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package jalview.schemabinding.version2; |
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import org.exolab.castor.xml.Marshaller; |
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import org.exolab.castor.xml.Unmarshaller; |
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@version |
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| 35.7% |
Uncovered Elements: 146 (227) |
Complexity: 96 |
Complexity Density: 0.76 |
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public class JSeq implements java.io.Serializable |
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{ |
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private int _colour; |
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private boolean _has_colour; |
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private int _start; |
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private boolean _has_start; |
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private int _end; |
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private boolean _has_end; |
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private java.lang.String _id; |
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private boolean _hidden; |
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private boolean _has_hidden; |
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private boolean _viewreference; |
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private boolean _has_viewreference; |
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private java.util.Vector _featuresList; |
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private java.util.Vector _pdbidsList; |
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private java.util.Vector _hiddenSequencesList; |
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private java.util.Vector _rnaViewerList; |
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
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public JSeq()... |
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{ |
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super(); |
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this._featuresList = new java.util.Vector(); |
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this._pdbidsList = new java.util.Vector(); |
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this._hiddenSequencesList = new java.util.Vector(); |
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this._rnaViewerList = new java.util.Vector(); |
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} |
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@param |
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@throws |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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44398 |
public void addFeatures(... |
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final jalview.schemabinding.version2.Features vFeatures) |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._featuresList.addElement(vFeatures); |
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} |
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@param |
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@param |
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@throws |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void addFeatures(final int index,... |
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final jalview.schemabinding.version2.Features vFeatures) |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._featuresList.add(index, vFeatures); |
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} |
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@param |
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@throws |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void addHiddenSequences(final int vHiddenSequences)... |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._hiddenSequencesList.addElement(new java.lang.Integer( |
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vHiddenSequences)); |
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} |
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@param |
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@param |
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@throws |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void addHiddenSequences(final int index, final int vHiddenSequences)... |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._hiddenSequencesList.add(index, new java.lang.Integer( |
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vHiddenSequences)); |
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} |
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@param |
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@throws |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void addPdbids(final jalview.schemabinding.version2.Pdbids vPdbids)... |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._pdbidsList.addElement(vPdbids); |
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} |
