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package jalview.gui; |
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import jalview.analysis.AlignSeq; |
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import jalview.datamodel.AlignmentAnnotation; |
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import jalview.datamodel.ColumnSelection; |
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import jalview.datamodel.HiddenColumns; |
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import jalview.datamodel.RnaViewerModel; |
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import jalview.datamodel.SequenceGroup; |
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import jalview.datamodel.SequenceI; |
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import jalview.ext.varna.RnaModel; |
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import jalview.structure.SecondaryStructureListener; |
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import jalview.structure.SelectionListener; |
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import jalview.structure.SelectionSource; |
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import jalview.structure.StructureSelectionManager; |
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import jalview.structure.VamsasSource; |
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import jalview.util.Comparison; |
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import jalview.util.MessageManager; |
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import jalview.util.ShiftList; |
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import java.awt.BorderLayout; |
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import java.awt.Color; |
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import java.util.Collection; |
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import java.util.Hashtable; |
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import java.util.LinkedHashMap; |
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import java.util.List; |
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import java.util.Map; |
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|
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import javax.swing.JInternalFrame; |
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import javax.swing.JSplitPane; |
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import javax.swing.event.InternalFrameAdapter; |
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import javax.swing.event.InternalFrameEvent; |
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import fr.orsay.lri.varna.VARNAPanel; |
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import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; |
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import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed; |
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import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses; |
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import fr.orsay.lri.varna.interfaces.InterfaceVARNASelectionListener; |
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import fr.orsay.lri.varna.models.BaseList; |
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import fr.orsay.lri.varna.models.FullBackup; |
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import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation; |
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import fr.orsay.lri.varna.models.rna.ModeleBase; |
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import fr.orsay.lri.varna.models.rna.RNA; |
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| 9.3% |
Uncovered Elements: 254 (280) |
Complexity: 73 |
Complexity Density: 0.4 |
|
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public class AppVarna extends JInternalFrame |
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implements SelectionListener, SecondaryStructureListener, |
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InterfaceVARNASelectionListener, VamsasSource |
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{ |
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private static final byte[] PAIRS = new byte[] { '(', ')', '[', ']', '{', |
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'}', '<', '>' }; |
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private AppVarnaBinding vab; |
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private AlignmentPanel ap; |
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private String viewId; |
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private StructureSelectionManager ssm; |
