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/* Copyright (c) 2009 Peter Troshin
*
* JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0
*
* This library is free software; you can redistribute it and/or modify it under the terms of the
* Apache License version 2 as published by the Apache Software Foundation
*
* This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
* even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
* License for more details.
*
* A copy of the license is in apache_license.txt. It is also available here:
* @see: http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Any republication or derived work distributed in source code form
* must include this copyright and license notice.
*/
package compbio.data.sequence;
import java.util.List;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlSeeAlso;
import compbio.util.annotation.Immutable;
/**
* Multiple sequence alignment.
*
* Does not give any guarantees on the content of individual FastaSequece
* records. It does not guarantee neither the uniqueness of the names of
* sequences nor it guarantees the uniqueness of the sequences.
*
* @see FastaSequence
* @see AlignmentMetadata
*
* @author pvtroshin
*
* @version 1.0 September 2009
*
*/
//@XmlSeeAlso({JpredAlignment.class})
@XmlAccessorType(XmlAccessType.FIELD)
public class Alignment {
protected AlignmentMetadata metadata;
protected List<FastaSequence> sequences;
protected Alignment() {
// This has to has a default constructor for JaxB
}
/**
* @param sequences
* @param program
* @param gapchar
*/
public Alignment(List<FastaSequence> sequences, Program program,
char gapchar) {
this.sequences = sequences;
this.metadata = new AlignmentMetadata(program, gapchar);
}
/**
*
* @param sequences
* @param metadata
*/
public Alignment(List<FastaSequence> sequences, AlignmentMetadata metadata) {
this.sequences = sequences;
this.metadata = metadata;
}
/**
*
* @return list of FastaSequence records
*/
public List<FastaSequence> getSequences() {
return sequences;
}
/**
*
* @return a number of sequence in the alignment
*/
public int getSize() {
return this.sequences.size();
}
/**
*
* @return AlignmentMetadata object
*/
public AlignmentMetadata getMetadata() {
return metadata;
}
@Override
public String toString() {
String sseq = "";
for (FastaSequence fs : getSequences()) {
sseq += fs.toString() + "\n";
}
return sseq;
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result
+ ((metadata == null) ? 0 : metadata.hashCode());
result = prime * result
+ ((sequences == null) ? 0 : sequences.hashCode());
return result;
}
/**
* Please note that this implementation does not take the order of sequences
* into account!
*/
@Override
public boolean equals(Object obj) {
if (obj == null) {
return false;
}
if (!(obj instanceof Alignment)) {
return false;
}
Alignment al = (Alignment) obj;
if (this.getSize() != al.getSize()) {
return false;
}
if (!this.getMetadata().equals(al.getMetadata())) {
return false;
}
int outerCounter = 0;
int matchCounter = 0;
for (FastaSequence fs : getSequences()) {
outerCounter++;
for (FastaSequence fs1 : al.getSequences()) {
if (fs.equals(fs1)) {
matchCounter++;
continue;
}
}
// Match for at lease one element was not found!
if (outerCounter != matchCounter) {
return false;
}
}
return true;
}
}
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