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package jalview.gui; |
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import jalview.analysis.AlignmentSorter; |
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import jalview.analysis.AverageDistanceTree; |
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import jalview.analysis.NJTree; |
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import jalview.analysis.TreeBuilder; |
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import jalview.analysis.TreeModel; |
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import jalview.analysis.scoremodels.ScoreModels; |
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import jalview.api.analysis.ScoreModelI; |
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import jalview.api.analysis.SimilarityParamsI; |
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import jalview.commands.CommandI; |
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import jalview.commands.OrderCommand; |
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import jalview.datamodel.Alignment; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.AlignmentView; |
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import jalview.datamodel.BinaryNode; |
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import jalview.datamodel.DBRefEntry; |
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import jalview.datamodel.HiddenColumns; |
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import jalview.datamodel.NodeTransformI; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceI; |
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import jalview.datamodel.SequenceNode; |
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import jalview.gui.ImageExporter.ImageWriterI; |
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import jalview.io.JalviewFileChooser; |
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import jalview.io.JalviewFileView; |
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import jalview.io.NewickFile; |
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import jalview.jbgui.GTreePanel; |
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import jalview.util.ImageMaker.TYPE; |
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import jalview.util.MessageManager; |
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import jalview.viewmodel.AlignmentViewport; |
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import java.awt.Font; |
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import java.awt.Graphics; |
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import java.awt.event.ActionEvent; |
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import java.awt.event.ActionListener; |
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import java.beans.PropertyChangeEvent; |
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import java.beans.PropertyChangeListener; |
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import java.io.File; |
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import java.io.FileOutputStream; |
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import java.util.ArrayList; |
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import java.util.List; |
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import javax.swing.ButtonGroup; |
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import javax.swing.JMenuItem; |
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import javax.swing.JRadioButtonMenuItem; |
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import javax.swing.event.InternalFrameAdapter; |
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import javax.swing.event.InternalFrameEvent; |
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import org.jibble.epsgraphics.EpsGraphics2D; |
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@author |
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@version |
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| 25.8% |
Uncovered Elements: 201 (271) |
Complexity: 72 |
Complexity Density: 0.39 |
|
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public class TreePanel extends GTreePanel |
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{ |
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String treeType; |
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String scoreModelName; |
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String treeTitle; |
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SimilarityParamsI similarityParams; |
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TreeCanvas treeCanvas; |
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TreeModel tree; |
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AlignViewport av; |
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@param |
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@param |
