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 _gapChar
  42      */
  43     private java.lang.String _gapChar;
  44
  45     /**
  46      * Field _aligned
  47      */
  48     private boolean _aligned;
  49
  50     /**
  51      * keeps track of state for field: _aligned
  52      */
  53     private boolean _has_aligned;
  54
  55     /**
  56      * Field _id
  57      */
  58     private java.lang.String _id;
  59
  60     /**
  61      * Field _alignmentAnnotations
  62      */
  63     private org.vamsas.objects.core.AlignmentAnnotations _alignmentAnnotations;
  64
  65     /**
  66      * Field _treeList
  67      */
  68     private java.util.Vector _treeList;
  69
  70     /**
  71      * Field _alignmentSequenceList
  72      */
  73     private java.util.Vector _alignmentSequenceList;
  74
  75     /**
  76      * Field _provenance
  77      */
  78     private org.vamsas.objects.core.Provenance _provenance;
  79
  80
  81       //----------------/
  82      //- Constructors -/
  83     //----------------/
  84
  85     public Alignment()
  86      {
  87         super();
  88         _treeList = new Vector();
  89         _alignmentSequenceList = new Vector();
  90     } //-- org.vamsas.objects.core.Alignment()
  91
  92
  93       //-----------/
  94      //- Methods -/
  95     //-----------/
  96
  97     /**
  98      * Method addAlignmentSequence
  99      *
 100      *
 101      *
 102      * @param vAlignmentSequence
 103      */
 104     public void addAlignmentSequence(org.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
 105         throws java.lang.IndexOutOfBoundsException
 106     {
 107         _alignmentSequenceList.addElement(vAlignmentSequence);
 108     } //-- void addAlignmentSequence(org.vamsas.objects.core.AlignmentSequence)
 109
 110     /**
 111      * Method addAlignmentSequence
 112      *
 113      *
 114      *
 115      * @param index
 116      * @param vAlignmentSequence
 117      */
 118     public void addAlignmentSequence(int index, org.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
 119         throws java.lang.IndexOutOfBoundsException
 120     {
 121         _alignmentSequenceList.insertElementAt(vAlignmentSequence, index);
 122     } //-- void addAlignmentSequence(int, org.vamsas.objects.core.AlignmentSequence)
 123
 124     /**
 125      * Method addTree
 126      *
 127      *
 128      *
 129      * @param vTree
 130      */
 131     public void addTree(org.vamsas.objects.core.Tree vTree)
 132         throws java.lang.IndexOutOfBoundsException
 133     {
 134         _treeList.addElement(vTree);
 135     } //-- void addTree(org.vamsas.objects.core.Tree)
 136
 137     /**
 138      * Method addTree
 139      *
 140      *
 141      *
 142      * @param index
 143      * @param vTree
 144      */
 145     public void addTree(int index, org.vamsas.objects.core.Tree vTree)
 146         throws java.lang.IndexOutOfBoundsException
 147     {
 148         _treeList.insertElementAt(vTree, index);
 149     } //-- void addTree(int, org.vamsas.objects.core.Tree)
 150
 151     /**
 152      * Method deleteAligned
 153      *
 154      */
 155     public void deleteAligned()
 156     {
 157         this._has_aligned= false;
 158     } //-- void deleteAligned()
 159
 160     /**
 161      * Method enumerateAlignmentSequence
 162      *
 163      *
 164      *
 165      * @return Enumeration
 166      */
 167     public java.util.Enumeration enumerateAlignmentSequence()
 168     {
 169         return _alignmentSequenceList.elements();
 170     } //-- java.util.Enumeration enumerateAlignmentSequence()
 171
 172     /**
 173      * Method enumerateTree
 174      *
 175      *
 176      *
 177      * @return Enumeration
 178      */
 179     public java.util.Enumeration enumerateTree()
 180     {
 181         return _treeList.elements();
 182     } //-- java.util.Enumeration enumerateTree()
 183
 184     /**
 185      * Note: hashCode() has not been overriden
 186      *
 187      * @param obj
 188      * @return boolean
 189      */
 190     public boolean equals(java.lang.Object obj)
 191     {
 192         if ( this == obj )
 193             return true;
 194
 195         if (super.equals(obj)==false)
 196             return false;
 197
 198         if (obj instanceof Alignment) {
 199
 200             Alignment temp = (Alignment)obj;
 201             if (this._gapChar != null) {
 202                 if (temp._gapChar == null) return false;
 203                 else if (!(this._gapChar.equals(temp._gapChar)))
 204                     return false;
 205             }
 206             else if (temp._gapChar != null)
 207                 return false;
 208             if (this._aligned != temp._aligned)
 209                 return false;
 210             if (this._has_aligned != temp._has_aligned)
 211                 return false;
 212             if (this._id != null) {
