2 * This class was automatically generated with
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3 * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
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8 package jalview.schemabinding.version2;
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10 //---------------------------------/
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11 //- Imported classes and packages -/
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12 //---------------------------------/
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14 import java.io.IOException;
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15 import java.io.Reader;
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16 import java.io.Serializable;
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17 import java.io.Writer;
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18 import java.util.Enumeration;
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19 import java.util.Vector;
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20 import org.exolab.castor.xml.MarshalException;
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21 import org.exolab.castor.xml.Marshaller;
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22 import org.exolab.castor.xml.Unmarshaller;
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23 import org.exolab.castor.xml.ValidationException;
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24 import org.xml.sax.ContentHandler;
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27 * Class SequenceSet.
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29 * @version $Revision$ $Date$
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31 public class SequenceSet implements java.io.Serializable {
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34 //--------------------------/
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35 //- Class/Member Variables -/
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36 //--------------------------/
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41 private java.lang.String _gapChar;
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44 * Field _sequenceList
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46 private java.util.Vector _sequenceList;
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49 * Field _annotationList
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51 private java.util.Vector _annotationList;
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54 * Field _sequenceSetPropertiesList
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56 private java.util.Vector _sequenceSetPropertiesList;
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63 public SequenceSet() {
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65 _sequenceList = new Vector();
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66 _annotationList = new Vector();
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67 _sequenceSetPropertiesList = new Vector();
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68 } //-- jalview.schemabinding.version2.SequenceSet()
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76 * Method addAnnotation
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80 * @param vAnnotation
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82 public void addAnnotation(jalview.schemabinding.version2.Annotation vAnnotation)
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83 throws java.lang.IndexOutOfBoundsException
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85 _annotationList.addElement(vAnnotation);
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86 } //-- void addAnnotation(jalview.schemabinding.version2.Annotation)
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89 * Method addAnnotation
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94 * @param vAnnotation
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96 public void addAnnotation(int index, jalview.schemabinding.version2.Annotation vAnnotation)
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97 throws java.lang.IndexOutOfBoundsException
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99 _annotationList.insertElementAt(vAnnotation, index);
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100 } //-- void addAnnotation(int, jalview.schemabinding.version2.Annotation)
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103 * Method addSequence
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109 public void addSequence(jalview.schemabinding.version2.Sequence vSequence)
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110 throws java.lang.IndexOutOfBoundsException
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112 _sequenceList.addElement(vSequence);
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113 } //-- void addSequence(jalview.schemabinding.version2.Sequence)
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116 * Method addSequence
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123 public void addSequence(int index, jalview.schemabinding.version2.Sequence vSequence)
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124 throws java.lang.IndexOutOfBoundsException
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126 _sequenceList.insertElementAt(vSequence, index);
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127 } //-- void addSequence(int, jalview.schemabinding.version2.Sequence)
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130 * Method addSequenceSetProperties
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134 * @param vSequenceSetProperties
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136 public void addSequenceSetProperties(jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
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137 throws java.lang.IndexOutOfBoundsException
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139 _sequenceSetPropertiesList.addElement(vSequenceSetProperties);
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140 } //-- void addSequenceSetProperties(jalview.schemabinding.version2.SequenceSetProperties)
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143 * Method addSequenceSetProperties
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148 * @param vSequenceSetProperties
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150 public void addSequenceSetProperties(int index, jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
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151 throws java.lang.IndexOutOfBoundsException
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153 _sequenceSetPropertiesList.insertElementAt(vSequenceSetProperties, index);
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154 } //-- void addSequenceSetProperties(int, jalview.schemabinding.version2.SequenceSetProperties)
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157 * Method enumerateAnnotation
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161 * @return Enumeration
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163 public java.util.Enumeration enumerateAnnotation()
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165 return _annotationList.elements();
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166 } //-- java.util.Enumeration enumerateAnnotation()
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169 * Method enumerateSequence
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173 * @return Enumeration
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175 public java.util.Enumeration enumerateSequence()
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177 return _sequenceList.elements();
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178 } //-- java.util.Enumeration enumerateSequence()
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181 * Method enumerateSequenceSetProperties
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185 * @return Enumeration
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187 public java.util.Enumeration enumerateSequenceSetProperties()
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189 return _sequenceSetPropertiesList.elements();
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190 } //-- java.util.Enumeration enumerateSequenceSetProperties()
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193 * Method getAnnotation
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198 * @return Annotation
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200 public jalview.schemabinding.version2.Annotation getAnnotation(int index)
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201 throws java.lang.IndexOutOfBoundsException
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203 //-- check bounds for index
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204 if ((index < 0) || (index > _annotationList.size())) {
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205 throw new IndexOutOfBoundsException();
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208 return (jalview.schemabinding.version2.Annotation) _annotationList.elementAt(index);
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209 } //-- jalview.schemabinding.version2.Annotation getAnnotation(int)
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212 * Method getAnnotation
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216 * @return Annotation
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218 public jalview.schemabinding.version2.Annotation[] getAnnotation()
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220 int size = _annotationList.size();
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221 jalview.schemabinding.version2.Annotation[] mArray = new jalview.schemabinding.version2.Annotation[size];
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222 for (int index = 0; index < size; index++) {
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223 mArray[index] = (jalview.schemabinding.version2.Annotation) _annotationList.elementAt(index);
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226 } //-- jalview.schemabinding.version2.Annotation[] getAnnotation()
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229 * Method getAnnotationCount
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235 public int getAnnotationCount()
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237 return _annotationList.size();
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238 } //-- int getAnnotationCount()
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241 * Returns the value of field 'gapChar'.