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@param |
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@param |
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| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
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public TreePanel(AlignmentPanel ap, String type, String modelName,... |
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SimilarityParamsI options) |
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{ |
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super(); |
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this.similarityParams = options; |
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initTreePanel(ap, type, modelName, null, null); |
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} |
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| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
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public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,... |
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String theTitle, AlignmentView inputData) |
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{ |
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super(); |
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this.treeTitle = theTitle; |
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initTreePanel(alignPanel, null, null, newtree, inputData); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public AlignmentI getAlignment()... |
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{ |
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return treeCanvas.av.getAlignment(); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public AlignmentViewport getViewPort()... |
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{ |
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return treeCanvas.av; |
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} |
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| 100% |
Uncovered Elements: 0 (11) |
Complexity: 1 |
Complexity Density: 0.09 |
|
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void initTreePanel(AlignmentPanel ap, String type, String modelName,... |
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NewickFile newTree, AlignmentView inputData) |
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{ |
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av = ap.av; |
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this.treeType = type; |
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this.scoreModelName = modelName; |
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treeCanvas = new TreeCanvas(this, ap, scrollPane); |
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scrollPane.setViewportView(treeCanvas); |
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PaintRefresher.Register(this, ap.av.getSequenceSetId()); |
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buildAssociatedViewMenu(); |
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final PropertyChangeListener listener = addAlignmentListener(); |
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addInternalFrameListener(new InternalFrameAdapter() |
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{ |
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| 75% |
Uncovered Elements: 1 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
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@Override... |
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public void internalFrameClosed(InternalFrameEvent evt) |
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{ |
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if (av != null) |
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{ |
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av.removePropertyChangeListener(listener); |
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} |
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} |
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}); |
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TreeLoader tl = new TreeLoader(newTree, inputData); |
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tl.start(); |
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} |
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@return |
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| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
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protected PropertyChangeListener addAlignmentListener()... |
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{ |
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final PropertyChangeListener listener = new PropertyChangeListener() |
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{ |
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| 0% |
Uncovered Elements: 15 (15) |
Complexity: 4 |
