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jannovar-core is a library for the functional annotation of genomic variants
package de.charite.compbio.jannovar.reference;
import java.io.Serializable;
import com.google.common.collect.ComparisonChain;
import de.charite.compbio.jannovar.Immutable;
import de.charite.compbio.jannovar.data.ReferenceDictionary;
import de.charite.compbio.jannovar.impl.util.StringUtil;
/**
* Representation of a genomic interval (chromsome, begin, end).
*
* Internally, positions are always stored zero-based, but the position type can be explicitely given to the constructor
* of {@link GenomeInterval}.
*
* @author Manuel Holtgrewe
*/
@Immutable
public final class GenomeInterval implements Serializable, Comparable {
private static final long serialVersionUID = 2L;
/** reference dictionary to use for coordinate translation */
final ReferenceDictionary refDict;
/** the strand that the position is located on */
private final Strand strand;
/** the chromosome number, as index in chromosome dictionary */
private final int chr;
/** the begin position on the chromosome */
private final int beginPos;
/** the end position on the chromosome */
private final int endPos;
/** construct genome interval with zero-based coordinate system */
public GenomeInterval(ReferenceDictionary refDict, Strand strand, int chr, int beginPos, int endPos) {
this.refDict = refDict;
this.strand = strand;
this.chr = chr;
this.beginPos = beginPos;
this.endPos = endPos;
}
/** construct genome interval with selected coordinate system */
public GenomeInterval(ReferenceDictionary refDict, Strand strand, int chr, int beginPos, int endPos,
PositionType positionType) {
this.refDict = refDict;
this.strand = strand;
this.chr = chr;
if (positionType == PositionType.ONE_BASED)
this.beginPos = beginPos - 1;
else
this.beginPos = beginPos;
this.endPos = endPos;
}
/** construct genome interval from other with selected coordinate system */
public GenomeInterval(GenomeInterval other) {
this.refDict = other.refDict;
this.strand = other.strand;
this.chr = other.chr;
this.beginPos = other.beginPos;
this.endPos = other.endPos;
}
/** construct genome interval from other with selected strand */
public GenomeInterval(GenomeInterval other, Strand strand) {
this.refDict = other.refDict;
this.strand = strand;
this.chr = other.chr;
// transform coordinate system
if (strand == other.strand) {
this.beginPos = other.beginPos;
this.endPos = other.endPos;
} else {
int beginPos = refDict.getContigIDToLength().get(other.chr) - other.beginPos;
int endPos = refDict.getContigIDToLength().get(other.chr) - other.endPos;
this.endPos = beginPos;
this.beginPos = endPos;
}
}
/** construct genome interval from {@link GenomePosition} with a length towards 3' of pos' coordinate system */
public GenomeInterval(GenomePosition pos, int length) {
this.refDict = pos.getRefDict();
this.strand = pos.getStrand();
this.chr = pos.getChr();
this.beginPos = pos.getPos();
this.endPos = pos.getPos() + length;
}
/** @return {@link ReferenceDictionary} to use */
public ReferenceDictionary getRefDict() {
return refDict;
}
/** @return {@link Strand} of this {@link GenomeInterval} */
public Strand getStrand() {
return strand;
}
/** @return numeric chromosome id */
public int getChr() {
return chr;
}
/** @return 0-based begin position */
public int getBeginPos() {
return beginPos;
}
/** @return 0-based end position */
public int getEndPos() {
return endPos;
}
/** convert into GenomeInterval of the given strand */
public GenomeInterval withStrand(Strand strand) {
return new GenomeInterval(this, strand);
}
/** return the genome begin position */
public GenomePosition getGenomeBeginPos() {
return new GenomePosition(refDict, strand, chr, beginPos, PositionType.ZERO_BASED);
}
/** return the genome end position */
public GenomePosition getGenomeEndPos() {
return new GenomePosition(refDict, strand, chr, endPos, PositionType.ZERO_BASED);
}
/** returns length of the interval */
public int length() {
return this.endPos - this.beginPos;
}
/**
* @return GenomeInterval with intersection of this and other
*/
public GenomeInterval intersection(GenomeInterval other) {
if (chr != other.chr)
return new GenomeInterval(refDict, strand, chr, beginPos, beginPos, PositionType.ZERO_BASED);
other = other.withStrand(strand);
int beginPos = Math.max(this.beginPos, other.beginPos);
int endPos = Math.min(this.endPos, other.endPos);
if (endPos < beginPos)
beginPos = endPos;
return new GenomeInterval(refDict, strand, chr, beginPos, endPos, PositionType.ZERO_BASED);
}
// TODO(holtgrewe): Test me!
/**
* @return GenomeInterval with union of this and other and everything in between,
* this if on different chromosomes. Result will be on the same strand as this.
