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

   1 /*
   2  * This class was automatically generated with
   3  * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
   4  * Schema.
   5  * $Id$
   6  */
   7
   8 package org.vamsas.client.objects;
   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.client.objects.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.client.objects.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.client.objects.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.client.objects.AlignmentSequence vAlignmentSequence)
  85         throws java.lang.IndexOutOfBoundsException
  86     {
  87         _alignmentSequenceList.addElement(vAlignmentSequence);
  88     } //-- void addAlignmentSequence(org.vamsas.client.objects.AlignmentSequence)
  89
  90     /**
  91      * Method addAlignmentSequence
  92      *
  93      *
  94      *
  95      * @param index
  96      * @param vAlignmentSequence
  97      */
  98     public void addAlignmentSequence(int index, org.vamsas.client.objects.AlignmentSequence vAlignmentSequence)
  99         throws java.lang.IndexOutOfBoundsException
 100     {
 101         _alignmentSequenceList.insertElementAt(vAlignmentSequence, index);
 102     } //-- void addAlignmentSequence(int, org.vamsas.client.objects.AlignmentSequence)
 103
 104     /**
 105      * Method addTree
 106      *
 107      *
 108      *
 109      * @param vTree
 110      */
 111     public void addTree(org.vamsas.client.objects.Tree vTree)
 112         throws java.lang.IndexOutOfBoundsException
 113     {
 114         _treeList.addElement(vTree);
 115     } //-- void addTree(org.vamsas.client.objects.Tree)
 116
 117     /**
 118      * Method addTree
 119      *
 120      *
 121      *
 122      * @param index
 123      * @param vTree
 124      */
 125     public void addTree(int index, org.vamsas.client.objects.Tree vTree)
 126         throws java.lang.IndexOutOfBoundsException
 127     {
 128         _treeList.insertElementAt(vTree, index);
 129     } //-- void addTree(int, org.vamsas.client.objects.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.client.objects.AlignmentAnnotations getAlignmentAnnotations()
 212     {
 213         return this._alignmentAnnotations;
 214     } //-- org.vamsas.client.objects.AlignmentAnnotations getAlignmentAnnotations()
 215
 216     /**
 217      * Method getAlignmentSequence
 218      *
 219      *
 220      *
 221      * @param index
 222      * @return AlignmentSequence
 223      */
 224     public org.vamsas.client.objects.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.client.objects.AlignmentSequence) _alignmentSequenceList.elementAt(index);
 233     } //-- org.vamsas.client.objects.AlignmentSequence getAlignmentSequence(int)
 234
 235     /**
 236      * Method getAlignmentSequence
 237      *
 238      *
 239      *
 240      * @return AlignmentSequence
 241      */
 242     public org.vamsas.client.objects.AlignmentSequence[] getAlignmentSequence()
 243     {
 244         int size = _alignmentSequenceList.size();
 245         org.vamsas.client.objects.AlignmentSequence[] mArray = new org.vamsas.client.objects.AlignmentSequence[size];
 246         for (int index = 0; index < size; index++) {
 247             mArray[index] = (org.vamsas.client.objects.AlignmentSequence) _alignmentSequenceList.elementAt(index);
 248         }
 249         return mArray;
 250     } //-- org.vamsas.client.objects.AlignmentSequence[] getAlignmentSequence()
 251
 252     /**
 253      * Method getAlignmentSequenceAsReference
 254      *
 255      * Returns a reference to 'alignmentSequence'. No type checking
 256      * is performed on any modications to the Vector.
 257      *
 258      * @return Vector
 259      * @return returns a reference to the Vector.
 260      */
 261     public java.util.Vector getAlignmentSequenceAsReference()
 262     {
 263         return _alignmentSequenceList;
 264     } //-- java.util.Vector getAlignmentSequenceAsReference()
 265
 266     /**
 267      * Method getAlignmentSequenceCount
 268      *
 269      *
 270      *
 271      * @return int
 272      */
 273     public int getAlignmentSequenceCount()
 274     {
 275         return _alignmentSequenceList.size();
 276     } //-- int getAlignmentSequenceCount()
 277
 278     /**
 279      * Returns the value of field 'provenance'.
 280      *
 281      * @return Provenance
 282      * @return the value of field 'provenance'.
 283      */
 284     public org.vamsas.client.objects.Provenance getProvenance()
 285     {
 286         return this._provenance;
 287     } //-- org.vamsas.client.objects.Provenance getProvenance()
 288
 289     /**
 290      * Method getTree
 291      *
 292      *
 293      *
 294      * @param index
 295      * @return Tree
 296      */
 297     public org.vamsas.client.objects.Tree getTree(int index)
 298         throws java.lang.IndexOutOfBoundsException
 299     {
 300         //-- check bounds for index
 301         if ((index < 0) || (index > _treeList.size())) {
 302             throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
 303         }
 304
 305         return (org.vamsas.client.objects.Tree) _treeList.elementAt(index);
 306     } //-- org.vamsas.client.objects.Tree getTree(int)
 307
 308     /**
 309      * Method getTree
 310      *
 311      *
 312      *
 313      * @return Tree
 314      */
 315     public org.vamsas.client.objects.Tree[] getTree()
 316     {
 317         int size = _treeList.size();
 318         org.vamsas.client.objects.Tree[] mArray = new org.vamsas.client.objects.Tree[size];
 319         for (int index = 0; index < size; index++) {
 320             mArray[index] = (org.vamsas.client.objects.Tree) _treeList.elementAt(index);
 321         }
 322         return mArray;
 323     } //-- org.vamsas.client.objects.Tree[] getTree()
 324
 325     /**
 326      * Method getTreeAsReference
 327      *
 328      * Returns a reference to 'tree'. No type checking is performed
 329      * on any modications to the Vector.
