |
764 |
|
{ |
765 |
0 |
return; |
766 |
|
} |
767 |
|
|
768 |
0 |
node.color = c; |
769 |
0 |
if (node.element() instanceof SequenceI) |
770 |
|
{ |
771 |
0 |
final SequenceI seq = (SequenceI) node.element(); |
772 |
0 |
AlignmentPanel[] aps = getAssociatedPanels(); |
773 |
0 |
if (aps != null) |
774 |
|
{ |
775 |
0 |
for (int a = 0; a < aps.length; a++) |
776 |
|
{ |
777 |
0 |
aps[a].av.setSequenceColour(seq, c); |
778 |
|
} |
779 |
|
} |
780 |
|
} |
781 |
0 |
setColor((BinaryNode) node.left(), c); |
782 |
0 |
setColor((BinaryNode) node.right(), c); |
783 |
|
} |
784 |
|
|
785 |
|
|
786 |
|
|
787 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
788 |
0 |
void startPrinting()... |
789 |
|
{ |
790 |
0 |
Thread thread = new Thread(this); |
791 |
0 |
thread.start(); |
792 |
|
} |
793 |
|
|
794 |
|
|
|
|
| 0% |
Uncovered Elements: 14 (14) |
Complexity: 4 |
Complexity Density: 0.4 |
|
795 |
0 |
@Override... |
796 |
|
public void run() |
797 |
|
{ |
798 |
0 |
PrinterJob printJob = PrinterJob.getPrinterJob(); |
799 |
0 |
PageFormat defaultPage = printJob.defaultPage(); |
800 |
0 |
PageFormat pf = printJob.pageDialog(defaultPage); |
801 |
|
|
802 |
0 |
if (defaultPage == pf) |
803 |
|
{ |
804 |
|
|
805 |
|
|
806 |
|
|
807 |
0 |
return; |
808 |
|
} |
809 |
|
|
810 |
0 |
printJob.setPrintable(this, pf); |
811 |
|
|
812 |
0 |
if (printJob.printDialog()) |
813 |
|
{ |
814 |
0 |
try |
815 |
|
{ |
816 |
0 |
printJob.print(); |
817 |
|
} catch (Exception PrintException) |
818 |
|
{ |
819 |
0 |
PrintException.printStackTrace(); |
820 |
|
} |
821 |
|
} |
822 |
|
} |
823 |
|
|
824 |
|
|
825 |
|
|
826 |
|
|
827 |
|
@param |
828 |
|
|
829 |
|
@param |
830 |
|
|
831 |
|
@param |
832 |
|
|
833 |
|
|
834 |
|
@return |
835 |
|
|
836 |
|
@throws |
837 |
|
|
838 |
|
|
|
|
| 0% |
Uncovered Elements: 28 (28) |
Complexity: 5 |
Complexity Density: 0.25 |
|
839 |
0 |
@Override... |
840 |
|
public int print(Graphics pg, PageFormat pf, int pi) |
841 |
|
throws PrinterException |
842 |
|
{ |
843 |
0 |
pg.setFont(font); |
844 |
0 |
pg.translate((int) pf.getImageableX(), (int) pf.getImageableY()); |
845 |
|
|
846 |
0 |
int pwidth = (int) pf.getImageableWidth(); |
847 |
0 |
int pheight = (int) pf.getImageableHeight(); |
848 |
|
|
849 |
0 |
int noPages = getHeight() / pheight; |
850 |
|
|
851 |
0 |
if (pi > noPages) |
852 |
|
{ |
853 |
0 |
return Printable.NO_SUCH_PAGE; |
854 |
|
} |
855 |
|
|
856 |
0 |
if (pwidth > getWidth()) |
857 |
|
{ |
858 |
0 |
pwidth = getWidth(); |
859 |
|
} |
860 |
|
|
861 |
0 |
if (fitToWindow) |
862 |
|
{ |
863 |
0 |
if (pheight > getHeight()) |
864 |
|
{ |
865 |
0 |
pheight = getHeight(); |
866 |
|
} |
867 |
|
|
868 |
0 |
noPages = 0; |
869 |
|
} |
870 |
|
else |
871 |
|
{ |
872 |
0 |
FontMetrics fm = pg.getFontMetrics(font); |
873 |
0 |
int height = fm.getHeight() * nameHash.size(); |
874 |
0 |
pg.translate(0, -pi * pheight); |
875 |
0 |
pg.setClip(0, pi * pheight, pwidth, (pi * pheight) + pheight); |
876 |
|
|
877 |
|
|
878 |
|
|
879 |
|
|
880 |
0 |
pheight = height; |
881 |
|
} |
882 |
|
|
883 |
0 |
draw(pg, pwidth, pheight); |
884 |
|
|
885 |
0 |
return Printable.PAGE_EXISTS; |
886 |
|
} |
887 |
|
|
888 |
|
|
889 |
|
|
890 |
|
|
891 |
|
@param |
892 |
|
|
893 |
|
|
|
|
| 0% |
Uncovered Elements: 20 (20) |
Complexity: 6 |
Complexity Density: 0.43 |
|
894 |
0 |
@Override... |
895 |
|
public void paintComponent(Graphics g) |
896 |
|
{ |
897 |
0 |
super.paintComponent(g); |
898 |
0 |
g.setFont(font); |
899 |
|
|
900 |
0 |
if (tree == null) |
901 |
|
{ |
