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MSFTBX - Mass Spectrometry File Tool Box
/*
* Copyright 2016 Dmitry Avtonomov.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package umich.ms.util.base64;
import umich.ms.fileio.exceptions.FileParsingException;
import java.nio.charset.StandardCharsets;
/**
* Follows implementation from Apache Commons Codec (org.apache.commons.codec.binary.Base64).
* @author Dmitry Avtonomov
*/
public class Base64 {
//////////////////////////////
//
// Fields from BaseNCodec
//
//////////////////////////////
static final int EOF = -1;
public static final int MIME_CHUNK_SIZE = 76;
public static final int PEM_CHUNK_SIZE = 64;
public static final int DEFAULT_BUFFER_RESIZE_FACTOR = 2;
public static final int DEFAULT_BUFFER_SIZE = 8192;
/**
* Mask used to extract 8 bits, used in decoding bytes
*/
protected static final int MASK_8BITS = 0xff;
/**
* Byte used to pad output.
*/
protected static final byte PAD_DEFAULT = '='; // Allow static access to default
protected final byte PAD = PAD_DEFAULT; // instance variable just in case it needs to vary later
/**
* Number of bytes in each full block of unencoded data, e.g. 4 for Base64
* and 5 for Base32
*/
private final int unencodedBlockSize;
/**
* Number of bytes in each full block of encoded data, e.g. 3 for Base64 and
* 8 for Base32
*/
private final int encodedBlockSize;
/**
* Chunksize for encoding. Not used when decoding. A value of zero or less
* implies no chunking of the encoded data. Rounded down to nearest multiple
* of encodedBlockSize.
*/
protected final int lineLength;
/**
* Size of chunk separator. Not used unless {@link #lineLength} > 0.
*/
private final int chunkSeparatorLength;
/**
* BASE32 characters are 6 bits in length. They are formed by taking a block
* of 3 octets to form a 24-bit string, which is converted into 4 BASE64
* characters.
*/
private static final int BITS_PER_ENCODED_BYTE = 6;
private static final int BYTES_PER_UNENCODED_BLOCK = 3;
private static final int BYTES_PER_ENCODED_BLOCK = 4;
/**
* Chunk separator per RFC 2045 section 2.1.
*
*
* N.B. The next major release may break compatibility and make this field
* private.
*
*
* @see RFC 2045 section
* 2.1
*/
static final byte[] CHUNK_SEPARATOR = {'\r', '\n'};
/**
* This array is a lookup table that translates 6-bit positive integer index
* values into their "Base64 Alphabet" equivalents as specified in Table 1
* of RFC 2045.
*
* Thanks to "commons" project in ws.apache.org for this code.
* http://svn.apache.org/repos/asf/webservices/commons/trunk/modules/util/
*/
private static final byte[] STANDARD_ENCODE_TABLE = {
'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M',
'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z',
'a', 'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j', 'k', 'l', 'm',
'n', 'o', 'p', 'q', 'r', 's', 't', 'u', 'v', 'w', 'x', 'y', 'z',
'0', '1', '2', '3', '4', '5', '6', '7', '8', '9', '+', '/'
};
/**
* This is a copy of the STANDARD_ENCODE_TABLE above, but with + and /
* changed to - and _ to make the encoded Base64 results more URL-SAFE. This
* table is only used when the Base64's mode is set to URL-SAFE.
*/
private static final byte[] URL_SAFE_ENCODE_TABLE = {
'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M',
'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z',
'a', 'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j', 'k', 'l', 'm',
'n', 'o', 'p', 'q', 'r', 's', 't', 'u', 'v', 'w', 'x', 'y', 'z',
'0', '1', '2', '3', '4', '5', '6', '7', '8', '9', '-', '_'
};
/**
* This array is a lookup table that translates Unicode characters drawn
* from the "Base64 Alphabet" (as specified in Table 1 of RFC 2045) into
* their 6-bit positive integer equivalents. Characters that are not in the
* Base64 alphabet but fall within the bounds of the array are translated to
* -1.
