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package jalview.javascript; |
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import jalview.api.AlignmentViewPanel; |
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import jalview.api.FeatureRenderer; |
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import jalview.api.SequenceRenderer; |
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import jalview.appletgui.AlignFrame; |
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import jalview.bin.JalviewLite; |
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import jalview.datamodel.SequenceI; |
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import jalview.ext.jmol.JmolCommands; |
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import jalview.structure.AtomSpec; |
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import jalview.structure.StructureListener; |
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import jalview.structure.StructureMapping; |
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import jalview.structure.StructureMappingcommandSet; |
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import jalview.structure.StructureSelectionManager; |
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import jalview.util.HttpUtils; |
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import java.util.ArrayList; |
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import java.util.List; |
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@author |
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| 0% |
Uncovered Elements: 106 (106) |
Complexity: 27 |
Complexity Density: 0.4 |
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public class MouseOverStructureListener extends JSFunctionExec |
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implements JsCallBack, StructureListener |
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{ |
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String _listenerfn; |
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String[] modelSet; |
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| 0% |
Uncovered Elements: 10 (10) |
Complexity: 3 |
Complexity Density: 0.5 |
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public MouseOverStructureListener(JalviewLite jalviewLite,... |
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String listener, String[] modelList) |
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{ |
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super(jalviewLite); |
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_listenerfn = listener; |
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modelSet = modelList; |
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if (modelSet != null) |
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{ |
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for (int i = 0; i < modelSet.length; i++) |
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{ |
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modelSet[i] = resolveModelFile(modelSet[i]); |
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} |
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} |
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} |
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@param |
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| 0% |
Uncovered Elements: 17 (17) |
Complexity: 4 |
Complexity Density: 0.36 |
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public String resolveModelFile(String file)... |
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{ |
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if (HttpUtils.isValidUrl(file)) |
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{ |
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return file; |
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} |
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String db = jvlite.getDocumentBase().toString(); |
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db = db.substring(0, db.lastIndexOf("/")); |
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String docBaseFile = db + "/" + file; |
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if (HttpUtils.isValidUrl(docBaseFile)) |
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{ |
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return docBaseFile; |
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} |
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String cb = jvlite.getCodeBase() + file; |
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if (HttpUtils.isValidUrl(cb)) |
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{ |
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return cb; |
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} |
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return file; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public String[] getStructureFiles() |
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{ |
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return modelSet; |
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} |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
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public void mouseOverStructure(int atomIndex, String strInfo)... |
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{ |
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} |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.4 |
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@Override... |
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public void highlightAtoms(List<AtomSpec> atoms) |
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{ |
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for (AtomSpec atom : atoms) |
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{ |
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try |
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{ |
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executeJavascriptFunction(_listenerfn, |
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new String[] |
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{ "mouseover", "" + atom.getPdbFile(), "" + atom.getChain(), |
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"" + (atom.getPdbResNum()), "" + atom.getAtomIndex() }); |
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} catch (Exception ex) |
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{ |
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System.err.println("Couldn't execute callback with " + _listenerfn |
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+ " for atomSpec: " + atom); |
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ex.printStackTrace(); |
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} |
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} |
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} |
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| 0% |
Uncovered Elements: 60 (60) |
Complexity: 12 |
Complexity Density: 0.29 |
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@Override... |
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public synchronized void updateColours(Object srce) |
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{ |
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final Object source = srce; |
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StructureSelectionManager ssm = StructureSelectionManager |
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.getStructureSelectionManager(jvlite); |
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if (JalviewLite.debug) |
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{ |
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System.err.println( |
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this.getClass().getName() + " modelSet[0]: " + modelSet[0]); |
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ssm.reportMapping(); |
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} |
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if (source instanceof jalview.api.AlignmentViewPanel) |
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{ |
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SequenceI[][] sequence = new SequenceI[modelSet.length][]; |
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for (int m = 0; m < modelSet.length; m++) |
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{ |
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StructureMapping[] sm = ssm.getMapping(modelSet[m]); |
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if (sm != null && sm.length > 0) |
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{ |
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sequence[m] = new SequenceI[sm.length]; |
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for (int i = 0; i < sm.length; i++) |
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{ |
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sequence[m][i] = sm[i].getSequence(); |
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} |
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} |
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else |
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{ |
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sequence[m] = new SequenceI[0]; |
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} |
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} |
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SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source) |
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.getSequenceRenderer(); |
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FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av |
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.isShowSequenceFeatures() |
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? new jalview.appletgui.FeatureRenderer( |
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((jalview.appletgui.AlignmentPanel) source).av) |
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: null; |
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if (fr != null) |
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{ |
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((jalview.appletgui.FeatureRenderer) fr).transferSettings( |
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((jalview.appletgui.AlignmentPanel) source) |
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.getFeatureRenderer()); |
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} |
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; |
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ArrayList<String[]> ccomands = new ArrayList<String[]>(); |
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ArrayList<String> pdbfn = new ArrayList<String>(); |
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StructureMappingcommandSet[] colcommands = JmolCommands |
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.getColourBySequenceCommand(ssm, modelSet, sequence, sr, |
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(AlignmentViewPanel) source); |
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if (colcommands == null) |
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{ |
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return; |
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} |
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int sz = 0; |
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for (jalview.structure.StructureMappingcommandSet ccset : colcommands) |
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{ |
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sz += ccset.commands.length; |
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ccomands.add(ccset.commands); |
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pdbfn.add(ccset.mapping); |
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} |
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String mclass, mhandle; |
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String ccomandset[] = new String[sz]; |
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sz = 0; |
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for (String[] ccset : ccomands) |
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{ |
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System.arraycopy(ccset, 0, ccomandset, sz, ccset.length); |
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sz += ccset.length; |
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} |
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if (jvlite.isJsMessageSetChanged(mclass = "colourstruct", |
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mhandle = ((jalview.appletgui.AlignmentPanel) source).av |
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.getViewId(), |
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ccomandset)) |
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{ |
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jvlite.setJsMessageSet(mclass, mhandle, ccomandset); |
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String st[] = new String[] { "colourstruct", |
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"" + ((jalview.appletgui.AlignmentPanel) source).av.getViewId(), |
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"" + ccomandset.length, jvlite.arrayToSeparatorList( |
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pdbfn.toArray(new String[pdbfn.size()])) }; |
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try |
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{ |
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executeJavascriptFunction(true, _listenerfn, st); |
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} catch (Exception ex) |
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{ |
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System.err.println("Couldn't execute callback with " + _listenerfn |
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+ " using args { " + st[0] + ", " + st[1] + ", " + st[2] |
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+ "," + st[3] + "}"); |
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ex.printStackTrace(); |
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} |
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} |
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} |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public AlignFrame getAlignFrame() |
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{ |
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return null; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public String getListenerFunction() |
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{ |
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return _listenerfn; |
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} |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
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@Override... |
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public void releaseReferences(Object svl) |
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{ |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public boolean isListeningFor(SequenceI seq) |
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{ |
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return true; |
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} |
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} |