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package jalview.schemabinding.version2.descriptors; |
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import jalview.schemabinding.version2.SequenceSet; |
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@version |
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| 74.9% |
Uncovered Elements: 42 (167) |
Complexity: 41 |
Complexity Density: 0.3 |
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public class SequenceSetDescriptor extends |
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org.exolab.castor.xml.util.XMLClassDescriptorImpl |
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{ |
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private boolean _elementDefinition; |
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private java.lang.String _nsPrefix; |
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private java.lang.String _nsURI; |
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private java.lang.String _xmlName; |
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| 100% |
Uncovered Elements: 0 (70) |
Complexity: 1 |
Complexity Density: 0.01 |
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public SequenceSetDescriptor()... |
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{ |
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super(); |
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_nsURI = "www.vamsas.ac.uk/jalview/version2"; |
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_xmlName = "SequenceSet"; |
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_elementDefinition = true; |
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setCompositorAsSequence(); |
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org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; |
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org.exolab.castor.mapping.FieldHandler handler = null; |
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org.exolab.castor.xml.FieldValidator fieldValidator = null; |
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desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( |
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java.lang.String.class, "_gapChar", "gapChar", |
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org.exolab.castor.xml.NodeType.Attribute); |
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desc.setImmutable(true); |
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handler = new org.exolab.castor.xml.XMLFieldHandler() |
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{ |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
74 |
58 |
public java.lang.Object getValue(java.lang.Object object)... |
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throws IllegalStateException |
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{ |
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SequenceSet target = (SequenceSet) object; |
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return target.getGapChar(); |
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} |
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| 75% |
Uncovered Elements: 1 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
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public void setValue(java.lang.Object object, java.lang.Object value)... |
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throws IllegalStateException, IllegalArgumentException |
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{ |
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try |
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{ |
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SequenceSet target = (SequenceSet) object; |
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target.setGapChar((java.lang.String) value); |
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} catch (java.lang.Exception ex) |
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{ |
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throw new IllegalStateException(ex.toString()); |
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} |
92 |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
public java.lang.Object newInstance(java.lang.Object parent)... |
95 |
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{ |
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return null; |
97 |
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} |
98 |
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}; |
99 |
137 |
desc.setHandler(handler); |
100 |
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desc.setRequired(true); |
101 |
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desc.setMultivalued(false); |
102 |
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addFieldDescriptor(desc); |
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fieldValidator = new org.exolab.castor.xml.FieldValidator(); |
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fieldValidator.setMinOccurs(1); |
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{ |
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org.exolab.castor.xml.validators.StringValidator typeValidator; |
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typeValidator = new org.exolab.castor.xml.validators.StringValidator(); |
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fieldValidator.setValidator(typeValidator); |
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typeValidator.setWhiteSpace("preserve"); |
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} |
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desc.setValidator(fieldValidator); |