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@param |
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@param |
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@throws |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void addPdbids(final int index,... |
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final jalview.schemabinding.version2.Pdbids vPdbids) |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._pdbidsList.add(index, vPdbids); |
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} |
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@param |
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@throws |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void addRnaViewer(... |
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final jalview.schemabinding.version2.RnaViewer vRnaViewer) |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._rnaViewerList.addElement(vRnaViewer); |
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} |
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@param |
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@param |
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@throws |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void addRnaViewer(final int index,... |
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final jalview.schemabinding.version2.RnaViewer vRnaViewer) |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._rnaViewerList.add(index, vRnaViewer); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void deleteColour()... |
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{ |
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this._has_colour = false; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void deleteEnd()... |
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{ |
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this._has_end = false; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void deleteHidden()... |
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{ |
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this._has_hidden = false; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void deleteStart()... |
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{ |
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this._has_start = false; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void deleteViewreference()... |
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{ |
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this._has_viewreference = false; |
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} |
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@return |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public java.util.Enumeration enumerateFeatures()... |
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{ |
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return this._featuresList.elements(); |
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} |
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@return |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public java.util.Enumeration enumerateHiddenSequences()... |
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{ |
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return this._hiddenSequencesList.elements(); |
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} |
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@return |
300 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
public java.util.Enumeration enumeratePdbids()... |
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{ |
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return this._pdbidsList.elements(); |
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} |
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@return |
311 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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0 |
public java.util.Enumeration enumerateRnaViewer()... |
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{ |
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return this._rnaViewerList.elements(); |
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} |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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2065 |
public int getColour()... |
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{ |
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2065 |
return this._colour; |
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} |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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3201 |
public int getEnd()... |
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{ |
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return this._end; |
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} |
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@param |
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@throws |
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@return |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
