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package jalview.xml.binding.jalview; |
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import java.util.ArrayList; |
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import java.util.List; |
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import javax.xml.bind.annotation.XmlAccessType; |
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import javax.xml.bind.annotation.XmlAccessorType; |
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import javax.xml.bind.annotation.XmlAttribute; |
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import javax.xml.bind.annotation.XmlElement; |
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import javax.xml.bind.annotation.XmlRootElement; |
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import javax.xml.bind.annotation.XmlType; |
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@XmlAccessorType(XmlAccessType.FIELD) |
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@XmlType( |
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name = "", |
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propOrder = |
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{ "annotationElement", "label", "description", "thresholdLine", |
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"contactmatrix", "property" }) |
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@XmlRootElement(name = "Annotation") |
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| 91.8% |
Uncovered Elements: 9 (110) |
Complexity: 49 |
Complexity Density: 0.89 |
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public class Annotation |
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{ |
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protected List<AnnotationElement> annotationElement; |
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@XmlElement(required = true) |
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protected String label; |
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protected String description; |
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protected Annotation.ThresholdLine thresholdLine; |
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protected List<MapOnAMatrixType> contactmatrix; |
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protected List<Property> property; |
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@XmlAttribute(name = "graph", required = true) |
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protected boolean graph; |
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@XmlAttribute(name = "graphType") |
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protected Integer graphType; |
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@XmlAttribute(name = "sequenceRef") |
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protected String sequenceRef; |
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@XmlAttribute(name = "groupRef") |
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protected String groupRef; |
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@XmlAttribute(name = "graphColour") |
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protected Integer graphColour; |
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@XmlAttribute(name = "graphGroup") |
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protected Integer graphGroup; |
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@XmlAttribute(name = "graphHeight") |
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protected Integer graphHeight; |
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@XmlAttribute(name = "id") |
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protected String id; |
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@XmlAttribute(name = "scoreOnly") |
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protected Boolean scoreOnly; |
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@XmlAttribute(name = "score") |
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protected Double score; |
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@XmlAttribute(name = "visible") |
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protected Boolean visible; |
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@XmlAttribute(name = "centreColLabels") |
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protected Boolean centreColLabels; |
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@XmlAttribute(name = "scaleColLabels") |
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protected Boolean scaleColLabels; |
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@XmlAttribute(name = "showAllColLabels") |
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protected Boolean showAllColLabels; |
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@XmlAttribute(name = "autoCalculated") |
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protected Boolean autoCalculated; |
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@XmlAttribute(name = "belowAlignment") |
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protected Boolean belowAlignment; |
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@XmlAttribute(name = "calcId") |
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protected String calcId; |
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@link |
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
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47480 |
public List<AnnotationElement> getAnnotationElement()... |
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{ |
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if (annotationElement == null) |
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{ |
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annotationElement = new ArrayList<AnnotationElement>(); |
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} |
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47480 |
return this.annotationElement; |
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} |
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@return@link |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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2166 |
public String getLabel()... |
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{ |
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return label; |
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} |
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@param |
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@link |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public void setLabel(String value)... |