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244 * @return the value of field 'gapChar'.
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246 public java.lang.String getGapChar()
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248 return this._gapChar;
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249 } //-- java.lang.String getGapChar()
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252 * Method getSequence
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259 public jalview.schemabinding.version2.Sequence getSequence(int index)
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260 throws java.lang.IndexOutOfBoundsException
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262 //-- check bounds for index
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263 if ((index < 0) || (index > _sequenceList.size())) {
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264 throw new IndexOutOfBoundsException();
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267 return (jalview.schemabinding.version2.Sequence) _sequenceList.elementAt(index);
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268 } //-- jalview.schemabinding.version2.Sequence getSequence(int)
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271 * Method getSequence
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277 public jalview.schemabinding.version2.Sequence[] getSequence()
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279 int size = _sequenceList.size();
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280 jalview.schemabinding.version2.Sequence[] mArray = new jalview.schemabinding.version2.Sequence[size];
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281 for (int index = 0; index < size; index++) {
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282 mArray[index] = (jalview.schemabinding.version2.Sequence) _sequenceList.elementAt(index);
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285 } //-- jalview.schemabinding.version2.Sequence[] getSequence()
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288 * Method getSequenceCount
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294 public int getSequenceCount()
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296 return _sequenceList.size();
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297 } //-- int getSequenceCount()
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300 * Method getSequenceSetProperties
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305 * @return SequenceSetProperties
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307 public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(int index)
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308 throws java.lang.IndexOutOfBoundsException
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310 //-- check bounds for index
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311 if ((index < 0) || (index > _sequenceSetPropertiesList.size())) {
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312 throw new IndexOutOfBoundsException();
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315 return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList.elementAt(index);
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316 } //-- jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(int)
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319 * Method getSequenceSetProperties
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323 * @return SequenceSetProperties
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325 public jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties()
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327 int size = _sequenceSetPropertiesList.size();
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328 jalview.schemabinding.version2.SequenceSetProperties[] mArray = new jalview.schemabinding.version2.SequenceSetProperties[size];
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329 for (int index = 0; index < size; index++) {
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330 mArray[index] = (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList.elementAt(index);
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333 } //-- jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties()
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336 * Method getSequenceSetPropertiesCount
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342 public int getSequenceSetPropertiesCount()
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344 return _sequenceSetPropertiesList.size();
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345 } //-- int getSequenceSetPropertiesCount()
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354 public boolean isValid()
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359 catch (org.exolab.castor.xml.ValidationException vex) {
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363 } //-- boolean isValid()
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372 public void marshal(java.io.Writer out)
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373 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
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376 Marshaller.marshal(this, out);
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377 } //-- void marshal(java.io.Writer)
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386 public void marshal(org.xml.sax.ContentHandler handler)
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387 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
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390 Marshaller.marshal(this, handler);
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391 } //-- void marshal(org.xml.sax.ContentHandler)
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394 * Method removeAllAnnotation
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397 public void removeAllAnnotation()
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399 _annotationList.removeAllElements();
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400 } //-- void removeAllAnnotation()
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403 * Method removeAllSequence
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406 public void removeAllSequence()
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408 _sequenceList.removeAllElements();
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409 } //-- void removeAllSequence()
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412 * Method removeAllSequenceSetProperties
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415 public void removeAllSequenceSetProperties()
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417 _sequenceSetPropertiesList.removeAllElements();
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418 } //-- void removeAllSequenceSetProperties()
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421 * Method removeAnnotation
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426 * @return Annotation
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428 public jalview.schemabinding.version2.Annotation removeAnnotation(int index)
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430 java.lang.Object obj = _annotationList.elementAt(index);
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431 _annotationList.removeElementAt(index);
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432 return (jalview.schemabinding.version2.Annotation) obj;
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433 } //-- jalview.schemabinding.version2.Annotation removeAnnotation(int)
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436 * Method removeSequence
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443 public jalview.schemabinding.version2.Sequence removeSequence(int index)