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0 |
public jalview.schemabinding.version2.Features getFeatures(final int index)... |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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if (index < 0 || index >= this._featuresList.size()) |
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{ |
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throw new IndexOutOfBoundsException("getFeatures: Index value '" |
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+ index + "' not in range [0.." |
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+ (this._featuresList.size() - 1) + "]"); |
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} |
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return (jalview.schemabinding.version2.Features) _featuresList |
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.get(index); |
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} |
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367 |
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368 |
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@return |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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1170 |
public jalview.schemabinding.version2.Features[] getFeatures()... |
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{ |
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1170 |
jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0]; |
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1170 |
return (jalview.schemabinding.version2.Features[]) this._featuresList |
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.toArray(array); |
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} |
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@return |
382 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
383 |
513 |
public int getFeaturesCount()... |
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{ |
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return this._featuresList.size(); |
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} |
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389 |
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391 |
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@return |
392 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
393 |
1676 |
public boolean getHidden()... |
394 |
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{ |
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1676 |
return this._hidden; |
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} |
397 |
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399 |
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@param |
402 |
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@throws |
403 |
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@return |
405 |
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| 60% |
Uncovered Elements: 2 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
406 |
2 |
public int getHiddenSequences(final int index)... |
407 |
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throws java.lang.IndexOutOfBoundsException |
408 |
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{ |
409 |
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410 |
2 |
if (index < 0 || index >= this._hiddenSequencesList.size()) |
411 |
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{ |
412 |
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throw new IndexOutOfBoundsException( |
413 |
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"getHiddenSequences: Index value '" + index |
414 |
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+ "' not in range [0.." |
415 |
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+ (this._hiddenSequencesList.size() - 1) + "]"); |
416 |
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} |
417 |
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2 |
return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue(); |
419 |
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} |
420 |
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421 |
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422 |
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423 |
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424 |
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425 |
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@return |
426 |
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| 100% |
Uncovered Elements: 0 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
427 |
930 |
public int[] getHiddenSequences()... |
428 |
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{ |
429 |
930 |
int size = this._hiddenSequencesList.size(); |
430 |
930 |
int[] array = new int[size]; |
431 |
930 |
java.util.Iterator iter = _hiddenSequencesList.iterator(); |
432 |
934 |
for (int index = 0; index < size; index++) |
433 |
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{ |
434 |
4 |
array[index] = ((java.lang.Integer) iter.next()).intValue(); |
435 |