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{ |
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this.label = value; |
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} |
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@return@link |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public String getDescription()... |
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{ |
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return description; |
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} |
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@param |
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@link |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public void setDescription(String value)... |
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{ |
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this.description = value; |
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} |
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@return@link |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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500 |
public Annotation.ThresholdLine getThresholdLine()... |
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{ |
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return thresholdLine; |
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} |
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@param |
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@link |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public void setThresholdLine(Annotation.ThresholdLine value)... |
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{ |
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this.thresholdLine = value; |
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} |
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@link |
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
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public List<MapOnAMatrixType> getContactmatrix()... |
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{ |
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if (contactmatrix == null) |
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{ |
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contactmatrix = new ArrayList<MapOnAMatrixType>(); |
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} |
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return this.contactmatrix; |
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} |
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@link |
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|
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| 80% |
Uncovered Elements: 1 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
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public List<Property> getProperty()... |
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{ |
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if (property == null) |
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{ |
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property = new ArrayList<Property>(); |
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} |
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return this.property; |
297 |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public boolean isGraph()... |
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{ |
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return graph; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public void setGraph(boolean value)... |
313 |
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{ |
314 |
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this.graph = value; |
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} |
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@return@link |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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410 |
public Integer getGraphType()... |
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{ |
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return graphType; |
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} |
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@param |
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@link |
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|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
335 |
283 |
public void setGraphType(Integer value)... |
336 |
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{ |
337 |
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this.graphType = value; |
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} |
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@return@link |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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594 |
public String getSequenceRef()... |
347 |
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{ |
348 |
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return sequenceRef; |
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} |
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@param |
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@link |
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|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
358 |
229 |
public void setSequenceRef(String value)... |
359 |
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{ |
360 |
229 |
this.sequenceRef = value; |
361 |
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} |
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@return@link |
367 |
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368 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
369 |
678 |
public String getGroupRef()... |
370 |
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{ |
371 |
678 |
return groupRef; |
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} |
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@param |
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@link |
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|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
381 |
12 |
public void setGroupRef(String value)... |
382 |
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{ |
383 |
12 |
this.groupRef = value; |
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} |
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@return@link |
390 |
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391 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
392 |
0 |
public Integer getGraphColour()... |
393 |
