Java Char Convert To charToCompressedBaseLow(final int base)

Description

Convert from ASCII byte to BAM nybble representation of a base in low-order nybble.

License

Open Source License

Parameter

Parameter	Description
base	One of =AaCcGgTtNn.

Return

Low-order nybble-encoded equivalent.

Declaration

private static byte charToCompressedBaseLow(final int base) 

Method Source Code

//package com.java2s;
/*/*ww  w .  j a  v a2s  .  c  o m*/
 * The MIT License
 *
 * Copyright (c) 2009 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.
 */

public class Main {
    private static final byte COMPRESSED_EQUAL_LOW = 0;
    private static final byte COMPRESSED_A_LOW = 1;
    private static final byte COMPRESSED_C_LOW = 2;
    private static final byte COMPRESSED_M_LOW = 3;
    private static final byte COMPRESSED_G_LOW = 4;
    private static final byte COMPRESSED_R_LOW = 5;
    private static final byte COMPRESSED_S_LOW = 6;
    private static final byte COMPRESSED_V_LOW = 7;
    private static final byte COMPRESSED_T_LOW = 8;
    private static final byte COMPRESSED_W_LOW = 9;
    private static final byte COMPRESSED_Y_LOW = 10;
    private static final byte COMPRESSED_H_LOW = 11;
    private static final byte COMPRESSED_K_LOW = 12;
    private static final byte COMPRESSED_D_LOW = 13;
    private static final byte COMPRESSED_B_LOW = 14;
    private static final byte COMPRESSED_N_LOW = 15;

    /**
     * Convert from ASCII byte to BAM nybble representation of a base in low-order nybble.
     * @param base One of =AaCcGgTtNn.
     * @return Low-order nybble-encoded equivalent.
     */
    private static byte charToCompressedBaseLow(final int base) {
        switch (base) {
        case '=':
            return COMPRESSED_EQUAL_LOW;
        case 'a':
        case 'A':
            return COMPRESSED_A_LOW;
        case 'c':
        case 'C':
            return COMPRESSED_C_LOW;
        case 'g':
        case 'G':
            return COMPRESSED_G_LOW;
        case 't':
        case 'T':
            return COMPRESSED_T_LOW;
        case 'n':
        case 'N':
        case '.':
            return COMPRESSED_N_LOW;

        // IUPAC ambiguity codes
        case 'M':
        case 'm':
            return COMPRESSED_M_LOW;
        case 'R':
        case 'r':
            return COMPRESSED_R_LOW;
        case 'S':
        case 's':
            return COMPRESSED_S_LOW;
        case 'V':
        case 'v':
            return COMPRESSED_V_LOW;
        case 'W':
        case 'w':
            return COMPRESSED_W_LOW;
        case 'Y':
        case 'y':
            return COMPRESSED_Y_LOW;
        case 'H':
        case 'h':
            return COMPRESSED_H_LOW;
        case 'K':
        case 'k':
            return COMPRESSED_K_LOW;
        case 'D':
        case 'd':
            return COMPRESSED_D_LOW;
        case 'B':
        case 'b':
            return COMPRESSED_B_LOW;
        default:
            throw new IllegalArgumentException("Bad  byte passed to charToCompressedBase: " + base);
        }
    }
}

Related

1. charToBasicType(char c, Class clazz)
2. charToBoolean(char c)
3. charToBuffer(char ch, byte[] ioBuffer)
4. charToCDATA(char ch)
5. charToCompressedBaseLow(final int base)
6. charToCp1252(char c)
7. charToDecimal(char c)
8. charToDigit(char c)
9. charToEscape(char ch)