902 |
0 |
g.drawString( |
903 |
|
MessageManager.getString("label.calculating_tree") + "....", |
904 |
|
20, getHeight() / 2); |
905 |
|
} |
906 |
|
else |
907 |
|
{ |
908 |
0 |
fm = g.getFontMetrics(font); |
909 |
|
|
910 |
0 |
int nameCount = nameHash.size(); |
911 |
0 |
if (nameCount == 0) |
912 |
|
{ |
913 |
0 |
repaint(); |
914 |
|
} |
915 |
|
|
916 |
0 |
if (fitToWindow || (!fitToWindow && (scrollPane |
917 |
|
.getHeight() > ((fm.getHeight() * nameCount) + offy)))) |
918 |
|
{ |
919 |
0 |
draw(g, scrollPane.getWidth(), scrollPane.getHeight()); |
920 |
0 |
setPreferredSize(null); |
921 |
|
} |
922 |
|
else |
923 |
|
{ |
924 |
0 |
setPreferredSize(new Dimension(scrollPane.getWidth(), |
925 |
|
fm.getHeight() * nameCount)); |
926 |
0 |
draw(g, scrollPane.getWidth(), fm.getHeight() * nameCount); |
927 |
|
} |
928 |
|
|
929 |
0 |
scrollPane.revalidate(); |
930 |
|
} |
931 |
|
} |
932 |
|
|
933 |
|
|
934 |
|
|
935 |
|
|
936 |
|
@param |
937 |
|
|
938 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
939 |
26 |
@Override... |
940 |
|
public void setFont(Font font) |
941 |
|
{ |
942 |
26 |
this.font = font; |
943 |
26 |
repaint(); |
944 |
|
} |
945 |
|
|
946 |
|
|
947 |
|
|
948 |
|
|
949 |
|
@param |
950 |
|
|
951 |
|
@param |
952 |
|
|
953 |
|
@param |
954 |
|
|
955 |
|
|
|
|
| 0% |
Uncovered Elements: 31 (31) |
Complexity: 6 |
Complexity Density: 0.26 |
|
956 |
0 |
public void draw(Graphics g1, int width, int height)... |
957 |
|
{ |
958 |
0 |
Graphics2D g2 = (Graphics2D) g1; |
959 |
0 |
g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, |
960 |
|
RenderingHints.VALUE_ANTIALIAS_ON); |
961 |
0 |
g2.setColor(Color.white); |
962 |
0 |
g2.fillRect(0, 0, width, height); |
963 |
0 |
g2.setFont(font); |
964 |
|
|
965 |
0 |
if (longestName == null || tree == null) |
966 |
|
{ |
967 |
0 |
g2.drawString("Calculating tree.", 20, 20); |
968 |
0 |
return; |
969 |
|
} |
970 |
0 |
offy = font.getSize() + 10; |
971 |
|
|
972 |
0 |
fm = g2.getFontMetrics(font); |
973 |
|
|
974 |
0 |
labelLength = fm.stringWidth(longestName) + 20; |
975 |
|
|
976 |
0 |
double wscale = (width - labelLength - (offx * 2)) |
977 |
|
/ tree.getMaxHeight(); |
978 |
|
|
979 |
0 |
BinaryNode top = tree.getTopNode(); |
980 |
|
|
981 |
0 |
if (top.count == 0) |
982 |
|
{ |
983 |
0 |
top.count = top.left().count + top.right().count; |
984 |
|
} |
985 |
|
|
986 |
0 |
float chunk = (float) (height - (offy)) / top.count; |
987 |
|
|
988 |
0 |
drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy); |
989 |
|
|
990 |
0 |
if (threshold != 0) |
991 |
|
{ |
992 |
0 |
if (av.getCurrentTree() == tree) |
993 |
|
{ |
994 |
0 |
g2.setColor(Color.red); |
995 |
|
} |
996 |
|
else |
997 |
|
{ |
998 |
0 |
g2.setColor(Color.gray); |
999 |
|
} |
1000 |
|
|
1001 |
0 |
int x = (int) ((threshold * (getWidth() - labelLength - (2 * offx))) |
1002 |
|
+ offx); |
1003 |
|
|
1004 |
0 |
g2.drawLine(x, 0, x, getHeight()); |
1005 |
|
} |
1006 |
|
} |
1007 |
|
|
1008 |
|
|
1009 |
|
|
1010 |
|
|
1011 |
|
@param |
1012 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1013 |
0 |
@Override... |
1014 |
|
public void mouseReleased(MouseEvent e) |
1015 |
|
{ |
1016 |
|
|
1017 |
|
|
1018 |
|
|
1019 |
0 |
if (e.isPopupTrigger()) |
1020 |
|
{ |
1021 |
0 |
chooseSubtreeColour(); |
1022 |
0 |
e.consume(); |
1023 |
|
} |
1024 |
|
} |
1025 |
|
|
1026 |
|
|
1027 |
|
|
1028 |
|
|
1029 |
|
@param |
1030 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
1031 |
0 |
@Override... |
1032 |
|
public void mouseEntered(MouseEvent e) |
