src/org/vamsas/objects/core/Alignment.java

   1 /*
   2  * This class was automatically generated with
   3  * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
   4  * Schema.
   5  * $Id$
   6  */
   7
   8 package org.vamsas.objects.core;
   9
  10   //---------------------------------/
  11  //- Imported classes and packages -/
  12 //---------------------------------/
  13
  14 import java.io.IOException;
  15 import java.io.Reader;
  16 import java.io.Serializable;
  17 import java.io.Writer;
  18 import java.util.Enumeration;
  19 import java.util.Vector;
  20 import org.exolab.castor.xml.MarshalException;
  21 import org.exolab.castor.xml.Marshaller;
  22 import org.exolab.castor.xml.Unmarshaller;
  23 import org.exolab.castor.xml.ValidationException;
  24 import org.xml.sax.ContentHandler;
  25
  26 /**
  27  * Class Alignment.
  28  *
  29  * @version $Revision$ $Date$
  30  */
  31 public class Alignment extends org.vamsas.client.object
  32 implements java.io.Serializable
  33 {
  34
  35
  36       //--------------------------/
  37      //- Class/Member Variables -/
  38     //--------------------------/
  39
  40     /**
  41      * Field _alignmentAnnotations
  42      */
  43     private org.vamsas.objects.core.AlignmentAnnotations _alignmentAnnotations;
  44
  45     /**
  46      * Field _treeList
  47      */
  48     private java.util.Vector _treeList;
  49
  50     /**
  51      * Field _alignmentSequenceList
  52      */
  53     private java.util.Vector _alignmentSequenceList;
  54
  55     /**
  56      * Field _provenance
  57      */
  58     private org.vamsas.objects.core.Provenance _provenance;
  59
  60
  61       //----------------/
  62      //- Constructors -/
  63     //----------------/
  64
  65     public Alignment()
  66      {
  67         super();
  68         _treeList = new Vector();
  69         _alignmentSequenceList = new Vector();
  70     } //-- org.vamsas.objects.core.Alignment()
  71
  72
  73       //-----------/
  74      //- Methods -/
  75     //-----------/
  76
  77     /**
  78      * Method addAlignmentSequence
  79      *
  80      *
  81      *
  82      * @param vAlignmentSequence
  83      */
  84     public void addAlignmentSequence(org.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
  85         throws java.lang.IndexOutOfBoundsException
  86     {
  87         _alignmentSequenceList.addElement(vAlignmentSequence);
  88     } //-- void addAlignmentSequence(org.vamsas.objects.core.AlignmentSequence)
  89
  90     /**
  91      * Method addAlignmentSequence
  92      *
  93      *
  94      *
  95      * @param index
  96      * @param vAlignmentSequence
  97      */
  98     public void addAlignmentSequence(int index, org.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
  99         throws java.lang.IndexOutOfBoundsException
 100     {
 101         _alignmentSequenceList.insertElementAt(vAlignmentSequence, index);
 102     } //-- void addAlignmentSequence(int, org.vamsas.objects.core.AlignmentSequence)
 103
 104     /**
 105      * Method addTree
 106      *
 107      *
 108      *
 109      * @param vTree
 110      */
 111     public void addTree(org.vamsas.objects.core.Tree vTree)
 112         throws java.lang.IndexOutOfBoundsException
 113     {
 114         _treeList.addElement(vTree);
 115     } //-- void addTree(org.vamsas.objects.core.Tree)
 116
 117     /**
 118      * Method addTree
 119      *
 120      *
 121      *
 122      * @param index
 123      * @param vTree
 124      */
 125     public void addTree(int index, org.vamsas.objects.core.Tree vTree)
 126         throws java.lang.IndexOutOfBoundsException
 127     {
 128         _treeList.insertElementAt(vTree, index);
 129     } //-- void addTree(int, org.vamsas.objects.core.Tree)
 130
 131     /**
 132      * Method enumerateAlignmentSequence
 133      *
 134      *
 135      *
 136      * @return Enumeration
 137      */
 138     public java.util.Enumeration enumerateAlignmentSequence()
 139     {
 140         return _alignmentSequenceList.elements();
 141     } //-- java.util.Enumeration enumerateAlignmentSequence()
 142
 143     /**
 144      * Method enumerateTree
 145      *
 146      *
 147      *
 148      * @return Enumeration
 149      */
 150     public java.util.Enumeration enumerateTree()
 151     {
