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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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| 27.3% |
Uncovered Elements: 128 (176) |
Complexity: 75 |
Complexity Density: 0.77 |
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public class SequenceSet implements java.io.Serializable |
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{ |
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private java.lang.String _gapChar; |
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private java.lang.String _datasetId; |
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private java.util.Vector _sequenceList; |
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private java.util.Vector _annotationList; |
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private java.util.Vector _sequenceSetPropertiesList; |
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private java.util.Vector _alcodonFrameList; |
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
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public SequenceSet()... |
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{ |
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super(); |
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this._sequenceList = new java.util.Vector(); |
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this._annotationList = new java.util.Vector(); |
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this._sequenceSetPropertiesList = new java.util.Vector(); |
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this._alcodonFrameList = new java.util.Vector(); |
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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 addAlcodonFrame(... |
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final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._alcodonFrameList.addElement(vAlcodonFrame); |
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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 addAlcodonFrame(final int index,... |
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final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._alcodonFrameList.add(index, vAlcodonFrame); |
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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 addAnnotation(... |
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final jalview.schemabinding.version2.Annotation vAnnotation) |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._annotationList.addElement(vAnnotation); |
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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 addAnnotation(final int index,... |
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final jalview.schemabinding.version2.Annotation vAnnotation) |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._annotationList.add(index, vAnnotation); |
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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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899 |
public void addSequence(... |
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final jalview.schemabinding.version2.Sequence vSequence) |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._sequenceList.addElement(vSequence); |
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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 addSequence(final int index,... |
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final jalview.schemabinding.version2.Sequence vSequence) |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._sequenceList.add(index, vSequence); |
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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 addSequenceSetProperties(... |
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final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._sequenceSetPropertiesList.addElement(vSequenceSetProperties); |
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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 addSequenceSetProperties(... |
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final int index, |
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final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._sequenceSetPropertiesList.add(index, vSequenceSetProperties); |
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} |
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@return |
199 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public java.util.Enumeration enumerateAlcodonFrame()... |
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{ |
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return this._alcodonFrameList.elements(); |
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} |
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@return |
210 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public java.util.Enumeration enumerateAnnotation()... |
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{ |
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return this._annotationList.elements(); |
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} |
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@return |
221 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public java.util.Enumeration enumerateSequence()... |
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{ |
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return this._sequenceList.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 enumerateSequenceSetProperties()... |
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{ |
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return this._sequenceSetPropertiesList.elements(); |
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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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public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame(... |
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final int index) throws java.lang.IndexOutOfBoundsException |
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{ |