*/
public GenomeInterval union(GenomeInterval other) {
if (chr != other.chr)
return new GenomeInterval(refDict, strand, chr, beginPos, beginPos, PositionType.ZERO_BASED);
other = other.withStrand(strand);
int beginPos = Math.min(this.beginPos, other.beginPos);
int endPos = Math.max(this.endPos, other.endPos);
if (endPos < beginPos)
beginPos = endPos;
return new GenomeInterval(refDict, strand, chr, beginPos, endPos, PositionType.ZERO_BASED);
}
/**
* @param pos
* query position
* @return true if the interval is truly left of the base that base pos points to
*/
public boolean isLeftOf(GenomePosition pos) {
if (chr != pos.getChr())
return false; // wrong chromosome
if (pos.getStrand() != strand)
pos = pos.withStrand(strand); // ensure that we are on the correct strand
return (pos.getPos() >= endPos);
}
/**
* @param pos
* query position
* @return true if the interval is truly right of the base that base pos points to
*/
public boolean isRightOf(GenomePosition pos) {
if (chr != pos.getChr())
return false; // wrong chromosome
if (pos.getStrand() != strand)
pos = pos.withStrand(strand); // ensure that we are on the correct strand
return (pos.getPos() < beginPos);
}
/**
* @param pos
* query position
* @return true if the interval is truly left of the gap between bases that pos points at
*/
public boolean isLeftOfGap(GenomePosition pos) {
if (chr != pos.getChr())
return false; // wrong chromosome
if (pos.getStrand() != strand)
pos = pos.withStrand(strand); // ensure that we are on the correct strand
return (pos.getPos() >= endPos);
}
/**
* @param pos
* query position
* @return true if the interval is truly right of the gap between bases that pos points at
*/
public boolean isRightOfGap(GenomePosition pos) {
if (chr != pos.getChr())
return false; // wrong chromosome
if (pos.getStrand() != strand)
pos = pos.withStrand(strand); // ensure that we are on the correct strand
return (pos.getPos() <= beginPos);
}
/**
* @param pos
* query position
* @return true if the interval contains pos
*/
public boolean contains(GenomePosition pos) {
if (chr != pos.getChr())
return false; // wrong chromosome
if (pos.getStrand() != strand)
pos = pos.withStrand(strand); // ensure that we are on the correct strand
return (pos.getPos() >= beginPos && pos.getPos() < endPos);
}
/**
* @param other
* other {@link GenomeInterval} to use for querying
* @return true if the interval contains other
*/
public boolean contains(GenomeInterval other) {
// TODO(holtgrem): Test this.
if (chr != other.chr)
return false; // wrong chromosome
if (other.strand != strand)
other = other.withStrand(strand); // ensure that we are on the correct strand
return (other.beginPos >= beginPos && other.endPos <= endPos);
}
/**
* @return a {@link GenomeInterval} that has padding more bases towards each side as padding
*/
public GenomeInterval withMorePadding(int padding) {
return withMorePadding(padding, padding);
}
/**
* @return a {@link GenomeInterval} that has padding more bases towards either side as padding.
*/
public GenomeInterval withMorePadding(int paddingUpstream, int paddingDownstream) {
// TODO(holtgrem): throw when going outside of chromosome?
return new GenomeInterval(refDict, strand, chr, beginPos - paddingUpstream, endPos + paddingDownstream,
PositionType.ZERO_BASED);
}
/**
* @param other
* other {@link GenomeInterval} to check with overlap for
* @return whether other overlaps with this
*/
public boolean overlapsWith(GenomeInterval other) {
// TODO(holtgrem): add test for this
if (chr != other.chr)
return false;
other = other.withStrand(strand);
return (other.beginPos < endPos && beginPos < other.endPos);
}
/*
* (non-Javadoc)
*
* @see java.lang.Object#toString()
*/
@Override
public String toString() {
if (strand.isReverse())
return withStrand(Strand.FWD).toString();
return StringUtil.concatenate(refDict.getContigIDToName().get(chr), ":g.", beginPos + 1, "_", endPos);
}
/*
* (non-Javadoc)
*
* @see java.lang.Object#hashCode()
*/
@Override
public int hashCode() {
if (strand.isReverse())
return withStrand(Strand.FWD).hashCode();
final int prime = 31;
int result = 1;
result = prime * result + beginPos;
result = prime * result + chr;
result = prime * result + endPos;
result = prime * result + strand.hashCode();
return result;
}
/*
* (non-Javadoc)
*
* @see java.lang.Object#equals(java.lang.Object)
*/
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
GenomeInterval other = (GenomeInterval) obj;
other = other.withStrand(strand);
if (beginPos != other.beginPos)
return false;
if (chr != other.chr)
return false;
if (endPos != other.endPos)
return false;
if (strand != other.strand)
return false;
return true;
}
@Override
public int compareTo(GenomeInterval other) {
other = other.withStrand(strand);
return ComparisonChain.start().compare(getChr(), other.getChr()).compare(getBeginPos(), other.getBeginPos())
.compare(getEndPos(), other.getEndPos()).result();
}
}
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