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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58 public SequenceSet() {
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60 _sequenceList = new Vector();
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61 _annotationList = new Vector();
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62 } //-- jalview.schemabinding.version2.SequenceSet()
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70 * Method addAnnotation
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74 * @param vAnnotation
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76 public void addAnnotation(jalview.schemabinding.version2.Annotation vAnnotation)
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77 throws java.lang.IndexOutOfBoundsException
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79 _annotationList.addElement(vAnnotation);
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80 } //-- void addAnnotation(jalview.schemabinding.version2.Annotation)
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83 * Method addAnnotation
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88 * @param vAnnotation
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90 public void addAnnotation(int index, jalview.schemabinding.version2.Annotation vAnnotation)
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91 throws java.lang.IndexOutOfBoundsException
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93 _annotationList.insertElementAt(vAnnotation, index);
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94 } //-- void addAnnotation(int, jalview.schemabinding.version2.Annotation)
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97 * Method addSequence
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103 public void addSequence(jalview.schemabinding.version2.Sequence vSequence)
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104 throws java.lang.IndexOutOfBoundsException
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106 _sequenceList.addElement(vSequence);
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107 } //-- void addSequence(jalview.schemabinding.version2.Sequence)
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110 * Method addSequence
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117 public void addSequence(int index, jalview.schemabinding.version2.Sequence vSequence)
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118 throws java.lang.IndexOutOfBoundsException
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120 _sequenceList.insertElementAt(vSequence, index);
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121 } //-- void addSequence(int, jalview.schemabinding.version2.Sequence)
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124 * Method enumerateAnnotation
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128 * @return Enumeration
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130 public java.util.Enumeration enumerateAnnotation()
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132 return _annotationList.elements();
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133 } //-- java.util.Enumeration enumerateAnnotation()
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136 * Method enumerateSequence
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140 * @return Enumeration
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142 public java.util.Enumeration enumerateSequence()
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144 return _sequenceList.elements();
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145 } //-- java.util.Enumeration enumerateSequence()
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148 * Method getAnnotation
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153 * @return Annotation
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155 public jalview.schemabinding.version2.Annotation getAnnotation(int index)
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156 throws java.lang.IndexOutOfBoundsException
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158 //-- check bounds for index
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159 if ((index < 0) || (index > _annotationList.size())) {
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160 throw new IndexOutOfBoundsException();
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163 return (jalview.schemabinding.version2.Annotation) _annotationList.elementAt(index);
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164 } //-- jalview.schemabinding.version2.Annotation getAnnotation(int)
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167 * Method getAnnotation
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171 * @return Annotation
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173 public jalview.schemabinding.version2.Annotation[] getAnnotation()
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175 int size = _annotationList.size();
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176 jalview.schemabinding.version2.Annotation[] mArray = new jalview.schemabinding.version2.Annotation[size];
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177 for (int index = 0; index < size; index++) {
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178 mArray[index] = (jalview.schemabinding.version2.Annotation) _annotationList.elementAt(index);
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181 } //-- jalview.schemabinding.version2.Annotation[] getAnnotation()
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184 * Method getAnnotationCount
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190 public int getAnnotationCount()
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192 return _annotationList.size();
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193 } //-- int getAnnotationCount()
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196 * Returns the value of field 'gapChar'.
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199 * @return the value of field 'gapChar'.
