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 _id
  42      */
  43     private java.lang.String _id;
  44
  45     /**
  46      * Field _alignmentAnnotations
  47      */
  48     private org.vamsas.objects.core.AlignmentAnnotations _alignmentAnnotations;
  49
  50     /**
  51      * Field _treeList
  52      */
  53     private java.util.Vector _treeList;
  54
  55     /**
  56      * Field _alignmentSequenceList
  57      */
  58     private java.util.Vector _alignmentSequenceList;
  59
  60     /**
  61      * Field _provenance
  62      */
  63     private org.vamsas.objects.core.Provenance _provenance;
  64
  65
  66       //----------------/
  67      //- Constructors -/
  68     //----------------/
  69
  70     public Alignment()
  71      {
  72         super();
  73         _treeList = new Vector();
  74         _alignmentSequenceList = new Vector();
  75     } //-- org.vamsas.objects.core.Alignment()
  76
  77
  78       //-----------/
  79      //- Methods -/
  80     //-----------/
  81
  82     /**
  83      * Method addAlignmentSequence
  84      *
  85      *
  86      *
  87      * @param vAlignmentSequence
  88      */
  89     public void addAlignmentSequence(org.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
  90         throws java.lang.IndexOutOfBoundsException
  91     {
  92         _alignmentSequenceList.addElement(vAlignmentSequence);
  93     } //-- void addAlignmentSequence(org.vamsas.objects.core.AlignmentSequence)
  94
  95     /**
  96      * Method addAlignmentSequence
  97      *
  98      *
  99      *
 100      * @param index
 101      * @param vAlignmentSequence
 102      */
 103     public void addAlignmentSequence(int index, org.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
 104         throws java.lang.IndexOutOfBoundsException
 105     {
 106         _alignmentSequenceList.insertElementAt(vAlignmentSequence, index);
 107     } //-- void addAlignmentSequence(int, org.vamsas.objects.core.AlignmentSequence)
 108
 109     /**
 110      * Method addTree
 111      *
 112      *
 113      *
 114      * @param vTree
 115      */
 116     public void addTree(org.vamsas.objects.core.Tree vTree)
 117         throws java.lang.IndexOutOfBoundsException
 118     {
 119         _treeList.addElement(vTree);
 120     } //-- void addTree(org.vamsas.objects.core.Tree)
 121
 122     /**
 123      * Method addTree
 124      *
 125      *
 126      *
 127      * @param index
 128      * @param vTree
 129      */
 130     public void addTree(int index, org.vamsas.objects.core.Tree vTree)
 131         throws java.lang.IndexOutOfBoundsException
 132     {
 133         _treeList.insertElementAt(vTree, index);
 134     } //-- void addTree(int, org.vamsas.objects.core.Tree)
 135
 136     /**
 137      * Method enumerateAlignmentSequence
 138      *
 139      *
 140      *
 141      * @return Enumeration
 142      */
 143     public java.util.Enumeration enumerateAlignmentSequence()
 144     {
 145         return _alignmentSequenceList.elements();
 146     } //-- java.util.Enumeration enumerateAlignmentSequence()
 147
 148     /**
 149      * Method enumerateTree
 150      *
 151      *
 152      *
 153      * @return Enumeration
 154      */
 155     public java.util.Enumeration enumerateTree()
 156     {
 157         return _treeList.elements();
 158     } //-- java.util.Enumeration enumerateTree()
 159
 160     /**
 161      * Note: hashCode() has not been overriden
 162      *
 163      * @param obj
 164      * @return boolean
 165      */
 166     public boolean equals(java.lang.Object obj)
 167     {
 168         if ( this == obj )
 169             return true;
 170
 171         if (super.equals(obj)==false)
 172             return false;
 173
 174         if (obj instanceof Alignment) {
 175
 176             Alignment temp = (Alignment)obj;
 177             if (this._id != null) {
 178                 if (temp._id == null) return false;
 179                 else if (!(this._id.equals(temp._id)))
 180                     return false;
 181             }
 182             else if (temp._id != null)
 183                 return false;
