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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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| 25.7% |
Uncovered Elements: 156 (210) |
Complexity: 89 |
Complexity Density: 0.76 |
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public class JalviewModelSequence implements java.io.Serializable |
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{ |
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private java.util.Vector _JSeqList; |
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private java.util.Vector _JGroupList; |
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private java.util.Vector _viewportList; |
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private java.util.Vector _userColoursList; |
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private java.util.Vector _treeList; |
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private jalview.schemabinding.version2.FeatureSettings _featureSettings; |
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| 100% |
Uncovered Elements: 0 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
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public JalviewModelSequence()... |
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{ |
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super(); |
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this._JSeqList = new java.util.Vector(); |
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this._JGroupList = new java.util.Vector(); |
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this._viewportList = new java.util.Vector(); |
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this._userColoursList = new java.util.Vector(); |
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this._treeList = 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 addJGroup(final jalview.schemabinding.version2.JGroup vJGroup)... |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._JGroupList.addElement(vJGroup); |
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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 addJGroup(final int index,... |
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final jalview.schemabinding.version2.JGroup vJGroup) |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._JGroupList.add(index, vJGroup); |
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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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1825 |
public void addJSeq(final jalview.schemabinding.version2.JSeq vJSeq)... |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._JSeqList.addElement(vJSeq); |
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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 addJSeq(final int index,... |
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final jalview.schemabinding.version2.JSeq vJSeq) |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._JSeqList.add(index, vJSeq); |
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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 addTree(final jalview.schemabinding.version2.Tree 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,... |
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final jalview.schemabinding.version2.Tree 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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@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 addUserColours(... |
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final jalview.schemabinding.version2.UserColours vUserColours) |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._userColoursList.addElement(vUserColours); |
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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 addUserColours(final int index,... |
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final jalview.schemabinding.version2.UserColours vUserColours) |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._userColoursList.add(index, vUserColours); |
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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 addViewport(... |
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final jalview.schemabinding.version2.Viewport vViewport) |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._viewportList.addElement(vViewport); |
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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 addViewport(final int index,... |
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final jalview.schemabinding.version2.Viewport vViewport) |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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this._viewportList.add(index, vViewport); |
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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 enumerateJGroup()... |
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{ |
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return this._JGroupList.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 enumerateJSeq()... |
