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;
029
030
031 import java.util.ArrayList;
032 import java.util.Arrays;
033 import java.util.List;
034
035
036 /**
037 * This object is {@code IntegerSequenceWithGap} with gaps defining a sequence
038 * of integers with missing integers at some intervals.
039 *
040 * @author nikitin
041 *
042 * @version 1.0
043 *
044 */
045 public final class IntegerSequenceWithGap {
046
047 /** the sequence of intervals */
048 private final List<IntegerSequence> sequence;
049
050 /** the number of integers in all intervals */
051 private int numOfInts;
052
053 /** construct an empty interval */
054 private IntegerSequenceWithGap() {
055 sequence = new ArrayList<IntegerSequence>();
056 }
057
058 public static IntegerSequenceWithGap newInstance() {
059 return new IntegerSequenceWithGap();
060 }
061
062 /**
063 * Build integer intervals
064 *
065 * @param ints the integers to place in intervals.
066 * @param by the increment of the sequence.
067 * @return an instance of {@code JPLIntervalSequence}
068 */
069 public static IntegerSequenceWithGap fromIntegers(final int[] ints,
070 final int by) {
071 final IntegerSequenceWithGap seq = new IntegerSequenceWithGap();
072
073 if ((ints != null) && (ints.length > 0)) {
074 int previousValue = ints[0];
075 int from = previousValue;
076 IntegerSequence interval = null;
077
078 for (final int currentValue : ints) {
079
080 // have to be sorted !!
081 if ((by > 0) && (currentValue < previousValue)) {
082 throw new IllegalStateException("integers have to be well"
083 + " sorted.");
084 } else if ((by < 0) && (currentValue > previousValue)) {
085 throw new IllegalStateException("integers have to be well"
086 + " sorted.");
087 }
088 // end of current interval
089 if ((by > 0) ? currentValue > previousValue + by
090 : currentValue < previousValue + by) {
091
092 if (by > 0) {
093 previousValue++;
094 } else {
095 from++;
096 }
097
098 interval =
099 new IntegerSequence.Builder(from, previousValue).by(by)
100 .build();
101
102 seq.add(interval);
103 from = currentValue;
104 }
105 previousValue = currentValue;
106 }
107
108 if (by > 0) {
109 previousValue++;
110 } else {
111 from++;
112 }
113
114 interval =
115 new IntegerSequence.Builder(from, previousValue).by(by).build();
116 seq.add(interval);
117 }
118
119 return seq;
120 }
121
122 public void add(final IntegerSequence interval) {
123 sequence.add(interval);
124 numOfInts += interval.size();
125 }
126
127 public final int getNumOfInts() {
128 return numOfInts;
129 }
130
131 public final IntegerSequence get(final int i) {
132 return sequence.get(i);
133 }
134
135 public final int size() {
136 return sequence.size();
137 }
138
139 public final int getLowerBound() {
140 if (sequence.size() == 0) {
141 throw new IllegalStateException("no existing intervals");
142 }
143 return sequence.get(0).getFrom();
144 }
145
146 public final int getUpperBound() {
147 if (sequence.size() == 0) {
148 throw new IllegalStateException("no existing intervals");
149 }
150 return sequence.get(sequence.size() - 1).getTo();
151 }
152
153 public int[] toInts() {
154 final int[] ints = new int[numOfInts];
155 int from = 0;
156 for (final IntegerSequence interval : sequence) {
157 System.arraycopy(interval.toInts(), 0, ints, from, interval.size());
158 from += interval.size();
159 }
160 return ints;
161 }
162
163 @Override
164 public String toString() {
165 final StringBuilder sb = new StringBuilder();
166
167 sb.append("Interval# = " + sequence.size() + "\n");
168 sb.append(Arrays.toString(toInts()));
169 return sb.toString();
170 }
171 }