118 lines
3.6 KiB
Java
118 lines
3.6 KiB
Java
/*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2009 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*/
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package edu.mit.broad.picard.illumina;
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import edu.mit.broad.sam.util.CoordMath;
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class SimpleMapping implements Comparable<SimpleMapping> {
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String arachneIndex;
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long startPos;
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long endPos;
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String sequenceName;
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public SimpleMapping(final String arachneIndex, final long startPos, final long endPos, final String sequenceName) {
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this.arachneIndex = arachneIndex;
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this.startPos = startPos;
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this.endPos = endPos;
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this.sequenceName = sequenceName;
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if (this.endPos < this.startPos) throw new IllegalArgumentException("startPos must be less than endPos!");
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}
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public String getArachneIndex() {
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return arachneIndex;
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}
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public void setArachneIndex(final String arachneIndex) {
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this.arachneIndex = arachneIndex;
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}
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public long getStartPos() {
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return startPos;
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}
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public void setStartPos(final long startPos) {
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this.startPos = startPos;
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}
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public long getEndPos() {
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return endPos;
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}
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public void setEndPos(final long endPos) {
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this.endPos = endPos;
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}
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public String getSequenceName() {
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return sequenceName;
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}
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public void setSequenceName(final String sequenceName) {
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this.sequenceName = sequenceName;
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}
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public SimpleMapping intersection(final SimpleMapping other) {
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if (this.intersects(other)) {
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return new SimpleMapping(this.getArachneIndex(),
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(this.getStartPos() >= other.getStartPos())?this.getStartPos():other.getStartPos(),
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(this.getEndPos() <= other.getEndPos())?this.getEndPos():other.getEndPos(), this.getSequenceName());
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}
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return null;
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}
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public boolean intersects(final SimpleMapping other) {
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return (this.getArachneIndex().equals(other.getArachneIndex()) &&
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CoordMath.overlaps(this.getStartPos(), this.getEndPos(), other.getStartPos(), other.getEndPos()));
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}
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public long length() {
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return CoordMath.getLength(startPos, endPos);
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}
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/**
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* Sort based on sequence.compareTo, then start pos, then end pos
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* with null objects coming lexically last
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*/
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public int compareTo(final SimpleMapping that) {
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if (that == null) return -1; // nulls last
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int result = this.getArachneIndex().compareTo(that.getArachneIndex());
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if (result == 0) {
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if (this.getStartPos() == that.getStartPos()) {
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result = ((int) (this.getEndPos() - that.getEndPos()));
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} else {
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result = ((int) (this.getStartPos() - that.getStartPos()));
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}
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}
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// normalize to -1, 0, 1
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if (result > 1) result = 1;
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else if (result < -1) result = -1;
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return result;
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}
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public boolean equals(final SimpleMapping that) {
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return (this.compareTo(that) == 0);
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}
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public int hashCode() {
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int result;
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result = arachneIndex.hashCode();
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result = 31 * result + (int) (startPos ^ (startPos >>> 32));
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result = 31 * result + (int) (endPos ^ (endPos >>> 32));
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return result;
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}
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public String toString() {
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return getArachneIndex() + ":" + getStartPos() + "-" + getEndPos();
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}
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}
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