001 /**
002 * Copyright (c) 2010, SIB. All rights reserved.
003 *
004 * SIB (Swiss Institute of Bioinformatics) - http://www.isb-sib.ch Host -
005 * https://sourceforge.net/projects/javaprotlib/
006 *
007 * Redistribution and use in source and binary forms, with or without
008 * modification, are permitted provided that the following conditions are met:
009 * Redistributions of source code must retain the above copyright notice, this
010 * list of conditions and the following disclaimer. Redistributions in binary
011 * form must reproduce the above copyright notice, this list of conditions and
012 * the following disclaimer in the documentation and/or other materials provided
013 * with the distribution. Neither the name of the SIB/GENEBIO nor the names of
014 * its contributors may be used to endorse or promote products derived from this
015 * software without specific prior written permission.
016 *
017 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
018 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
019 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
020 * ARE DISCLAIMED. IN NO EVENT SHALL SIB/GENEBIO BE LIABLE FOR ANY DIRECT,
021 * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
022 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
023 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
024 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
025 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
026 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
027 */
028 package org.expasy.jpl.commons.collection.symbol.seq;
029
030
031 import java.util.NoSuchElementException;
032 import org.expasy.jpl.commons.collection.IndexIterable;
033
034
035 /**
036 * This class provides a skeletal implementation of the PositionIterable
037 * interface, to minimize the effort required to implement this interface.
038 *
039 * To implement a JPL positioner on a Sequence, the programmer needs only to
040 * extend this class and provide implementations for the iterator. (The iterator
041 * returned by the iterator method must implement the
042 * <code>foundNextPosition()</code> method).
043 *
044 * @author nikitin
045 *
046 * @version 1.0
047 *
048 */
049 public abstract class AbstractSequencePositioner<T> implements
050 SequenceIterable<T> {
051
052 /** Iterator will iterate over found positions on this sequence. */
053 protected SymbolSequence<T> sequence;
054
055 protected int numberOfPositions;
056
057 /**
058 * This inner class provides implementations for <code>next()</code> and
059 * <code>hasNext()</code> needed from <code>Iterator</code> interface. It
060 * announces and provides the mechanism of searching in a sequence and
061 * storing all positions matching an expression. (@see JPLRegExpPositioner
062 * and JPLSimpleAAPositioner).
063 */
064 public abstract class Iterator extends IndexIterable.Iterator {
065
066 protected Integer nextPosition;
067
068 public Iterator() {
069 if (sequence == null) {
070 throw new IllegalStateException("sequence not defined");
071 }
072
073 numberOfPositions = 0;
074 nextPosition = -1;
075 }
076
077 /**
078 * Has found next match ? [method implemented to respect Iterator
079 * contract].
080 */
081 public boolean hasNext() {
082 return ((nextPosition == -1) ? foundNextPosition() : true);
083 }
084
085 /**
086 * Returns the next <code>Integer</code> element [method implemented to
087 * respect Iterator contract].
088 *
089 */
090 public Integer next() {
091 if (nextPosition != -1) {
092 return consumePosition();
093 }
094
095 if (!foundNextPosition()) {
096 throw new NoSuchElementException("No more elements");
097 }
098
099 return consumePosition();
100 }
101
102 /**
103 * Returns the next position found in the sequence.
104 *
105 * @return Integer
106 */
107 private Integer consumePosition() {
108 final Integer pos = nextPosition;
109
110 nextPosition = -1;
111
112 if (pos < sequence.length()) {
113 numberOfPositions++;
114 }
115
116 return pos;
117 }
118
119 /**
120 * This function will have to set nextPosition to its value and will
121 * return true if a valid position is found otherwise false.
122 */
123 public abstract boolean foundNextPosition();
124 }
125
126 /**
127 * Set the sequence for future searches.
128 *
129 * @param sequence the sequence where motif search will be done.
130 *
131 * @throws IllegalArgumentException if sequence is not defined.
132 */
133 public void setSequence(final SymbolSequence<T> sequence) {
134 if (sequence == null) {
135 throw new IllegalArgumentException("sequence cannot be null.");
136 }
137 this.sequence = sequence;
138 }
139
140 public int getNumberOfSites() {
141 return numberOfPositions;
142 }
143
144 public IndexIterable.Iterator iterator(SymbolSequence<T> sequence) {
145 setSequence(sequence);
146 return iterator();
147 }
148 }