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desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( |
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java.lang.String.class, "_datasetId", "datasetId", |
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org.exolab.castor.xml.NodeType.Attribute); |
118 |
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desc.setImmutable(true); |
119 |
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handler = new org.exolab.castor.xml.XMLFieldHandler() |
120 |
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{ |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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58 |
public java.lang.Object getValue(java.lang.Object object)... |
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throws IllegalStateException |
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{ |
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SequenceSet target = (SequenceSet) object; |
125 |
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return target.getDatasetId(); |
126 |
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} |
127 |
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| 75% |
Uncovered Elements: 1 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
|
128 |
29 |
public void setValue(java.lang.Object object, java.lang.Object value)... |
129 |
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throws IllegalStateException, IllegalArgumentException |
130 |
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{ |
131 |
29 |
try |
132 |
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{ |
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SequenceSet target = (SequenceSet) object; |
134 |
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target.setDatasetId((java.lang.String) value); |
135 |
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} catch (java.lang.Exception ex) |
136 |
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{ |
137 |
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throw new IllegalStateException(ex.toString()); |
138 |
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} |
139 |
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} |
140 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
141 |
0 |
public java.lang.Object newInstance(java.lang.Object parent)... |
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{ |
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return null; |
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} |
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}; |
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desc.setHandler(handler); |
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desc.setMultivalued(false); |
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addFieldDescriptor(desc); |
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150 |
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fieldValidator = new org.exolab.castor.xml.FieldValidator(); |
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{ |
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org.exolab.castor.xml.validators.StringValidator typeValidator; |
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typeValidator = new org.exolab.castor.xml.validators.StringValidator(); |
155 |
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fieldValidator.setValidator(typeValidator); |
156 |
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typeValidator.setWhiteSpace("preserve"); |
157 |
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} |
158 |
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desc.setValidator(fieldValidator); |
159 |
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160 |
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desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( |
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jalview.schemabinding.version2.Sequence.class, "_sequenceList", |
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"Sequence", org.exolab.castor.xml.NodeType.Element); |
165 |
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handler = new org.exolab.castor.xml.XMLFieldHandler() |
166 |
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{ |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
167 |
58 |
public java.lang.Object getValue(java.lang.Object object)... |
168 |
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throws IllegalStateException |
169 |
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{ |
170 |
58 |
SequenceSet target = (SequenceSet) object; |
171 |
58 |
return target.getSequence(); |
172 |
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} |
173 |
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| 75% |
Uncovered Elements: 1 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
|
174 |
482 |
public void setValue(java.lang.Object object, java.lang.Object value)... |
175 |
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throws IllegalStateException, IllegalArgumentException |
176 |
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{ |
177 |
482 |
try |
178 |
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{ |
179 |
482 |
SequenceSet target = (SequenceSet) object; |
180 |
482 |
target.addSequence((jalview.schemabinding.version2.Sequence) value); |
181 |
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} catch (java.lang.Exception ex) |
182 |
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{ |
183 |
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throw new IllegalStateException(ex.toString()); |
184 |
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} |
185 |
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} |