 213                 if (temp._id == null) return false;
 214                 else if (!(this._id.equals(temp._id)))
 215                     return false;
 216             }
 217             else if (temp._id != null)
 218                 return false;
 219             if (this._alignmentAnnotations != null) {
 220                 if (temp._alignmentAnnotations == null) return false;
 221                 else if (!(this._alignmentAnnotations.equals(temp._alignmentAnnotations)))
 222                     return false;
 223             }
 224             else if (temp._alignmentAnnotations != null)
 225                 return false;
 226             if (this._treeList != null) {
 227                 if (temp._treeList == null) return false;
 228                 else if (!(this._treeList.equals(temp._treeList)))
 229                     return false;
 230             }
 231             else if (temp._treeList != null)
 232                 return false;
 233             if (this._alignmentSequenceList != null) {
 234                 if (temp._alignmentSequenceList == null) return false;
 235                 else if (!(this._alignmentSequenceList.equals(temp._alignmentSequenceList)))
 236                     return false;
 237             }
 238             else if (temp._alignmentSequenceList != null)
 239                 return false;
 240             if (this._provenance != null) {
 241                 if (temp._provenance == null) return false;
 242                 else if (!(this._provenance.equals(temp._provenance)))
 243                     return false;
 244             }
 245             else if (temp._provenance != null)
 246                 return false;
 247             return true;
 248         }
 249         return false;
 250     } //-- boolean equals(java.lang.Object)
 251
 252     /**
 253      * Returns the value of field 'aligned'.
 254      *
 255      * @return boolean
 256      * @return the value of field 'aligned'.
 257      */
 258     public boolean getAligned()
 259     {
 260         return this._aligned;
 261     } //-- boolean getAligned()
 262
 263     /**
 264      * Returns the value of field 'alignmentAnnotations'.
 265      *
 266      * @return AlignmentAnnotations
 267      * @return the value of field 'alignmentAnnotations'.
 268      */
 269     public org.vamsas.objects.core.AlignmentAnnotations getAlignmentAnnotations()
 270     {
 271         return this._alignmentAnnotations;
 272     } //-- org.vamsas.objects.core.AlignmentAnnotations getAlignmentAnnotations()
 273
 274     /**
 275      * Method getAlignmentSequence
 276      *
 277      *
 278      *
 279      * @param index
 280      * @return AlignmentSequence
 281      */
 282     public org.vamsas.objects.core.AlignmentSequence getAlignmentSequence(int index)
 283         throws java.lang.IndexOutOfBoundsException
 284     {
 285         //-- check bounds for index
 286         if ((index < 0) || (index > _alignmentSequenceList.size())) {
 287             throw new IndexOutOfBoundsException("getAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]");
 288         }
 289
 290         return (org.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index);
 291     } //-- org.vamsas.objects.core.AlignmentSequence getAlignmentSequence(int)
 292
 293     /**
 294      * Method getAlignmentSequence
 295      *
 296      *
 297      *
 298      * @return AlignmentSequence
 299      */
 300     public org.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence()
 301     {
 302         int size = _alignmentSequenceList.size();
 303         org.vamsas.objects.core.AlignmentSequence[] mArray = new org.vamsas.objects.core.AlignmentSequence[size];
 304         for (int index = 0; index < size; index++) {
 305             mArray[index] = (org.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index);
 306         }
 307         return mArray;
 308     } //-- org.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence()
 309
 310     /**
 311      * Method getAlignmentSequenceCount
 312      *
 313      *
 314      *
 315      * @return int
 316      */
 317     public int getAlignmentSequenceCount()
 318     {
 319         return _alignmentSequenceList.size();
 320     } //-- int getAlignmentSequenceCount()
 321
 322     /**
 323      * Returns the value of field 'gapChar'.
 324      *
 325      * @return String
 326      * @return the value of field 'gapChar'.
 327      */
 328     public java.lang.String getGapChar()
 329     {
 330         return this._gapChar;
 331     } //-- java.lang.String getGapChar()
 332
 333     /**
 334      * Returns the value of field 'id'.
 335      *
 336      * @return String
 337      * @return the value of field 'id'.
 338      */
 339     public java.lang.String getId()
 340     {
 341         return this._id;
 342     } //-- java.lang.String getId()
 343
 344     /**
 345      * Returns the value of field 'provenance'.