 152         return _treeList.elements();
 153     } //-- java.util.Enumeration enumerateTree()
 154
 155     /**
 156      * Note: hashCode() has not been overriden
 157      *
 158      * @param obj
 159      * @return boolean
 160      */
 161     public boolean equals(java.lang.Object obj)
 162     {
 163         if ( this == obj )
 164             return true;
 165
 166         if (super.equals(obj)==false)
 167             return false;
 168
 169         if (obj instanceof Alignment) {
 170
 171             Alignment temp = (Alignment)obj;
 172             if (this._alignmentAnnotations != null) {
 173                 if (temp._alignmentAnnotations == null) return false;
 174                 else if (!(this._alignmentAnnotations.equals(temp._alignmentAnnotations)))
 175                     return false;
 176             }
 177             else if (temp._alignmentAnnotations != null)
 178                 return false;
 179             if (this._treeList != null) {
 180                 if (temp._treeList == null) return false;
 181                 else if (!(this._treeList.equals(temp._treeList)))
 182                     return false;
 183             }
 184             else if (temp._treeList != null)
 185                 return false;
 186             if (this._alignmentSequenceList != null) {
 187                 if (temp._alignmentSequenceList == null) return false;
 188                 else if (!(this._alignmentSequenceList.equals(temp._alignmentSequenceList)))
 189                     return false;
 190             }
 191             else if (temp._alignmentSequenceList != null)
 192                 return false;
 193             if (this._provenance != null) {
 194                 if (temp._provenance == null) return false;
 195                 else if (!(this._provenance.equals(temp._provenance)))
 196                     return false;
 197             }
 198             else if (temp._provenance != null)
 199                 return false;
 200             return true;
 201         }
 202         return false;
 203     } //-- boolean equals(java.lang.Object)
 204
 205     /**
 206      * Returns the value of field 'alignmentAnnotations'.
 207      *
 208      * @return AlignmentAnnotations
 209      * @return the value of field 'alignmentAnnotations'.
 210      */
 211     public org.vamsas.objects.core.AlignmentAnnotations getAlignmentAnnotations()
 212     {
 213         return this._alignmentAnnotations;
 214     } //-- org.vamsas.objects.core.AlignmentAnnotations getAlignmentAnnotations()
 215
 216     /**
 217      * Method getAlignmentSequence
 218      *
 219      *
 220      *
 221      * @param index
 222      * @return AlignmentSequence
 223      */
 224     public org.vamsas.objects.core.AlignmentSequence getAlignmentSequence(int index)
 225         throws java.lang.IndexOutOfBoundsException
 226     {
 227         //-- check bounds for index
 228         if ((index < 0) || (index > _alignmentSequenceList.size())) {
 229             throw new IndexOutOfBoundsException("getAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]");
 230         }
 231
 232         return (org.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index);
 233     } //-- org.vamsas.objects.core.AlignmentSequence getAlignmentSequence(int)
 234
 235     /**
 236      * Method getAlignmentSequence
 237      *
 238      *
 239      *
 240      * @return AlignmentSequence
 241      */
 242     public org.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence()
 243     {
 244         int size = _alignmentSequenceList.size();
 245         org.vamsas.objects.core.AlignmentSequence[] mArray = new org.vamsas.objects.core.AlignmentSequence[size];
 246         for (int index = 0; index < size; index++) {
 247             mArray[index] = (org.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index);
 248         }
 249         return mArray;
 250     } //-- org.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence()
 251
 252     /**
 253      * Method getAlignmentSequenceCount
 254      *
 255      *
 256      *
 257      * @return int
 258      */
 259     public int getAlignmentSequenceCount()
 260     {
 261         return _alignmentSequenceList.size();
 262     } //-- int getAlignmentSequenceCount()
 263
 264     /**
 265      * Returns the value of field 'provenance'.
