/*
* 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
* 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.
*/
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.broad.igv.sam;
public class AlignmentBlockImpl implements AlignmentBlock {
private int start;
private byte[] bases;
private int basesLength = -1;
public byte[] qualities;
private boolean softClipped = false;
private int pixelStart;
private int pixelEnd;
private int padding = 0;
public AlignmentBlockImpl(int start, byte[] bases, byte[] qualities) {
this.start = start;
this.bases = bases;
this.basesLength = bases.length;
this.qualities = qualities;
}
@Override
public void setPixelRange(int s, int e) {
this.pixelStart = s;
this.pixelEnd = e;
}
@Override
public boolean containsPixel(int x) {
return x >= this.pixelStart && x <= this.pixelEnd;
}
@Override
public int getPadding() {
return padding;
}
@Override
public boolean contains(int position) {
int offset = position - start;
return offset >= 0 && offset < getLength();
}
@Override
public int getLength() {
return basesLength + padding;
}
@Override
public byte getBase(int offset) {
return bases != null && offset < bases.length ? bases[offset] : 0;
}
/**
* Return AlignmentBlock bases. May be null
*
* @return
*/
@Override
public byte[] getBases() {
return bases;
}
@Override
public int getStart() {
return start;
}
@Override
public byte getQuality(int offset) {
return qualities == null || offset >= qualities.length ? (byte) 126 : qualities[offset];
}
@Override
public byte[] getQualities() {
return qualities;
}
@Override
public int getEnd() {
return start + getLength();
}
@Override
public boolean isSoftClipped() {
return softClipped;
}
public void setSoftClipped(boolean softClipped) {
this.softClipped = softClipped;
}
@Override
public String toString() {
StringBuffer sb = new StringBuffer();
sb.append("[block ");
sb.append(isSoftClipped() ? "softClipped " : " ");
sb.append(getStart());
sb.append("-");
sb.append(getEnd());
sb.append(" ");
for (int i = 0; i < bases.length; i++) {
sb.append((char) bases[i]);
}
sb.append("]");
return sb.toString();
}
/**
* Whether this AlignmentBlock has non-null bases
*
* @return
*/
@Override
public boolean hasBases() {
return this.bases != null;
}
public void setPadding(int padding) {
this.padding = padding;
}
}