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/* Copyright (c) 2011 Peter Troshin
*
* JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0
*
* 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.regex.Matcher;
import java.util.regex.Pattern;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import compbio.util.SysPrefs;
import compbio.util.annotation.Immutable;
/**
* A FASTA formatted sequence. Please note that this class does not make any
* assumptions as to what sequence it stores e.g. it could be nucleotide,
* protein or even gapped alignment sequence! The only guarantee it makes is
* that the sequence does not contain white space characters e.g. spaces, new
* lines etc
*
* @author pvtroshin
*
* @version 1.0 September 2009
*/
@XmlAccessorType(XmlAccessType.FIELD)
@Immutable
public class FastaSequence {
/**
* Sequence id
*/
private String id;
// TODO what about gapped sequence here! should be indicated
/**
* Returns the string representation of sequence
*/
private String sequence;
FastaSequence() {
// Default constructor for JaxB
}
/**
* Upon construction the any whitespace characters are removed from the
* sequence
*
* @param id
* @param sequence
*/
public FastaSequence(String id, String sequence) {
this.id = id;
this.sequence = SequenceUtil.cleanSequence(sequence);
}
/**
* Gets the value of id
*
* @return the value of id
*/
public String getId() {
return this.id;
}
/**
* Gets the value of sequence
*
* @return the value of sequence
*/
public String getSequence() {
return this.sequence;
}
public static int countMatchesInSequence(final String theString,
final String theRegExp) {
final Pattern p = Pattern.compile(theRegExp);
final Matcher m = p.matcher(theString);
int cnt = 0;
while (m.find()) {
cnt++;
}
return cnt;
}
public String getFormattedFasta() {
return getFormatedSequence(80);
}
/**
*
* @return one line name, next line sequence, no matter what the sequence
* length is
*/
public String getOnelineFasta() {
String fasta = ">" + getId() + SysPrefs.newlinechar;
fasta += getSequence() + SysPrefs.newlinechar;
return fasta;
}
/**
* Format sequence per width letter in one string. Without spaces.
*
* @return multiple line formated sequence, one line width letters length
*
*/
public String getFormatedSequence(final int width) {
if (sequence == null) {
return "";
}
assert width >= 0 : "Wrong width parameter ";
final StringBuilder sb = new StringBuilder(sequence);
// int tail = nrOfWindows % WIN_SIZE;
// final int turns = (nrOfWindows - tail) / WIN_SIZE;
int tailLen = sequence.length() % width;
// add up inserted new line chars
int nchunks = (sequence.length() - tailLen) / width;
int nlineCharcounter = 0;
int insPos = 0;
for (int i = 1; i <= nchunks; i++) {
insPos = width * i + nlineCharcounter;
// to prevent inserting new line in the very end of a sequence then
// it would have failed.
if (sb.length() <= insPos) {
break;
}
sb.insert(insPos, "\n");
nlineCharcounter++;
}
// sb.insert(insPos + tailLen, "\n");
return sb.toString();
}
/**
*
* @return sequence length
*/
public int getLength() {
return this.sequence.length();
}
/**
* Same as oneLineFasta
*/
@Override
public String toString() {
return this.getOnelineFasta();
}
@Override
public int hashCode() {
final int prime = 17;
int result = 1;
result = prime * result + ((id == null) ? 0 : id.hashCode());
result = prime * result
+ ((sequence == null) ? 0 : sequence.hashCode());
return result;
}
@Override
public boolean equals(Object obj) {
if (obj == null) {
return false;
}
if (!(obj instanceof FastaSequence)) {
return false;
}
FastaSequence fs = (FastaSequence) obj;
if (!fs.getId().equals(this.getId())) {
return false;
}
if (!fs.getSequence().equalsIgnoreCase(this.getSequence())) {
return false;
}
return true;
}
}
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