 266      *
 267      * @return Provenance
 268      * @return the value of field 'provenance'.
 269      */
 270     public org.vamsas.objects.core.Provenance getProvenance()
 271     {
 272         return this._provenance;
 273     } //-- org.vamsas.objects.core.Provenance getProvenance()
 274
 275     /**
 276      * Method getTree
 277      *
 278      *
 279      *
 280      * @param index
 281      * @return Tree
 282      */
 283     public org.vamsas.objects.core.Tree getTree(int index)
 284         throws java.lang.IndexOutOfBoundsException
 285     {
 286         //-- check bounds for index
 287         if ((index < 0) || (index > _treeList.size())) {
 288             throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
 289         }
 290
 291         return (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
 292     } //-- org.vamsas.objects.core.Tree getTree(int)
 293
 294     /**
 295      * Method getTree
 296      *
 297      *
 298      *
 299      * @return Tree
 300      */
 301     public org.vamsas.objects.core.Tree[] getTree()
 302     {
 303         int size = _treeList.size();
 304         org.vamsas.objects.core.Tree[] mArray = new org.vamsas.objects.core.Tree[size];
 305         for (int index = 0; index < size; index++) {
 306             mArray[index] = (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
 307         }
 308         return mArray;
 309     } //-- org.vamsas.objects.core.Tree[] getTree()
 310
 311     /**
 312      * Method getTreeCount
 313      *
 314      *
 315      *
 316      * @return int
 317      */
 318     public int getTreeCount()
 319     {
 320         return _treeList.size();
 321     } //-- int getTreeCount()
 322
 323     /**
 324      * Method isValid
 325      *
 326      *
 327      *
 328      * @return boolean
 329      */
 330     public boolean isValid()
 331     {
 332         try {
 333             validate();
 334         }
 335         catch (org.exolab.castor.xml.ValidationException vex) {
 336             return false;
 337         }
 338         return true;
 339     } //-- boolean isValid()
 340
 341     /**
 342      * Method marshal
 343      *
 344      *
 345      *
 346      * @param out
 347      */
 348     public void marshal(java.io.Writer out)
 349         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 350     {
 351
 352         Marshaller.marshal(this, out);
 353     } //-- void marshal(java.io.Writer)
 354
 355     /**
 356      * Method marshal
 357      *
 358      *
 359      *
 360      * @param handler
 361      */
 362     public void marshal(org.xml.sax.ContentHandler handler)
 363         throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 364     {
 365
 366         Marshaller.marshal(this, handler);
 367     } //-- void marshal(org.xml.sax.ContentHandler)
 368
 369     /**
 370      * Method removeAlignmentSequence
 371      *
 372      *
 373      *
 374      * @param index
 375      * @return AlignmentSequence
 376      */
 377     public org.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int index)
 378     {
 379         java.lang.Object obj = _alignmentSequenceList.elementAt(index);
 380         _alignmentSequenceList.removeElementAt(index);
 381         return (org.vamsas.objects.core.AlignmentSequence) obj;
 382     } //-- org.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int)
 383
 384     /**
 385      * Method removeAllAlignmentSequence
 386      *
 387      */
 388     public void removeAllAlignmentSequence()
 389     {
 390         _alignmentSequenceList.removeAllElements();
 391     } //-- void removeAllAlignmentSequence()
 392
 393     /**
 394      * Method removeAllTree
 395      *
 396      */
 397     public void removeAllTree()
 398     {
 399         _treeList.removeAllElements();
 400     } //-- void removeAllTree()
 401
 402     /**
 403      * Method removeTree
 404      *
 405      *
 406      *
 407      * @param index
 408      * @return Tree
 409      */
 410     public org.vamsas.objects.core.Tree removeTree(int index)
 411     {
 412         java.lang.Object obj = _treeList.elementAt(index);
 413         _treeList.removeElementAt(index);
 414         return (org.vamsas.objects.core.Tree) obj;
 415     } //-- org.vamsas.objects.core.Tree removeTree(int)
 416
 417     /**
 418      * Sets the value of field 'alignmentAnnotations'.