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} |
436 |
930 |
return array; |
437 |
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} |
438 |
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439 |
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440 |
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441 |
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442 |
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@return |
443 |
|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
444 |
992 |
public int getHiddenSequencesCount()... |
445 |
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{ |
446 |
992 |
return this._hiddenSequencesList.size(); |
447 |
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} |
448 |
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449 |
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450 |
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451 |
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452 |
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@return |
453 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
454 |
2346 |
public java.lang.String getId()... |
455 |
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{ |
456 |
2346 |
return this._id; |
457 |
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} |
458 |
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459 |
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460 |
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461 |
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462 |
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@param |
463 |
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@throws |
464 |
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465 |
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@return |
466 |
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467 |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
468 |
0 |
public jalview.schemabinding.version2.Pdbids getPdbids(final int index)... |
469 |
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throws java.lang.IndexOutOfBoundsException |
470 |
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{ |
471 |
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|
472 |
0 |
if (index < 0 || index >= this._pdbidsList.size()) |
473 |
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{ |
474 |
0 |
throw new IndexOutOfBoundsException("getPdbids: Index value '" |
475 |
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+ index + "' not in range [0.." |
476 |
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+ (this._pdbidsList.size() - 1) + "]"); |
477 |
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} |
478 |
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|
479 |
0 |
return (jalview.schemabinding.version2.Pdbids) _pdbidsList.get(index); |
480 |
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} |
481 |
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482 |
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483 |
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484 |
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485 |
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486 |
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487 |
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488 |
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489 |
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@return |
490 |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
491 |
1173 |
public jalview.schemabinding.version2.Pdbids[] getPdbids()... |
492 |
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{ |
493 |
1173 |
jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0]; |
494 |
1173 |
return (jalview.schemabinding.version2.Pdbids[]) this._pdbidsList |
495 |
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.toArray(array); |
496 |
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} |
497 |
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498 |
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|
499 |
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|
500 |
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|
501 |
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@return |
502 |
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|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
503 |
1617 |
public int getPdbidsCount()... |
504 |
|
{ |
505 |
1617 |
return this._pdbidsList.size(); |
506 |
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} |
507 |
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508 |
|
|
509 |
|
|
510 |
|
|
511 |
|
@param |
512 |
|
@throws |
513 |
|
|
514 |
|
@return |
515 |
|
|
516 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
517 |
0 |
public jalview.schemabinding.version2.RnaViewer getRnaViewer(... |
518 |
|
final int index) throws java.lang.IndexOutOfBoundsException |
519 |
|
{ |
520 |
|
|
521 |
0 |
if (index < 0 || index >= this._rnaViewerList.size()) |
522 |
|
{ |
523 |
0 |
throw new IndexOutOfBoundsException("getRnaViewer: Index value '" |
524 |
|
+ index + "' not in range [0.." |