1033 |
|
{ |
1034 |
|
} |
1035 |
|
|
1036 |
|
|
1037 |
|
|
1038 |
|
|
1039 |
|
@param |
1040 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
1041 |
0 |
@Override... |
1042 |
|
public void mouseExited(MouseEvent e) |
1043 |
|
{ |
1044 |
|
} |
1045 |
|
|
1046 |
|
|
1047 |
|
|
1048 |
|
|
1049 |
|
|
1050 |
|
|
1051 |
|
@param |
1052 |
|
|
|
|
| 0% |
Uncovered Elements: 23 (23) |
Complexity: 5 |
Complexity Density: 0.33 |
|
1053 |
0 |
@Override... |
1054 |
|
public void mouseClicked(MouseEvent evt) |
1055 |
|
{ |
1056 |
0 |
if (highlightNode == null) |
1057 |
|
{ |
1058 |
0 |
return; |
1059 |
|
} |
1060 |
|
|
1061 |
0 |
if (evt.getClickCount() > 1) |
1062 |
|
{ |
1063 |
0 |
tree.swapNodes(highlightNode); |
1064 |
0 |
tree.reCount(tree.getTopNode()); |
1065 |
0 |
tree.findHeight(tree.getTopNode()); |
1066 |
|
} |
1067 |
|
else |
1068 |
|
{ |
1069 |
0 |
Vector<BinaryNode> leaves = tree.findLeaves(highlightNode); |
1070 |
0 |
if (tp.isColumnWise()) |
1071 |
|
{ |
1072 |
0 |
markColumnsFor(getAssociatedPanels(), leaves, Color.red, false); |
1073 |
|
} |
1074 |
|
else |
1075 |
|
{ |
1076 |
0 |
for (int i = 0; i < leaves.size(); i++) |
1077 |
|
{ |
1078 |
0 |
SequenceI seq = (SequenceI) leaves.elementAt(i).element(); |
1079 |
0 |
treeSelectionChanged(seq); |
1080 |
|
} |
1081 |
|
} |
1082 |
0 |
av.sendSelection(); |
1083 |
|
} |
1084 |
|
|
1085 |
0 |
PaintRefresher.Refresh(tp, av.getSequenceSetId()); |
1086 |
0 |
repaint(); |
1087 |
|
} |
1088 |
|
|
1089 |
|
|
1090 |
|
|
1091 |
|
|
1092 |
|
|
1093 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
1094 |
0 |
void chooseSubtreeColour()... |
1095 |
|
{ |
1096 |
0 |
String ttl = MessageManager.getString("label.select_subtree_colour"); |
1097 |
0 |
ColourChooserListener listener = new ColourChooserListener() |
1098 |
|
{ |
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
1099 |
0 |
@Override... |
1100 |
|
public void colourSelected(Color c) |
1101 |
|
{ |
1102 |
0 |
setColor(highlightNode, c); |
1103 |
0 |
PaintRefresher.Refresh(tp, ap.av.getSequenceSetId()); |
1104 |
0 |
repaint(); |
1105 |
|
} |
1106 |
|
}; |
1107 |
0 |
JalviewColourChooser.showColourChooser(this, ttl, highlightNode.color, |
1108 |
|
listener); |
1109 |
|
} |
1110 |
|
|
|
|
| 0% |
Uncovered Elements: 29 (29) |
Complexity: 4 |
Complexity Density: 0.17 |
|
1111 |
0 |
@Override... |
1112 |
|
public void mouseMoved(MouseEvent evt) |
1113 |
|
{ |
1114 |
0 |
av.setCurrentTree(tree); |
1115 |
|
|
1116 |
0 |
Object ob = findElement(evt.getX(), evt.getY()); |
1117 |
|
|
1118 |
|
|
1119 |
0 |
int mouseX = evt.getX(); |
1120 |
0 |
int mouseY = evt.getY(); |
1121 |
|
|
1122 |
0 |
if (ob instanceof BinaryNode) |
1123 |
|
{ |
1124 |
0 |
highlightNode = (BinaryNode) ob; |
1125 |
0 |
this.setToolTipText( |
1126 |
|
"<html>" + MessageManager.getString("label.highlightnode")); |
1127 |
0 |
repaint(); |
1128 |
|
|
1129 |
|
} |
1130 |
|
else |
1131 |
|
{ |
1132 |
|
|
1133 |
0 |
if (highlightNode != null) |
1134 |
|
{ |
1135 |
0 |
highlightNode = null; |
1136 |
0 |
setToolTipText(null); |
1137 |
0 |
repaint(); |
1138 |
|
} |
1139 |
|
|
1140 |
|
|
1141 |
0 |
for (Map.Entry<BinaryNode, List<Rectangle>> entry : labelBoundsMap.entrySet()) { |
1142 |
0 |
BinaryNode node = entry.getKey(); |
1143 |
0 |
List<Rectangle> boundsList = entry.getValue(); |
1144 |
|
|
1145 |
|
|
1146 |
0 |
for (Rectangle labelBounds : boundsList) { |
1147 |
0 |
if (labelBounds.contains(mouseX, mouseY)) { |
1148 |
|
|
1149 |
0 |
String nodeLabel = node.getDisplayName(); |
1150 |
0 |