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private Map<RNA, RnaModel> models = new LinkedHashMap<RNA, RnaModel>(); |
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private Map<RNA, ShiftList> offsets = new Hashtable<RNA, ShiftList>(); |
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|
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private Map<RNA, ShiftList> offsetsInv = new Hashtable<RNA, ShiftList>(); |
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private JSplitPane split; |
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private VarnaHighlighter mouseOverHighlighter = new VarnaHighlighter(); |
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private VarnaHighlighter selectionHighlighter = new VarnaHighlighter(); |
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| 0% |
Uncovered Elements: 31 (31) |
Complexity: 10 |
Complexity Density: 0.53 |
|
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private class VarnaHighlighter |
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{ |
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private HighlightRegionAnnotation _lastHighlight; |
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|
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private RNA _lastRNAhighlighted = null; |
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|
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
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0 |
public VarnaHighlighter()... |
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{ |
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} |
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@param |
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| 0% |
Uncovered Elements: 6 (6) |
Complexity: 3 |
Complexity Density: 0.75 |
|
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public VarnaHighlighter(RNA rna)... |
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{ |
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_lastRNAhighlighted = rna; |
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List<HighlightRegionAnnotation> highlights = rna.getHighlightRegion(); |
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if (highlights != null && !highlights.isEmpty()) |
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{ |
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_lastHighlight = highlights.get(0); |
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} |
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} |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
|
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0 |
public void highlightRegion(RNA rna, int start, int end)... |
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{ |
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0 |
clearLastSelection(); |
126 |
0 |
HighlightRegionAnnotation highlight = new HighlightRegionAnnotation( |
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rna.getBasesBetween(start, end)); |
128 |
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rna.addHighlightRegion(highlight); |
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_lastHighlight = highlight; |
130 |
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_lastRNAhighlighted = rna; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
133 |
0 |
public HighlightRegionAnnotation getLastHighlight()... |
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{ |
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0 |
return _lastHighlight; |
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} |
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|
140 |
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| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
141 |
0 |
public void clearSelection()... |
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{ |
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0 |
if (_lastRNAhighlighted != null) |
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{ |
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_lastRNAhighlighted.getHighlightRegion().clear(); |
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0 |
vab.updateSelectedRNA(_lastRNAhighlighted); |
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_lastRNAhighlighted = null; |
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_lastHighlight = null; |
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} |
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} |
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153 |
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154 |
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| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