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if (index < 0 || index >= this._alcodonFrameList.size()) |
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{ |
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throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '" |
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+ index + "' not in range [0.." |
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+ (this._alcodonFrameList.size() - 1) + "]"); |
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} |
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return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList |
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.get(index); |
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} |
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@return |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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public jalview.schemabinding.version2.AlcodonFrame[] getAlcodonFrame()... |
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{ |
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jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0]; |
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return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList |
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.toArray(array); |
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} |
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@return |
283 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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82 |
public int getAlcodonFrameCount()... |
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{ |
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return this._alcodonFrameList.size(); |
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} |
288 |
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@param |
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@throws |
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@return |
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297 |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
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0 |
public jalview.schemabinding.version2.Annotation getAnnotation(... |
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final int index) throws java.lang.IndexOutOfBoundsException |
300 |
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{ |
301 |
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302 |
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if (index < 0 || index >= this._annotationList.size()) |
303 |
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{ |
304 |
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throw new IndexOutOfBoundsException("getAnnotation: Index value '" |
305 |
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+ index + "' not in range [0.." |
306 |
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+ (this._annotationList.size() - 1) + "]"); |
307 |
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} |
308 |
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return (jalview.schemabinding.version2.Annotation) _annotationList |
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.get(index); |
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} |
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@return |
321 |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
322 |
135 |
public jalview.schemabinding.version2.Annotation[] getAnnotation()... |
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{ |
324 |
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jalview.schemabinding.version2.Annotation[] array = new jalview.schemabinding.version2.Annotation[0]; |
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return (jalview.schemabinding.version2.Annotation[]) this._annotationList |
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.toArray(array); |
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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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82 |
public int getAnnotationCount()... |
335 |
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{ |
336 |
82 |
return this._annotationList.size(); |
337 |
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} |
338 |
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342 |
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345 |
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@return |
346 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
347 |
268 |
public java.lang.String getDatasetId()... |
348 |
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{ |
349 |
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return this._datasetId; |
350 |
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} |
351 |
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352 |
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353 |
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354 |
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@return |
356 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
357 |
58 |
public java.lang.String getGapChar()... |
358 |
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{ |
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return this._gapChar; |
360 |
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} |
361 |
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362 |
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363 |
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364 |
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365 |
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@param |
366 |
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@throws |
367 |
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368 |
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@return |
369 |
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370 |
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| 60% |
Uncovered Elements: 2 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
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353 |