this.setToolTipText(nodeLabel); |
1151 |
0 |
repaint(); |
1152 |
0 |
return; |
1153 |
|
} |
1154 |
|
} |
1155 |
|
} |
1156 |
|
|
1157 |
0 |
setToolTipText(null); |
1158 |
0 |
repaint(); |
1159 |
|
|
1160 |
|
} |
1161 |
|
} |
1162 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
1163 |
0 |
@Override... |
1164 |
|
public void mouseDragged(MouseEvent ect) |
1165 |
|
{ |
1166 |
|
} |
1167 |
|
|
1168 |
|
|
1169 |
|
|
1170 |
|
|
1171 |
|
|
1172 |
|
|
1173 |
|
|
1174 |
|
@param |
1175 |
|
|
|
|
| 0% |
Uncovered Elements: 55 (55) |
Complexity: 10 |
Complexity Density: 0.27 |
|
1176 |
0 |
@Override... |
1177 |
|
public void mousePressed(MouseEvent e) |
1178 |
|
{ |
1179 |
0 |
av.setCurrentTree(tree); |
1180 |
|
|
1181 |
|
|
1182 |
|
|
1183 |
|
|
1184 |
|
|
1185 |
0 |
if (e.isPopupTrigger()) |
1186 |
|
{ |
1187 |
0 |
if (highlightNode != null) |
1188 |
|
{ |
1189 |
0 |
chooseSubtreeColour(); |
1190 |
|
} |
1191 |
0 |
return; |
1192 |
|
} |
1193 |
|
|
1194 |
|
|
1195 |
|
|
1196 |
|
|
1197 |
|
|
1198 |
|
|
1199 |
|
|
1200 |
0 |
if (SwingUtilities.isRightMouseButton(e)) |
1201 |
|
{ |
1202 |
0 |
return; |
1203 |
|
} |
1204 |
|
|
1205 |
0 |
int x = e.getX(); |
1206 |
0 |
int y = e.getY(); |
1207 |
|
|
1208 |
0 |
Object ob = findElement(x, y); |
1209 |
|
|
1210 |
0 |
if (ob instanceof SequenceI) |
1211 |
|
{ |
1212 |
0 |
treeSelectionChanged((Sequence) ob); |
1213 |
0 |
PaintRefresher.Refresh(tp, |
1214 |
|
getAssociatedPanel().av.getSequenceSetId()); |
1215 |
0 |
repaint(); |
1216 |
0 |
av.sendSelection(); |
1217 |
0 |
return; |
1218 |
|
} |
1219 |
0 |
else if (!(ob instanceof BinaryNode)) |
1220 |
|
{ |
1221 |
|
|
1222 |
0 |
if (tree.getMaxHeight() != 0) |
1223 |
|
{ |
1224 |
0 |
threshold = (float) (x - offx) |
1225 |
|
/ (float) (getWidth() - labelLength - (2 * offx)); |
1226 |
|
|
1227 |
0 |
List<BinaryNode> groups = tree.groupNodes(threshold); |
1228 |
0 |
setColor(tree.getTopNode(), Color.black); |
1229 |
|
|
1230 |
0 |
AlignmentPanel[] aps = getAssociatedPanels(); |
1231 |
|
|
1232 |
|
|
1233 |
|
|
1234 |
0 |
for (int a = 0; a < aps.length; a++) |
1235 |
|
{ |
1236 |
0 |
aps[a].av.setSelectionGroup(null); |
1237 |
0 |
aps[a].av.getAlignment().deleteAllGroups(); |
1238 |
0 |
aps[a].av.clearSequenceColours(); |
1239 |
0 |
if (aps[a].av.getCodingComplement() != null) |
1240 |
|
{ |
1241 |
0 |
aps[a].av.getCodingComplement().setSelectionGroup(null); |
1242 |
0 |
aps[a].av.getCodingComplement().getAlignment() |
1243 |
|
.deleteAllGroups(); |
1244 |
0 |
aps[a].av.getCodingComplement().clearSequenceColours(); |
1245 |
|
} |
1246 |
0 |
aps[a].av.setUpdateStructures(true); |
1247 |
|
} |
1248 |
0 |
colourGroups(groups); |
1249 |
|
|
1250 |
|
|
1251 |
|
|
1252 |
|
|
1253 |
|
|
1254 |
0 |
if (groups.isEmpty()) |
1255 |
|
{ |
1256 |
0 |
threshold = 0f; |
1257 |
|
} |
1258 |
|
} |
1259 |
0 |
Console.log.debug("Tree cut threshold set at:" + threshold); |
1260 |
0 |
PaintRefresher.Refresh(tp, |
1261 |
|
getAssociatedPanel().av.getSequenceSetId()); |
1262 |
0 |
repaint(); |
1263 |
|
} |
1264 |
|
|
1265 |
|
} |
1266 |
|
|
|
|
| 0% |
Uncovered Elements: 40 (40) |
Complexity: 8 |
Complexity Density: 0.31 |
|
1267 |
0 |
void colourGroups(List<BinaryNode> groups)... |
1268 |
|
{ |
1269 |
0 |
AlignmentPanel[] aps = getAssociatedPanels(); |
1270 |
0 |
List<BitSet> colGroups = new ArrayList<>(); |
1271 |
0 |
Map<BitSet, Color> colors = new HashMap(); |
1272 |
0 |
for (int i = 0; i < groups.size(); i++) |
1273 |
|
{ |
1274 |
0 |
Color col = ColorUtils.getARandomColor(); |
1275 |