 184             if (this._alignmentAnnotations != null) {
 185                 if (temp._alignmentAnnotations == null) return false;
 186                 else if (!(this._alignmentAnnotations.equals(temp._alignmentAnnotations)))
 187                     return false;
 188             }
 189             else if (temp._alignmentAnnotations != null)
 190                 return false;
 191             if (this._treeList != null) {
 192                 if (temp._treeList == null) return false;
 193                 else if (!(this._treeList.equals(temp._treeList)))
 194                     return false;
 195             }
 196             else if (temp._treeList != null)
 197                 return false;
 198             if (this._alignmentSequenceList != null) {
 199                 if (temp._alignmentSequenceList == null) return false;
 200                 else if (!(this._alignmentSequenceList.equals(temp._alignmentSequenceList)))
 201                     return false;
 202             }
 203             else if (temp._alignmentSequenceList != null)
 204                 return false;
 205             if (this._provenance != null) {
 206                 if (temp._provenance == null) return false;
 207                 else if (!(this._provenance.equals(temp._provenance)))
 208                     return false;
 209             }
 210             else if (temp._provenance != null)
 211                 return false;
 212             return true;
 213         }
 214         return false;
 215     } //-- boolean equals(java.lang.Object)
 216
 217     /**
 218      * Returns the value of field 'alignmentAnnotations'.
 219      *
 220      * @return AlignmentAnnotations
 221      * @return the value of field 'alignmentAnnotations'.
 222      */
 223     public org.vamsas.objects.core.AlignmentAnnotations getAlignmentAnnotations()
 224     {
 225         return this._alignmentAnnotations;
 226     } //-- org.vamsas.objects.core.AlignmentAnnotations getAlignmentAnnotations()
 227
 228     /**
 229      * Method getAlignmentSequence
 230      *
 231      *
 232      *
 233      * @param index
 234      * @return AlignmentSequence
 235      */
 236     public org.vamsas.objects.core.AlignmentSequence getAlignmentSequence(int index)
 237         throws java.lang.IndexOutOfBoundsException
 238     {
 239         //-- check bounds for index
 240         if ((index < 0) || (index > _alignmentSequenceList.size())) {
 241             throw new IndexOutOfBoundsException("getAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]");
 242         }
 243
 244         return (org.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index);
 245     } //-- org.vamsas.objects.core.AlignmentSequence getAlignmentSequence(int)
 246
 247     /**
 248      * Method getAlignmentSequence
 249      *
 250      *
 251      *
 252      * @return AlignmentSequence
 253      */
 254     public org.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence()
 255     {
 256         int size = _alignmentSequenceList.size();
 257         org.vamsas.objects.core.AlignmentSequence[] mArray = new org.vamsas.objects.core.AlignmentSequence[size];
 258         for (int index = 0; index < size; index++) {
 259             mArray[index] = (org.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index);
 260         }
 261         return mArray;
 262     } //-- org.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence()
 263
 264     /**
 265      * Method getAlignmentSequenceCount
 266      *
 267      *
 268      *
 269      * @return int
 270      */
 271     public int getAlignmentSequenceCount()
 272     {
 273         return _alignmentSequenceList.size();
 274     } //-- int getAlignmentSequenceCount()
 275
 276     /**
 277      * Returns the value of field 'id'.
 278      *
 279      * @return String
 280      * @return the value of field 'id'.
 281      */
 282     public java.lang.String getId()
 283     {
 284         return this._id;
 285     } //-- java.lang.String getId()
 286
 287     /**
 288      * Returns the value of field 'provenance'.
 289      *
 290      * @return Provenance
 291      * @return the value of field 'provenance'.