public jalview.schemabinding.version2.Sequence getSequence(final int index)... |
372 |
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throws java.lang.IndexOutOfBoundsException |
373 |
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{ |
374 |
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353 |
if (index < 0 || index >= this._sequenceList.size()) |
376 |
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{ |
377 |
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throw new IndexOutOfBoundsException("getSequence: Index value '" |
378 |
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+ index + "' not in range [0.." |
379 |
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+ (this._sequenceList.size() - 1) + "]"); |
380 |
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} |
381 |
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382 |
353 |
return (jalview.schemabinding.version2.Sequence) _sequenceList |
383 |
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.get(index); |
384 |
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} |
385 |
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386 |
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387 |
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388 |
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389 |
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390 |
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391 |
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392 |
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393 |
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@return |
394 |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
395 |
140 |
public jalview.schemabinding.version2.Sequence[] getSequence()... |
396 |
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{ |
397 |
140 |
jalview.schemabinding.version2.Sequence[] array = new jalview.schemabinding.version2.Sequence[0]; |
398 |
140 |
return (jalview.schemabinding.version2.Sequence[]) this._sequenceList |
399 |
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.toArray(array); |
400 |
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} |
401 |
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402 |
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403 |
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404 |
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405 |
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@return |
406 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
407 |
32 |
public int getSequenceCount()... |
408 |
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{ |
409 |
32 |
return this._sequenceList.size(); |
410 |
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} |
411 |
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412 |
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413 |
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414 |
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415 |
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@param |
416 |
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@throws |
417 |
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418 |
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@return |
419 |
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420 |
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421 |
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| 60% |
Uncovered Elements: 2 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
422 |
21 |
public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(... |
423 |
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final int index) throws java.lang.IndexOutOfBoundsException |
424 |
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{ |
425 |
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|
426 |
21 |
if (index < 0 || index >= this._sequenceSetPropertiesList.size()) |
427 |
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{ |
428 |
0 |
throw new IndexOutOfBoundsException( |
429 |
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"getSequenceSetProperties: Index value '" + index |
430 |
|
+ "' not in range [0.." |
431 |
|
+ (this._sequenceSetPropertiesList.size() - 1) + "]"); |
432 |
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} |
433 |
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|
434 |
21 |
return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList |
435 |
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.get(index); |
436 |
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} |
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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443 |
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444 |
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445 |
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446 |
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@return |
447 |
|
|
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
448 |
58 |
public jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties()... |
449 |
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{ |
450 |
58 |
jalview.schemabinding.version2.SequenceSetProperties[] array = new jalview.schemabinding.version2.SequenceSetProperties[0]; |
451 |
58 |
return (jalview.schemabinding.version2.SequenceSetProperties[]) this._sequenceSetPropertiesList |
452 |
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.toArray(array); |
453 |
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} |
454 |
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455 |
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456 |
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457 |
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458 |
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@return |
459 |
|
|
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|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
460 |
103 |
public int getSequenceSetPropertiesCount()... |
461 |
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{ |
462 |
103 |
return this._sequenceSetPropertiesList.size(); |
463 |
