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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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| 17.4% |
Uncovered Elements: 76 (92) |
Complexity: 39 |
Complexity Density: 0.75 |
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public class VAMSAS implements java.io.Serializable |
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{ |
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private java.util.Vector _treeList; |
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private java.util.Vector _sequenceSetList; |
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| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
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public VAMSAS()... |
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{ |
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super(); |
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this._treeList = new java.util.Vector(); |
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this._sequenceSetList = 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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public void addSequenceSet(... |
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final jalview.schemabinding.version2.SequenceSet vSequenceSet) |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._sequenceSetList.addElement(vSequenceSet); |
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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 addSequenceSet(final int index,... |
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final jalview.schemabinding.version2.SequenceSet vSequenceSet) |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._sequenceSetList.add(index, vSequenceSet); |
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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 addTree(final java.lang.String vTree)... |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._treeList.addElement(vTree); |
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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 addTree(final int index, final java.lang.String vTree)... |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._treeList.add(index, vTree); |
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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 enumerateSequenceSet()... |
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{ |
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return this._sequenceSetList.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 enumerateTree()... |
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{ |
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return this._treeList.elements(); |
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} |
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@param |
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@throws |
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@return |
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| 60% |
Uncovered Elements: 2 (5) |
Complexity: 3 |
Complexity Density: 1 |
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public jalview.schemabinding.version2.SequenceSet getSequenceSet(... |
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final int index) throws java.lang.IndexOutOfBoundsException |
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{ |
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if (index < 0 || index >= this._sequenceSetList.size()) |
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{ |
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throw new IndexOutOfBoundsException("getSequenceSet: Index value '" |
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+ index + "' not in range [0.." |
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+ (this._sequenceSetList.size() - 1) + "]"); |
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} |
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return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList |
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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.SequenceSet[] getSequenceSet()... |
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{ |
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jalview.schemabinding.version2.SequenceSet[] array = new jalview.schemabinding.version2.SequenceSet[0]; |
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return (jalview.schemabinding.version2.SequenceSet[]) this._sequenceSetList |
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.toArray(array); |
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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 int getSequenceSetCount()... |
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{ |
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return this._sequenceSetList.size(); |
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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 java.lang.String getTree(final int index)... |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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if (index < 0 || index >= this._treeList.size()) |
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{ |
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throw new IndexOutOfBoundsException("getTree: Index value '" + index |
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+ "' not in range [0.." + (this._treeList.size() - 1) + "]"); |
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} |
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return (java.lang.String) _treeList.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 java.lang.String[] getTree()... |
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{ |
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java.lang.String[] array = new java.lang.String[0]; |
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return (java.lang.String[]) this._treeList.toArray(array); |
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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 int getTreeCount()... |
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{ |
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return this._treeList.size(); |
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} |
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@return |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
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public boolean isValid()... |
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{ |
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try |
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{ |
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validate(); |
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} catch (org.exolab.castor.xml.ValidationException vex) |
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{ |
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return false; |
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} |
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return true; |
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} |
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@param |
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@throws |
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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 marshal(final java.io.Writer out)... |
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throws org.exolab.castor.xml.MarshalException, |
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org.exolab.castor.xml.ValidationException |
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{ |
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Marshaller.marshal(this, out); |
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} |
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@param |
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@throws |
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@throws |
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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 marshal(final org.xml.sax.ContentHandler handler)... |
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throws java.io.IOException, |
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org.exolab.castor.xml.MarshalException, |
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org.exolab.castor.xml.ValidationException |
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{ |
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Marshaller.marshal(this, handler); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void removeAllSequenceSet()... |
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{ |
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this._sequenceSetList.clear(); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public void removeAllTree()... |
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{ |
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this._treeList.clear(); |
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} |
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@param |
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@return |
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| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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0 |
public boolean removeSequenceSet(... |
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final jalview.schemabinding.version2.SequenceSet vSequenceSet) |
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{ |
304 |
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boolean removed = _sequenceSetList.remove(vSequenceSet); |
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return removed; |
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} |
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@param |
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@return |
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| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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public jalview.schemabinding.version2.SequenceSet removeSequenceSetAt(... |
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final int index) |
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{ |
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java.lang.Object obj = this._sequenceSetList.remove(index); |
318 |
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return (jalview.schemabinding.version2.SequenceSet) obj; |
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} |
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@param |
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@return |
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| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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public boolean removeTree(final java.lang.String vTree)... |
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{ |
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boolean removed = _treeList.remove(vTree); |
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return removed; |
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} |
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@param |
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@return |
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| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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public java.lang.String removeTreeAt(final int index)... |
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{ |
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java.lang.Object obj = this._treeList.remove(index); |
342 |
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return (java.lang.String) obj; |
343 |
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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: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
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public void setSequenceSet(final int index,... |
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final jalview.schemabinding.version2.SequenceSet vSequenceSet) |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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if (index < 0 || index >= this._sequenceSetList.size()) |
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{ |
360 |
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throw new IndexOutOfBoundsException("setSequenceSet: Index value '" |
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+ index + "' not in range [0.." |
362 |
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+ (this._sequenceSetList.size() - 1) + "]"); |
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} |
364 |
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this._sequenceSetList.set(index, vSequenceSet); |
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} |
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@param |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
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public void setSequenceSet(... |
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final jalview.schemabinding.version2.SequenceSet[] vSequenceSetArray) |
375 |
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{ |
376 |
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|
377 |
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_sequenceSetList.clear(); |
378 |
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379 |
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for (int i = 0; i < vSequenceSetArray.length; i++) |
380 |
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{ |
381 |
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this._sequenceSetList.add(vSequenceSetArray[i]); |
382 |
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} |
383 |
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} |
384 |
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385 |
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@param |
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@param |
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@throws |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
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public void setTree(final int index, final java.lang.String vTree)... |
394 |
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throws java.lang.IndexOutOfBoundsException |
395 |
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{ |
396 |
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|
397 |
0 |
if (index < 0 || index >= this._treeList.size()) |
398 |
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{ |
399 |
0 |
throw new IndexOutOfBoundsException("setTree: Index value '" + index |
400 |
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+ "' not in range [0.." + (this._treeList.size() - 1) + "]"); |
401 |
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} |
402 |
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403 |
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this._treeList.set(index, vTree); |
404 |
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} |
405 |
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406 |
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407 |
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408 |
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409 |
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@param |
410 |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
411 |
0 |
public void setTree(final java.lang.String[] vTreeArray)... |
412 |
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{ |
413 |
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|
414 |
0 |
_treeList.clear(); |
415 |
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|
416 |
0 |
for (int i = 0; i < vTreeArray.length; i++) |
417 |
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{ |
418 |
0 |
this._treeList.add(vTreeArray[i]); |
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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@param |
426 |
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@throws |
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428 |
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429 |
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@throws |
430 |
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431 |
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@return |
432 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
433 |
0 |
public static jalview.schemabinding.version2.VAMSAS unmarshal(... |
434 |
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final java.io.Reader reader) |
435 |
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throws org.exolab.castor.xml.MarshalException, |
436 |
|
org.exolab.castor.xml.ValidationException |
437 |
|
{ |
438 |
0 |
return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal( |
439 |
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jalview.schemabinding.version2.VAMSAS.class, reader); |
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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@throws |
446 |
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|
447 |
|
|
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|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
448 |
0 |
public void validate() throws org.exolab.castor.xml.ValidationException... |
449 |
|
{ |
450 |
0 |
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); |
451 |
0 |
validator.validate(this); |
452 |
|
} |
453 |
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|
454 |
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} |