 330      *
 331      * @return Vector
 332      * @return returns a reference to the Vector.
 333      */
 334     public java.util.Vector getTreeAsReference()
 335     {
 336         return _treeList;
 337     } //-- java.util.Vector getTreeAsReference()
 338
 339     /**
 340      * Method getTreeCount
 341      *
 342      *
 343      *
 344      * @return int
 345      */
 346     public int getTreeCount()
 347     {
 348         return _treeList.size();
 349     } //-- int getTreeCount()
 350
 351     /**
 352      * Method isValid
 353      *
 354      *
 355      *
 356      * @return boolean
 357      */
 358     public boolean isValid()
 359     {
 360         try {
 361             validate();
 362         }
 363         catch (org.exolab.castor.xml.ValidationException vex) {
 364             return false;
 365         }
 366         return true;
 367     } //-- boolean isValid()
 368
 369     /**
 370      * Method marshal
 371      *
 372      *
 373      *
 374      * @param out
 375      */
 376     public void marshal(java.io.Writer out)
 377         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 378     {
 379
 380         Marshaller.marshal(this, out);
 381     } //-- void marshal(java.io.Writer)
 382
 383     /**
 384      * Method marshal
 385      *
 386      *
 387      *
 388      * @param handler
 389      */
 390     public void marshal(org.xml.sax.ContentHandler handler)
 391         throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 392     {
 393
 394         Marshaller.marshal(this, handler);
 395     } //-- void marshal(org.xml.sax.ContentHandler)
 396
 397     /**
 398      * Method removeAlignmentSequence
 399      *
 400      *
 401      *
 402      * @param index
 403      * @return AlignmentSequence
 404      */
 405     public org.vamsas.client.objects.AlignmentSequence removeAlignmentSequence(int index)
 406     {
 407         java.lang.Object obj = _alignmentSequenceList.elementAt(index);
 408         _alignmentSequenceList.removeElementAt(index);
 409         return (org.vamsas.client.objects.AlignmentSequence) obj;
 410     } //-- org.vamsas.client.objects.AlignmentSequence removeAlignmentSequence(int)
 411
 412     /**
 413      * Method removeAllAlignmentSequence
 414      *
 415      */
 416     public void removeAllAlignmentSequence()
 417     {
 418         _alignmentSequenceList.removeAllElements();
 419     } //-- void removeAllAlignmentSequence()
 420
 421     /**
 422      * Method removeAllTree
 423      *
 424      */
 425     public void removeAllTree()
 426     {
 427         _treeList.removeAllElements();
 428     } //-- void removeAllTree()
 429
 430     /**
 431      * Method removeTree
 432      *
 433      *
 434      *
 435      * @param index
 436      * @return Tree
 437      */
 438     public org.vamsas.client.objects.Tree removeTree(int index)
 439     {
 440         java.lang.Object obj = _treeList.elementAt(index);
 441         _treeList.removeElementAt(index);
 442         return (org.vamsas.client.objects.Tree) obj;
 443     } //-- org.vamsas.client.objects.Tree removeTree(int)
 444
 445     /**
 446      * Sets the value of field 'alignmentAnnotations'.
 447      *
 448      * @param alignmentAnnotations the value of field
 449      * 'alignmentAnnotations'.
 450      */
 451     public void setAlignmentAnnotations(org.vamsas.client.objects.AlignmentAnnotations alignmentAnnotations)
 452     {
 453         this._alignmentAnnotations = alignmentAnnotations;
 454     } //-- void setAlignmentAnnotations(org.vamsas.client.objects.AlignmentAnnotations)
 455
 456     /**
 457      * Method setAlignmentSequence
 458      *
 459      *
 460      *
 461      * @param index
 462      * @param vAlignmentSequence
 463      */
 464     public void setAlignmentSequence(int index, org.vamsas.client.objects.AlignmentSequence vAlignmentSequence)
 465         throws java.lang.IndexOutOfBoundsException
 466     {
 467         //-- check bounds for index
 468         if ((index < 0) || (index > _alignmentSequenceList.size())) {
 469             throw new IndexOutOfBoundsException("setAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]");
 470         }
 471         _alignmentSequenceList.setElementAt(vAlignmentSequence, index);
 472     } //-- void setAlignmentSequence(int, org.vamsas.client.objects.AlignmentSequence)
 473
 474     /**
 475      * Method setAlignmentSequence
 476      *
 477      *
 478      *
 479      * @param alignmentSequenceArray
 480      */
 481     public void setAlignmentSequence(org.vamsas.client.objects.AlignmentSequence[] alignmentSequenceArray)
 482     {
 483         //-- copy array
 484         _alignmentSequenceList.removeAllElements();
 485         for (int i = 0; i < alignmentSequenceArray.length; i++) {
 486             _alignmentSequenceList.addElement(alignmentSequenceArray[i]);
 487         }
 488     } //-- void setAlignmentSequence(org.vamsas.client.objects.AlignmentSequence)
 489
 490     /**
 491      * Method setAlignmentSequence
 492      *
 493      * Sets the value of 'alignmentSequence' by copying the given
 494      * Vector.