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} |
464 |
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465 |
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466 |
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467 |
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|
468 |
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@return |
469 |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
|
470 |
0 |
public boolean isValid()... |
471 |
|
{ |
472 |
0 |
try |
473 |
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{ |
474 |
0 |
validate(); |
475 |
|
} catch (org.exolab.castor.xml.ValidationException vex) |
476 |
|
{ |
477 |
0 |
return false; |
478 |
|
} |
479 |
0 |
return true; |
480 |
|
} |
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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@param |
486 |
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@throws |
487 |
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488 |
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|
489 |
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@throws |
490 |
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|
491 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
492 |
0 |
public void marshal(final java.io.Writer out)... |
493 |
|
throws org.exolab.castor.xml.MarshalException, |
494 |
|
org.exolab.castor.xml.ValidationException |
495 |
|
{ |
496 |
0 |
Marshaller.marshal(this, out); |
497 |
|
} |
498 |
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|
499 |
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|
500 |
|
|
501 |
|
|
502 |
|
@param |
503 |
|
@throws |
504 |
|
|
505 |
|
@throws |
506 |
|
|
507 |
|
@throws |
508 |
|
|
509 |
|
|
510 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
511 |
0 |
public void marshal(final org.xml.sax.ContentHandler handler)... |
512 |
|
throws java.io.IOException, |
513 |
|
org.exolab.castor.xml.MarshalException, |
514 |
|
org.exolab.castor.xml.ValidationException |
515 |
|
{ |
516 |
0 |
Marshaller.marshal(this, handler); |
517 |
|
} |
518 |
|
|
519 |
|
|
520 |
|
|
521 |
|
|
522 |
|
@param |
523 |
|
@return |
524 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
525 |
0 |
public boolean removeAlcodonFrame(... |
526 |
|
final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) |
527 |
|
{ |
528 |
0 |
boolean removed = _alcodonFrameList.remove(vAlcodonFrame); |
529 |
0 |
return removed; |
530 |
|
} |
531 |
|
|
532 |
|
|
533 |
|
|
534 |
|
|
535 |
|
@param |
536 |
|
@return |
537 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
538 |
0 |
public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt(... |
539 |
|
final int index) |
540 |
|
{ |
541 |
0 |
java.lang.Object obj = this._alcodonFrameList.remove(index); |
542 |
0 |
return (jalview.schemabinding.version2.AlcodonFrame) obj; |
543 |
|
} |
544 |
|
|
545 |
|
|
546 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
547 |
0 |
public void removeAllAlcodonFrame()... |
548 |
|
{ |
549 |
0 |
this._alcodonFrameList.clear(); |
550 |
|
} |
551 |
|
|
552 |
|
|
553 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
554 |
0 |
public void removeAllAnnotation()... |
555 |
|
{ |
556 |
0 |
this._annotationList.clear(); |
557 |
|
} |
558 |
|
|
559 |
|
|
560 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
561 |
0 |
public void removeAllSequence()... |
562 |
|
{ |
563 |
0 |
this._sequenceList.clear(); |
564 |
|
} |
565 |
|
|
566 |
|
|
567 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
568 |
0 |
public void removeAllSequenceSetProperties()... |
569 |
|
{ |
570 |
0 |
this._sequenceSetPropertiesList.clear(); |
571 |
|
} |
572 |
|
|
573 |
|
|
574 |
|
|
575 |
|
|
576 |
|
@param |
577 |
|
@return |
578 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
579 |
0 |
public boolean removeAnnotation(... |
580 |
|
final jalview.schemabinding.version2.Annotation vAnnotation) |
581 |
|
{ |
582 |
0 |
boolean removed = _annotationList.remove(vAnnotation); |
583 |
0 |
return removed; |
584 |
|
} |
585 |
|
|
586 |
|
|
587 |
|
|
588 |
|
|
589 |
|
@param |
590 |
|
@return |
591 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
592 |
0 |
public jalview.schemabinding.version2.Annotation removeAnnotationAt(... |
593 |
|
final int index) |
594 |
|
{ |
595 |
0 |
java.lang.Object obj = this._annotationList.remove(index); |
596 |
0 |
return (jalview.schemabinding.version2.Annotation) obj; |
597 |
|
} |
598 |
|
|
599 |
|
|
600 |
|
|
601 |
|
|
602 |
|
@param |
603 |
|
@return |
604 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
605 |
0 |
public boolean removeSequence(... |
606 |
|
final jalview.schemabinding.version2.Sequence vSequence) |
607 |
|
{ |
608 |
0 |
boolean removed = _sequenceList.remove(vSequence); |
609 |
0 |
return removed; |
610 |
|
} |
611 |
|
|
612 |
|
|
613 |
|
|
614 |
|
|
615 |
|
@param |
616 |
|
@return |
617 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
618 |
0 |
public jalview.schemabinding.version2.Sequence removeSequenceAt(... |
619 |
|
final int index) |
620 |
|
{ |
621 |
0 |
java.lang.Object obj = this._sequenceList.remove(index); |
622 |
0 |
return (jalview.schemabinding.version2.Sequence) obj; |
623 |
|
} |
624 |
|
|
625 |
|
|
626 |
|
|
627 |
|
|
628 |
|
@param |
629 |
|
@return |
630 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
631 |
0 |
public boolean removeSequenceSetProperties(... |
632 |
|
final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) |
633 |
|
{ |
634 |
0 |
boolean removed = _sequenceSetPropertiesList |
635 |
|
.remove(vSequenceSetProperties); |
636 |
0 |
return removed; |
637 |
|
} |
638 |
|
|
639 |
|
|
640 |
|
|
641 |
|
|
642 |
|
@param |
643 |
|
@return |
644 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
645 |
0 |
public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetPropertiesAt(... |
646 |
|
final int index) |
647 |
|
{ |
648 |
0 |
java.lang.Object obj = this._sequenceSetPropertiesList.remove(index); |
649 |
0 |
return (jalview.schemabinding.version2.SequenceSetProperties) obj; |
650 |
|
} |
651 |
|
|
652 |
|
|
653 |
|
|
654 |
|
|
655 |
|
@param |
656 |
|
@param |
657 |
|
@throws |
658 |
|
|
659 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
660 |
0 |
