/*
* 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.
*/
package org.broad.igv.util;
/**
* User: jrobinso
* Date: Feb 21, 2010
*/
public class SOLIDUtils {
/**
* Return the sequence in Color Space (SOLID alignment encoding)
*/
public static byte[] convertToColorSpace(byte[] baseSequence) {
// We need to know the base just to the left of the start
if (baseSequence == null || baseSequence.length == 0) {
return baseSequence;
}
byte[] csSequence = new byte[baseSequence.length];
// Can't know the first base
csSequence[0] = baseSequence[0]; //
int c1 = baseToCS(baseSequence[0]);
for (int i = 1; i < baseSequence.length; i++) {
int c2 = baseToCS(baseSequence[i]);
if (c2 == 4 && c1 != 4) {
csSequence[i] = 4;
} else if (c1 == 4 && c2 != 4) {
csSequence[i] = 5;
} else if (c1 == 4 && c2 == 4) {
csSequence[i] = 6;
} else {
csSequence[i] = (byte) (c1 ^ c2);
}
c1 = c2;
}
return csSequence;
}
public static int baseToCS(byte base) {
switch (base) {
case 'A':
case 'a':
return 0;
case 'C':
case 'c':
return 1;
case 'G':
case 'g':
return 2;
case 'T':
case 't':
return 3;
case 'N':
case 'n':
return 4;
}
return -1;
}
}