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/*
* The MIT License
*
* Copyright (c) 2013 The 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
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.tribble.bed;
import htsjdk.tribble.annotation.Strand;
import java.util.ArrayList;
/**
* Object for full BED file.
*/
public class FullBEDFeature extends SimpleBEDFeature implements BEDFeature {
private java.util.List exons = new ArrayList();
public FullBEDFeature(String chr, int start, int end) {
super(start, end, chr);
}
@Override
public java.util.List getExons() {
return exons;
}
public void setExons(java.util.List exons) {
this.exons = exons;
}
public void addExon(Exon exon) {
if (exon == null) {
this.exons = new ArrayList();
}
exons.add(exon);
}
public void addExon(int exonStart, int exonEnd, int cdStart, int cdEnd, int exonNumber) {
Exon exon = new Exon(exonStart, exonEnd);
exon.setCodingStart(cdStart);
exon.setCodingEnd(cdEnd);
exon.setNumber(exonNumber);
addExon(exon);
}
/**
* A sub region of a feature. For example, a Gene exon
*
* @author jrobinso
*/
public class Exon {
int start;
int end;
/**
* The index of the exon relative to the start codon. The exon with the start
* codon is number "1".
*/
private int number;
private int readingFrame = -1;
/**
* Coding start position. This is the leftmost position of the coding region, not neccessarily the 5'utr end
*/
private int codingStart;
private int codingEnd;
boolean utr = false;
// The position of the first base of this exon relative to the start of the mRNA. This will correspond
// to either the beginning or end of the exon, depending on the strand
private int mrnaBase = -1;
public void setMrnaBase(int base) {
this.mrnaBase = base;
}
/**
* Constructs ...
*
* @param start
* @param end
*/
public Exon(int start, int end) {
this.start = start;
this.end = end;
// By default the entre exon is a coding region
this.codingStart = start;
this.codingEnd = end;
}
/**
* Flag indicating that the entire exon is the UTR.
*
* @param utr
*/
public void setUTR(boolean utr) {
this.utr = utr;
if (strand == Strand.POSITIVE) {
codingStart = codingEnd = end;
} else {
codingStart = codingEnd = start;
}
}
/**
* Method description
*
* @param codingStart
*/
public void setCodingStart(int codingStart) {
this.codingStart = Math.max(start, codingStart);
}
/**
* Method description
*
* @param codingEnd
*/
public void setCodingEnd(int codingEnd) {
this.codingEnd = Math.min(end, codingEnd);
}
/**
* Method description
*
* @param offset
*/
public void setReadingFrame(int offset) {
this.readingFrame = offset;
}
/**
* Method description
*
* @param phase
*/
public void setPhase(int phase) {
if (strand == Strand.POSITIVE) {
readingFrame = phase;
} else if (strand == Strand.NEGATIVE) {
int modLen = (getCodingLength() - phase) % 3;
readingFrame = modLen;
}
}
/**
* Method description
*
* @return
*/
public int getCdStart() {
return codingStart;
}
/**
* Method description
*
* @return
*/
public int getCdEnd() {
return this.codingEnd;
}
/**
* Method description
*
* @return
*/
public int getCodingLength() {
return utr ? 0 : Math.max(0, codingEnd - codingStart + 1);
}
/**
* This is exposed for unit tests.
*
* @return
*/
int getReadingShift() {
return readingFrame;
}
public String getValueString(double position) {
String msg = number > 0 ? "Exon number: " + number : "";
return msg;
}
public int getNumber() {
return number;
}
public void setNumber(int number) {
this.number = number;
}
}
public class Exon2 {
/**
* The index of the exon relative to the start codon. The exon with the start
* codon is number "1".