 292      */
 293     public org.vamsas.objects.core.Provenance getProvenance()
 294     {
 295         return this._provenance;
 296     } //-- org.vamsas.objects.core.Provenance getProvenance()
 297
 298     /**
 299      * Method getTree
 300      *
 301      *
 302      *
 303      * @param index
 304      * @return Tree
 305      */
 306     public org.vamsas.objects.core.Tree getTree(int index)
 307         throws java.lang.IndexOutOfBoundsException
 308     {
 309         //-- check bounds for index
 310         if ((index < 0) || (index > _treeList.size())) {
 311             throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
 312         }
 313
 314         return (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
 315     } //-- org.vamsas.objects.core.Tree getTree(int)
 316
 317     /**
 318      * Method getTree
 319      *
 320      *
 321      *
 322      * @return Tree
 323      */
 324     public org.vamsas.objects.core.Tree[] getTree()
 325     {
 326         int size = _treeList.size();
 327         org.vamsas.objects.core.Tree[] mArray = new org.vamsas.objects.core.Tree[size];
 328         for (int index = 0; index < size; index++) {
 329             mArray[index] = (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
 330         }
 331         return mArray;
 332     } //-- org.vamsas.objects.core.Tree[] getTree()
 333
 334     /**
 335      * Method getTreeCount
 336      *
 337      *
 338      *
 339      * @return int
 340      */
 341     public int getTreeCount()
 342     {
 343         return _treeList.size();
 344     } //-- int getTreeCount()
 345
 346     /**
 347      * Method isValid
 348      *
 349      *
 350      *
 351      * @return boolean
 352      */
 353     public boolean isValid()
 354     {
 355         try {
 356             validate();
 357         }
 358         catch (org.exolab.castor.xml.ValidationException vex) {
 359             return false;
 360         }
 361         return true;
 362     } //-- boolean isValid()
 363
 364     /**
 365      * Method marshal
 366      *
 367      *
 368      *
 369      * @param out
 370      */
 371     public void marshal(java.io.Writer out)
 372         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 373     {
 374
 375         Marshaller.marshal(this, out);
 376     } //-- void marshal(java.io.Writer)
 377
 378     /**
 379      * Method marshal
 380      *
 381      *
 382      *
 383      * @param handler
 384      */
 385     public void marshal(org.xml.sax.ContentHandler handler)
 386         throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 387     {
 388
 389         Marshaller.marshal(this, handler);
 390     } //-- void marshal(org.xml.sax.ContentHandler)
 391
 392     /**
 393      * Method removeAlignmentSequence
 394      *
 395      *
 396      *
 397      * @param index
 398      * @return AlignmentSequence
 399      */
 400     public org.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int index)
 401     {
 402         java.lang.Object obj = _alignmentSequenceList.elementAt(index);
 403         _alignmentSequenceList.removeElementAt(index);
 404         return (org.vamsas.objects.core.AlignmentSequence) obj;
 405     } //-- org.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int)
 406
 407     /**
 408      * Method removeAllAlignmentSequence
 409      *
 410      */
 411     public void removeAllAlignmentSequence()
 412     {
 413         _alignmentSequenceList.removeAllElements();
 414     } //-- void removeAllAlignmentSequence()
 415
 416     /**
 417      * Method removeAllTree
 418      *
 419      */
 420     public void removeAllTree()
 421     {
 422         _treeList.removeAllElements();
 423     } //-- void removeAllTree()
 424
 425     /**
 426      * Method removeTree
 427      *
 428      *
 429      *
 430      * @param index
 431      * @return Tree
 432      */
 433     public org.vamsas.objects.core.Tree removeTree(int index)
 434     {
 435         java.lang.Object obj = _treeList.elementAt(index);
 436         _treeList.removeElementAt(index);
 437         return (org.vamsas.objects.core.Tree) obj;
 438     } //-- org.vamsas.objects.core.Tree removeTree(int)
 439
 440     /**
 441      * Sets the value of field 'alignmentAnnotations'.
 442      *
 443      * @param alignmentAnnotations the value of field
 444      * 'alignmentAnnotations'.