Complexity Density: 0.44 |
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@Override... |
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public void propertyChange(PropertyChangeEvent evt) |
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{ |
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if (evt.getPropertyName().equals("alignment")) |
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{ |
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if (tree == null) |
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{ |
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System.out.println("tree is null"); |
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return; |
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} |
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if (evt.getNewValue() == null) |
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{ |
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System.out.println( |
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"new alignment sequences vector value is null"); |
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} |
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tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue()); |
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treeCanvas.nameHash.clear(); |
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repaint(); |
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} |
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} |
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}; |
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av.addPropertyChangeListener(listener); |
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return listener; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
206 |
0 |
@Override... |
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public void viewMenu_menuSelected() |
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{ |
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buildAssociatedViewMenu(); |
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} |
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| 86.2% |
Uncovered Elements: 4 (29) |
Complexity: 5 |
Complexity Density: 0.22 |
|
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12 |
void buildAssociatedViewMenu()... |
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{ |
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AlignmentPanel[] aps = PaintRefresher |
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.getAssociatedPanels(av.getSequenceSetId()); |
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if (aps.length == 1 && treeCanvas.ap == aps[0]) |
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{ |
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associateLeavesMenu.setVisible(false); |
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return; |
220 |
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} |
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associateLeavesMenu.setVisible(true); |
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|
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if ((viewMenu |
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.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem)) |
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{ |
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viewMenu.insertSeparator(viewMenu.getItemCount() - 1); |
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} |
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associateLeavesMenu.removeAll(); |
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JRadioButtonMenuItem item; |
233 |
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ButtonGroup buttonGroup = new ButtonGroup(); |
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int i, iSize = aps.length; |
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final TreePanel thisTreePanel = this; |
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48 |
for (i = 0; i < iSize; i++) |
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{ |
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36 |
final AlignmentPanel ap = aps[i]; |
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item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap); |
240 |
36 |
buttonGroup.add(item); |
241 |
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item.addActionListener(new ActionListener() |
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{ |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
243 |
0 |
@Override... |
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public void actionPerformed(ActionEvent evt) |
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{ |
246 |
0 |
treeCanvas.applyToAllViews = false; |
247 |
0 |
treeCanvas.ap = ap; |
248 |
0 |
treeCanvas.av = ap.av; |
249 |
0 |
PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId()); |
250 |