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{ |
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return this._JSeqList.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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@return |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public java.util.Enumeration enumerateUserColours()... |
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{ |
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return this._userColoursList.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 enumerateViewport()... |
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{ |
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return this._viewportList.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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public jalview.schemabinding.version2.FeatureSettings getFeatureSettings()... |
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{ |
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return this._featureSettings; |
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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.JGroup getJGroup(final int index)... |
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throws java.lang.IndexOutOfBoundsException |
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{ |
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if (index < 0 || index >= this._JGroupList.size()) |
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{ |
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throw new IndexOutOfBoundsException("getJGroup: Index value '" |
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+ index + "' not in range [0.." |
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+ (this._JGroupList.size() - 1) + "]"); |
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} |
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return (jalview.schemabinding.version2.JGroup) _JGroupList.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.JGroup[] getJGroup()... |
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{ |
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jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0]; |
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return (jalview.schemabinding.version2.JGroup[]) this._JGroupList |
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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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public int getJGroupCount()... |
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{ |
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return this._JGroupList.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 jalview.schemabinding.version2.JSeq getJSeq(final int index)... |
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throws java.lang.IndexOutOfBoundsException |
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{ |
345 |
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346 |
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if (index < 0 || index >= this._JSeqList.size()) |
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{ |
348 |
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throw new IndexOutOfBoundsException("getJSeq: Index value '" + index |
349 |
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+ "' not in range [0.." + (this._JSeqList.size() - 1) + "]"); |
350 |
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} |
351 |
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return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index); |
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} |
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@return |
363 |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
364 |
140 |
public jalview.schemabinding.version2.JSeq[] getJSeq()... |
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{ |
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jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0]; |
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return (jalview.schemabinding.version2.JSeq[]) this._JSeqList |
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.toArray(array); |
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} |
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@return |
375 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
public int getJSeqCount()... |
377 |
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{ |
378 |
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return this._JSeqList.size(); |
379 |
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} |
380 |
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@param |
385 |
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@throws |
386 |
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387 |
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@return |
388 |
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389 |
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| 60% |