186 |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
|
187 |
0 |
public void resetValue(Object object) throws IllegalStateException,... |
188 |
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IllegalArgumentException |
189 |
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{ |
190 |
0 |
try |
191 |
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{ |
192 |
0 |
SequenceSet target = (SequenceSet) object; |
193 |
0 |
target.removeAllSequence(); |
194 |
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} catch (java.lang.Exception ex) |
195 |
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{ |
196 |
0 |
throw new IllegalStateException(ex.toString()); |
197 |
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} |
198 |
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} |
199 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
200 |
482 |
public java.lang.Object newInstance(java.lang.Object parent)... |
201 |
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{ |
202 |
482 |
return new jalview.schemabinding.version2.Sequence(); |
203 |
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} |
204 |
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}; |
205 |
137 |
desc.setHandler(handler); |
206 |
137 |
desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); |
207 |
137 |
desc.setMultivalued(true); |
208 |
137 |
addFieldDescriptor(desc); |
209 |
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210 |
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211 |
137 |
fieldValidator = new org.exolab.castor.xml.FieldValidator(); |
212 |
137 |
fieldValidator.setMinOccurs(0); |
213 |
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{ |
214 |
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} |
215 |
137 |
desc.setValidator(fieldValidator); |
216 |
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|
217 |
137 |
desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( |
218 |
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jalview.schemabinding.version2.Annotation.class, |
219 |
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"_annotationList", "Annotation", |
220 |
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org.exolab.castor.xml.NodeType.Element); |
221 |
137 |
handler = new org.exolab.castor.xml.XMLFieldHandler() |
222 |
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{ |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
223 |
58 |
public java.lang.Object getValue(java.lang.Object object)... |
224 |
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throws IllegalStateException |
225 |
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{ |
226 |
58 |
SequenceSet target = (SequenceSet) object; |
227 |
58 |
return target.getAnnotation(); |
228 |
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} |
229 |
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| 75% |
Uncovered Elements: 1 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
|
230 |
545 |
public void setValue(java.lang.Object object, java.lang.Object value)... |
231 |
|
throws IllegalStateException, IllegalArgumentException |
232 |
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{ |
233 |
545 |
try |
234 |
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{ |
235 |
545 |
SequenceSet target = (SequenceSet) object; |
236 |
545 |
target.addAnnotation((jalview.schemabinding.version2.Annotation) value); |
237 |
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} catch (java.lang.Exception ex) |
238 |
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{ |
239 |
0 |
throw new IllegalStateException(ex.toString()); |
240 |
|
} |
241 |
|
} |
242 |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
|
243 |
0 |
public void resetValue(Object object) throws IllegalStateException,... |
244 |
|
IllegalArgumentException |
245 |
|
{ |
246 |
0 |
try |
247 |
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{ |
248 |
0 |
SequenceSet target = (SequenceSet) object; |
249 |
0 |
target.removeAllAnnotation(); |
250 |
|
} catch (java.lang.Exception ex) |
251 |
|
{ |
252 |
0 |
throw new IllegalStateException(ex.toString()); |
253 |
|
} |
254 |
|
} |
255 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
256 |
545 |
public java.lang.Object newInstance(java.lang.Object parent)... |
257 |
|
{ |
258 |
545 |
return new jalview.schemabinding.version2.Annotation(); |
259 |
|
} |
260 |
|
}; |
261 |
137 |
desc.setHandler(handler); |
262 |
137 |
desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); |
263 |
137 |
desc.setMultivalued(true); |
264 |
137 |
addFieldDescriptor(desc); |
265 |
|
|
266 |
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|
267 |
137 |
fieldValidator = new org.exolab.castor.xml.FieldValidator(); |
268 |
137 |
fieldValidator.setMinOccurs(0); |
269 |
|
{ |
270 |
|
} |
271 |
137 |
desc.setValidator(fieldValidator); |
272 |
|
|
273 |
137 |
desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( |
274 |
|
jalview.schemabinding.version2.SequenceSetProperties.class, |
275 |
|
"_sequenceSetPropertiesList", "sequenceSetProperties", |
276 |
|
org.exolab.castor.xml.NodeType.Element); |
277 |
137 |
handler = new org.exolab.castor.xml.XMLFieldHandler() |
278 |
|
{ |
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
279 |
58 |
public java.lang.Object getValue(java.lang.Object object)... |
280 |
|
throws IllegalStateException |
281 |
|
{ |
282 |
58 |
SequenceSet target = (SequenceSet) object; |
283 |
58 |
return target.getSequenceSetProperties(); |
284 |
|
} |
285 |
|
|
|
|
| 75% |
Uncovered Elements: 1 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
|
286 |
21 |
public void setValue(java.lang.Object object, java.lang.Object value)... |
287 |
|
throws IllegalStateException, IllegalArgumentException |