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0 |
public void clearLastSelection()... |
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{ |
157 |
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if (_lastRNAhighlighted != null) |
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{ |
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_lastRNAhighlighted.removeHighlightRegion(_lastHighlight); |
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_lastRNAhighlighted = null; |
161 |
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_lastHighlight = null; |
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} |
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} |
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} |
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@param |
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@param |
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@param |
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| 0% |
Uncovered Elements: 16 (16) |
Complexity: 3 |
Complexity Density: 0.25 |
|
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public AppVarna(SequenceI seq, AlignmentAnnotation aa, AlignmentPanel ap)... |
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{ |
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this(ap); |
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|
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String sname = aa.sequenceRef == null |
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? "secondary structure (alignment)" |
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: seq.getName() + " structure"; |
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String theTitle = sname |
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+ (aa.sequenceRef == null ? " trimmed to " + seq.getName() |
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: ""); |
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theTitle = MessageManager.formatMessage("label.varna_params", |
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new String[] |
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{ theTitle }); |
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setTitle(theTitle); |
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|
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0 |
String gappedTitle = sname + " (with gaps)"; |
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RnaModel gappedModel = new RnaModel(gappedTitle, aa, seq, null, true); |
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addModel(gappedModel, gappedTitle); |
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|
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String trimmedTitle = "trimmed " + sname; |
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RnaModel trimmedModel = new RnaModel(trimmedTitle, aa, seq, null, |
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false); |
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addModel(trimmedModel, trimmedTitle); |
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vab.setSelectedIndex(0); |
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} |
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203 |
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204 |
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|
206 |
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@param |
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|
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| 0% |
Uncovered Elements: 8 (8) |
Complexity: 1 |
Complexity Density: 0.12 |
|
208 |
0 |
protected AppVarna(AlignmentPanel ap)... |
209 |
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{ |
210 |
0 |
this.ap = ap; |
211 |
0 |
this.viewId = System.currentTimeMillis() + "." + this.hashCode(); |
212 |
0 |
vab = new AppVarnaBinding(); |
213 |
0 |
initVarna(); |
214 |
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|
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0 |
this.ssm = ap.getStructureSelectionManager(); |
216 |
0 |
ssm.addStructureViewerListener(this); |
217 |
0 |
ssm.addSelectionListener(this); |
218 |
0 |
addInternalFrameListener(new InternalFrameAdapter() |
219 |
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{ |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
220 |
0 |
@Override... |
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public void internalFrameClosed(InternalFrameEvent evt) |
222 |
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{ |
223 |
0 |
close(); |
224 |
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} |
225 |
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}); |