525 |
|
+ (this._rnaViewerList.size() - 1) + "]"); |
526 |
|
} |
527 |
|
|
528 |
0 |
return (jalview.schemabinding.version2.RnaViewer) _rnaViewerList |
529 |
|
.get(index); |
530 |
|
} |
531 |
|
|
532 |
|
|
533 |
|
|
534 |
|
|
535 |
|
|
536 |
|
|
537 |
|
|
538 |
|
|
539 |
|
@return |
540 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
541 |
930 |
public jalview.schemabinding.version2.RnaViewer[] getRnaViewer()... |
542 |
|
{ |
543 |
930 |
jalview.schemabinding.version2.RnaViewer[] array = new jalview.schemabinding.version2.RnaViewer[0]; |
544 |
930 |
return (jalview.schemabinding.version2.RnaViewer[]) this._rnaViewerList |
545 |
|
.toArray(array); |
546 |
|
} |
547 |
|
|
548 |
|
|
549 |
|
|
550 |
|
|
551 |
|
@return |
552 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
553 |
1104 |
public int getRnaViewerCount()... |
554 |
|
{ |
555 |
1104 |
return this._rnaViewerList.size(); |
556 |
|
} |
557 |
|
|
558 |
|
|
559 |
|
|
560 |
|
|
561 |
|
@return |
562 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
563 |
3201 |
public int getStart()... |
564 |
|
{ |
565 |
3201 |
return this._start; |
566 |
|
} |
567 |
|
|
568 |
|
|
569 |
|
|
570 |
|
|
571 |
|
@return |
572 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
573 |
240 |
public boolean getViewreference()... |
574 |
|
{ |
575 |
240 |
return this._viewreference; |
576 |
|
} |
577 |
|
|
578 |
|
|
579 |
|
|
580 |
|
|
581 |
|
@return |
582 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
583 |
930 |
public boolean hasColour()... |
584 |
|
{ |
585 |
930 |
return this._has_colour; |
586 |
|
} |
587 |
|
|
588 |
|
|
589 |
|
|
590 |
|
|
591 |
|
@return |
592 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
593 |
930 |
public boolean hasEnd()... |
594 |
|
{ |
595 |
930 |
return this._has_end; |
596 |
|
} |
597 |
|
|
598 |
|
|
599 |
|
|
600 |
|
|
601 |
|
@return |
602 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
603 |
930 |
public boolean hasHidden()... |
604 |
|
{ |
605 |
930 |
return this._has_hidden; |
606 |
|
} |
607 |
|
|
608 |
|
|
609 |
|
|
610 |
|
|
611 |
|
@return |
612 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
613 |
930 |
public boolean hasStart()... |
614 |
|
{ |
615 |
930 |
return this._has_start; |
616 |
|
} |
617 |
|
|
618 |
|
|
619 |
|
|
620 |
|
|
621 |
|
@return |
622 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
623 |
2226 |
public boolean hasViewreference()... |
624 |
|
{ |
625 |
2226 |
return this._has_viewreference; |
626 |
|
} |
627 |
|
|
628 |
|
|
629 |
|
|
630 |
|
|
631 |
|
@return |
632 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
633 |
0 |
public boolean isHidden()... |
634 |
|
{ |
635 |
0 |
return this._hidden; |
636 |
|
} |
637 |
|
|
638 |
|
|
639 |
|
|
640 |
|
|
641 |
|
@return |
642 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
|
643 |
0 |
public boolean isValid()... |
644 |
|
{ |
645 |
0 |
try |
646 |
|
{ |
647 |
0 |
validate(); |
648 |
|
} catch (org.exolab.castor.xml.ValidationException vex) |
649 |
|
{ |
650 |
0 |
return false; |
651 |
|
} |
652 |
0 |
return true; |
653 |
|
} |
654 |
|
|
655 |
|
|
656 |
|
|
657 |
|
|
658 |
|
@return |
659 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
660 |
0 |
public boolean isViewreference()... |
661 |
|
{ |
662 |
0 |
return this._viewreference; |
663 |
|
} |
664 |
|
|
665 |
|
|
666 |
|
|
667 |
|
|
668 |
|
@param |
669 |
|
@throws |
670 |
|
|
671 |
|
|
672 |
|
@throws |
673 |
|
|
674 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
675 |
0 |
public void marshal(final java.io.Writer out)... |
676 |
|
throws org.exolab.castor.xml.MarshalException, |
677 |
|
org.exolab.castor.xml.ValidationException |
678 |
|
{ |
679 |
0 |
Marshaller.marshal(this, out); |
680 |
|
} |
681 |
|
|
682 |
|
|
683 |
|
|
684 |
|
|
685 |
|
@param |
686 |
|
@throws |
687 |
|
|
688 |
|
@throws |
689 |
|
|
690 |
|
@throws |
691 |
|
|
692 |
|
|
693 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
694 |
0 |
public void marshal(final org.xml.sax.ContentHandler handler)... |
695 |
|
throws java.io.IOException, |
696 |
|
org.exolab.castor.xml.MarshalException, |
697 |
|
org.exolab.castor.xml.ValidationException |
698 |
|
{ |
699 |
0 |
Marshaller.marshal(this, handler); |
700 |
|
} |
701 |
|
|
702 |
|
|
703 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
704 |
0 |
public void removeAllFeatures()... |
705 |
|
{ |
706 |
0 |
this._featuresList.clear(); |
707 |
|
} |
708 |
|
|
709 |
|
|
710 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
711 |
0 |
public void removeAllHiddenSequences()... |
712 |
|
{ |
713 |
0 |
this._hiddenSequencesList.clear(); |
714 |
|
} |
715 |
|
|
716 |
|
|
717 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
718 |
0 |
public void removeAllPdbids()... |
719 |
|
{ |
720 |
0 |
this._pdbidsList.clear(); |
721 |
|
} |
722 |
|
|
723 |
|
|
724 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
725 |
0 |
public void removeAllRnaViewer()... |
726 |
|
{ |
727 |
0 |
this._rnaViewerList.clear(); |
728 |
|
} |
729 |
|
|
730 |
|
|
731 |
|
|
732 |
|
|
733 |
|
@param |
734 |
|
@return |
735 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