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} |
251 |
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}); |
252 |
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|
253 |
36 |
associateLeavesMenu.add(item); |
254 |
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} |
255 |
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|
256 |
12 |
final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem( |
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MessageManager.getString("label.all_views")); |
258 |
12 |
buttonGroup.add(itemf); |
259 |
12 |
itemf.setSelected(treeCanvas.applyToAllViews); |
260 |
12 |
itemf.addActionListener(new ActionListener() |
261 |
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{ |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
262 |
0 |
@Override... |
263 |
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public void actionPerformed(ActionEvent evt) |
264 |
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{ |
265 |
0 |
treeCanvas.applyToAllViews = itemf.isSelected(); |
266 |
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} |
267 |
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}); |
268 |
12 |
associateLeavesMenu.add(itemf); |
269 |
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|
270 |
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} |
271 |
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| 65.6% |
Uncovered Elements: 11 (32) |
Complexity: 7 |
Complexity Density: 0.35 |
|
272 |
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class TreeLoader extends Thread |
273 |
|
{ |
274 |
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private NewickFile newtree; |
275 |
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|
276 |
|
private AlignmentView odata = null; |
277 |
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| 85.7% |
Uncovered Elements: 1 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
278 |
12 |
public TreeLoader(NewickFile newickFile, AlignmentView inputData)... |
279 |
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{ |
280 |
12 |
this.newtree = newickFile; |
281 |
12 |
this.odata = inputData; |
282 |
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|
283 |
12 |
if (newickFile != null) |
284 |
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{ |
285 |
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|
286 |
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|
287 |
12 |
showBootstrap(newickFile.HasBootstrap()); |
288 |
12 |
showDistances(newickFile.HasDistances()); |
289 |
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} |
290 |
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} |
291 |
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|
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| 56.5% |
Uncovered Elements: 10 (23) |
Complexity: 5 |
Complexity Density: 0.33 |
|
292 |
12 |
@Override... |
293 |
|
public void run() |
294 |
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{ |
295 |
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|
296 |
12 |
if (newtree != null) |
297 |
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{ |
298 |
12 |
tree = new TreeModel(av.getAlignment().getSequencesArray(), odata, |
299 |
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newtree); |
300 |
12 |
if (tree.getOriginalData() == null) |
301 |
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{ |
302 |
12 |
originalSeqData.setVisible(false); |
303 |
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} |
304 |
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} |
305 |
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else |
306 |
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{ |
307 |
0 |
ScoreModelI sm = ScoreModels.getInstance() |
308 |
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.getScoreModel(scoreModelName, treeCanvas.ap); |
309 |
0 |
TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) |
310 |
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? new NJTree(av, sm, similarityParams) |
311 |
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: new AverageDistanceTree(av, sm, similarityParams); |
312 |
0 |
tree = new TreeModel(njtree); |
313 |
0 |
showDistances(true); |
314 |
|
} |
315 |
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|
316 |
12 |
tree.reCount(tree.getTopNode()); |
317 |
12 |
tree.findHeight(tree.getTopNode()); |
318 |
12 |
treeCanvas.setTree(tree); |
319 |
12 |
treeCanvas.repaint(); |
320 |
12 |
av.setCurrentTree(tree); |
321 |
12 |
if (av.getSortByTree()) |
322 |
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{ |
323 |
0 |
sortByTree_actionPerformed(); |
324 |
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} |
325 |
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} |
326 |
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} |
327 |
|
|
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|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