226 |
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} |
227 |
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|
231 |
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@param |
232 |
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@param |
233 |
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|
234 |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
|
235 |
0 |
public AppVarna(RnaViewerModel model, AlignmentPanel ap)... |
236 |
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{ |
237 |
0 |
this(ap); |
238 |
0 |
setTitle(model.title); |
239 |
0 |
this.viewId = model.viewId; |
240 |
0 |
setBounds(model.x, model.y, model.width, model.height); |
241 |
0 |
this.split.setDividerLocation(model.dividerLocation); |
242 |
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} |
243 |
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244 |
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245 |
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246 |
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247 |
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| 0% |
Uncovered Elements: 9 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
|
248 |
0 |
public void initVarna()... |
249 |
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{ |
250 |
0 |
VARNAPanel varnaPanel = vab.get_varnaPanel(); |
251 |
0 |
setBackground(Color.white); |
252 |
0 |
split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, true, |
253 |
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vab.getListPanel(), varnaPanel); |
254 |
0 |
getContentPane().setLayout(new BorderLayout()); |
255 |
0 |
getContentPane().add(split, BorderLayout.CENTER); |
256 |
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|
257 |
0 |
varnaPanel.addSelectionListener(this); |
258 |
0 |
jalview.gui.Desktop.addInternalFrame(this, "", getBounds().width, |
259 |
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getBounds().height); |
260 |
0 |
this.pack(); |
261 |
0 |
showPanel(true); |
262 |
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} |
263 |
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264 |
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265 |
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266 |
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267 |
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|
268 |
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@param |
269 |
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@param |
270 |
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@return |
271 |
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| 0% |
Uncovered Elements: 48 (48) |
Complexity: 11 |
Complexity Density: 0.31 |
|
272 |
0 |
public RNA trimRNA(RNA rna, String name)... |
273 |
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{ |
274 |
0 |
ShiftList offset = new ShiftList(); |
275 |
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|
276 |
0 |
RNA rnaTrim = new RNA(name); |
277 |
0 |
try |
278 |
|
{ |
279 |
0 |
String structDBN = rna.getStructDBN(true); |
280 |
0 |
rnaTrim.setRNA(rna.getSeq(), replaceOddGaps(structDBN)); |
281 |
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} catch (ExceptionUnmatchedClosingParentheses e2) |
282 |
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{ |
283 |
0 |
e2.printStackTrace(); |
284 |
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} catch (ExceptionFileFormatOrSyntax e3) |
285 |
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{ |
286 |
0 |
e3.printStackTrace(); |
287 |
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} |
288 |
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|
289 |
0 |
String seq = rnaTrim.getSeq(); |
290 |
0 |
StringBuilder struc = new StringBuilder(256); |
291 |
0 |
struc.append(rnaTrim.getStructDBN(true)); |
292 |
0 |
int ofstart = -1; |
293 |
0 |
int sleng = seq.length(); |
294 |
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|
295 |
0 |
for (int i = 0; i < sleng; i++) |
296 |
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{ |
297 |
0 |
if (Comparison.isGap(seq.charAt(i))) |
298 |
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{ |
299 |
0 |
if (ofstart == -1) |
300 |
|
{ |
301 |
0 |
ofstart = i; |
302 |
|
} |
303 |
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|
304 |
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|
305 |
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|
306 |
0 |
if (!rnaTrim.findPair(i).isEmpty()) |
307 |
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{ |
308 |
0 |
int m = rnaTrim.findPair(i).get(1); |
309 |
0 |
int l = rnaTrim.findPair(i).get(0); |
310 |
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|
