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The Bouncy Castle Java APIs for CMS, PKCS, EAC, TSP, CMP, CRMF, OCSP, and certificate generation. This jar contains APIs for JDK 1.5 to JDK 1.8. The APIs can be used in conjunction with a JCE/JCA provider such as the one provided with the Bouncy Castle Cryptography APIs.

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package org.bouncycastle.mime.encoding;

import java.io.EOFException;
import java.io.IOException;
import java.io.InputStream;

/**
 * Reader for Base64 armored objects which converts them into binary data.
 */
public class Base64InputStream
    extends InputStream
{
    /*
     * set up the decoding table.
     */
    private static final byte[] decodingTable;

    static
    {
        decodingTable = new byte[128];

        for (int i = 'A'; i <= 'Z'; i++)
        {
            decodingTable[i] = (byte)(i - 'A');
        }

        for (int i = 'a'; i <= 'z'; i++)
        {
            decodingTable[i] = (byte)(i - 'a' + 26);
        }

        for (int i = '0'; i <= '9'; i++)
        {
            decodingTable[i] = (byte)(i - '0' + 52);
        }

        decodingTable['+'] = 62;
        decodingTable['/'] = 63;
    }

    /**
     * decode the base 64 encoded input data.
     *
     * @return the offset the data starts in out.
     */
    private int decode(
        int      in0,
        int      in1,
        int      in2,
        int      in3,
        int[]    out)
        throws EOFException
    {
        int    b1, b2, b3, b4;

        if (in3 < 0)
        {
            throw new EOFException("unexpected end of file in armored stream.");
        }

        if (in2 == '=')
        {
            b1 = decodingTable[in0] &0xff;
            b2 = decodingTable[in1] & 0xff;

            out[2] = ((b1 << 2) | (b2 >> 4)) & 0xff;

            return 2;
        }
        else if (in3 == '=')
        {
            b1 = decodingTable[in0];
            b2 = decodingTable[in1];
            b3 = decodingTable[in2];

            out[1] = ((b1 << 2) | (b2 >> 4)) & 0xff;
            out[2] = ((b2 << 4) | (b3 >> 2)) & 0xff;

            return 1;
        }
        else
        {
            b1 = decodingTable[in0];
            b2 = decodingTable[in1];
            b3 = decodingTable[in2];
            b4 = decodingTable[in3];

            out[0] = ((b1 << 2) | (b2 >> 4)) & 0xff;
            out[1] = ((b2 << 4) | (b3 >> 2)) & 0xff;
            out[2] = ((b3 << 6) | b4) & 0xff;

            return 0;
        }
    }

    InputStream    in;
    int[]          outBuf = new int[3];
    int            bufPtr = 3;
//    boolean        isEndOfStream;

    public Base64InputStream(
        InputStream    in)
    {
        this.in = in;
    }

    public int available()
        throws IOException
    {
        // We can't guarantee 'in.available()' bytes aren't all spaces
        return 0;
    }

    public int read()
        throws IOException
    {
        if (bufPtr > 2)
        {
            int in0 = readIgnoreSpaceFirst();
            if (in0 < 0)
            {
//                isEndOfStream = true;
                return -1;
            }

            int in1 = readIgnoreSpace();
            int in2 = readIgnoreSpace();
            int in3 = readIgnoreSpace();

            bufPtr = decode(in0, in1, in2, in3, outBuf);
        }

        return outBuf[bufPtr++];
    }

    public void close()
        throws IOException
    {
        in.close();
    }

    private int readIgnoreSpace()
        throws IOException
    {
        for (;;)
        {
            int c;
            switch (c = in.read())
            {
            case ' ':
            case '\t':
                break;
            default:
                return c;
            }
        }
    }

    private int readIgnoreSpaceFirst()
        throws IOException
    {
        for (;;)
        {
            int c;
            switch (c = in.read())
            {
            case ' ':
            case '\n':
            case '\r':
            case '\t':
                break;
            default:
                return c;
            }
        }
    }
}