/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* THE SOFTWARE.
*/
package org.broad.igv.feature;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.track.SequenceTrack;
/**
* @author Jim Robinson
* @date 12/26/11
*/
class Codon {
// Position in protein coordinates, first amino acid is numbered 1
private int proteinPosition;
// Triplet -- genomic (base) positions
// in "zero" based (UCSC style) coordinates
private int[] genomePositions = new int[]{-1, -1, -1};
private int nextPos = 0;
private AminoAcid aminoAcid;
private Strand strand;
private int incr = 1;
private String chr;
private String sequence;
Codon(String chr, int proteinPosition) {
this(chr, proteinPosition, Strand.POSITIVE);
}
public Codon(String chr, int proteinPosition, Strand strand) {
this.proteinPosition = proteinPosition;
this.strand = strand;
this.chr = chr;
if (this.strand == Strand.NEGATIVE) {
this.nextPos = 2;
this.incr = -1;
}
}
/**
* If on positive strand, will add each successive
* gp at end. If on negative strand, they will be added in reverse order.
*
* @param gp
*/
void setNextGenomePosition(int gp) {
try {
genomePositions[nextPos] = gp;
nextPos += incr;
} catch (IndexOutOfBoundsException e) {
throw new IllegalStateException("Genome positions have already been set, cannot set any more");
}
}
boolean isGenomePositionsSet() {
boolean set = true;
for (int ii : genomePositions) {
set &= ii >= 0;
}
return set;
}
public void setAminoAcid(AminoAcid aa) {
this.aminoAcid = aa;
}
public int getProteinPosition() {
return proteinPosition;
}
public int[] getGenomePositions() {
return genomePositions;
}
public AminoAcid getAminoAcid() {
return aminoAcid;
}
public void calcSequence(Genome genome) {
if (!this.isGenomePositionsSet()) {
throw new IllegalStateException("Must set genome positions first");
}
int[] positions = this.getGenomePositions();
String aas = "";
for (int start : positions) {
final byte[] nucSequence = genome.getSequence(chr, start, start + 1);
if (nucSequence == null) {
// No sequence.
} else {
aas += new String(nucSequence);
}
}
if (strand == Strand.NEGATIVE) {
aas = SequenceTrack.getReverseComplement(aas);
}
this.sequence = aas;
}
String getSequence() {
return sequence;
}
}