311 |
0 |
struc.replace(m, m + 1, "*"); |
312 |
0 |
struc.replace(l, l + 1, "*"); |
313 |
|
} |
314 |
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else |
315 |
|
{ |
316 |
0 |
struc.replace(i, i + 1, "*"); |
317 |
|
} |
318 |
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} |
319 |
|
else |
320 |
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{ |
321 |
0 |
if (ofstart > -1) |
322 |
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{ |
323 |
0 |
offset.addShift(offset.shift(ofstart), ofstart - i); |
324 |
0 |
ofstart = -1; |
325 |
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} |
326 |
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} |
327 |
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} |
328 |
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|
329 |
0 |
if (ofstart > -1) |
330 |
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{ |
331 |
0 |
offset.addShift(offset.shift(ofstart), ofstart - sleng); |
332 |
0 |
ofstart = -1; |
333 |
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} |
334 |
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|
335 |
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|
336 |
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|
337 |
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|
338 |
0 |
String newStruc = struc.toString().replace("*", ""); |
339 |
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|
340 |
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|
341 |
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|
342 |
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|
343 |
0 |
String newSeq = AlignSeq.extractGaps(Comparison.GapChars, seq); |
344 |
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|
345 |
0 |
try |
346 |
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{ |
347 |
0 |
rnaTrim.setRNA(newSeq, newStruc); |
348 |
0 |
registerOffset(rnaTrim, offset); |
349 |
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} catch (ExceptionUnmatchedClosingParentheses e) |
350 |
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{ |
351 |
0 |
e.printStackTrace(); |
352 |
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} catch (ExceptionFileFormatOrSyntax e) |
353 |
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{ |
354 |
0 |
e.printStackTrace(); |
355 |
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} |
356 |
0 |
return rnaTrim; |
357 |
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} |
358 |
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|
359 |
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|
360 |
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|
361 |
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|
362 |
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@param |
363 |
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@param |
364 |
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|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
365 |
0 |
private void registerOffset(RNA rnaTrim, ShiftList offset)... |
366 |
|
{ |
367 |
0 |
offsets.put(rnaTrim, offset); |
368 |
0 |
offsetsInv.put(rnaTrim, offset.getInverse()); |
369 |
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} |
370 |
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|
|
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
371 |
0 |
public void showPanel(boolean show)... |
372 |
|
{ |
373 |
0 |
this.setVisible(show); |
374 |
|
} |
375 |
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376 |
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377 |
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378 |
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379 |
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380 |
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381 |
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382 |
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@param |
383 |
|
@param |
384 |
|
|
385 |
|
@param |
386 |
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|
387 |
|
|
|
|
| 0% |
Uncovered Elements: 14 (14) |
Complexity: 4 |
Complexity Density: 0.5 |
|
388 |
0 |
@Override... |
389 |
|
public void mouseOverSequence(SequenceI sequence, final int index, |
390 |
|
final int position) |
391 |
|
{ |
392 |
0 |
RNA rna = vab.getSelectedRNA(); |
393 |
0 |
if (rna == null) |
394 |
|
{ |
395 |
0 |
return; |
396 |
|
} |
397 |
0 |
RnaModel rnaModel = models.get(rna); |
398 |
0 |
if (rnaModel.seq == sequence) |
399 |
|
{ |
400 |
0 |
int highlightPos = rnaModel.gapped ? index : position - 1; |
401 |
0 |
mouseOverHighlighter.highlightRegion(rna, highlightPos, highlightPos); |
402 |
0 |
vab.updateSelectedRNA(rna); |
403 |
|
} |
404 |
|
} |
405 |