 445      */
 446     public void setAlignmentAnnotations(org.vamsas.objects.core.AlignmentAnnotations alignmentAnnotations)
 447     {
 448         this._alignmentAnnotations = alignmentAnnotations;
 449     } //-- void setAlignmentAnnotations(org.vamsas.objects.core.AlignmentAnnotations)
 450
 451     /**
 452      * Method setAlignmentSequence
 453      *
 454      *
 455      *
 456      * @param index
 457      * @param vAlignmentSequence
 458      */
 459     public void setAlignmentSequence(int index, org.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
 460         throws java.lang.IndexOutOfBoundsException
 461     {
 462         //-- check bounds for index
 463         if ((index < 0) || (index > _alignmentSequenceList.size())) {
 464             throw new IndexOutOfBoundsException("setAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]");
 465         }
 466         _alignmentSequenceList.setElementAt(vAlignmentSequence, index);
 467     } //-- void setAlignmentSequence(int, org.vamsas.objects.core.AlignmentSequence)
 468
 469     /**
 470      * Method setAlignmentSequence
 471      *
 472      *
 473      *
 474      * @param alignmentSequenceArray
 475      */
 476     public void setAlignmentSequence(org.vamsas.objects.core.AlignmentSequence[] alignmentSequenceArray)
 477     {
 478         //-- copy array
 479         _alignmentSequenceList.removeAllElements();
 480         for (int i = 0; i < alignmentSequenceArray.length; i++) {
 481             _alignmentSequenceList.addElement(alignmentSequenceArray[i]);
 482         }
 483     } //-- void setAlignmentSequence(org.vamsas.objects.core.AlignmentSequence)
 484
 485     /**
 486      * Sets the value of field 'id'.
 487      *
 488      * @param id the value of field 'id'.
 489      */
 490     public void setId(java.lang.String id)
 491     {
 492         this._id = id;
 493     } //-- void setId(java.lang.String)
 494
 495     /**
 496      * Sets the value of field 'provenance'.
 497      *
 498      * @param provenance the value of field 'provenance'.
 499      */
 500     public void setProvenance(org.vamsas.objects.core.Provenance provenance)
 501     {
 502         this._provenance = provenance;
 503     } //-- void setProvenance(org.vamsas.objects.core.Provenance)
 504
 505     /**
 506      * Method setTree
 507      *
 508      *
 509      *
 510      * @param index
 511      * @param vTree
 512      */
 513     public void setTree(int index, org.vamsas.objects.core.Tree vTree)
 514         throws java.lang.IndexOutOfBoundsException
 515     {
 516         //-- check bounds for index
 517         if ((index < 0) || (index > _treeList.size())) {
 518             throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
 519         }
 520         _treeList.setElementAt(vTree, index);
 521     } //-- void setTree(int, org.vamsas.objects.core.Tree)
 522
 523     /**
 524      * Method setTree
 525      *
 526      *
 527      *
 528      * @param treeArray
 529      */
 530     public void setTree(org.vamsas.objects.core.Tree[] treeArray)
 531     {
 532         //-- copy array
 533         _treeList.removeAllElements();
 534         for (int i = 0; i < treeArray.length; i++) {
 535             _treeList.addElement(treeArray[i]);
 536         }
 537     } //-- void setTree(org.vamsas.objects.core.Tree)
 538
 539     /**
 540      * Method unmarshal
 541      *
 542      *
 543      *
 544      * @param reader
 545      * @return Alignment
 546      */
 547     public static org.vamsas.objects.core.Alignment unmarshal(java.io.Reader reader)
 548         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 549     {
 550         return (org.vamsas.objects.core.Alignment) Unmarshaller.unmarshal(org.vamsas.objects.core.Alignment.class, reader);
 551     } //-- org.vamsas.objects.core.Alignment unmarshal(java.io.Reader)
 552
 553     /**
 554      * Method validate
 555      *
 556      */
 557     public void validate()
 558         throws org.exolab.castor.xml.ValidationException
 559     {
 560         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
 561         validator.validate(this);
 562     } //-- void validate()
 563
 564 }