|
|
1276 |
0 |
setColor(groups.get(i), col.brighter()); |
1277 |
|
|
1278 |
0 |
Vector<BinaryNode> l = tree.findLeaves(groups.get(i)); |
1279 |
|
|
1280 |
0 |
if (!tp.isColumnWise()) |
1281 |
|
{ |
1282 |
0 |
createSeqGroupFor(aps, l, col, groups.get(i).getLabel()); |
1283 |
|
} |
1284 |
|
else |
1285 |
|
{ |
1286 |
0 |
BitSet gp = createColumnGroupFor(l, col); |
1287 |
|
|
1288 |
0 |
colGroups.add(gp); |
1289 |
0 |
colors.put(gp, col); |
1290 |
|
} |
1291 |
|
} |
1292 |
0 |
if (tp.isColumnWise()) |
1293 |
|
{ |
1294 |
0 |
AlignmentAnnotation aa = tp.getAssocAnnotation(); |
1295 |
0 |
if (aa != null) |
1296 |
|
{ |
1297 |
0 |
ContactMatrixI cm = av.getContactMatrix(aa); |
1298 |
0 |
if (cm != null) |
1299 |
|
{ |
1300 |
0 |
cm.updateGroups(colGroups); |
1301 |
0 |
for (BitSet gp : colors.keySet()) |
1302 |
|
{ |
1303 |
0 |
cm.setColorForGroup(gp, colors.get(gp)); |
1304 |
|
} |
1305 |
|
} |
1306 |
0 |
cm.transferGroupColorsTo(aa); |
1307 |
|
} |
1308 |
|
} |
1309 |
|
|
1310 |
|
|
1311 |
|
|
1312 |
0 |
for (int a = 0; a < aps.length; a++) |
1313 |
|
{ |
1314 |
0 |
aps[a].updateAnnotation(); |
1315 |
0 |
final AlignViewportI codingComplement = aps[a].av |
1316 |
|
.getCodingComplement(); |
1317 |
0 |
if (codingComplement != null) |
1318 |
|
{ |
1319 |
0 |
((AlignViewport) codingComplement).getAlignPanel() |
1320 |
|
.updateAnnotation(); |
1321 |
|
} |
1322 |
|
} |
1323 |
|
} |
1324 |
|
|
|
|
| 0% |
Uncovered Elements: 16 (16) |
Complexity: 3 |
Complexity Density: 0.25 |
|
1325 |
0 |
private void gatherLabelsTo(BinaryNode binaryNode, Vector<BinaryNode> l)... |
1326 |
|
{ |
1327 |
0 |
LinkedHashSet<String> labelsForNode = new LinkedHashSet<String>(); |
1328 |
0 |
for (BinaryNode leaf : l) |
1329 |
|
{ |
1330 |
0 |
if (leaf.hasLabel()) |
1331 |
|
{ |
1332 |
0 |
labelsForNode.add(leaf.getLabel()); |
1333 |
|
} |
1334 |
|
} |
1335 |
0 |
StringBuilder sb = new StringBuilder(); |
1336 |
0 |
boolean first = true; |
1337 |
0 |
for (String label : labelsForNode) |
1338 |
|
{ |
1339 |
0 |
if (!first) |
1340 |
|
{ |
1341 |
0 |
sb.append(" | "); |
1342 |
|
} |
1343 |
0 |
first = false; |
1344 |
|
|
1345 |
|
|
1346 |
|
|
1347 |
|
|
1348 |
0 |
sb.append(label); |
1349 |
|
|
1350 |
|
} |
1351 |
0 |
binaryNode.setLabel(sb.toString()); |
1352 |
|
} |
1353 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1354 |
0 |
private int parseColumnNode(BinaryNode bn) throws NumberFormatException... |
1355 |
|
{ |
1356 |
0 |
return Integer.parseInt( |
1357 |
|
bn.getName().substring(bn.getName().indexOf("c") + 1)); |
1358 |
|
} |
1359 |
|
|
|
|
| 0% |
Uncovered Elements: 42 (42) |
Complexity: 10 |
Complexity Density: 0.36 |
|
1360 |
0 |
private boolean isColumnForNodeSelected(BinaryNode bn)... |
1361 |
|
{ |
1362 |
0 |
SequenceI rseq = tp.assocAnnotation.sequenceRef; |
1363 |
0 |
int colm = -1; |
1364 |
0 |
try |
1365 |
|
{ |
1366 |
0 |
colm = parseColumnNode(bn); |
1367 |
|
} catch (Exception e) |
1368 |
|
{ |
1369 |
0 |
return false; |
1370 |
|
} |
1371 |
0 |
if (av == null || av.getAlignment() == null) |
1372 |
|
{ |
1373 |
|
|
1374 |
0 |
return false; |
1375 |
|
} |
1376 |
0 |
ColumnSelection cs = av.getColumnSelection(); |
1377 |
0 |
HiddenColumns hc = av.getAlignment().getHiddenColumns(); |
1378 |
0 |
AlignmentAnnotation aa = tp.getAssocAnnotation(); |
1379 |
0 |
int offp = -1; |
1380 |
0 |
if (aa != null) |
1381 |
|
{ |
1382 |
0 |
ContactMatrixI cm = av.getContactMatrix(aa); |
1383 |
|
|
1384 |
|
|
1385 |
|
|
1386 |
0 |
if (cm instanceof MappableContactMatrixI) |
1387 |