328 |
24 |
public void showDistances(boolean b)... |
329 |
|
{ |
330 |
24 |
treeCanvas.setShowDistances(b); |
331 |
24 |
distanceMenu.setSelected(b); |
332 |
|
} |
333 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
334 |
24 |
public void showBootstrap(boolean b)... |
335 |
|
{ |
336 |
24 |
treeCanvas.setShowBootstrap(b); |
337 |
24 |
bootstrapMenu.setSelected(b); |
338 |
|
} |
339 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
340 |
12 |
public void showPlaceholders(boolean b)... |
341 |
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{ |
342 |
12 |
placeholdersMenu.setState(b); |
343 |
12 |
treeCanvas.setMarkPlaceholders(b); |
344 |
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} |
345 |
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|
346 |
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|
347 |
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|
348 |
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|
349 |
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@return |
350 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
351 |
16 |
public TreeModel getTree()... |
352 |
|
{ |
353 |
16 |
return tree; |
354 |
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} |
355 |
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|
356 |
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|
357 |
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|
358 |
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|
359 |
|
@param |
360 |
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|
361 |
|
|
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|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 2 |
Complexity Density: 0.25 |
|
362 |
0 |
@Override... |
363 |
|
public void textbox_actionPerformed(ActionEvent e) |
364 |
|
{ |
365 |
0 |
CutAndPasteTransfer cap = new CutAndPasteTransfer(); |
366 |
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|
367 |
0 |
String newTitle = getPanelTitle(); |
368 |
|
|
369 |
0 |
NewickFile fout = new NewickFile(tree.getTopNode()); |
370 |
0 |
try |
371 |
|
{ |
372 |
0 |
cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(), |
373 |
|
tree.hasRootDistance())); |
374 |
0 |
Desktop.addInternalFrame(cap, newTitle, 500, 100); |
375 |
|
} catch (OutOfMemoryError oom) |
376 |
|
{ |
377 |
0 |
new OOMWarning("generating newick tree file", oom); |
378 |
0 |
cap.dispose(); |
379 |
|
} |
380 |
|
|
381 |
|
} |
382 |
|
|
383 |
|
|
384 |
|
|
385 |
|
|
386 |
|
@param |
387 |
|
|
388 |
|
|
|
|
| 0% |
Uncovered Elements: 17 (17) |
Complexity: 3 |
Complexity Density: 0.2 |
|
389 |
0 |
@Override... |
390 |
|
public void saveAsNewick_actionPerformed(ActionEvent e) |
391 |
|
{ |
392 |
|
|
393 |
0 |
JalviewFileChooser chooser = new JalviewFileChooser( |
394 |
|
jalview.bin.Cache.getProperty("LAST_DIRECTORY")); |
395 |
0 |
chooser.setFileView(new JalviewFileView()); |
396 |
0 |
chooser.setDialogTitle( |
397 |
|
MessageManager.getString("label.save_tree_as_newick")); |
398 |
0 |
chooser.setToolTipText(MessageManager.getString("action.save")); |
399 |
|
|
400 |
0 |
int value = chooser.showSaveDialog(null); |
401 |
|
|
402 |
0 |
if (value == JalviewFileChooser.APPROVE_OPTION) |
403 |
|
{ |
404 |
0 |
String choice = chooser.getSelectedFile().getPath(); |
405 |
0 |
jalview.bin.Cache.setProperty("LAST_DIRECTORY", |
406 |
|
chooser.getSelectedFile().getParent()); |
407 |
|
|
408 |
0 |
try |
409 |
|
{ |
410 |
0 |
jalview.io.NewickFile fout = new jalview.io.NewickFile( |
411 |
|
tree.getTopNode()); |
412 |
0 |
String output = fout.print(tree.hasBootstrap(), tree.hasDistances(), |
413 |
|
tree.hasRootDistance()); |
414 |
0 |
java.io.PrintWriter out = new java.io.PrintWriter( |
415 |
|
new java.io.FileWriter(choice)); |
416 |
0 |
out.println(output); |
417 |
0 |
out.close(); |
418 |
|
} catch (Exception ex) |
419 |
|
{ |
420 |
0 |
ex.printStackTrace(); |
421 |
|
} |
422 |
|
} |
423 |
|
} |
424 |
|
|
425 |
|
|
426 |
|
|
427 |
|
|
428 |
|
@param |
429 |
|
|
430 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
431 |
0 |
@Override... |
432 |
|
public void printMenu_actionPerformed(ActionEvent e) |
433 |
|
{ |
434 |
|
|
435 |
0 |
treeCanvas.startPrinting(); |
436 |
|
} |
437 |
|
|
|
|
| 0% |
Uncovered Elements: 24 (24) |
Complexity: 8 |
Complexity Density: 0.5 |
|
438 |
0 |
@Override... |
439 |
|
public void originalSeqData_actionPerformed(ActionEvent e) |
440 |
|
{ |
441 |
0 |
AlignmentView originalData = tree.getOriginalData(); |
442 |
0 |
if (originalData == null) |
443 |
|
{ |
444 |
0 |
jalview.bin.Cache.log.info( |
445 |
|
"Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); |
446 |
0 |
return; |
447 |
|
} |
448 |
|
|
449 |
|
|
450 |
|
|
451 |
|
|
452 |
|
|
453 |
|
|
454 |
0 |
char gc = '-'; |
455 |
0 |
try |
456 |
|
{ |
457 |
|
|
458 |
|
|
459 |
0 |
gc = av.getGapCharacter(); |
460 |
|
|
461 |
|
} catch (Exception ex) |
462 |
|
{ |
463 |
|
} |
464 |
|
|
465 |
0 |
Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc); |
466 |
|
|
467 |
0 |
if (alAndColsel != null && alAndColsel[0] != null) |
468 |
|
{ |
469 |
|
|
470 |
|
|
471 |
0 |
AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]); |
472 |
0 |
AlignmentI dataset = (av != null && av.getAlignment() != null) |
473 |
|
? av.getAlignment().getDataset() |
474 |
|
: null; |
475 |
0 |
if (dataset != null) |
476 |
|
{ |
477 |
0 |
al.setDataset(dataset); |
478 |
|
} |
479 |
|
|
480 |
0 |
if (true) |
481 |
|
{ |
482 |
|
|
483 |
0 |
AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1], |
484 |
|
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); |
485 |
|
|
486 |
|
|
487 |
|
|
488 |
|
|
489 |
|
|
490 |
|
|
491 |
|
|
492 |
|
|
493 |
0 |
Desktop.addInternalFrame(af, MessageManager.formatMessage( |
494 |
|
"label.original_data_for_params", new Object[] |
495 |
|
{ this.title }), AlignFrame.DEFAULT_WIDTH, |
496 |
|
AlignFrame.DEFAULT_HEIGHT); |
497 |
|
} |
498 |
|
} |
499 |
|
} |
500 |
|
|
501 |
|
|
502 |
|
|
503 |
|
|
504 |
|
@param |
505 |
|
|
506 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
507 |
12 |
@Override... |
508 |
|
public void fitToWindow_actionPerformed(ActionEvent e) |
509 |
|
{ |
510 |
12 |
treeCanvas.fitToWindow = fitToWindow.isSelected(); |
511 |
12 |
repaint(); |
512 |
|
} |
513 |
|
|
514 |
|
|
515 |
|
|
516 |
|
|
517 |
|
@param |
518 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 2 |
Complexity Density: 0.25 |
|
519 |
0 |
@Override... |
520 |
|
public void sortByTree_actionPerformed() |
521 |
|
{ |
522 |
|
|
523 |
0 |
if (treeCanvas.applyToAllViews) |
524 |
|
{ |
525 |
0 |
final ArrayList<CommandI> commands = new ArrayList<>(); |
526 |
0 |
for (AlignmentPanel ap : PaintRefresher |
527 |
|
.getAssociatedPanels(av.getSequenceSetId())) |
528 |
|
{ |
529 |
0 |
commands.add(sortAlignmentIn(ap.av.getAlignPanel())); |
530 |
|
} |
531 |
0 |
av.getAlignPanel().alignFrame.addHistoryItem(new CommandI() |
532 |
|
{ |
533 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
534 |
0 |
@Override... |
535 |
|
public void undoCommand(AlignmentI[] views) |
536 |
|
{ |
537 |
0 |
for (CommandI tsort : commands) |
538 |
|
{ |
539 |
0 |
tsort.undoCommand(views); |
540 |
|
} |
541 |
|
} |
542 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
543 |
0 |
@Override... |
544 |
|
public int getSize() |
545 |
|
{ |
546 |
0 |
return commands.size(); |
547 |
|
} |
548 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
549 |
0 |
@Override... |
550 |
|
public String getDescription() |
551 |
|
{ |
552 |
0 |
return "Tree Sort (many views)"; |
553 |
|
} |
554 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
555 |
0 |
@Override... |
556 |
|
public void doCommand(AlignmentI[] views) |
557 |
|
{ |
558 |
|
|
559 |
0 |
for (CommandI tsort : commands) |
560 |
|
{ |
561 |
0 |
tsort.doCommand(views); |
562 |
|
} |
563 |
|
} |
564 |
|
}); |
565 |
0 |
for (AlignmentPanel ap : PaintRefresher |
566 |
|
.getAssociatedPanels(av.getSequenceSetId())) |
567 |
|
{ |
568 |
|
|
569 |
0 |
ap.alignFrame.updateEditMenuBar(); |
570 |
|
} |
571 |
|
} |
572 |
|
else |
573 |
|
{ |
574 |
0 |
treeCanvas.ap.alignFrame |
575 |
|
.addHistoryItem(sortAlignmentIn(treeCanvas.ap)); |
576 |
|
} |
577 |
|
|
578 |
|
} |
579 |
|
|
|
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 1 |
Complexity Density: 0.14 |
|
580 |
0 |
public CommandI sortAlignmentIn(AlignmentPanel ap)... |
581 |
|
{ |
582 |
|
|
583 |
0 |
AlignmentViewport viewport = ap.av; |
584 |
0 |
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
585 |
0 |
AlignmentSorter.sortByTree(viewport.getAlignment(), tree); |
586 |
0 |
CommandI undo; |
587 |
0 |
undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment()); |
588 |
|
|
589 |
0 |
ap.paintAlignment(true, false); |
590 |
0 |
return undo; |
591 |
|
} |
592 |
|
|
593 |
|
|
594 |
|
|
595 |
|
|
596 |
|
@param |
597 |
|
|
598 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
599 |
0 |
@Override... |
600 |
|
public void font_actionPerformed(ActionEvent e) |
601 |
|
{ |
602 |
0 |
if (treeCanvas == null) |
603 |
|
{ |
604 |
0 |
return; |
605 |
|
} |
606 |
|
|
607 |
0 |
new FontChooser(this); |
608 |
|
} |
609 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
610 |
6 |
public Font getTreeFont()... |
611 |
|
{ |
612 |
6 |
return treeCanvas.font; |
613 |
|
} |
614 |
|
|
|
|
| 75% |
Uncovered Elements: 1 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
615 |
12 |
public void setTreeFont(Font f)... |
616 |
|
{ |
617 |
12 |
if (treeCanvas != null) |
618 |
|
{ |
619 |
12 |
treeCanvas.setFont(f); |
620 |
|
} |
621 |
|
} |
622 |
|
|
623 |
|
|
624 |
|
|
625 |
|
|
626 |
|
@param |
627 |
|
|
628 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
629 |
0 |
@Override... |
630 |
|
public void distanceMenu_actionPerformed(ActionEvent e) |
631 |
|
{ |
632 |
0 |
treeCanvas.setShowDistances(distanceMenu.isSelected()); |
633 |
|
} |
634 |
|
|
635 |
|
|
636 |
|
|
637 |
|
|
638 |
|
@param |