*/
private int number;
private int readingFrame = -1;
/**
* Coding start position. This is the leftmost position of the coding region, not neccessarily the 5'utr end
*/
private int start;
private int end;
private int codingStart;
private int codingEnd;
//private AminoAcidSequence aminoAcidSequence;
boolean utr = false;
// The position of the first base of this exon relative to the start of the mRNA. This will correspond
// to either the beginning or end of the exon, depending on the strand
private int mrnaBase = -1;
public Exon2(int start, int end, int codingStart, int codingDne) {
this.start = start;
this.end = end;
this.codingStart = codingStart;
this.codingEnd = codingDne;
}
public void setMrnaBase(int base) {
this.mrnaBase = base;
}
public int getAminoAcidNumber(int genomeCoordinate) {
if (mrnaBase < 0) {
return -1;
}
if (genomeCoordinate < getStart() || genomeCoordinate > getEnd()) {
throw new IndexOutOfBoundsException();
}
if (getStrand() == Strand.POSITIVE) {
int mrnaCoord = mrnaBase + (genomeCoordinate - codingStart) - 1;
return mrnaCoord < 0 ? -1 : mrnaCoord / 3 + 1;
} else if (getStrand() == Strand.NEGATIVE) {
int mrnaCoord = mrnaBase + (codingEnd - genomeCoordinate);
return mrnaCoord < 0 ? -1 : mrnaCoord / 3 + 1;
} else {
return 0;
}
}
/**
* Flag indicating that the entire exon is the UTR.
*
* @param utr
*/
public void setUTR(boolean utr) {
this.utr = utr;
if (getStrand() == Strand.POSITIVE) {
codingStart = codingEnd = getEnd();
} else {
codingStart = codingEnd = getStart();
}
}
/**
* Method description
*
* @param codingStart
*/
public void setCodingStart(int codingStart) {
this.codingStart = Math.max(getStart(), codingStart);
}
/**
* Method description
*
* @param codingEnd
*/
public void setCodingEnd(int codingEnd) {
this.codingEnd = Math.min(getEnd(), codingEnd);
}
/**
* Method description
*
* @param offset
*/
public void setReadingFrame(int offset) {
this.readingFrame = offset;
}
/**
* Method description
*
* @param phase
*/
public void setPhase(int phase) {
if (getStrand() == Strand.POSITIVE) {
readingFrame = phase;
} else if (getStrand() == Strand.NEGATIVE) {
int modLen = (getCodingLength() - phase) % 3;
readingFrame = modLen;
}
}
/**
* Method description
*
* @return
*/
public int getCdStart() {
return codingStart;
}
/**
* Method description
*
* @return
*/
public int getCdEnd() {
return this.codingEnd;
}
/**
* Method description
*
* @return
*/
public int getCodingLength() {
return utr ? 0 : Math.max(0, codingEnd - codingStart);
}
/**
* This is exposed for unit tests.
*
* @return
*/
int getReadingShift() {
return readingFrame;
}
/**
* Method description
*
* @return
*/
/*
public AminoAcidSequence getAminoAcidSequence() {
if (aminoAcidSequence == null) {
computeAminoAcidSequence();
}
return aminoAcidSequence;
}
*/
/*
public void setAminoAcidSequence(AminoAcidSequence aminoAcidSequence) {
this.aminoAcidSequence = aminoAcidSequence;
}
*/
/*
private void computeAminoAcidSequence() {
if (utr) {
return;
}
int start = getStart();
int end = getEnd();
String chr = getChr();
if (readingFrame >= 0) {
int readStart = (codingStart > start) ? codingStart : start + readingFrame;
int readEnd = Math.min(end, codingEnd);
if (readEnd > readStart + 3) {
String genome = IGVModel.getInstance().getViewContext().getGenomeId();
aminoAcidSequence = AminoAcidManager.getAminoAcidSequence(genome, chr, readStart,
readEnd, getStrand());
}
}
}
*/
public String getValueString(double position) {
String msg = number > 0 ? "Exon number: " + number : "";
int aaNumber = this.getAminoAcidNumber((int) position);
if (aaNumber > 0) {
msg += " Amino acid number: " + aaNumber;
}
return msg;
}
public int getNumber() {
return number;
}
public void setNumber(int number) {
this.number = number;
}
}
}