|
{ |
1388 |
0 |
int[] pos; |
1389 |
|
|
1390 |
|
|
1391 |
0 |
MappableContactMatrixI mcm = (MappableContactMatrixI) cm; |
1392 |
0 |
pos = mcm.getMappedPositionsFor(rseq, colm + 1); |
1393 |
|
|
1394 |
0 |
if (pos != null) |
1395 |
|
{ |
1396 |
0 |
offp = rseq.findIndex(pos[0]); |
1397 |
|
} |
1398 |
|
} |
1399 |
|
else |
1400 |
|
{ |
1401 |
0 |
offp = colm; |
1402 |
|
} |
1403 |
|
} |
1404 |
0 |
if (offp <= 0) |
1405 |
|
{ |
1406 |
0 |
return false; |
1407 |
|
} |
1408 |
|
|
1409 |
0 |
offp -= 2; |
1410 |
0 |
if (!av.hasHiddenColumns()) |
1411 |
|
{ |
1412 |
0 |
return cs.contains(offp); |
1413 |
|
} |
1414 |
0 |
if (hc.isVisible(offp)) |
1415 |
|
{ |
1416 |
0 |
return cs.contains(offp); |
1417 |
|
|
1418 |
|
} |
1419 |
0 |
return false; |
1420 |
|
} |
1421 |
|
|
|
|
| 0% |
Uncovered Elements: 12 (12) |
Complexity: 4 |
Complexity Density: 0.4 |
|
1422 |
0 |
private BitSet createColumnGroupFor(Vector<BinaryNode> l, Color col)... |
1423 |
|
{ |
1424 |
0 |
BitSet gp = new BitSet(); |
1425 |
0 |
for (BinaryNode bn : l) |
1426 |
|
{ |
1427 |
0 |
int colm = -1; |
1428 |
0 |
if (bn.element() != null && bn.element() instanceof Integer) |
1429 |
|
{ |
1430 |
0 |
colm = (Integer) bn.element(); |
1431 |
|
} |
1432 |
|
else |
1433 |
|
{ |
1434 |
|
|
1435 |
0 |
try |
1436 |
|
{ |
1437 |
0 |
colm = parseColumnNode(bn); |
1438 |
|
} catch (Exception e) |
1439 |
|
{ |
1440 |
0 |
continue; |
1441 |
|
} |
1442 |
|
} |
1443 |
0 |
gp.set(colm); |
1444 |
|
} |
1445 |
0 |
return gp; |
1446 |
|
} |
1447 |
|
|
|
|
| 0% |
Uncovered Elements: 40 (40) |
Complexity: 12 |
Complexity Density: 0.46 |
|
1448 |
0 |
private void markColumnsFor(AlignmentPanel[] aps, Vector<BinaryNode> l,... |
1449 |
|
Color col, boolean clearSelected) |
1450 |
|
{ |
1451 |
0 |
SequenceI rseq = tp.assocAnnotation.sequenceRef; |
1452 |
0 |
if (av == null || av.getAlignment() == null) |
1453 |
|
{ |
1454 |
|
|
1455 |
0 |
return; |
1456 |
|
} |
1457 |
|
|
1458 |
|
|
1459 |
0 |
ColumnSelection cs = av.getColumnSelection(); |
1460 |
0 |
HiddenColumns hc = av.getAlignment().getHiddenColumns(); |
1461 |
0 |
ContactMatrixI cm = av.getContactMatrix(tp.assocAnnotation); |
1462 |
0 |
MappableContactMatrixI mcm = null; |
1463 |
0 |
int offp; |
1464 |
0 |
if (cm instanceof MappableContactMatrixI) |
1465 |
|
{ |
1466 |
0 |
mcm = (MappableContactMatrixI) cm; |
1467 |
|
} |
1468 |
0 |
for (BinaryNode bn : l) |
1469 |
|
{ |
1470 |
0 |
int colm = -1; |
1471 |
0 |
try |
1472 |
|
{ |
1473 |
0 |
colm = Integer.parseInt( |
1474 |
|
bn.getName().substring(bn.getName().indexOf("c") + 1)); |
1475 |
|
} catch (Exception e) |
1476 |
|
{ |
1477 |
0 |
continue; |
1478 |
|
} |
1479 |
0 |
if (mcm != null) |
1480 |
|
{ |
1481 |
0 |
int[] seqpos = mcm.getMappedPositionsFor(rseq, colm); |
1482 |
0 |
if (seqpos == null) |
1483 |
|
{ |
1484 |
|
|
1485 |
0 |
continue; |
1486 |
|
} |
1487 |
|
|
1488 |
0 |
offp = rseq.findIndex(seqpos[0]) - 1; |
1489 |
|
} |
1490 |
|
else |
1491 |
|
{ |
1492 |
0 |
offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm) |
1493 |
|
: colm; |
1494 |
|
} |
1495 |
0 |
if (!av.hasHiddenColumns() || hc.isVisible(offp)) |
1496 |
|
{ |
1497 |
0 |
if (clearSelected || cs.contains(offp)) |
1498 |
|
{ |
1499 |
0 |
cs.removeElement(offp); |
1500 |
|
} |
1501 |
|
else |
1502 |
|
{ |
1503 |
0 |
cs.addElement(offp); |
1504 |
|
} |
1505 |
|
} |
1506 |
|
} |
1507 |
0 |
PaintRefresher.Refresh(tp, av.getSequenceSetId()); |
1508 |
|
} |
1509 |
|
|
|
|
| 0% |
Uncovered Elements: 61 (61) |
Complexity: 13 |
Complexity Density: 0.32 |
