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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29 * @version $Revision$ $Date$
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31 public class VAMSAS 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.util.Vector _treeList;
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44 * Field _sequenceSetList
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46 private java.util.Vector _sequenceSetList;
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55 _treeList = new Vector();
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56 _sequenceSetList = new Vector();
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57 } //-- jalview.schemabinding.version2.VAMSAS()
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65 * Method addSequenceSet
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69 * @param vSequenceSet
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71 public void addSequenceSet(jalview.schemabinding.version2.SequenceSet vSequenceSet)
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72 throws java.lang.IndexOutOfBoundsException
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74 _sequenceSetList.addElement(vSequenceSet);
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75 } //-- void addSequenceSet(jalview.schemabinding.version2.SequenceSet)
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78 * Method addSequenceSet
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83 * @param vSequenceSet
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85 public void addSequenceSet(int index, jalview.schemabinding.version2.SequenceSet vSequenceSet)
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86 throws java.lang.IndexOutOfBoundsException
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88 _sequenceSetList.insertElementAt(vSequenceSet, index);
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89 } //-- void addSequenceSet(int, jalview.schemabinding.version2.SequenceSet)
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98 public void addTree(java.lang.String vTree)
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99 throws java.lang.IndexOutOfBoundsException
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101 _treeList.addElement(vTree);
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102 } //-- void addTree(java.lang.String)
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112 public void addTree(int index, java.lang.String vTree)
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113 throws java.lang.IndexOutOfBoundsException
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115 _treeList.insertElementAt(vTree, index);
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116 } //-- void addTree(int, java.lang.String)
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119 * Method enumerateSequenceSet
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123 * @return Enumeration
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125 public java.util.Enumeration enumerateSequenceSet()
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127 return _sequenceSetList.elements();
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128 } //-- java.util.Enumeration enumerateSequenceSet()
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131 * Method enumerateTree
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135 * @return Enumeration
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137 public java.util.Enumeration enumerateTree()
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139 return _treeList.elements();
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140 } //-- java.util.Enumeration enumerateTree()
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143 * Method getSequenceSet
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148 * @return SequenceSet
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150 public jalview.schemabinding.version2.SequenceSet getSequenceSet(int index)
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151 throws java.lang.IndexOutOfBoundsException
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153 //-- check bounds for index
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154 if ((index < 0) || (index > _sequenceSetList.size())) {
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155 throw new IndexOutOfBoundsException();
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158 return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.elementAt(index);
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159 } //-- jalview.schemabinding.version2.SequenceSet getSequenceSet(int)
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162 * Method getSequenceSet
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166 * @return SequenceSet
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168 public jalview.schemabinding.version2.SequenceSet[] getSequenceSet()
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170 int size = _sequenceSetList.size();
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171 jalview.schemabinding.version2.SequenceSet[] mArray = new jalview.schemabinding.version2.SequenceSet[size];
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172 for (int index = 0; index < size; index++) {
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173 mArray[index] = (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.elementAt(index);
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176 } //-- jalview.schemabinding.version2.SequenceSet[] getSequenceSet()
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179 * Method getSequenceSetCount
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185 public int getSequenceSetCount()
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187 return _sequenceSetList.size();
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188 } //-- int getSequenceSetCount()
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198 public java.lang.String getTree(int index)
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199 throws java.lang.IndexOutOfBoundsException
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201 //-- check bounds for index
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202 if ((index < 0) || (index > _treeList.size())) {
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203 throw new IndexOutOfBoundsException();
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206 return (String)_treeList.elementAt(index);
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207 } //-- java.lang.String getTree(int)
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216 public java.lang.String[] getTree()
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218 int size = _treeList.size();
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219 java.lang.String[] mArray = new java.lang.String[size];
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220 for (int index = 0; index < size; index++) {
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221 mArray[index] = (String)_treeList.elementAt(index);
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224 } //-- java.lang.String[] getTree()
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227 * Method getTreeCount
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233 public int getTreeCount()
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235 return _treeList.size();
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236 } //-- int getTreeCount()
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245 public boolean isValid()
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250 catch (org.exolab.castor.xml.ValidationException vex) {
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254 } //-- boolean isValid()
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263 public void marshal(java.io.Writer out)
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264 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
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267 Marshaller.marshal(this, out);
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268 } //-- void marshal(java.io.Writer)
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277 public void marshal(org.xml.sax.ContentHandler handler)
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278 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
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281 Marshaller.marshal(this, handler);
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282 } //-- void marshal(org.xml.sax.ContentHandler)
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285 * Method removeAllSequenceSet
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288 public void removeAllSequenceSet()
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290 _sequenceSetList.removeAllElements();
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291 } //-- void removeAllSequenceSet()
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294 * Method removeAllTree
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297 public void removeAllTree()
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299 _treeList.removeAllElements();
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300 } //-- void removeAllTree()
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303 * Method removeSequenceSet
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308 * @return SequenceSet
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310 public jalview.schemabinding.version2.SequenceSet removeSequenceSet(int index)
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312 java.lang.Object obj = _sequenceSetList.elementAt(index);
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313 _sequenceSetList.removeElementAt(index);
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314 return (jalview.schemabinding.version2.SequenceSet) obj;
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315 } //-- jalview.schemabinding.version2.SequenceSet removeSequenceSet(int)
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318 * Method removeTree
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325 public java.lang.String removeTree(int index)
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327 java.lang.Object obj = _treeList.elementAt(index);
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328 _treeList.removeElementAt(index);
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329 return (String)obj;
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330 } //-- java.lang.String removeTree(int)
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333 * Method setSequenceSet
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338 * @param vSequenceSet
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340 public void setSequenceSet(int index, jalview.schemabinding.version2.SequenceSet vSequenceSet)
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341 throws java.lang.IndexOutOfBoundsException
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343 //-- check bounds for index
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344 if ((index < 0) || (index > _sequenceSetList.size())) {
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345 throw new IndexOutOfBoundsException();
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347 _sequenceSetList.setElementAt(vSequenceSet, index);
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348 } //-- void setSequenceSet(int, jalview.schemabinding.version2.SequenceSet)
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351 * Method setSequenceSet
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355 * @param sequenceSetArray
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357 public void setSequenceSet(jalview.schemabinding.version2.SequenceSet[] sequenceSetArray)
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360 _sequenceSetList.removeAllElements();
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361 for (int i = 0; i < sequenceSetArray.length; i++) {
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362 _sequenceSetList.addElement(sequenceSetArray[i]);
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364 } //-- void setSequenceSet(jalview.schemabinding.version2.SequenceSet)
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374 public void setTree(int index, java.lang.String vTree)
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375 throws java.lang.IndexOutOfBoundsException
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377 //-- check bounds for index
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378 if ((index < 0) || (index > _treeList.size())) {
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379 throw new IndexOutOfBoundsException();
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381 _treeList.setElementAt(vTree, index);
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382 } //-- void setTree(int, java.lang.String)
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391 public void setTree(java.lang.String[] treeArray)
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394 _treeList.removeAllElements();
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395 for (int i = 0; i < treeArray.length; i++) {
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396 _treeList.addElement(treeArray[i]);
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398 } //-- void setTree(java.lang.String)
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408 public static java.lang.Object unmarshal(java.io.Reader reader)
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409 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
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411 return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(jalview.schemabinding.version2.VAMSAS.class, reader);
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412 } //-- java.lang.Object unmarshal(java.io.Reader)
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418 public void validate()
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419 throws org.exolab.castor.xml.ValidationException
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421 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
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422 validator.validate(this);
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423 } //-- void validate()
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