736 |
0 |
public boolean removeFeatures(... |
737 |
|
final jalview.schemabinding.version2.Features vFeatures) |
738 |
|
{ |
739 |
0 |
boolean removed = _featuresList.remove(vFeatures); |
740 |
0 |
return removed; |
741 |
|
} |
742 |
|
|
743 |
|
|
744 |
|
|
745 |
|
|
746 |
|
@param |
747 |
|
@return |
748 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
749 |
0 |
public jalview.schemabinding.version2.Features removeFeaturesAt(... |
750 |
|
final int index) |
751 |
|
{ |
752 |
0 |
java.lang.Object obj = this._featuresList.remove(index); |
753 |
0 |
return (jalview.schemabinding.version2.Features) obj; |
754 |
|
} |
755 |
|
|
756 |
|
|
757 |
|
|
758 |
|
|
759 |
|
@param |
760 |
|
@return |
761 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
762 |
0 |
public boolean removeHiddenSequences(final int vHiddenSequences)... |
763 |
|
{ |
764 |
0 |
boolean removed = _hiddenSequencesList.remove(new java.lang.Integer( |
765 |
|
vHiddenSequences)); |
766 |
0 |
return removed; |
767 |
|
} |
768 |
|
|
769 |
|
|
770 |
|
|
771 |
|
|
772 |
|
@param |
773 |
|
@return |
774 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
775 |
0 |
public int removeHiddenSequencesAt(final int index)... |
776 |
|
{ |
777 |
0 |
java.lang.Object obj = this._hiddenSequencesList.remove(index); |
778 |
0 |
return ((java.lang.Integer) obj).intValue(); |
779 |
|
} |
780 |
|
|
781 |
|
|
782 |
|
|
783 |
|
|
784 |
|
@param |
785 |
|
@return |
786 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
787 |
0 |
public boolean removePdbids(... |
788 |
|
final jalview.schemabinding.version2.Pdbids vPdbids) |
789 |
|
{ |
790 |
0 |
boolean removed = _pdbidsList.remove(vPdbids); |
791 |
0 |
return removed; |
792 |
|
} |
793 |
|
|
794 |
|
|
795 |
|
|
796 |
|
|
797 |
|
@param |
798 |
|
@return |
799 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
800 |
0 |
public jalview.schemabinding.version2.Pdbids removePdbidsAt(... |
801 |
|
final int index) |
802 |
|
{ |
803 |
0 |
java.lang.Object obj = this._pdbidsList.remove(index); |
804 |
0 |
return (jalview.schemabinding.version2.Pdbids) obj; |
805 |
|
} |
806 |
|
|
807 |
|
|
808 |
|
|
809 |
|
|
810 |
|
@param |
811 |
|
@return |
812 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
813 |
0 |
public boolean removeRnaViewer(... |
814 |
|
final jalview.schemabinding.version2.RnaViewer vRnaViewer) |
815 |
|
{ |
816 |
0 |
boolean removed = _rnaViewerList.remove(vRnaViewer); |
817 |
0 |
return removed; |
818 |
|
} |
819 |
|
|
820 |
|
|
821 |
|
|
822 |
|
|
823 |
|
@param |
824 |
|
@return |
825 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
826 |
0 |
public jalview.schemabinding.version2.RnaViewer removeRnaViewerAt(... |
827 |
|
final int index) |
828 |
|
{ |
829 |
0 |
java.lang.Object obj = this._rnaViewerList.remove(index); |
830 |
0 |
return (jalview.schemabinding.version2.RnaViewer) obj; |
831 |
|
} |
832 |
|
|
833 |
|
|
834 |
|
|
835 |
|
|
836 |
|
@param |
837 |
|
|
838 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
839 |
1825 |
public void setColour(final int colour)... |
840 |
|
{ |
841 |
1825 |
this._colour = colour; |
842 |
1825 |
this._has_colour = true; |
843 |
|
} |
844 |
|
|
845 |
|
|
846 |
|
|
847 |
|
|
848 |
|
@param |
849 |
|
|
850 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
851 |
1825 |
public void setEnd(final int end)... |
852 |
|
{ |
853 |
1825 |
this._end = end; |
854 |
1825 |
this._has_end = true; |
855 |
|
} |
856 |
|
|
857 |
|
|
858 |
|
|
859 |
|
|
860 |
|
@param |
861 |
|
@param |
862 |
|
@throws |
863 |
|
|
864 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
865 |
0 |
public void setFeatures(final int index,... |
866 |
|
final jalview.schemabinding.version2.Features vFeatures) |
867 |
|
throws java.lang.IndexOutOfBoundsException |
868 |
|
{ |
869 |
|
|
870 |
0 |
if (index < 0 || index >= this._featuresList.size()) |
871 |
|
{ |
872 |
0 |
throw new IndexOutOfBoundsException("setFeatures: Index value '" |
873 |
|
+ index + "' not in range [0.." |
874 |
|
+ (this._featuresList.size() - 1) + "]"); |
875 |
|
} |
876 |
|
|
877 |
0 |
this._featuresList.set(index, vFeatures); |
878 |
|
} |
879 |
|
|
880 |
|
|
881 |
|
|
882 |
|
|
883 |
|
@param |
884 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
885 |
0 |
public void setFeatures(... |
886 |
|
final jalview.schemabinding.version2.Features[] vFeaturesArray) |
887 |
|
{ |
888 |
|
|
889 |
0 |
_featuresList.clear(); |
890 |
|
|
891 |
0 |
for (int i = 0; i < vFeaturesArray.length; i++) |
892 |
|
{ |
893 |
0 |
this._featuresList.add(vFeaturesArray[i]); |
894 |
|
} |
895 |
|
} |
896 |
|
|
897 |
|
|
898 |
|
|
899 |
|
|
900 |
|
@param |
901 |
|
|
902 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
903 |
1180 |
public void setHidden(final boolean hidden)... |
904 |
|
{ |
905 |
1180 |
this._hidden = hidden; |
906 |
1180 |
this._has_hidden = true; |
907 |
|
} |
908 |
|
|
909 |
|
|
910 |
|
|
911 |
|
|
912 |
|
@param |
913 |
|
@param |
914 |
|
@throws |
915 |
|
|
916 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
917 |
0 |
public void setHiddenSequences(final int index, final int vHiddenSequences)... |