Uncovered Elements: 2 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
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12 |
public jalview.schemabinding.version2.Tree getTree(final int index)... |
391 |
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throws java.lang.IndexOutOfBoundsException |
392 |
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{ |
393 |
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394 |
12 |
if (index < 0 || index >= this._treeList.size()) |
395 |
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{ |
396 |
0 |
throw new IndexOutOfBoundsException("getTree: Index value '" + index |
397 |
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+ "' not in range [0.." + (this._treeList.size() - 1) + "]"); |
398 |
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} |
399 |
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400 |
12 |
return (jalview.schemabinding.version2.Tree) _treeList.get(index); |
401 |
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} |
402 |
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403 |
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406 |
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407 |
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408 |
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409 |
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410 |
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@return |
411 |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
412 |
58 |
public jalview.schemabinding.version2.Tree[] getTree()... |
413 |
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{ |
414 |
58 |
jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0]; |
415 |
58 |
return (jalview.schemabinding.version2.Tree[]) this._treeList |
416 |
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.toArray(array); |
417 |
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} |
418 |
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419 |
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420 |
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421 |
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422 |
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@return |
423 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
424 |
81 |
public int getTreeCount()... |
425 |
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{ |
426 |
81 |
return this._treeList.size(); |
427 |
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} |
428 |
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429 |
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430 |
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431 |
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432 |
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@param |
433 |
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@throws |
434 |
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435 |
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@return |
436 |
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437 |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
438 |
0 |
public jalview.schemabinding.version2.UserColours getUserColours(... |
439 |
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final int index) throws java.lang.IndexOutOfBoundsException |
440 |
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{ |
441 |
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|
442 |
0 |
if (index < 0 || index >= this._userColoursList.size()) |
443 |
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{ |
444 |
0 |
throw new IndexOutOfBoundsException("getUserColours: Index value '" |
445 |
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+ index + "' not in range [0.." |
446 |
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+ (this._userColoursList.size() - 1) + "]"); |
447 |
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} |
448 |
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|
449 |
0 |
return (jalview.schemabinding.version2.UserColours) _userColoursList |
450 |
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.get(index); |
451 |
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} |
452 |
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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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459 |
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460 |
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@return |
461 |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
462 |
58 |
public jalview.schemabinding.version2.UserColours[] getUserColours()... |
463 |
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{ |
464 |
58 |
jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0]; |
465 |
58 |
return (jalview.schemabinding.version2.UserColours[]) this._userColoursList |
466 |
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.toArray(array); |
467 |
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} |
468 |
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469 |