 419      *
 420      * @param alignmentAnnotations the value of field
 421      * 'alignmentAnnotations'.
 422      */
 423     public void setAlignmentAnnotations(org.vamsas.objects.core.AlignmentAnnotations alignmentAnnotations)
 424     {
 425         this._alignmentAnnotations = alignmentAnnotations;
 426     } //-- void setAlignmentAnnotations(org.vamsas.objects.core.AlignmentAnnotations)
 427
 428     /**
 429      * Method setAlignmentSequence
 430      *
 431      *
 432      *
 433      * @param index
 434      * @param vAlignmentSequence
 435      */
 436     public void setAlignmentSequence(int index, org.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
 437         throws java.lang.IndexOutOfBoundsException
 438     {
 439         //-- check bounds for index
 440         if ((index < 0) || (index > _alignmentSequenceList.size())) {
 441             throw new IndexOutOfBoundsException("setAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]");
 442         }
 443         _alignmentSequenceList.setElementAt(vAlignmentSequence, index);
 444     } //-- void setAlignmentSequence(int, org.vamsas.objects.core.AlignmentSequence)
 445
 446     /**
 447      * Method setAlignmentSequence
 448      *
 449      *
 450      *
 451      * @param alignmentSequenceArray
 452      */
 453     public void setAlignmentSequence(org.vamsas.objects.core.AlignmentSequence[] alignmentSequenceArray)
 454     {
 455         //-- copy array
 456         _alignmentSequenceList.removeAllElements();
 457         for (int i = 0; i < alignmentSequenceArray.length; i++) {
 458             _alignmentSequenceList.addElement(alignmentSequenceArray[i]);
 459         }
 460     } //-- void setAlignmentSequence(org.vamsas.objects.core.AlignmentSequence)
 461
 462     /**
 463      * Sets the value of field 'provenance'.
 464      *
 465      * @param provenance the value of field 'provenance'.
 466      */
 467     public void setProvenance(org.vamsas.objects.core.Provenance provenance)
 468     {
 469         this._provenance = provenance;
 470     } //-- void setProvenance(org.vamsas.objects.core.Provenance)
 471
 472     /**
 473      * Method setTree
 474      *
 475      *
 476      *
 477      * @param index
 478      * @param vTree
 479      */
 480     public void setTree(int index, org.vamsas.objects.core.Tree vTree)
 481         throws java.lang.IndexOutOfBoundsException
 482     {
 483         //-- check bounds for index
 484         if ((index < 0) || (index > _treeList.size())) {
 485             throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
 486         }
 487         _treeList.setElementAt(vTree, index);
 488     } //-- void setTree(int, org.vamsas.objects.core.Tree)
 489
 490     /**
 491      * Method setTree
 492      *
 493      *
 494      *
 495      * @param treeArray
 496      */
 497     public void setTree(org.vamsas.objects.core.Tree[] treeArray)
 498     {
 499         //-- copy array
 500         _treeList.removeAllElements();
 501         for (int i = 0; i < treeArray.length; i++) {
 502             _treeList.addElement(treeArray[i]);
 503         }
 504     } //-- void setTree(org.vamsas.objects.core.Tree)
 505
 506     /**
 507      * Method unmarshal
 508      *
 509      *
 510      *
 511      * @param reader
 512      * @return Alignment
 513      */
 514     public static org.vamsas.objects.core.Alignment unmarshal(java.io.Reader reader)
 515         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 516     {
 517         return (org.vamsas.objects.core.Alignment) Unmarshaller.unmarshal(org.vamsas.objects.core.Alignment.class, reader);
 518     } //-- org.vamsas.objects.core.Alignment unmarshal(java.io.Reader)
 519
 520     /**
 521      * Method validate
 522      *
 523      */
 524     public void validate()
 525         throws org.exolab.castor.xml.ValidationException
 526     {
 527         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
 528         validator.validate(this);
 529     } //-- void validate()
 530
 531 }