288 |
|
{ |
289 |
21 |
try |
290 |
|
{ |
291 |
21 |
SequenceSet target = (SequenceSet) object; |
292 |
21 |
target.addSequenceSetProperties((jalview.schemabinding.version2.SequenceSetProperties) value); |
293 |
|
} catch (java.lang.Exception ex) |
294 |
|
{ |
295 |
0 |
throw new IllegalStateException(ex.toString()); |
296 |
|
} |
297 |
|
} |
298 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
|
299 |
0 |
public void resetValue(Object object) throws IllegalStateException,... |
300 |
|
IllegalArgumentException |
301 |
|
{ |
302 |
0 |
try |
303 |
|
{ |
304 |
0 |
SequenceSet target = (SequenceSet) object; |
305 |
0 |
target.removeAllSequenceSetProperties(); |
306 |
|
} catch (java.lang.Exception ex) |
307 |
|
{ |
308 |
0 |
throw new IllegalStateException(ex.toString()); |
309 |
|
} |
310 |
|
} |
311 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
312 |
21 |
public java.lang.Object newInstance(java.lang.Object parent)... |
313 |
|
{ |
314 |
21 |
return new jalview.schemabinding.version2.SequenceSetProperties(); |
315 |
|
} |
316 |
|
}; |
317 |
137 |
desc.setHandler(handler); |
318 |
137 |
desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); |
319 |
137 |
desc.setMultivalued(true); |
320 |
137 |
addFieldDescriptor(desc); |
321 |
|
|
322 |
|
|
323 |
137 |
fieldValidator = new org.exolab.castor.xml.FieldValidator(); |
324 |
137 |
fieldValidator.setMinOccurs(0); |
325 |
|
{ |
326 |
|
} |
327 |
137 |
desc.setValidator(fieldValidator); |
328 |
|
|
329 |
137 |
desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( |
330 |
|
jalview.schemabinding.version2.AlcodonFrame.class, |
331 |
|
"_alcodonFrameList", "AlcodonFrame", |
332 |
|
org.exolab.castor.xml.NodeType.Element); |
333 |
137 |
handler = new org.exolab.castor.xml.XMLFieldHandler() |
334 |
|
{ |
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
335 |
58 |
public java.lang.Object getValue(java.lang.Object object)... |
336 |
|
throws IllegalStateException |
337 |
|
{ |
338 |
58 |
SequenceSet target = (SequenceSet) object; |
339 |
58 |
return target.getAlcodonFrame(); |
340 |
|
} |
341 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
|
342 |
0 |
public void setValue(java.lang.Object object, java.lang.Object value)... |
343 |
|
throws IllegalStateException, IllegalArgumentException |
344 |
|
{ |
345 |
0 |
try |
346 |
|
{ |
347 |
0 |
SequenceSet target = (SequenceSet) object; |
348 |
0 |
target.addAlcodonFrame((jalview.schemabinding.version2.AlcodonFrame) value); |
349 |
|
} catch (java.lang.Exception ex) |
350 |
|
{ |
351 |
0 |
throw new IllegalStateException(ex.toString()); |
352 |
|
} |
353 |
|
} |
354 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
|
355 |
0 |
public void resetValue(Object object) throws IllegalStateException,... |
356 |
|
IllegalArgumentException |
357 |
|
{ |
358 |
0 |
try |
359 |
|
{ |
360 |
0 |
SequenceSet target = (SequenceSet) object; |
361 |
0 |
target.removeAllAlcodonFrame(); |
362 |
|
} catch (java.lang.Exception ex) |
363 |
|
{ |
364 |
0 |
throw new IllegalStateException(ex.toString()); |
365 |
|
} |
366 |
|
} |
367 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
368 |
0 |
public java.lang.Object newInstance(java.lang.Object parent)... |
369 |
|
{ |
370 |
0 |
return new jalview.schemabinding.version2.AlcodonFrame(); |
371 |
|
} |
372 |
|
}; |
373 |
137 |
desc.setHandler(handler); |
374 |
137 |
desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); |
375 |
137 |
desc.setMultivalued(true); |
376 |
137 |
addFieldDescriptor(desc); |
377 |
|
|
378 |
|
|
379 |
137 |
fieldValidator = new org.exolab.castor.xml.FieldValidator(); |
380 |
137 |
fieldValidator.setMinOccurs(0); |
381 |
|
{ |
382 |
|
} |
383 |
137 |
desc.setValidator(fieldValidator); |
384 |
|
} |
385 |
|
|
386 |
|
|
387 |
|
|
388 |
|
|
389 |
|
|
390 |
|
|
391 |
|
|
392 |
|
|
393 |
|
@return |
394 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
395 |
0 |
public org.exolab.castor.mapping.AccessMode getAccessMode()... |
396 |
|
{ |
397 |
0 |
return null; |
398 |
|
} |
399 |
|
|
400 |
|
|
401 |
|
|
402 |
|
|
403 |
|
@return |
404 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
405 |
137 |
public org.exolab.castor.mapping.FieldDescriptor getIdentity()... |
406 |
|
{ |
407 |
137 |
return super.getIdentity(); |
408 |
|
} |
409 |
|
|
410 |
|
|
411 |
|
|
412 |
|
|
413 |
|
@return |
414 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
415 |
108 |
public java.lang.Class getJavaClass()... |
416 |
|
{ |
417 |
108 |
return jalview.schemabinding.version2.SequenceSet.class; |
418 |
|
} |
419 |
|
|
420 |
|
|
421 |
|
|
422 |
|
|
423 |
|
@return |
424 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
425 |
29 |
public java.lang.String getNameSpacePrefix()... |
426 |
|
{ |
427 |
29 |
return _nsPrefix; |
428 |
|
} |
429 |
|
|
430 |
|
|
431 |
|
|
432 |
|
|
433 |
|
@return |
434 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
435 |
0 |
public java.lang.String getNameSpaceURI()... |
436 |
|
{ |
437 |
0 |
return _nsURI; |
438 |
|
} |
439 |
|
|
440 |
|
|
441 |
|
|
442 |
|
|
443 |
|
@return |
444 |
|
|
445 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
446 |
29 |
public org.exolab.castor.xml.TypeValidator getValidator()... |
447 |
|
{ |
448 |
29 |
return this; |
449 |
|
} |
450 |
|
|
451 |
|
|
452 |
|
|
453 |
|
|
454 |
|
@return |
455 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
456 |
274 |
public java.lang.String getXMLName()... |
457 |
|
{ |
458 |
274 |
return _xmlName; |
459 |
|
} |
460 |
|
|
461 |
|
|
462 |
|
|
463 |
|
|
464 |
|
@return |
465 |
|
|
466 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
467 |
0 |
public boolean isElementDefinition()... |
468 |
|
{ |
469 |
0 |
return _elementDefinition; |
470 |
|
} |
471 |
|
|
472 |
|
} |