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470 |
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471 |
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472 |
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@return |
473 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
474 |
0 |
public int getUserColoursCount()... |
475 |
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{ |
476 |
0 |
return this._userColoursList.size(); |
477 |
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} |
478 |
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479 |
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480 |
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481 |
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482 |
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@param |
483 |
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@throws |
484 |
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485 |
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@return |
486 |
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|
487 |
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| 60% |
Uncovered Elements: 2 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
488 |
75 |
public jalview.schemabinding.version2.Viewport getViewport(final int index)... |
489 |
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throws java.lang.IndexOutOfBoundsException |
490 |
|
{ |
491 |
|
|
492 |
75 |
if (index < 0 || index >= this._viewportList.size()) |
493 |
|
{ |
494 |
0 |
throw new IndexOutOfBoundsException("getViewport: Index value '" |
495 |
|
+ index + "' not in range [0.." |
496 |
|
+ (this._viewportList.size() - 1) + "]"); |
497 |
|
} |
498 |
|
|
499 |
75 |
return (jalview.schemabinding.version2.Viewport) _viewportList |
500 |
|
.get(index); |
501 |
|
} |
502 |
|
|
503 |
|
|
504 |
|
|
505 |
|
|
506 |
|
|
507 |
|
|
508 |
|
|
509 |
|
|
510 |
|
@return |
511 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
512 |
58 |
public jalview.schemabinding.version2.Viewport[] getViewport()... |
513 |
|
{ |
514 |
58 |
jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0]; |
515 |
58 |
return (jalview.schemabinding.version2.Viewport[]) this._viewportList |
516 |
|
.toArray(array); |
517 |
|
} |
518 |
|
|
519 |
|
|
520 |
|
|
521 |
|
|
522 |
|
@return |
523 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
524 |
183 |
public int getViewportCount()... |
525 |
|
{ |
526 |
183 |
return this._viewportList.size(); |
527 |
|
} |
528 |
|
|
529 |
|
|
530 |
|
|
531 |
|
|
532 |
|
@return |
533 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
|
534 |
0 |
public boolean isValid()... |
535 |
|
{ |
536 |
0 |
try |
537 |
|
{ |
538 |
0 |
validate(); |
539 |
|
} catch (org.exolab.castor.xml.ValidationException vex) |
540 |
|
{ |
541 |
0 |
return false; |
542 |
|
} |
543 |
0 |
return true; |
544 |
|
} |
545 |
|
|
546 |
|
|
547 |
|
|
548 |
|
|
549 |
|
@param |
550 |
|
@throws |
551 |
|
|
552 |
|
|
553 |
|
@throws |
554 |
|
|
555 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
556 |
0 |
public void marshal(final java.io.Writer out)... |
557 |
|
throws org.exolab.castor.xml.MarshalException, |
558 |
|
org.exolab.castor.xml.ValidationException |
559 |
|
{ |
560 |
0 |
Marshaller.marshal(this, out); |
561 |
|
} |
562 |
|
|
563 |
|
|
564 |
|
|
565 |
|
|
566 |
|
@param |
567 |
|
@throws |
568 |
|
|
569 |
|
@throws |
570 |
|
|
571 |
|
@throws |
572 |
|
|
573 |
|
|
574 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
575 |
0 |
public void marshal(final org.xml.sax.ContentHandler handler)... |
576 |
|
throws java.io.IOException, |
577 |
|
org.exolab.castor.xml.MarshalException, |
578 |
|
org.exolab.castor.xml.ValidationException |
579 |
|
{ |
580 |
0 |
Marshaller.marshal(this, handler); |
581 |
|
} |
582 |
|
|
583 |
|
|
584 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
585 |
0 |
public void removeAllJGroup()... |
586 |
|
{ |
587 |
0 |
this._JGroupList.clear(); |
588 |
|
} |
589 |
|
|
590 |
|
|
591 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
592 |
0 |
public void removeAllJSeq()... |
593 |
|
{ |
594 |
0 |
this._JSeqList.clear(); |
595 |
|
} |
596 |
|
|
597 |
|
|
598 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
599 |
0 |
public void removeAllTree()... |
600 |
|
{ |
601 |
0 |
this._treeList.clear(); |
602 |
|
} |
603 |
|
|
604 |
|
|
605 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
606 |
0 |
public void removeAllUserColours()... |
607 |
|
{ |
608 |
0 |
this._userColoursList.clear(); |
609 |
|
} |
610 |
|
|
611 |
|
|
612 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
613 |
0 |
public void removeAllViewport()... |
614 |
|
{ |
615 |
0 |
this._viewportList.clear(); |
616 |
|
} |
617 |
|
|
618 |
|
|
619 |
|
|
620 |
|
|
621 |
|
@param |
622 |
|
@return |
623 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
624 |
0 |
public boolean removeJGroup(... |
625 |
|
final jalview.schemabinding.version2.JGroup vJGroup) |
626 |
|
{ |
627 |
0 |
boolean removed = _JGroupList.remove(vJGroup); |
628 |
0 |
return removed; |
629 |
|
} |
630 |
|
|
631 |
|
|
632 |
|
|
633 |
|
|
634 |
|