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{ |
394 |
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return graphColour; |
395 |
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} |
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@param |
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@link |
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|
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
404 |
0 |
public void setGraphColour(Integer value)... |
405 |
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{ |
406 |
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this.graphColour = value; |
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} |
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410 |
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@return@link |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
415 |
410 |
public Integer getGraphGroup()... |
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{ |
417 |
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return graphGroup; |
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} |
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@param |
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@link |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
427 |
283 |
public void setGraphGroup(Integer value)... |
428 |
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{ |
429 |
283 |
this.graphGroup = value; |
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} |
431 |
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433 |
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434 |
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435 |
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@return@link |
436 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
438 |
1188 |
public Integer getGraphHeight()... |
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{ |
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1188 |
return graphHeight; |
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} |
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444 |
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445 |
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|
@param |
447 |
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@link |
448 |
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|
449 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
450 |
447 |
public void setGraphHeight(Integer value)... |
451 |
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{ |
452 |
447 |
this.graphHeight = value; |
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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@link |
459 |
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|
460 |
|
|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
461 |
1774 |
public String getId()... |
462 |
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{ |
463 |
1774 |
return id; |
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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|
469 |
|
@param |
470 |
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@link |
471 |
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|
472 |
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|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
473 |
751 |
public void setId(String value)... |
474 |
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{ |
475 |
751 |
this.id = value; |
476 |
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} |
477 |
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478 |
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479 |
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|
480 |
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|
481 |
|
@return@link |
482 |
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|
483 |
|
|
|
|
| 60% |
Uncovered Elements: 2 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
484 |
594 |
public boolean isScoreOnly()... |
485 |
|
{ |
486 |
594 |
if (scoreOnly == null) |
487 |
|
{ |
488 |
0 |
return false; |
489 |
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} |
490 |
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else |
491 |
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{ |
492 |
594 |
return scoreOnly; |
493 |
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} |
494 |
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} |
495 |
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496 |
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497 |
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498 |
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|
499 |
|
@param |
500 |
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@link |
501 |
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|
502 |
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|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
503 |
447 |
public void setScoreOnly(Boolean value)... |
504 |
|
{ |
505 |
447 |
this.scoreOnly = value; |
506 |
|
} |
507 |
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508 |
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|
509 |
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|
510 |
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|
511 |
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@return@link |
512 |
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|
513 |
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|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
514 |
733 |
public Double getScore()... |
515 |
|
{ |
516 |
733 |
return score; |
517 |
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} |
518 |
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519 |
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520 |
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521 |
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522 |
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@param |
523 |
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@link |
524 |
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|
525 |
|
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|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
526 |
139 |
public void setScore(Double value)... |
527 |
|
{ |
528 |
139 |
this.score = value; |
529 |
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} |
530 |
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|
531 |
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|
532 |
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|
533 |
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|
534 |
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@return@link |
