/*
* The MIT License
*
* Copyright (c) 2011 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 picard.illumina.parser;
import picard.PicardException;
/**
* Store the information from Illumina files for a single cluster with one or more reads.
*
* @author jburke@broadinstitute.org
*/
public class ClusterData {
private int lane = -1;
private int tile = -1;
private int x = -1;
private int y = -1;
private final ReadData [] reads;
private Boolean pf;
private String matchedBarcode;
/** Used for testing, reads is set directly with no copying to the input array */
public ClusterData(final ReadData ... reads) {
this.reads = reads;
}
/** Creates a ClusterData with one read for each type provided */
public ClusterData(final ReadType [] readTypes) {
reads = new ReadData[readTypes.length];
for(int i = 0; i < readTypes.length; i++) {
reads[i] = new ReadData(readTypes[i]);
}
}
public String toString() {
return "ClusterData(lane: " + lane + "; tile: " + tile + "; x: " + x + "; y: " + y + "; pf: " + pf +
"; matchedBarcode: " + matchedBarcode + ")";
}
public int getTile() {
return tile;
}
public void setTile(final int tile) {
this.tile = tile;
}
public boolean tileIsSet() {
return tile != -1;
}
public ReadData getRead(final int index) {
return reads[index];
}
public int getNumReads() {
return reads.length;
}
/**
* Either set this value if not already set, or if already set, throw an exception if new value != current value.
*/
public void setOrCheckTile(final int tile) {
if (tileIsSet()) {
if (this.tile != tile) {
throw new PicardException("Tile number mismatch for " + this + " : " + this.tile + " != " + tile);
}
} else {
this.tile = tile;
}
}
public int getLane() {
return lane;
}
public void setLane(final int lane) {
this.lane = lane;
}
public boolean laneIsSet() {
return lane != -1;
}
/**
* Either set this value if not already set, or if already set, throw an exception if new value != current value.
*/
public void setOrCheckLane(final int lane) {
if (laneIsSet()) {
if (this.lane != lane) {
throw new PicardException("Lane number mismatch for " + this + " : " + this.lane + " != " + lane);
}
} else {
this.lane = lane;
}
}
public int getX() {
return x;
}
public void setX(final int x) {
this.x = x;
}
public boolean xIsSet() {
return x != -1;
}
/**
* Either set this value if not already set, or if already set, throw an exception if new value != current value.
*/
public void setOrCheckX(final int x) {
if (xIsSet()) {
if (this.x != x) {
throw new PicardException("X value mismatch for " + this + " : " + this.x + " != " + x);
}
} else {
this.x = x;
}
}
public int getY() {
return y;
}
public void setY(final int y) {
this.y = y;
}
public boolean yIsSet() {
return y != -1;
}
/**
* Either set this value if not already set, or if already set, throw an exception if new value != current value.
*/
public void setOrCheckY(final int y) {
if (yIsSet()) {
if (this.y != y) {
throw new PicardException("Y value mismatch for " + this + " : " + this.y + " != " + y);
}
} else {
this.y = y;
}
}
public Boolean isPf() {
return pf;
}
public void setPf(final boolean pf) {
this.pf = pf;
}
/**
* Either set this value if not already set, or if already set, throw an exception if new value != current value.
*/
public void setOrCheckPf(final boolean pf) {
if (this.pf == null) {
this.pf = pf;
} else if (this.pf != pf) {
throw new PicardException("PF value mismatch for " + this + " : ");
}
}
/**
* @return The barcode matched (not the actual sequence from the read, which may not perfectly match
* the barcode).
*/
public String getMatchedBarcode() {
return matchedBarcode;
}
public void setMatchedBarcode(final String matchedBarcode) {
this.matchedBarcode = matchedBarcode;
}
}