@param |
635 |
|
@return |
636 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
637 |
0 |
public jalview.schemabinding.version2.JGroup removeJGroupAt(... |
638 |
|
final int index) |
639 |
|
{ |
640 |
0 |
java.lang.Object obj = this._JGroupList.remove(index); |
641 |
0 |
return (jalview.schemabinding.version2.JGroup) obj; |
642 |
|
} |
643 |
|
|
644 |
|
|
645 |
|
|
646 |
|
|
647 |
|
@param |
648 |
|
@return |
649 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
650 |
0 |
public boolean removeJSeq(final jalview.schemabinding.version2.JSeq vJSeq)... |
651 |
|
{ |
652 |
0 |
boolean removed = _JSeqList.remove(vJSeq); |
653 |
0 |
return removed; |
654 |
|
} |
655 |
|
|
656 |
|
|
657 |
|
|
658 |
|
|
659 |
|
@param |
660 |
|
@return |
661 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
662 |
0 |
public jalview.schemabinding.version2.JSeq removeJSeqAt(final int index)... |
663 |
|
{ |
664 |
0 |
java.lang.Object obj = this._JSeqList.remove(index); |
665 |
0 |
return (jalview.schemabinding.version2.JSeq) obj; |
666 |
|
} |
667 |
|
|
668 |
|
|
669 |
|
|
670 |
|
|
671 |
|
@param |
672 |
|
@return |
673 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
674 |
0 |
public boolean removeTree(final jalview.schemabinding.version2.Tree vTree)... |
675 |
|
{ |
676 |
0 |
boolean removed = _treeList.remove(vTree); |
677 |
0 |
return removed; |
678 |
|
} |
679 |
|
|
680 |
|
|
681 |
|
|
682 |
|
|
683 |
|
@param |
684 |
|
@return |
685 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
686 |
0 |
public jalview.schemabinding.version2.Tree removeTreeAt(final int index)... |
687 |
|
{ |
688 |
0 |
java.lang.Object obj = this._treeList.remove(index); |
689 |
0 |
return (jalview.schemabinding.version2.Tree) obj; |
690 |
|
} |
691 |
|
|
692 |
|
|
693 |
|
|
694 |
|
|
695 |
|
@param |
696 |
|
@return |
697 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
698 |
0 |
public boolean removeUserColours(... |
699 |
|
final jalview.schemabinding.version2.UserColours vUserColours) |
700 |
|
{ |
701 |
0 |
boolean removed = _userColoursList.remove(vUserColours); |
702 |
0 |
return removed; |
703 |
|
} |
704 |
|
|
705 |
|
|
706 |
|
|
707 |
|
|
708 |
|
@param |
709 |
|
@return |
710 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
711 |
0 |
public jalview.schemabinding.version2.UserColours removeUserColoursAt(... |
712 |
|
final int index) |
713 |
|
{ |
714 |
0 |
java.lang.Object obj = this._userColoursList.remove(index); |
715 |
0 |
return (jalview.schemabinding.version2.UserColours) obj; |
716 |
|
} |
717 |
|
|
718 |
|
|
719 |
|
|
720 |
|
|
721 |
|
@param |
722 |
|
@return |
723 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
724 |
0 |
public boolean removeViewport(... |
725 |
|
final jalview.schemabinding.version2.Viewport vViewport) |
726 |
|
{ |
727 |
0 |
boolean removed = _viewportList.remove(vViewport); |
728 |
0 |
return removed; |
729 |
|
} |
730 |
|
|
731 |
|
|
732 |
|
|
733 |
|
|
734 |
|
@param |
735 |
|
@return |
736 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
737 |
0 |
public jalview.schemabinding.version2.Viewport removeViewportAt(... |
738 |
|
final int index) |
739 |
|
{ |
740 |
0 |
java.lang.Object obj = this._viewportList.remove(index); |
741 |
0 |
return (jalview.schemabinding.version2.Viewport) obj; |
742 |
|
} |
743 |
|
|
744 |
|
|
745 |
|
|
746 |
|
|
747 |
|
@param |
748 |
|
|
749 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
750 |
62 |
public void setFeatureSettings(... |
751 |
|
final jalview.schemabinding.version2.FeatureSettings featureSettings) |
752 |
|
{ |
753 |
62 |
this._featureSettings = featureSettings; |
754 |
|
} |
755 |
|
|
756 |
|
|
757 |
|
|
758 |
|
|
759 |
|
@param |
760 |
|
@param |
761 |
|
@throws |
762 |
|
|
763 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
764 |
0 |
public void setJGroup(final int index,... |
765 |
|
final jalview.schemabinding.version2.JGroup vJGroup) |
766 |
|
throws java.lang.IndexOutOfBoundsException |
767 |
|
{ |
768 |
|
|
769 |
0 |
if (index < 0 || index >= this._JGroupList.size()) |
770 |
|
{ |
771 |
0 |
throw new IndexOutOfBoundsException("setJGroup: Index value '" |
772 |
|
+ index + "' not in range [0.." |
773 |
|
+ (this._JGroupList.size() - 1) + "]"); |
774 |
|
} |
775 |
|
|
776 |
0 |
this._JGroupList.set(index, vJGroup); |
777 |
|
} |
778 |
|
|
779 |
|
|
780 |
|
|
781 |
|
|
782 |
|
@param |
783 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
784 |
36 |
public void setJGroup(... |
785 |
|
final jalview.schemabinding.version2.JGroup[] vJGroupArray) |
786 |
|
{ |
787 |
|
|
788 |
36 |
_JGroupList.clear(); |
789 |
|
|
790 |
49 |
for (int i = 0; i < vJGroupArray.length; i++) |
791 |
|
{ |
792 |
13 |
this._JGroupList.add(vJGroupArray[i]); |
793 |
|
} |
794 |
|
} |
795 |
|
|
796 |
|
|
797 |
|
|
798 |
|
|
799 |
|
@param |
800 |
|
@param |
801 |
|
@throws |
802 |
|
|
803 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
804 |
0 |
public void setJSeq(final int index,... |
805 |
|
final jalview.schemabinding.version2.JSeq vJSeq) |
806 |
|
throws java.lang.IndexOutOfBoundsException |
807 |
|
{ |
808 |
|
|
809 |
0 |