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445 java.lang.Object obj = _sequenceList.elementAt(index);
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446 _sequenceList.removeElementAt(index);
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447 return (jalview.schemabinding.version2.Sequence) obj;
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448 } //-- jalview.schemabinding.version2.Sequence removeSequence(int)
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451 * Method removeSequenceSetProperties
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456 * @return SequenceSetProperties
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458 public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetProperties(int index)
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460 java.lang.Object obj = _sequenceSetPropertiesList.elementAt(index);
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461 _sequenceSetPropertiesList.removeElementAt(index);
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462 return (jalview.schemabinding.version2.SequenceSetProperties) obj;
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463 } //-- jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetProperties(int)
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466 * Method setAnnotation
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471 * @param vAnnotation
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473 public void setAnnotation(int index, jalview.schemabinding.version2.Annotation vAnnotation)
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474 throws java.lang.IndexOutOfBoundsException
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476 //-- check bounds for index
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477 if ((index < 0) || (index > _annotationList.size())) {
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478 throw new IndexOutOfBoundsException();
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480 _annotationList.setElementAt(vAnnotation, index);
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481 } //-- void setAnnotation(int, jalview.schemabinding.version2.Annotation)
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484 * Method setAnnotation
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488 * @param annotationArray
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490 public void setAnnotation(jalview.schemabinding.version2.Annotation[] annotationArray)
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493 _annotationList.removeAllElements();
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494 for (int i = 0; i < annotationArray.length; i++) {
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495 _annotationList.addElement(annotationArray[i]);
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497 } //-- void setAnnotation(jalview.schemabinding.version2.Annotation)
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500 * Sets the value of field 'gapChar'.
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502 * @param gapChar the value of field 'gapChar'.
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504 public void setGapChar(java.lang.String gapChar)
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506 this._gapChar = gapChar;
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507 } //-- void setGapChar(java.lang.String)
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510 * Method setSequence
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517 public void setSequence(int index, jalview.schemabinding.version2.Sequence vSequence)
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518 throws java.lang.IndexOutOfBoundsException
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520 //-- check bounds for index
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521 if ((index < 0) || (index > _sequenceList.size())) {
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522 throw new IndexOutOfBoundsException();
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524 _sequenceList.setElementAt(vSequence, index);
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525 } //-- void setSequence(int, jalview.schemabinding.version2.Sequence)
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528 * Method setSequence
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532 * @param sequenceArray
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534 public void setSequence(jalview.schemabinding.version2.Sequence[] sequenceArray)
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537 _sequenceList.removeAllElements();
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538 for (int i = 0; i < sequenceArray.length; i++) {
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539 _sequenceList.addElement(sequenceArray[i]);
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541 } //-- void setSequence(jalview.schemabinding.version2.Sequence)
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544 * Method setSequenceSetProperties
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549 * @param vSequenceSetProperties
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551 public void setSequenceSetProperties(int index, jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
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552 throws java.lang.IndexOutOfBoundsException
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554 //-- check bounds for index
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555 if ((index < 0) || (index > _sequenceSetPropertiesList.size())) {
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556 throw new IndexOutOfBoundsException();
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558 _sequenceSetPropertiesList.setElementAt(vSequenceSetProperties, index);
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559 } //-- void setSequenceSetProperties(int, jalview.schemabinding.version2.SequenceSetProperties)
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562 * Method setSequenceSetProperties
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566 * @param sequenceSetPropertiesArray
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568 public void setSequenceSetProperties(jalview.schemabinding.version2.SequenceSetProperties[] sequenceSetPropertiesArray)
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571 _sequenceSetPropertiesList.removeAllElements();
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572 for (int i = 0; i < sequenceSetPropertiesArray.length; i++) {
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573 _sequenceSetPropertiesList.addElement(sequenceSetPropertiesArray[i]);
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575 } //-- void setSequenceSetProperties(jalview.schemabinding.version2.SequenceSetProperties)
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585 public static java.lang.Object unmarshal(java.io.Reader reader)
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586 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
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588 return (jalview.schemabinding.version2.SequenceSet) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceSet.class, reader);
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589 } //-- java.lang.Object unmarshal(java.io.Reader)
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595 public void validate()
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596 throws org.exolab.castor.xml.ValidationException
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598 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
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599 validator.validate(this);
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600 } //-- void validate()
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