 346      *
 347      * @return Provenance
 348      * @return the value of field 'provenance'.
 349      */
 350     public org.vamsas.objects.core.Provenance getProvenance()
 351     {
 352         return this._provenance;
 353     } //-- org.vamsas.objects.core.Provenance getProvenance()
 354
 355     /**
 356      * Method getTree
 357      *
 358      *
 359      *
 360      * @param index
 361      * @return Tree
 362      */
 363     public org.vamsas.objects.core.Tree getTree(int index)
 364         throws java.lang.IndexOutOfBoundsException
 365     {
 366         //-- check bounds for index
 367         if ((index < 0) || (index > _treeList.size())) {
 368             throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
 369         }
 370
 371         return (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
 372     } //-- org.vamsas.objects.core.Tree getTree(int)
 373
 374     /**
 375      * Method getTree
 376      *
 377      *
 378      *
 379      * @return Tree
 380      */
 381     public org.vamsas.objects.core.Tree[] getTree()
 382     {
 383         int size = _treeList.size();
 384         org.vamsas.objects.core.Tree[] mArray = new org.vamsas.objects.core.Tree[size];
 385         for (int index = 0; index < size; index++) {
 386             mArray[index] = (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
 387         }
 388         return mArray;
 389     } //-- org.vamsas.objects.core.Tree[] getTree()
 390
 391     /**
 392      * Method getTreeCount
 393      *
 394      *
 395      *
 396      * @return int
 397      */
 398     public int getTreeCount()
 399     {
 400         return _treeList.size();
 401     } //-- int getTreeCount()
 402
 403     /**
 404      * Method hasAligned
 405      *
 406      *
 407      *
 408      * @return boolean
 409      */
 410     public boolean hasAligned()
 411     {
 412         return this._has_aligned;
 413     } //-- boolean hasAligned()
 414
 415     /**
 416      * Method isValid
 417      *
 418      *
 419      *
 420      * @return boolean
 421      */
 422     public boolean isValid()
 423     {
 424         try {
 425             validate();
 426         }
 427         catch (org.exolab.castor.xml.ValidationException vex) {
 428             return false;
 429         }
 430         return true;
 431     } //-- boolean isValid()
 432
 433     /**
 434      * Method marshal
 435      *
 436      *
 437      *
 438      * @param out
 439      */
 440     public void marshal(java.io.Writer out)
 441         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 442     {
 443
 444         Marshaller.marshal(this, out);
 445     } //-- void marshal(java.io.Writer)
 446
 447     /**
 448      * Method marshal
 449      *
 450      *
 451      *
 452      * @param handler
 453      */
 454     public void marshal(org.xml.sax.ContentHandler handler)
 455         throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 456     {
 457
 458         Marshaller.marshal(this, handler);
 459     } //-- void marshal(org.xml.sax.ContentHandler)
 460
 461     /**
 462      * Method removeAlignmentSequence
 463      *
 464      *
 465      *
 466      * @param index
 467      * @return AlignmentSequence
 468      */
 469     public org.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int index)
 470     {
 471         java.lang.Object obj = _alignmentSequenceList.elementAt(index);
 472         _alignmentSequenceList.removeElementAt(index);
 473         return (org.vamsas.objects.core.AlignmentSequence) obj;
 474     } //-- org.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int)
 475
 476     /**
 477      * Method removeAllAlignmentSequence
 478      *
 479      */
 480     public void removeAllAlignmentSequence()
 481     {
 482         _alignmentSequenceList.removeAllElements();
 483     } //-- void removeAllAlignmentSequence()
 484
 485     /**
 486      * Method removeAllTree
 487      *
 488      */
 489     public void removeAllTree()
 490     {
 491         _treeList.removeAllElements();
 492     } //-- void removeAllTree()
 493
 494     /**
 495      * Method removeTree
 496      *
 497      *
 498      *
 499      * @param index
 500      * @return Tree
 501      */
 502     public org.vamsas.objects.core.Tree removeTree(int index)
 503     {
 504         java.lang.Object obj = _treeList.elementAt(index);
 505         _treeList.removeElementAt(index);
 506         return (org.vamsas.objects.core.Tree) obj;
 507     } //-- org.vamsas.objects.core.Tree removeTree(int)
 508
 509     /**
 510      * Sets the value of field 'aligned'.
 511      *
 512      * @param aligned the value of field 'aligned'.
 513      */
 514     public void setAligned(boolean aligned)
 515     {
 516         this._aligned = aligned;
 517         this._has_aligned = true;
 518     } //-- void setAligned(boolean)
 519
 520     /**
 521      * Sets the value of field 'alignmentAnnotations'.