if (index < 0 || index >= this._JSeqList.size()) |
810 |
|
{ |
811 |
0 |
throw new IndexOutOfBoundsException("setJSeq: Index value '" + index |
812 |
|
+ "' not in range [0.." + (this._JSeqList.size() - 1) + "]"); |
813 |
|
} |
814 |
|
|
815 |
0 |
this._JSeqList.set(index, vJSeq); |
816 |
|
} |
817 |
|
|
818 |
|
|
819 |
|
|
820 |
|
|
821 |
|
@param |
822 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
823 |
0 |
public void setJSeq(final jalview.schemabinding.version2.JSeq[] vJSeqArray)... |
824 |
|
{ |
825 |
|
|
826 |
0 |
_JSeqList.clear(); |
827 |
|
|
828 |
0 |
for (int i = 0; i < vJSeqArray.length; i++) |
829 |
|
{ |
830 |
0 |
this._JSeqList.add(vJSeqArray[i]); |
831 |
|
} |
832 |
|
} |
833 |
|
|
834 |
|
|
835 |
|
|
836 |
|
|
837 |
|
@param |
838 |
|
@param |
839 |
|
@throws |
840 |
|
|
841 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
842 |
0 |
public void setTree(final int index,... |
843 |
|
final jalview.schemabinding.version2.Tree vTree) |
844 |
|
throws java.lang.IndexOutOfBoundsException |
845 |
|
{ |
846 |
|
|
847 |
0 |
if (index < 0 || index >= this._treeList.size()) |
848 |
|
{ |
849 |
0 |
throw new IndexOutOfBoundsException("setTree: Index value '" + index |
850 |
|
+ "' not in range [0.." + (this._treeList.size() - 1) + "]"); |
851 |
|
} |
852 |
|
|
853 |
0 |
this._treeList.set(index, vTree); |
854 |
|
} |
855 |
|
|
856 |
|
|
857 |
|
|
858 |
|
|
859 |
|
@param |
860 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
861 |
0 |
public void setTree(final jalview.schemabinding.version2.Tree[] vTreeArray)... |
862 |
|
{ |
863 |
|
|
864 |
0 |
_treeList.clear(); |
865 |
|
|
866 |
0 |
for (int i = 0; i < vTreeArray.length; i++) |
867 |
|
{ |
868 |
0 |
this._treeList.add(vTreeArray[i]); |
869 |
|
} |
870 |
|
} |
871 |
|
|
872 |
|
|
873 |
|
|
874 |
|
|
875 |
|
@param |
876 |
|
@param |
877 |
|
@throws |
878 |
|
|
879 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
880 |
0 |
public void setUserColours(final int index,... |
881 |
|
final jalview.schemabinding.version2.UserColours vUserColours) |
882 |
|
throws java.lang.IndexOutOfBoundsException |
883 |
|
{ |
884 |
|
|
885 |
0 |
if (index < 0 || index >= this._userColoursList.size()) |
886 |
|
{ |
887 |
0 |
throw new IndexOutOfBoundsException("setUserColours: Index value '" |
888 |
|
+ index + "' not in range [0.." |
889 |
|
+ (this._userColoursList.size() - 1) + "]"); |
890 |
|
} |
891 |
|
|
892 |
0 |
this._userColoursList.set(index, vUserColours); |
893 |
|
} |
894 |
|
|
895 |
|
|
896 |
|
|
897 |
|
|
898 |
|
@param |
899 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
900 |
0 |
public void setUserColours(... |
901 |
|
final jalview.schemabinding.version2.UserColours[] vUserColoursArray) |
902 |
|
{ |
903 |
|
|
904 |
0 |
_userColoursList.clear(); |
905 |
|
|
906 |
0 |
for (int i = 0; i < vUserColoursArray.length; i++) |
907 |
|
{ |
908 |
0 |
this._userColoursList.add(vUserColoursArray[i]); |
909 |
|
} |
910 |
|
} |
911 |
|
|
912 |
|
|
913 |
|
|
914 |
|
|
915 |
|
@param |
916 |
|
@param |
917 |
|
@throws |
918 |
|
|
919 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
920 |
0 |
public void setViewport(final int index,... |
921 |
|
final jalview.schemabinding.version2.Viewport vViewport) |
922 |
|
throws java.lang.IndexOutOfBoundsException |
923 |
|
{ |
924 |
|
|
925 |
0 |
if (index < 0 || index >= this._viewportList.size()) |
926 |
|
{ |
927 |
0 |
throw new IndexOutOfBoundsException("setViewport: Index value '" |
928 |
|
+ index + "' not in range [0.." |
929 |
|
+ (this._viewportList.size() - 1) + "]"); |
930 |
|
} |
931 |
|
|
932 |
0 |
this._viewportList.set(index, vViewport); |
933 |
|
} |
934 |
|
|
935 |
|
|
936 |
|
|
937 |
|
|
938 |
|
@param |
939 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
940 |
0 |
public void setViewport(... |
941 |
|
final jalview.schemabinding.version2.Viewport[] vViewportArray) |
942 |
|
{ |
943 |
|
|
944 |
0 |
_viewportList.clear(); |
945 |
|
|
946 |
0 |
for (int i = 0; i < vViewportArray.length; i++) |
947 |
|
{ |
948 |
0 |
this._viewportList.add(vViewportArray[i]); |
949 |
|
} |
950 |
|
} |
951 |
|
|
952 |
|
|
953 |
|
|
954 |
|
|
955 |
|
@param |
956 |
|
@throws |
957 |
|
|
958 |
|
|
959 |
|
@throws |
960 |
|
|
961 |
|
@return |
962 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
963 |
0 |
public static jalview.schemabinding.version2.JalviewModelSequence unmarshal(... |
964 |
|
final java.io.Reader reader) |
965 |
|
throws org.exolab.castor.xml.MarshalException, |
966 |
|
org.exolab.castor.xml.ValidationException |
967 |
|
{ |
968 |
0 |
return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller |
969 |
|
.unmarshal( |
970 |
|
jalview.schemabinding.version2.JalviewModelSequence.class, |
971 |
|
reader); |
972 |
|
} |
973 |
|
|
974 |
|
|
975 |
|
|
976 |
|
|
977 |
|
@throws |
978 |
|
|
979 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
980 |
0 |
public void validate() throws org.exolab.castor.xml.ValidationException... |
981 |
|
{ |
982 |
0 |
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); |
983 |
0 |
validator.validate(this); |
984 |
|
} |
985 |
|
|
986 |
|
} |