|
|
|
|
| 0% |
Uncovered Elements: 23 (23) |
Complexity: 6 |
Complexity Density: 0.4 |
|
406 |
0 |
@Override... |
407 |
|
public void selection(SequenceGroup seqsel, ColumnSelection colsel, |
408 |
|
HiddenColumns hidden, SelectionSource source) |
409 |
|
{ |
410 |
0 |
if (source != ap.av) |
411 |
|
{ |
412 |
|
|
413 |
|
|
414 |
0 |
return; |
415 |
|
} |
416 |
0 |
RNA rna = vab.getSelectedRNA(); |
417 |
0 |
if (rna == null) |
418 |
|
{ |
419 |
0 |
return; |
420 |
|
} |
421 |
0 |
if (seqsel != null && seqsel.getSize() > 0) |
422 |
|
{ |
423 |
0 |
int start = seqsel.getStartRes(), end = seqsel.getEndRes(); |
424 |
0 |
ShiftList shift = offsets.get(rna); |
425 |
0 |
if (shift != null) |
426 |
|
{ |
427 |
0 |
start = shift.shift(start); |
428 |
0 |
end = shift.shift(end); |
429 |
|
} |
430 |
0 |
selectionHighlighter.highlightRegion(rna, start, end); |
431 |
0 |
selectionHighlighter.getLastHighlight() |
432 |
|
.setOutlineColor(seqsel.getOutlineColour()); |
433 |
|
|
434 |
0 |
vab.updateSelectedRNA(rna); |
435 |
|
} |
436 |
|
else |
437 |
|
{ |
438 |
0 |
selectionHighlighter.clearSelection(); |
439 |
|
} |
440 |
|
} |
441 |
|
|
442 |
|
|
443 |
|
|
444 |
|
|
|
|
| 0% |
Uncovered Elements: 12 (12) |
Complexity: 4 |
Complexity Density: 0.5 |
|
445 |
0 |
@Override... |
446 |
|
public void onHoverChanged(ModeleBase previousBase, ModeleBase newBase) |
447 |
|
{ |
448 |
0 |
RNA rna = vab.getSelectedRNA(); |
449 |
0 |
ShiftList shift = offsetsInv.get(rna); |
450 |
0 |
SequenceI seq = models.get(rna).seq; |
451 |
0 |
if (newBase != null && seq != null) |
452 |
|
{ |
453 |
0 |
if (shift != null) |
454 |
|
{ |
455 |
0 |
int i = shift.shift(newBase.getIndex()); |
456 |
|
|
457 |
0 |
ssm.mouseOverVamsasSequence(seq, i, this); |
458 |
|
} |
459 |
|
else |
460 |
|
{ |
461 |
0 |
ssm.mouseOverVamsasSequence(seq, newBase.getIndex(), this); |
462 |
|
} |
463 |
|
} |
464 |
|
} |
465 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
466 |
0 |
@Override... |
467 |
|
public void onSelectionChanged(BaseList arg0, BaseList arg1, |
468 |
|
BaseList arg2) |
469 |
|
{ |
470 |
|
|
471 |
|
|
472 |
|
|
473 |
|
} |
474 |
|
|
475 |
|
|
476 |
|
|
477 |
|
|
478 |
|
|
479 |
|
@param |
480 |
|
|
481 |
|
@return |
482 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
483 |
0 |
public String getStateInfo(RNA rna)... |
484 |
|
{ |
485 |
0 |
return vab.getStateInfo(rna); |
486 |
|
} |
487 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
488 |
0 |
public AlignmentPanel getAlignmentPanel()... |
489 |
|
{ |
490 |
0 |
return ap; |
491 |
|
} |
492 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
493 |
0 |
public String getViewId()... |
494 |
|
{ |
495 |
0 |
return viewId; |
496 |
|
} |
497 |
|
|
498 |
|
|
499 |
|
|
500 |
|
|
501 |
|
|
502 |
|
@param |
503 |
|
@return |
504 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
505 |
0 |
public boolean isListeningFor(SequenceI seq)... |
506 |
|
{ |
507 |
0 |
for (RnaModel model : models.values()) |
508 |
|
{ |
509 |
0 |
if (model.seq == seq) |
510 |
|
{ |
511 |
0 |
return true; |
512 |
|
} |
513 |
|
} |
514 |
0 |
return false; |
515 |
|
} |
516 |
|
|
517 |
|
|
518 |
|
|
519 |
|
|
520 |
|
@return |
521 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
522 |
0 |
public int getDividerLocation()... |
523 |
|
{ |
524 |
0 |
return split == null ? 0 : split.getDividerLocation(); |
525 |
|
} |
526 |
|
|
527 |
|
|
528 |
|
|
529 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
530 |
0 |
protected void close()... |
531 |
|
{ |
532 |
|
|
533 |
|
|
534 |
|
|
535 |
0 |
if (ssm != null) |
536 |
|
{ |
537 |
0 |
ssm.removeStructureViewerListener(AppVarna.this, null); |
538 |
0 |
ssm.removeSelectionListener(AppVarna.this); |
539 |
|
} |
540 |
|
} |
541 |
|
|
542 |
|
|
543 |
|
|
544 |
|
|
545 |
|
|
546 |
|
@return |
547 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
548 |
0 |
public AlignmentAnnotation getAnnotation(SequenceI seq)... |
549 |
|
{ |
550 |
0 |
for (RnaModel model : models.values()) |
551 |
|
{ |
552 |
0 |
if (model.seq == seq) |
553 |
|
{ |
554 |
0 |
return model.ann; |
555 |
|
} |
556 |
|
} |
557 |
0 |
return null; |
558 |
|
} |
559 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
560 |
0 |
public int getSelectedIndex()... |
561 |
|
{ |
562 |
0 |
return this.vab.getSelectedIndex(); |
563 |
|
} |
564 |
|
|
565 |
|
|
566 |
|
|
567 |
|
|
568 |
|
@return |
569 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
570 |
0 |
public Collection<RnaModel> getModels()... |
571 |
|
{ |
572 |
0 |
return models.values(); |
573 |
|
} |
574 |
|
|
575 |
|
|
576 |
|
|
577 |
|
|
578 |
|
@param |
579 |
|
@param |
580 |
|
|
|
|
| 0% |
Uncovered Elements: 19 (19) |
Complexity: 5 |
Complexity Density: 0.33 |
|