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201 public java.lang.String getGapChar()
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203 return this._gapChar;
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204 } //-- java.lang.String getGapChar()
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207 * Method getSequence
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214 public jalview.schemabinding.version2.Sequence getSequence(int index)
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215 throws java.lang.IndexOutOfBoundsException
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217 //-- check bounds for index
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218 if ((index < 0) || (index > _sequenceList.size())) {
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219 throw new IndexOutOfBoundsException();
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222 return (jalview.schemabinding.version2.Sequence) _sequenceList.elementAt(index);
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223 } //-- jalview.schemabinding.version2.Sequence getSequence(int)
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226 * Method getSequence
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232 public jalview.schemabinding.version2.Sequence[] getSequence()
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234 int size = _sequenceList.size();
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235 jalview.schemabinding.version2.Sequence[] mArray = new jalview.schemabinding.version2.Sequence[size];
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236 for (int index = 0; index < size; index++) {
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237 mArray[index] = (jalview.schemabinding.version2.Sequence) _sequenceList.elementAt(index);
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240 } //-- jalview.schemabinding.version2.Sequence[] getSequence()
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243 * Method getSequenceCount
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249 public int getSequenceCount()
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251 return _sequenceList.size();
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252 } //-- int getSequenceCount()
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261 public boolean isValid()
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266 catch (org.exolab.castor.xml.ValidationException vex) {
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270 } //-- boolean isValid()
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279 public void marshal(java.io.Writer out)
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280 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
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283 Marshaller.marshal(this, out);
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284 } //-- void marshal(java.io.Writer)
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293 public void marshal(org.xml.sax.ContentHandler handler)
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294 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
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297 Marshaller.marshal(this, handler);
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298 } //-- void marshal(org.xml.sax.ContentHandler)
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301 * Method removeAllAnnotation
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304 public void removeAllAnnotation()
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306 _annotationList.removeAllElements();
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307 } //-- void removeAllAnnotation()
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310 * Method removeAllSequence
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313 public void removeAllSequence()
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315 _sequenceList.removeAllElements();
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316 } //-- void removeAllSequence()
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319 * Method removeAnnotation
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324 * @return Annotation
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326 public jalview.schemabinding.version2.Annotation removeAnnotation(int index)
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328 java.lang.Object obj = _annotationList.elementAt(index);
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329 _annotationList.removeElementAt(index);
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330 return (jalview.schemabinding.version2.Annotation) obj;
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331 } //-- jalview.schemabinding.version2.Annotation removeAnnotation(int)
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334 * Method removeSequence
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341 public jalview.schemabinding.version2.Sequence removeSequence(int index)
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343 java.lang.Object obj = _sequenceList.elementAt(index);
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344 _sequenceList.removeElementAt(index);
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345 return (jalview.schemabinding.version2.Sequence) obj;
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346 } //-- jalview.schemabinding.version2.Sequence removeSequence(int)
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349 * Method setAnnotation
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354 * @param vAnnotation
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356 public void setAnnotation(int index, jalview.schemabinding.version2.Annotation vAnnotation)
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357 throws java.lang.IndexOutOfBoundsException
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359 //-- check bounds for index
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360 if ((index < 0) || (index > _annotationList.size())) {
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361 throw new IndexOutOfBoundsException();
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363 _annotationList.setElementAt(vAnnotation, index);
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364 } //-- void setAnnotation(int, jalview.schemabinding.version2.Annotation)
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367 * Method setAnnotation
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371 * @param annotationArray
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373 public void setAnnotation(jalview.schemabinding.version2.Annotation[] annotationArray)
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376 _annotationList.removeAllElements();
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377 for (int i = 0; i < annotationArray.length; i++) {
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378 _annotationList.addElement(annotationArray[i]);
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380 } //-- void setAnnotation(jalview.schemabinding.version2.Annotation)
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383 * Sets the value of field 'gapChar'.
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385 * @param gapChar the value of field 'gapChar'.
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387 public void setGapChar(java.lang.String gapChar)
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389 this._gapChar = gapChar;
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390 } //-- void setGapChar(java.lang.String)
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393 * Method setSequence
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400 public void setSequence(int index, jalview.schemabinding.version2.Sequence vSequence)
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401 throws java.lang.IndexOutOfBoundsException
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403 //-- check bounds for index
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404 if ((index < 0) || (index > _sequenceList.size())) {
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405 throw new IndexOutOfBoundsException();
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407 _sequenceList.setElementAt(vSequence, index);
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408 } //-- void setSequence(int, jalview.schemabinding.version2.Sequence)
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411 * Method setSequence
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415 * @param sequenceArray
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417 public void setSequence(jalview.schemabinding.version2.Sequence[] sequenceArray)
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420 _sequenceList.removeAllElements();
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421 for (int i = 0; i < sequenceArray.length; i++) {
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422 _sequenceList.addElement(sequenceArray[i]);
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424 } //-- void setSequence(jalview.schemabinding.version2.Sequence)
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434 public static java.lang.Object unmarshal(java.io.Reader reader)
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435 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
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437 return (jalview.schemabinding.version2.SequenceSet) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceSet.class, reader);
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438 } //-- java.lang.Object unmarshal(java.io.Reader)
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444 public void validate()
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445 throws org.exolab.castor.xml.ValidationException
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447 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
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448 validator.validate(this);
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449 } //-- void validate()
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