|
1510 |
0 |
public void createSeqGroupFor(AlignmentPanel[] aps, Vector<BinaryNode> l,... |
1511 |
|
Color col, String label) |
1512 |
|
{ |
1513 |
|
|
1514 |
0 |
Vector<SequenceI> sequences = new Vector<>(); |
1515 |
|
|
1516 |
0 |
for (int j = 0; j < l.size(); j++) |
1517 |
|
{ |
1518 |
0 |
SequenceI s1 = (SequenceI) l.elementAt(j).element(); |
1519 |
|
|
1520 |
0 |
if (!sequences.contains(s1)) |
1521 |
|
{ |
1522 |
0 |
sequences.addElement(s1); |
1523 |
|
} |
1524 |
|
} |
1525 |
|
|
1526 |
0 |
ColourSchemeI cs = null; |
1527 |
0 |
SequenceGroup _sg = new SequenceGroup(sequences, null, cs, true, true, |
1528 |
|
false, 0, av.getAlignment().getWidth() - 1); |
1529 |
|
|
1530 |
|
|
1531 |
0 |
if(label != null && !label.isEmpty()) { |
1532 |
|
|
1533 |
0 |
List<SequenceGroup> existingGroups = av.getAlignment().getGroups(); |
1534 |
|
|
1535 |
|
|
1536 |
0 |
label = AlignmentUtils.reduceLabelLength(label); |
1537 |
|
|
1538 |
|
|
1539 |
0 |
String newGroupName = "JTreeGroup:" + label; |
1540 |
|
|
1541 |
|
|
1542 |
0 |
int noOfGroupsWithSameName = 0; |
1543 |
|
|
1544 |
|
|
1545 |
0 |
for (SequenceGroup sg : existingGroups) { |
1546 |
0 |
if (sg.getName().equals(newGroupName) || sg.getName().matches(newGroupName + " \\d+")) { |
1547 |
|
|
1548 |
0 |
noOfGroupsWithSameName++; |
1549 |
|
|
1550 |
|
|
1551 |
0 |
if(sg.getName().equals(newGroupName) ) { |
1552 |
0 |
String updatedGroupName = sg.getName() + " " + noOfGroupsWithSameName; |
1553 |
0 |
sg.setName(updatedGroupName); |
1554 |
|
} |
1555 |
|
} |
1556 |
|
} |
1557 |
|
|
1558 |
|
|
1559 |
0 |
if(noOfGroupsWithSameName>0) { |
1560 |
0 |
noOfGroupsWithSameName++; |
1561 |
0 |
newGroupName = newGroupName + " " + noOfGroupsWithSameName; |
1562 |
|
} |
1563 |
|
|
1564 |
0 |
_sg.setName(newGroupName); |
1565 |
|
} |
1566 |
|
else { |
1567 |
0 |
_sg.setName("JTreeGroup:" + _sg.hashCode()); |
1568 |
|
} |
1569 |
0 |
_sg.setIdColour(col); |
1570 |
|
|
1571 |
0 |
for (int a = 0; a < aps.length; a++) |
1572 |
|
{ |
1573 |
0 |
SequenceGroup sg = new SequenceGroup(_sg); |
1574 |
0 |
AlignViewport viewport = aps[a].av; |
1575 |
|
|
1576 |
|
|
1577 |
0 |
if (viewport.getGlobalColourScheme() != null) |
1578 |
|
{ |
1579 |
0 |
cs = viewport.getGlobalColourScheme().getInstance(viewport, sg); |
1580 |
0 |
sg.setColourScheme(cs); |
1581 |
0 |
sg.getGroupColourScheme().setThreshold( |
1582 |
|
viewport.getResidueShading().getThreshold(), |
1583 |
|
viewport.isIgnoreGapsConsensus()); |
1584 |
|
|
1585 |
0 |
if (viewport.getResidueShading().conservationApplied()) |
1586 |
|
{ |
1587 |
0 |
Conservation c = new Conservation("Group", sg.getSequences(null), |
1588 |
|
sg.getStartRes(), sg.getEndRes()); |
1589 |
0 |
c.calculate(); |
1590 |
0 |
c.verdict(false, viewport.getConsPercGaps()); |
1591 |
0 |
sg.cs.setConservation(c); |
1592 |
|
} |
1593 |
0 |
if (viewport.getResidueShading() |
1594 |
|
.isConsensusSecondaryStructureColouring()) |
1595 |
|
{ |
1596 |
0 |
sg.getGroupColourScheme().setConsensusSecondaryStructureThreshold( |
1597 |
|
viewport.getResidueShading().getThreshold()); |
1598 |
0 |
sg.getGroupColourScheme() |
1599 |
|
.setConsensusSecondaryStructureColouring(true); |
1600 |
|
} |
1601 |
|
} |
1602 |
|
|
1603 |
0 |
viewport.setUpdateStructures(true); |
1604 |
|
|
1605 |
0 |
viewport.addSequenceGroup(sg); |
1606 |
|
} |
1607 |
|
} |
1608 |
|
|
1609 |
|
|
1610 |
|
|
1611 |
|
|
1612 |
|
@param |
1613 |
|
|
1614 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1615 |
40 |
public void setShowDistances(boolean state)... |