639 |
|
|
640 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
641 |
0 |
@Override... |
642 |
|
public void bootstrapMenu_actionPerformed(ActionEvent e) |
643 |
|
{ |
644 |
0 |
treeCanvas.setShowBootstrap(bootstrapMenu.isSelected()); |
645 |
|
} |
646 |
|
|
647 |
|
|
648 |
|
|
649 |
|
|
650 |
|
@param |
651 |
|
|
652 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
653 |
0 |
@Override... |
654 |
|
public void placeholdersMenu_actionPerformed(ActionEvent e) |
655 |
|
{ |
656 |
0 |
treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected()); |
657 |
|
} |
658 |
|
|
659 |
|
|
660 |
|
|
661 |
|
|
662 |
|
|
663 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
|
664 |
0 |
@Override... |
665 |
|
public void writeTreeImage(TYPE imageFormat) |
666 |
|
{ |
667 |
0 |
int width = treeCanvas.getWidth(); |
668 |
0 |
int height = treeCanvas.getHeight(); |
669 |
0 |
ImageWriterI writer = new ImageWriterI() |
670 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
671 |
0 |
@Override... |
672 |
|
public void exportImage(Graphics g) throws Exception |
673 |
|
{ |
674 |
0 |
treeCanvas.draw(g, width, height); |
675 |
|
} |
676 |
|
}; |
677 |
0 |
String tree = MessageManager.getString("label.tree"); |
678 |
0 |
ImageExporter exporter = new ImageExporter(writer, null, imageFormat, |
679 |
|
tree); |
680 |
0 |
exporter.doExport(null, this, width, height, tree.toLowerCase()); |
681 |
|
} |
682 |
|
|
683 |
|
|
684 |
|
|
685 |
|
|
686 |
|
|
687 |
|
|
688 |
|
|
689 |
|
@param |
690 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
691 |
0 |
public void changeNames(final String labelClass)... |
692 |
|
{ |
693 |
0 |
tree.applyToNodes(new NodeTransformI() |
694 |
|
{ |
695 |
|
|
|
|
| 0% |
Uncovered Elements: 34 (34) |
Complexity: 11 |
Complexity Density: 0.61 |
|
696 |
0 |
@Override... |
697 |
|
public void transform(BinaryNode node) |
698 |
|
{ |
699 |
0 |
if (node instanceof SequenceNode |
700 |
|
&& !((SequenceNode) node).isPlaceholder() |
701 |
|
&& !((SequenceNode) node).isDummy()) |
702 |
|
{ |
703 |
0 |
String newname = null; |
704 |
0 |
SequenceI sq = (SequenceI) ((SequenceNode) node).element(); |
705 |
0 |
if (sq != null) |
706 |
|
{ |
707 |
|
|
708 |
0 |
DBRefEntry[] refs = jalview.util.DBRefUtils |
709 |
|
.selectRefs(sq.getDBRefs(), new String[] |
710 |
|
{ labelClass.toUpperCase() }); |
711 |
0 |
if (refs != null) |
712 |
|
{ |
713 |
0 |
for (int i = 0; i < refs.length; i++) |
714 |
|
{ |
715 |
0 |
if (newname == null) |
716 |
|
{ |
717 |
0 |
newname = new String(refs[i].getAccessionId()); |
718 |
|
} |
719 |
|
else |
720 |
|
{ |
721 |
0 |
newname = newname + "; " + refs[i].getAccessionId(); |
722 |
|
} |
723 |
|
} |
724 |
|
} |
725 |
0 |
if (newname == null) |
726 |
|
{ |
727 |
0 |
List<SequenceFeature> features = sq.getFeatures() |
728 |
|
.getPositionalFeatures(labelClass); |
729 |
0 |
for (SequenceFeature feature : features) |
730 |
|
{ |
731 |
0 |
if (newname == null) |
732 |
|
{ |
733 |
0 |
newname = feature.getDescription(); |
734 |
|
} |
735 |
|
else |
736 |
|
{ |
737 |
0 |
newname = newname + "; " + feature.getDescription(); |
738 |
|
} |
739 |
|
} |
740 |
|
} |
741 |
|
} |
742 |
0 |
if (newname != null) |
743 |
|
{ |
744 |
|
|
745 |
|
|
746 |
0 |
((SequenceNode) node).setName(newname); |
747 |
|
} |
748 |
|
} |
749 |
|
} |
750 |
|
}); |
751 |
|
} |
752 |
|
|
753 |
|
|
754 |
|
|
755 |
|
|
756 |
|
|
757 |
|
|
758 |
|
|
759 |
|
|
760 |
|
@return |
761 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
762 |
0 |
public String getPanelTitle()... |
763 |
|
{ |
764 |
0 |
if (treeTitle != null) |
765 |
|
{ |
766 |
0 |
return treeTitle; |
767 |
|
} |
768 |
|
|
769 |
|
|
770 |
|
|
771 |
|
|
772 |
0 |
String treecalcnm = MessageManager |
773 |
|
.getString("label.tree_calc_" + treeType.toLowerCase()); |
774 |
|
|
775 |
|
|
776 |
|
|
777 |
|
|
778 |
0 |
String smn = scoreModelName; |
779 |
|
|
780 |
|
|
781 |
|
|
782 |
|
|
783 |
0 |
final String ttl = MessageManager.formatMessage("label.treecalc_title", |
784 |
|
treecalcnm, smn); |
785 |
0 |
return ttl; |
786 |
|
} |
787 |
|
|
788 |
|
|
789 |
|
|
790 |
|
|
791 |
|
@param |
792 |
|
@param |
793 |
|
|
794 |
|
|
|
|
| 0% |
Uncovered Elements: 11 (11) |
Complexity: 2 |
Complexity Density: 0.18 |
|
795 |
0 |
protected void writeEpsFile(File outFile, boolean textOption)... |
796 |
|
{ |
797 |
0 |
try |
798 |
|
{ |
799 |
0 |
int width = treeCanvas.getWidth(); |
800 |
0 |
int height = treeCanvas.getHeight(); |
801 |
|
|
802 |
0 |
FileOutputStream out = new FileOutputStream( |
803 |
|
outFile); |
804 |
0 |
EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, |
805 |
|
height); |
806 |
0 |
pg.setAccurateTextMode(!textOption); |
807 |
0 |
treeCanvas.draw(pg, width, height); |
808 |
|
|
809 |
0 |
pg.flush(); |
810 |
0 |
pg.close(); |
811 |
|
} catch (Exception ex) |
812 |
|
{ |
813 |
0 |
System.err.println("Error writing tree as EPS"); |
814 |
0 |
ex.printStackTrace(); |
815 |
|
} |
816 |
|
} |
817 |
|
} |