public void setAlcodonFrame(final int index,... |
661 |
|
final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) |
662 |
|
throws java.lang.IndexOutOfBoundsException |
663 |
|
{ |
664 |
|
|
665 |
0 |
if (index < 0 || index >= this._alcodonFrameList.size()) |
666 |
|
{ |
667 |
0 |
throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '" |
668 |
|
+ index + "' not in range [0.." |
669 |
|
+ (this._alcodonFrameList.size() - 1) + "]"); |
670 |
|
} |
671 |
|
|
672 |
0 |
this._alcodonFrameList.set(index, vAlcodonFrame); |
673 |
|
} |
674 |
|
|
675 |
|
|
676 |
|
|
677 |
|
|
678 |
|
@param |
679 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
680 |
0 |
public void setAlcodonFrame(... |
681 |
|
final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray) |
682 |
|
{ |
683 |
|
|
684 |
0 |
_alcodonFrameList.clear(); |
685 |
|
|
686 |
0 |
for (int i = 0; i < vAlcodonFrameArray.length; i++) |
687 |
|
{ |
688 |
0 |
this._alcodonFrameList.add(vAlcodonFrameArray[i]); |
689 |
|
} |
690 |
|
} |
691 |
|
|
692 |
|
|
693 |
|
|
694 |
|
|
695 |
|
@param |
696 |
|
@param |
697 |
|
@throws |
698 |
|
|
699 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
700 |
0 |
public void setAnnotation(final int index,... |
701 |
|
final jalview.schemabinding.version2.Annotation vAnnotation) |
702 |
|
throws java.lang.IndexOutOfBoundsException |
703 |
|
{ |
704 |
|
|
705 |
0 |
if (index < 0 || index >= this._annotationList.size()) |
706 |
|
{ |
707 |
0 |
throw new IndexOutOfBoundsException("setAnnotation: Index value '" |
708 |
|
+ index + "' not in range [0.." |
709 |
|
+ (this._annotationList.size() - 1) + "]"); |
710 |
|
} |
711 |
|
|
712 |
0 |
this._annotationList.set(index, vAnnotation); |
713 |
|
} |
714 |
|
|
715 |
|
|
716 |
|
|
717 |
|
|
718 |
|
@param |
719 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
720 |
0 |
public void setAnnotation(... |
721 |
|
final jalview.schemabinding.version2.Annotation[] vAnnotationArray) |
722 |
|
{ |
723 |
|
|
724 |
0 |
_annotationList.clear(); |
725 |
|
|
726 |
0 |
for (int i = 0; i < vAnnotationArray.length; i++) |
727 |
|
{ |
728 |
0 |
this._annotationList.add(vAnnotationArray[i]); |
729 |
|
} |
730 |
|
} |
731 |
|
|
732 |
|
|
733 |
|
|
734 |
|
|
735 |
|
|
736 |
|
|
737 |
|
|
738 |
|
@param |
739 |
|
|
740 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
741 |
65 |
public void setDatasetId(final java.lang.String datasetId)... |
742 |
|
{ |
743 |
65 |
this._datasetId = datasetId; |
744 |
|
} |
745 |
|
|
746 |
|
|
747 |
|
|
748 |
|
|
749 |
|
@param |
750 |
|
|
751 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
752 |
115 |
public void setGapChar(final java.lang.String gapChar)... |
753 |
|
{ |
754 |
115 |
this._gapChar = gapChar; |
755 |
|
} |
756 |
|
|
757 |
|
|
758 |
|
|
759 |
|
|
760 |
|
@param |
761 |
|
@param |
762 |
|
@throws |
763 |
|
|
764 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
765 |
0 |
public void setSequence(final int index,... |
766 |
|
final jalview.schemabinding.version2.Sequence vSequence) |
767 |
|
throws java.lang.IndexOutOfBoundsException |
768 |
|
{ |
769 |
|
|
770 |
0 |
if (index < 0 || index >= this._sequenceList.size()) |
771 |
|
{ |
772 |
0 |
throw new IndexOutOfBoundsException("setSequence: Index value '" |
773 |
|
+ index + "' not in range [0.." |
774 |
|
+ (this._sequenceList.size() - 1) + "]"); |
775 |
|
} |
776 |
|
|
777 |
0 |
this._sequenceList.set(index, vSequence); |
778 |
|
} |
779 |
|
|
780 |
|
|
781 |
|
|
782 |
|
|
783 |
|
@param |
784 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
785 |
0 |
public void setSequence(... |
786 |
|
final jalview.schemabinding.version2.Sequence[] vSequenceArray) |
787 |
|
{ |
788 |
|
|
789 |
0 |
_sequenceList.clear(); |
790 |
|
|
791 |
0 |
for (int i = 0; i < vSequenceArray.length; i++) |
792 |
|
{ |
793 |
0 |
this._sequenceList.add(vSequenceArray[i]); |
794 |
|
} |
795 |
|
} |
796 |
|
|
797 |
|
|
798 |
|
|
799 |
|
|
800 |
|
@param |
801 |
|
@param |
802 |
|
@throws |
803 |
|
|
804 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
805 |
0 |
public void setSequenceSetProperties(... |
806 |
|
final int index, |
807 |
|
final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) |
808 |
|
throws java.lang.IndexOutOfBoundsException |
809 |
|
{ |
810 |
|
|
811 |
0 |
if (index < 0 || index >= this._sequenceSetPropertiesList.size()) |
812 |
|
{ |
813 |
0 |
throw new IndexOutOfBoundsException( |
814 |
|
"setSequenceSetProperties: Index value '" + index |
815 |
|
+ "' not in range [0.." |
816 |
|
+ (this._sequenceSetPropertiesList.size() - 1) + "]"); |
817 |
|
} |
818 |
|
|
819 |
0 |
this._sequenceSetPropertiesList.set(index, vSequenceSetProperties); |
820 |
|
} |
821 |
|
|
822 |
|
|
823 |
|
|
824 |
|
|
825 |
|
@param |
826 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
827 |
0 |
public void setSequenceSetProperties(... |
828 |
|
final jalview.schemabinding.version2.SequenceSetProperties[] vSequenceSetPropertiesArray) |
829 |
|
{ |
830 |
|
|
831 |
0 |
_sequenceSetPropertiesList.clear(); |
832 |
|
|
833 |
0 |
for (int i = 0; i < vSequenceSetPropertiesArray.length; i++) |
834 |
|
{ |
835 |
0 |
this._sequenceSetPropertiesList.add(vSequenceSetPropertiesArray[i]); |
836 |
|
} |
837 |
|
} |
838 |
|
|
839 |
|
|
840 |
|
|
841 |
|
|
842 |
|
@param |
843 |
|
@throws |
844 |
|
|
845 |
|
|
846 |
|
@throws |
847 |
|
|
848 |
|
@return |
849 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
850 |
0 |
public static jalview.schemabinding.version2.SequenceSet unmarshal(... |
851 |
|
final java.io.Reader reader) |
852 |
|
throws org.exolab.castor.xml.MarshalException, |
853 |
|
org.exolab.castor.xml.ValidationException |
854 |
|
{ |
855 |
0 |
return (jalview.schemabinding.version2.SequenceSet) Unmarshaller |
856 |
|
.unmarshal(jalview.schemabinding.version2.SequenceSet.class, |
857 |
|
reader); |
858 |
|
} |
859 |
|
|
860 |
|
|
861 |
|
|
862 |
|
|
863 |
|
@throws |
864 |
|
|
865 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
866 |
0 |
public void validate() throws org.exolab.castor.xml.ValidationException... |
867 |
|
{ |
868 |
0 |
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); |
869 |
0 |
validator.validate(this); |
870 |
|
} |
871 |
|
|
872 |
|
} |