eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/SequenceIDIterator.java

   1 // $Id$
   2 /**
   3 * Copyright (C) 2016 EDIT
   4 * European Distributed Institute of Taxonomy
   5 * http://www.e-taxonomy.eu
   6 *
   7 * The contents of this file are subject to the Mozilla Public License Version 1.1
   8 * See LICENSE.TXT at the top of this package for the full license terms.
   9 */
  10 package eu.etaxonomy.taxeditor.molecular.io;
  11
  12 import java.util.Iterator;
  13 import java.util.NoSuchElementException;
  14
  15 import eu.etaxonomy.taxeditor.molecular.l10n.Messages;
  16
  17
  18
  19 /**
  20  * Iterator implementation used internally be {@link CDMSequenceMatrixAdapter}.
  21  *
  22  * @author Ben Stöver
  23  * @date 29.04.2016
  24  */
  25 class SequenceIDIterator implements Iterator<String> {
  26     private boolean containsConsensus;
  27     private int singleReadPos;
  28     private int singleReadCount;
  29
  30
  31     /**
  32      * Creates a new instance of this class.
  33      *
  34      * @param singleReadCount the number of single read IDs to be returned by this iterator before the consensus sequence
  35      */
  36     public SequenceIDIterator(int singleReadCount, boolean containsConsensus) {
  37         super();
  38         this.containsConsensus = containsConsensus;
  39         this.singleReadCount = singleReadCount;
  40         this.singleReadPos = 0;
  41     }
  42
  43
  44     @Override
  45     public boolean hasNext() {
  46         return (singleReadPos < singleReadCount) || (containsConsensus && (singleReadPos <= singleReadCount));
  47     }
  48
  49
  50     @Override
  51     public String next() {
  52         if (singleReadPos < singleReadCount) {
  53             return CDMSequenceMatrixAdapter.SINGLE_READ_SEQUENCE_ID_PREFIX + (singleReadPos++);
  54         }
  55         else if (containsConsensus && (singleReadPos == singleReadCount)) {
  56             singleReadPos++;
  57             return CDMSequenceMatrixAdapter.CONSENSUS_SEQUENCE_ID;
  58         }
  59         else {
  60             throw new NoSuchElementException(Messages.SequenceIDIterator_NO_MORE_SEQUENCES);
  61         }
  62     }
  63
  64
  65     @Override
  66     public void remove() {
  67         throw new UnsupportedOperationException(Messages.SequenceIDIterator_REMOVE_NOT_SUPPORTED);
  68     }
  69 }