 495      *
 496      * @param alignmentSequenceVector the Vector to copy.
 497      */
 498     public void setAlignmentSequence(java.util.Vector alignmentSequenceVector)
 499     {
 500         //-- copy vector
 501         _alignmentSequenceList.removeAllElements();
 502         for (int i = 0; i < alignmentSequenceVector.size(); i++) {
 503             _alignmentSequenceList.addElement((org.vamsas.client.objects.AlignmentSequence)alignmentSequenceVector.elementAt(i));
 504         }
 505     } //-- void setAlignmentSequence(java.util.Vector)
 506
 507     /**
 508      * Method setAlignmentSequenceAsReference
 509      *
 510      * Sets the value of 'alignmentSequence' by setting it to the
 511      * given Vector. No type checking is performed.
 512      *
 513      * @param alignmentSequenceVector the Vector to copy.
 514      */
 515     public void setAlignmentSequenceAsReference(java.util.Vector alignmentSequenceVector)
 516     {
 517         _alignmentSequenceList = alignmentSequenceVector;
 518     } //-- void setAlignmentSequenceAsReference(java.util.Vector)
 519
 520     /**
 521      * Sets the value of field 'provenance'.
 522      *
 523      * @param provenance the value of field 'provenance'.
 524      */
 525     public void setProvenance(org.vamsas.client.objects.Provenance provenance)
 526     {
 527         this._provenance = provenance;
 528     } //-- void setProvenance(org.vamsas.client.objects.Provenance)
 529
 530     /**
 531      * Method setTree
 532      *
 533      *
 534      *
 535      * @param index
 536      * @param vTree
 537      */
 538     public void setTree(int index, org.vamsas.client.objects.Tree vTree)
 539         throws java.lang.IndexOutOfBoundsException
 540     {
 541         //-- check bounds for index
 542         if ((index < 0) || (index > _treeList.size())) {
 543             throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
 544         }
 545         _treeList.setElementAt(vTree, index);
 546     } //-- void setTree(int, org.vamsas.client.objects.Tree)
 547
 548     /**
 549      * Method setTree
 550      *
 551      *
 552      *
 553      * @param treeArray
 554      */
 555     public void setTree(org.vamsas.client.objects.Tree[] treeArray)
 556     {
 557         //-- copy array
 558         _treeList.removeAllElements();
 559         for (int i = 0; i < treeArray.length; i++) {
 560             _treeList.addElement(treeArray[i]);
 561         }
 562     } //-- void setTree(org.vamsas.client.objects.Tree)
 563
 564     /**
 565      * Method setTree
 566      *
 567      * Sets the value of 'tree' by copying the given Vector.
 568      *
 569      * @param treeVector the Vector to copy.
 570      */
 571     public void setTree(java.util.Vector treeVector)
 572     {
 573         //-- copy vector
 574         _treeList.removeAllElements();
 575         for (int i = 0; i < treeVector.size(); i++) {
 576             _treeList.addElement((org.vamsas.client.objects.Tree)treeVector.elementAt(i));
 577         }
 578     } //-- void setTree(java.util.Vector)
 579
 580     /**
 581      * Method setTreeAsReference
 582      *
 583      * Sets the value of 'tree' by setting it to the given Vector.
 584      * No type checking is performed.
 585      *
 586      * @param treeVector the Vector to copy.
 587      */
 588     public void setTreeAsReference(java.util.Vector treeVector)
 589     {
 590         _treeList = treeVector;
 591     } //-- void setTreeAsReference(java.util.Vector)
 592
 593     /**
 594      * Method unmarshal
 595      *
 596      *
 597      *
 598      * @param reader
 599      * @return Alignment
 600      */
 601     public static org.vamsas.client.objects.Alignment unmarshal(java.io.Reader reader)
 602         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 603     {
 604         return (org.vamsas.client.objects.Alignment) Unmarshaller.unmarshal(org.vamsas.client.objects.Alignment.class, reader);
 605     } //-- org.vamsas.client.objects.Alignment unmarshal(java.io.Reader)
 606
 607     /**
 608      * Method validate
 609      *
 610      */
 611     public void validate()
 612         throws org.exolab.castor.xml.ValidationException
 613     {
 614         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
 615         validator.validate(this);
 616     } //-- void validate()
 617
 618 }