 522      *
 523      * @param alignmentAnnotations the value of field
 524      * 'alignmentAnnotations'.
 525      */
 526     public void setAlignmentAnnotations(org.vamsas.objects.core.AlignmentAnnotations alignmentAnnotations)
 527     {
 528         this._alignmentAnnotations = alignmentAnnotations;
 529     } //-- void setAlignmentAnnotations(org.vamsas.objects.core.AlignmentAnnotations)
 530
 531     /**
 532      * Method setAlignmentSequence
 533      *
 534      *
 535      *
 536      * @param index
 537      * @param vAlignmentSequence
 538      */
 539     public void setAlignmentSequence(int index, org.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
 540         throws java.lang.IndexOutOfBoundsException
 541     {
 542         //-- check bounds for index
 543         if ((index < 0) || (index > _alignmentSequenceList.size())) {
 544             throw new IndexOutOfBoundsException("setAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]");
 545         }
 546         _alignmentSequenceList.setElementAt(vAlignmentSequence, index);
 547     } //-- void setAlignmentSequence(int, org.vamsas.objects.core.AlignmentSequence)
 548
 549     /**
 550      * Method setAlignmentSequence
 551      *
 552      *
 553      *
 554      * @param alignmentSequenceArray
 555      */
 556     public void setAlignmentSequence(org.vamsas.objects.core.AlignmentSequence[] alignmentSequenceArray)
 557     {
 558         //-- copy array
 559         _alignmentSequenceList.removeAllElements();
 560         for (int i = 0; i < alignmentSequenceArray.length; i++) {
 561             _alignmentSequenceList.addElement(alignmentSequenceArray[i]);
 562         }
 563     } //-- void setAlignmentSequence(org.vamsas.objects.core.AlignmentSequence)
 564
 565     /**
 566      * Sets the value of field 'gapChar'.
 567      *
 568      * @param gapChar the value of field 'gapChar'.
 569      */
 570     public void setGapChar(java.lang.String gapChar)
 571     {
 572         this._gapChar = gapChar;
 573     } //-- void setGapChar(java.lang.String)
 574
 575     /**
 576      * Sets the value of field 'id'.
 577      *
 578      * @param id the value of field 'id'.
 579      */
 580     public void setId(java.lang.String id)
 581     {
 582         this._id = id;
 583     } //-- void setId(java.lang.String)
 584
 585     /**
 586      * Sets the value of field 'provenance'.
 587      *
 588      * @param provenance the value of field 'provenance'.
 589      */
 590     public void setProvenance(org.vamsas.objects.core.Provenance provenance)
 591     {
 592         this._provenance = provenance;
 593     } //-- void setProvenance(org.vamsas.objects.core.Provenance)
 594
 595     /**
 596      * Method setTree
 597      *
 598      *
 599      *
 600      * @param index
 601      * @param vTree
 602      */
 603     public void setTree(int index, org.vamsas.objects.core.Tree vTree)
 604         throws java.lang.IndexOutOfBoundsException
 605     {
 606         //-- check bounds for index
 607         if ((index < 0) || (index > _treeList.size())) {
 608             throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
 609         }
 610         _treeList.setElementAt(vTree, index);
 611     } //-- void setTree(int, org.vamsas.objects.core.Tree)
 612
 613     /**
 614      * Method setTree
 615      *
 616      *
 617      *
 618      * @param treeArray
 619      */
 620     public void setTree(org.vamsas.objects.core.Tree[] treeArray)
 621     {
 622         //-- copy array
 623         _treeList.removeAllElements();
 624         for (int i = 0; i < treeArray.length; i++) {
 625             _treeList.addElement(treeArray[i]);
 626         }
 627     } //-- void setTree(org.vamsas.objects.core.Tree)
 628
 629     /**
 630      * Method unmarshal
 631      *
 632      *
 633      *
 634      * @param reader
 635      * @return Alignment
 636      */
 637     public static org.vamsas.objects.core.Alignment unmarshal(java.io.Reader reader)
 638         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 639     {
 640         return (org.vamsas.objects.core.Alignment) Unmarshaller.unmarshal(org.vamsas.objects.core.Alignment.class, reader);
 641     } //-- org.vamsas.objects.core.Alignment unmarshal(java.io.Reader)
 642
 643     /**
 644      * Method validate
 645      *
 646      */
 647     public void validate()
 648         throws org.exolab.castor.xml.ValidationException
 649     {
 650         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
 651         validator.validate(this);
 652     } //-- void validate()
 653
 654 }