535 |
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|
536 |
|
|
|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
537 |
1200 |
public Boolean isVisible()... |
538 |
|
{ |
539 |
1200 |
return visible; |
540 |
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} |
541 |
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|
542 |
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|
543 |
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|
544 |
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|
545 |
|
@param |
546 |
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@link |
547 |
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|
548 |
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|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
549 |
447 |
public void setVisible(Boolean value)... |
550 |
|
{ |
551 |
447 |
this.visible = value; |
552 |
|
} |
553 |
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|
554 |
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|
555 |
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|
556 |
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|
557 |
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@return@link |
558 |
|
|
559 |
|
|
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|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
560 |
1188 |
public Boolean isCentreColLabels()... |
561 |
|
{ |
562 |
1188 |
return centreColLabels; |
563 |
|
} |
564 |
|
|
565 |
|
|
566 |
|
|
567 |
|
|
568 |
|
@param |
569 |
|
@link |
570 |
|
|
571 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
572 |
447 |
public void setCentreColLabels(Boolean value)... |
573 |
|
{ |
574 |
447 |
this.centreColLabels = value; |
575 |
|
} |
576 |
|
|
577 |
|
|
578 |
|
|
579 |
|
|
580 |
|
@return@link |
581 |
|
|
582 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
583 |
1188 |
public Boolean isScaleColLabels()... |
584 |
|
{ |
585 |
1188 |
return scaleColLabels; |
586 |
|
} |
587 |
|
|
588 |
|
|
589 |
|
|
590 |
|
|
591 |
|
@param |
592 |
|
@link |
593 |
|
|
594 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
595 |
447 |
public void setScaleColLabels(Boolean value)... |
596 |
|
{ |
597 |
447 |
this.scaleColLabels = value; |
598 |
|
} |
599 |
|
|
600 |
|
|
601 |
|
|
602 |
|
|
603 |
|
@return@link |
604 |
|
|
605 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
606 |
0 |
public Boolean isShowAllColLabels()... |
607 |
|
{ |
608 |
0 |
return showAllColLabels; |
609 |
|
} |
610 |
|
|
611 |
|
|
612 |
|
|
613 |
|
|
614 |
|
@param |
615 |
|
@link |
616 |
|
|
617 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
618 |
447 |
public void setShowAllColLabels(Boolean value)... |
619 |
|
{ |
620 |
447 |
this.showAllColLabels = value; |
621 |
|
} |
622 |
|
|
623 |
|
|
624 |
|
|
625 |
|
|
626 |
|
@return@link |
627 |
|
|
628 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
629 |
1142 |
public boolean isAutoCalculated()... |
630 |
|
{ |
631 |
1142 |
if (autoCalculated == null) |
632 |
|
{ |
633 |
692 |
return false; |
634 |
|
} |
635 |
|
else |
636 |
|
{ |
637 |
450 |
return autoCalculated; |
638 |
|
} |
639 |
|
} |
640 |
|
|
641 |
|
|
642 |
|
|
643 |
|
|
644 |
|
@param |
645 |
|
@link |
646 |
|
|
647 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
648 |
193 |
public void setAutoCalculated(Boolean value)... |
649 |
|
{ |
650 |
193 |
this.autoCalculated = value; |
651 |
|
} |
652 |
|
|
653 |
|
|
654 |
|
|
655 |
|
|
656 |
|
@return@link |
657 |
|
|
658 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
659 |
594 |
public boolean isBelowAlignment()... |
660 |
|
{ |
661 |
594 |
if (belowAlignment == null) |
662 |
|
{ |
663 |
144 |
return true; |
664 |
|
} |
665 |
|
else |
666 |
|
{ |
667 |
450 |
return belowAlignment; |
668 |
|
} |
669 |
|
} |
670 |
|
|
671 |
|
|
672 |
|
|
673 |
|
|
674 |
|
@param |
675 |
|
@link |
676 |
|
|
677 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
678 |
447 |
public void setBelowAlignment(Boolean value)... |
679 |
|
{ |
680 |
447 |
this.belowAlignment = value; |
681 |
|
} |
682 |
|
|
683 |
|
|
684 |
|
|
685 |
|
|
686 |
|
@return@link |
687 |
|
|
688 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
689 |
594 |
public String getCalcId()... |
690 |
|
{ |
691 |
594 |
return calcId; |
692 |
|
} |
693 |
|
|
694 |
|
|
695 |
|
|
696 |
|
|
697 |
|
@param |
698 |
|
@link |
699 |
|
|
700 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
701 |
423 |
public void setCalcId(String value)... |
702 |
|
{ |
703 |
423 |
this.calcId = value; |
704 |
|
} |
705 |
|
|
706 |
|
|
707 |
|
|
708 |
|
|
709 |
|
|
710 |
|
|
711 |
|
|
712 |
|
|
713 |
|
|
714 |
|
|
715 |
|
|
716 |
|
|
717 |
|
|
718 |
|
|
719 |
|
|
720 |
|
|
721 |
|
|
722 |
|
|
723 |
|
|
724 |
|
@XmlAccessorType(XmlAccessType.FIELD) |
725 |
|
@XmlType(name = "") |
|
|
| 100% |
Uncovered Elements: 0 (12) |
Complexity: 6 |
Complexity Density: 1 |
|
726 |
|
public static class ThresholdLine |
727 |
|
{ |
728 |
|
|
729 |
|
@XmlAttribute(name = "label") |
730 |
|
protected String label; |
731 |
|
|
732 |
|
@XmlAttribute(name = "value") |
733 |
|
protected Float value; |
734 |
|
|
735 |
|
@XmlAttribute(name = "colour") |
736 |
|
protected Integer colour; |
737 |
|
|
738 |
|
|
739 |
|
|
740 |
|
|
741 |
|
@return@link |
742 |
|
|
743 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
744 |
30 |
public String getLabel()... |
745 |
|
{ |
746 |
30 |
return label; |
747 |
|
} |
748 |
|
|
749 |
|
|
750 |
|
|
751 |
|
|
752 |
|
@param |
753 |
|
@link |
754 |
|
|
755 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
756 |
30 |
public void setLabel(String value)... |
757 |
|
{ |
758 |
30 |
this.label = value; |
759 |
|
} |
760 |
|
|
761 |
|
|
762 |
|
|
763 |
|
|
764 |
|
@return@link |
765 |
|
|
766 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
767 |
30 |
public Float getValue()... |
768 |
|
{ |
769 |
30 |
return value; |
770 |
|
} |
771 |
|
|
772 |
|
|
773 |
|
|
774 |
|
|
775 |
|
@param |
776 |
|
@link |
777 |
|
|
778 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
779 |
30 |
public void setValue(Float value)... |
780 |
|
{ |
781 |
30 |
this.value = value; |
782 |
|
} |
783 |
|
|
784 |
|
|
785 |
|
|
786 |
|
|
787 |
|
@return@link |
788 |
|
|
789 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
790 |
30 |
public Integer getColour()... |
791 |
|
{ |
792 |
30 |
return colour; |
793 |
|
} |
794 |
|
|
795 |
|
|
796 |
|
|
797 |
|
|
798 |
|
@param |
799 |
|
@link |
800 |
|
|
801 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
802 |
30 |
public void setColour(Integer value)... |
803 |
|
{ |
804 |
30 |
this.colour = value; |
805 |
|
} |
806 |
|
|
807 |
|
} |
808 |
|
|
809 |
|
} |