918 |
|
throws java.lang.IndexOutOfBoundsException |
919 |
|
{ |
920 |
|
|
921 |
0 |
if (index < 0 || index >= this._hiddenSequencesList.size()) |
922 |
|
{ |
923 |
0 |
throw new IndexOutOfBoundsException( |
924 |
|
"setHiddenSequences: Index value '" + index |
925 |
|
+ "' not in range [0.." |
926 |
|
+ (this._hiddenSequencesList.size() - 1) + "]"); |
927 |
|
} |
928 |
|
|
929 |
0 |
this._hiddenSequencesList.set(index, new java.lang.Integer( |
930 |
|
vHiddenSequences)); |
931 |
|
} |
932 |
|
|
933 |
|
|
934 |
|
|
935 |
|
|
936 |
|
@param |
937 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
938 |
0 |
public void setHiddenSequences(final int[] vHiddenSequencesArray)... |
939 |
|
{ |
940 |
|
|
941 |
0 |
_hiddenSequencesList.clear(); |
942 |
|
|
943 |
0 |
for (int i = 0; i < vHiddenSequencesArray.length; i++) |
944 |
|
{ |
945 |
0 |
this._hiddenSequencesList.add(new java.lang.Integer( |
946 |
|
vHiddenSequencesArray[i])); |
947 |
|
} |
948 |
|
} |
949 |
|
|
950 |
|
|
951 |
|
|
952 |
|
|
953 |
|
@param |
954 |
|
|
955 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
956 |
1825 |
public void setId(final java.lang.String id)... |
957 |
|
{ |
958 |
1825 |
this._id = id; |
959 |
|
} |
960 |
|
|
961 |
|
|
962 |
|
|
963 |
|
|
964 |
|
@param |
965 |
|
@param |
966 |
|
@throws |
967 |
|
|
968 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
969 |
0 |
public void setPdbids(final int index,... |
970 |
|
final jalview.schemabinding.version2.Pdbids vPdbids) |
971 |
|
throws java.lang.IndexOutOfBoundsException |
972 |
|
{ |
973 |
|
|
974 |
0 |
if (index < 0 || index >= this._pdbidsList.size()) |
975 |
|
{ |
976 |
0 |
throw new IndexOutOfBoundsException("setPdbids: Index value '" |
977 |
|
+ index + "' not in range [0.." |
978 |
|
+ (this._pdbidsList.size() - 1) + "]"); |
979 |
|
} |
980 |
|
|
981 |
0 |
this._pdbidsList.set(index, vPdbids); |
982 |
|
} |
983 |
|
|
984 |
|
|
985 |
|
|
986 |
|
|
987 |
|
@param |
988 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
989 |
0 |
public void setPdbids(... |
990 |
|
final jalview.schemabinding.version2.Pdbids[] vPdbidsArray) |
991 |
|
{ |
992 |
|
|
993 |
0 |
_pdbidsList.clear(); |
994 |
|
|
995 |
0 |
for (int i = 0; i < vPdbidsArray.length; i++) |
996 |
|
{ |
997 |
0 |
this._pdbidsList.add(vPdbidsArray[i]); |
998 |
|
} |
999 |
|
} |
1000 |
|
|
1001 |
|
|
1002 |
|
|
1003 |
|
|
1004 |
|
@param |
1005 |
|
@param |
1006 |
|
@throws |
1007 |
|
|
1008 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
1009 |
0 |
public void setRnaViewer(final int index,... |
1010 |
|
final jalview.schemabinding.version2.RnaViewer vRnaViewer) |
1011 |
|
throws java.lang.IndexOutOfBoundsException |
1012 |
|
{ |
1013 |
|
|
1014 |
0 |
if (index < 0 || index >= this._rnaViewerList.size()) |
1015 |
|
{ |
1016 |
0 |
throw new IndexOutOfBoundsException("setRnaViewer: Index value '" |
1017 |
|
+ index + "' not in range [0.." |
1018 |
|
+ (this._rnaViewerList.size() - 1) + "]"); |
1019 |
|
} |
1020 |
|
|
1021 |
0 |
this._rnaViewerList.set(index, vRnaViewer); |
1022 |
|
} |
1023 |
|
|
1024 |
|
|
1025 |
|
|
1026 |
|
|
1027 |
|
@param |
1028 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1029 |
0 |
public void setRnaViewer(... |
1030 |
|
final jalview.schemabinding.version2.RnaViewer[] vRnaViewerArray) |
1031 |
|
{ |
1032 |
|
|
1033 |
0 |
_rnaViewerList.clear(); |
1034 |
|
|
1035 |
0 |
for (int i = 0; i < vRnaViewerArray.length; i++) |
1036 |
|
{ |
1037 |
0 |
this._rnaViewerList.add(vRnaViewerArray[i]); |
1038 |
|
} |
1039 |
|
} |
1040 |
|
|
1041 |
|
|
1042 |
|
|
1043 |
|
|
1044 |
|
@param |
1045 |
|
|
1046 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1047 |
1825 |
public void setStart(final int start)... |
1048 |
|
{ |
1049 |
1825 |
this._start = start; |
1050 |
1825 |
this._has_start = true; |
1051 |
|
} |
1052 |
|
|
1053 |
|
|
1054 |
|
|
1055 |
|
|
1056 |
|
@param |
1057 |
|
|
1058 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1059 |
160 |
public void setViewreference(final boolean viewreference)... |
1060 |
|
{ |
1061 |
160 |
this._viewreference = viewreference; |
1062 |
160 |
this._has_viewreference = true; |
1063 |
|
} |
1064 |
|
|
1065 |
|
|
1066 |
|
|
1067 |
|
|
1068 |
|
@param |
1069 |
|
@throws |
1070 |
|
|
1071 |
|
|
1072 |
|
@throws |
1073 |
|
|
1074 |
|
@return |
1075 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1076 |
0 |
public static jalview.schemabinding.version2.JSeq unmarshal(... |
1077 |
|
final java.io.Reader reader) |
1078 |
|
throws org.exolab.castor.xml.MarshalException, |
1079 |
|
org.exolab.castor.xml.ValidationException |
1080 |
|
{ |
1081 |
0 |
return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal( |
1082 |
|
jalview.schemabinding.version2.JSeq.class, reader); |
1083 |
|
} |
1084 |
|
|
1085 |
|
|
1086 |
|
|
1087 |
|
|
1088 |
|
@throws |
1089 |
|
|
1090 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1091 |
0 |
public void validate() throws org.exolab.castor.xml.ValidationException... |
1092 |
|
{ |
1093 |
0 |
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); |
1094 |
0 |
validator.validate(this); |
1095 |
|
} |
1096 |
|
|
1097 |
|
} |