581 |
0 |
public RNA addModel(RnaModel model, String modelName)... |
582 |
|
{ |
583 |
0 |
if (!model.ann.isValidStruc()) |
584 |
|
{ |
585 |
0 |
throw new IllegalArgumentException( |
586 |
|
"Invalid RNA structure annotation"); |
587 |
|
} |
588 |
|
|
589 |
|
|
590 |
|
|
591 |
|
|
592 |
0 |
RNA rna = new RNA(modelName); |
593 |
0 |
String struc = model.ann.getRNAStruc(); |
594 |
0 |
struc = replaceOddGaps(struc); |
595 |
|
|
596 |
0 |
String strucseq = model.seq.getSequenceAsString(); |
597 |
0 |
try |
598 |
|
{ |
599 |
0 |
rna.setRNA(strucseq, struc); |
600 |
|
} catch (ExceptionUnmatchedClosingParentheses e2) |
601 |
|
{ |
602 |
0 |
e2.printStackTrace(); |
603 |
|
} catch (ExceptionFileFormatOrSyntax e3) |
604 |
|
{ |
605 |
0 |
e3.printStackTrace(); |
606 |
|
} |
607 |
|
|
608 |
0 |
if (!model.gapped) |
609 |
|
{ |
610 |
0 |
rna = trimRNA(rna, modelName); |
611 |
|
} |
612 |
0 |
models.put(rna, new RnaModel(modelName, model.ann, model.seq, rna, |
613 |
|
model.gapped)); |
614 |
0 |
vab.addStructure(rna); |
615 |
0 |
return rna; |
616 |
|
} |
617 |
|
|
618 |
|
|
619 |
|
|
620 |
|
|
621 |
|
@param |
622 |
|
@return |
623 |
|
|
|
|
| 0% |
Uncovered Elements: 24 (24) |
Complexity: 6 |
Complexity Density: 0.43 |
|
624 |
0 |
protected ShiftList buildOffset(SequenceI seq)... |
625 |
|
{ |
626 |
|
|
627 |
|
|
628 |
0 |
ShiftList offset = new ShiftList(); |
629 |
0 |
int ofstart = -1; |
630 |
0 |
int sleng = seq.getLength(); |
631 |
|
|
632 |
0 |
for (int i = 0; i < sleng; i++) |
633 |
|
{ |
634 |
0 |
if (Comparison.isGap(seq.getCharAt(i))) |
635 |
|
{ |
636 |
0 |
if (ofstart == -1) |
637 |
|
{ |
638 |
0 |
ofstart = i; |
639 |
|
} |
640 |
|
} |
641 |
|
else |
642 |
|
{ |
643 |
0 |
if (ofstart > -1) |
644 |
|
{ |
645 |
0 |
offset.addShift(offset.shift(ofstart), ofstart - i); |
646 |
0 |
ofstart = -1; |
647 |
|
} |
648 |
|
} |
649 |
|
} |
650 |
|
|
651 |
0 |
if (ofstart > -1) |
652 |
|
{ |
653 |
0 |
offset.addShift(offset.shift(ofstart), ofstart - sleng); |
654 |
0 |
ofstart = -1; |
655 |
|
} |
656 |
0 |
return offset; |
657 |
|
} |
658 |
|
|
659 |
|
|
660 |
|
|
661 |
|
|
662 |
|
@param |
663 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
|
664 |
0 |
public void setInitialSelection(final int selectedIndex)... |
665 |
|
{ |
666 |
|
|
667 |
|
|
668 |
|
|
669 |
|
|
670 |
|
|
671 |
0 |
synchronized (this) |
672 |
|
{ |
673 |
0 |
try |
674 |
|
{ |
675 |
0 |
wait(1000); |
676 |
|
} catch (InterruptedException e) |
677 |
|
{ |
678 |
|
|
679 |
|
} |
680 |
|
} |
681 |
0 |
vab.setSelectedIndex(selectedIndex); |
682 |
|
} |
683 |
|
|
684 |
|
|
685 |
|
|
686 |
|
|
687 |
|
@param |
688 |
|
@param |
689 |
|
|
|
|
| 0% |
Uncovered Elements: 18 (18) |
Complexity: 4 |
Complexity Density: 0.29 |
|
690 |
0 |
public RNA addModelSession(RnaModel model, String modelName,... |
691 |
|
String sessionFile) |
692 |
|
{ |
693 |
0 |
if (!model.ann.isValidStruc()) |
694 |
|
{ |
695 |
0 |
throw new IllegalArgumentException( |
696 |
|
"Invalid RNA structure annotation"); |
697 |
|
} |
698 |
|
|
699 |
0 |
try |
700 |
|
{ |
701 |
0 |
FullBackup fromSession = vab.vp.loadSession(sessionFile); |
702 |
0 |
vab.addStructure(fromSession.rna, fromSession.config); |
703 |
0 |
RNA rna = fromSession.rna; |
704 |
|
|
705 |
0 |
RnaModel newModel = new RnaModel(model.title, model.ann, model.seq, |
706 |
|
rna, model.gapped); |
707 |
0 |
if (!model.gapped) |
708 |
|
{ |
709 |
0 |
registerOffset(rna, buildOffset(model.seq)); |
710 |
|
} |
711 |
0 |
models.put(rna, newModel); |
712 |
|
|
713 |
0 |
selectionHighlighter = new VarnaHighlighter(rna); |
714 |
0 |
return fromSession.rna; |
715 |
|
} catch (ExceptionLoadingFailed e) |
716 |
|
{ |
717 |
0 |
System.err |
718 |
|
.println("Error restoring Varna session: " + e.getMessage()); |
719 |
0 |
return null; |
720 |
|
} |
721 |
|
} |
722 |
|
|
723 |
|
|
724 |
|
|
725 |
|
|
726 |
|
@param |
727 |
|
@return |
728 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (25) |
Complexity: 8 |
Complexity Density: 0.62 |
|
729 |
5 |
public static String replaceOddGaps(String s)... |
730 |
|
{ |
731 |
5 |
if (s == null) |
732 |
|
{ |
733 |
1 |
return null; |
734 |
|
} |
735 |
|
|
736 |
|
|
737 |
4 |
boolean changed = false; |
738 |
4 |
byte[] bytes = s.getBytes(); |
739 |
30 |
for (int i = 0; i < bytes.length; i++) |
740 |
|
{ |
741 |
26 |
boolean ok = false; |
742 |
|
|
743 |
|
|
744 |
183 |
for (int j = 0; !ok && (j < PAIRS.length); j++) |
745 |
|
{ |
746 |
157 |
if (bytes[i] == PAIRS[j]) |
747 |
|
{ |
748 |
15 |
ok = true; |
749 |
|
} |
750 |
|
} |
751 |
26 |
if (!ok) |
752 |
|
{ |
753 |
11 |
bytes[i] = '.'; |
754 |
11 |
changed = true; |
755 |
|
} |
756 |
|
} |
757 |
4 |
return changed ? new String(bytes) : s; |
758 |
|
} |
759 |
|
} |