1616 |
|
{ |
1617 |
40 |
this.showDistances = state; |
1618 |
40 |
repaint(); |
1619 |
|
} |
1620 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
1621 |
0 |
public void hideStructureProviders(boolean state)... |
1622 |
|
{ |
1623 |
0 |
if(state) { |
1624 |
0 |
this.showStructureProviderColouredLines = false; |
1625 |
0 |
this.showStructureProviderLabels = false; |
1626 |
0 |
repaint(); |
1627 |
|
} |
1628 |
|
} |
1629 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
1630 |
0 |
public void setShowStructureProviderColouredLines(boolean state)... |
1631 |
|
{ |
1632 |
0 |
this.showStructureProviderColouredLines = state; |
1633 |
0 |
if(state) { |
1634 |
0 |
this.showStructureProviderLabels = false; |
1635 |
|
} |
1636 |
0 |
repaint(); |
1637 |
|
} |
1638 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
1639 |
0 |
public void setShowStructureProviderLabels(boolean state)... |
1640 |
|
{ |
1641 |
0 |
this.showStructureProviderLabels = state; |
1642 |
0 |
if(state) { |
1643 |
0 |
this.showStructureProviderColouredLines = false; |
1644 |
|
} |
1645 |
0 |
repaint(); |
1646 |
|
} |
1647 |
|
|
1648 |
|
|
1649 |
|
|
1650 |
|
|
1651 |
|
|
1652 |
|
@param |
1653 |
|
|
1654 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1655 |
26 |
public void setShowBootstrap(boolean state)... |
1656 |
|
{ |
1657 |
26 |
this.showBootstrap = state; |
1658 |
26 |
repaint(); |
1659 |
|
} |
1660 |
|
|
1661 |
|
|
1662 |
|
|
1663 |
|
|
1664 |
|
@param |
1665 |
|
|
1666 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1667 |
26 |
public void setMarkPlaceholders(boolean state)... |
1668 |
|
{ |
1669 |
26 |
this.markPlaceholders = state; |
1670 |
26 |
repaint(); |
1671 |
|
} |
1672 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1673 |
0 |
AlignmentPanel[] getAssociatedPanels()... |
1674 |
|
{ |
1675 |
0 |
if (applyToAllViews) |
1676 |
|
{ |
1677 |
0 |
return PaintRefresher.getAssociatedPanels(av.getSequenceSetId()); |
1678 |
|
} |
1679 |
|
else |
1680 |
|
{ |
1681 |
0 |
return new AlignmentPanel[] { getAssociatedPanel() }; |
1682 |
|
} |
1683 |
|
} |
1684 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1685 |
32 |
public AlignmentPanel getAssociatedPanel()... |
1686 |
|
{ |
1687 |
32 |
return ap; |
1688 |
|
} |
1689 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1690 |
14 |
public void setAssociatedPanel(AlignmentPanel ap)... |
1691 |
|
{ |
1692 |
14 |
this.ap = ap; |
1693 |
|
} |
1694 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1695 |
4 |
public AlignViewport getViewport()... |
1696 |
|
{ |
1697 |
4 |
return av; |
1698 |
|
} |
1699 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1700 |
0 |
public void setViewport(AlignViewport av)... |
1701 |
|
{ |
1702 |
0 |
this.av = av; |
1703 |
|
} |
1704 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1705 |
4 |
public float getThreshold()... |
1706 |
|
{ |
1707 |
4 |
return threshold; |
1708 |
|
} |
1709 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1710 |
12 |
public void setThreshold(float threshold)... |
1711 |
|
{ |
1712 |
12 |
this.threshold = threshold; |
1713 |
|
} |
1714 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1715 |
4 |
public boolean isApplyToAllViews()... |
1716 |
|
{ |
1717 |
4 |
return this.applyToAllViews; |
1718 |
|
} |
1719 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1720 |
12 |
public void setApplyToAllViews(boolean applyToAllViews)... |
1721 |
|
{ |
1722 |
12 |
this.applyToAllViews = applyToAllViews; |
1723 |
|
} |
1724 |
|
} |