*
* Note: '+' and '-' both decode to 62. '/' and '_' both decode to 63. This
* means decoder seamlessly handles both URL_SAFE and STANDARD base64. (The
* encoder, on the other hand, needs to know ahead of time what to emit).
*
* Thanks to "commons" project in ws.apache.org for this code.
* http://svn.apache.org/repos/asf/webservices/commons/trunk/modules/util/
*/
private static final byte[] DECODE_TABLE = {
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, 62, -1, 62, -1, 63, 52, 53, 54,
55, 56, 57, 58, 59, 60, 61, -1, -1, -1, -1, -1, -1, -1, 0, 1, 2, 3, 4,
5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
24, 25, -1, -1, -1, -1, 63, -1, 26, 27, 28, 29, 30, 31, 32, 33, 34,
35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51
};
/**
* Base64 uses 6-bit fields.
*/
/**
* Mask used to extract 6 bits, used when encoding
*/
private static final int MASK_6BITS = 0x3f;
// The static final fields above are used for the original static byte[] methods on Base64.
// The private member fields below are used with the new streaming approach, which requires
// some state be preserved between calls of encode() and decode().
/**
* Encode table to use: either STANDARD or URL_SAFE. Note: the DECODE_TABLE
* above remains static because it is able to decode both STANDARD and
* URL_SAFE streams, but the encodeTable must be a member variable so we can
* switch between the two modes.
*/
private final byte[] encodeTable;
// Only one decode table currently; keep for consistency with Base32 code
private final byte[] decodeTable = DECODE_TABLE;
/**
* Line separator for encoding. Not used when decoding. Only used if
* lineLength > 0.
*/
private final byte[] lineSeparator;
/**
* Convenience variable to help us determine when our buffer is going to run
* out of room and needs resizing.
* decodeSize = 3 + lineSeparator.length;
*/
private final int decodeSize;
/**
* Convenience variable to help us determine when our buffer is going to run
* out of room and needs resizing.
* encodeSize = 4 + lineSeparator.length;
*/
private final int encodeSize;
/**
* Creates a Base64 codec used for decoding (all modes) and encoding in
* URL-unsafe mode.
*
* When encoding the line length is 0 (no chunking), and the encoding table
* is STANDARD_ENCODE_TABLE.
*
*
*
* When decoding all variants are supported.
*
*/
public Base64() {
this(0);
}
protected Base64(final int lineLength) {
this(lineLength, CHUNK_SEPARATOR, false);
}
/**
* Creates a Base64 codec used for decoding (all modes) and encoding in
* URL-unsafe mode.
*
* When encoding the line length and line separator are given in the
* constructor, and the encoding table is STANDARD_ENCODE_TABLE.
*
*
* Line lengths that aren't multiples of 4 will still essentially end up
* being multiples of 4 in the encoded data.
*
*
* When decoding all variants are supported.
*
*
* @param lineLength Each line of encoded data will be at most of the given
* length (rounded down to nearest multiple of 4). If lineLength <= 0, then
* the output will not be divided into lines (chunks). Ignored when
* decoding. @param lineSeparator Each line of encoded data will end with
* this sequence of
* bytes.
* @param urlSafe Instead of emitting '+' and '/' we emit '-' and '_'
* respectively. urlSafe is only applied to encode operations. Decoding
* seamlessly handles both modes.
* Note: no padding is added when using the URL-safe alphabet.
* @throws IllegalArgumentException The provided lineSeparator included some
* base64 characters. That's not going to work!
* @since 1.4
*/
public Base64(final int lineLength, final byte[] lineSeparator, final boolean urlSafe) {
this.unencodedBlockSize = BYTES_PER_UNENCODED_BLOCK;
this.encodedBlockSize = BYTES_PER_ENCODED_BLOCK;
this.chunkSeparatorLength = lineSeparator == null ? 0 : lineSeparator.length;
final boolean useChunking = lineLength > 0 && chunkSeparatorLength > 0;
this.lineLength = useChunking ? (lineLength / encodedBlockSize) * encodedBlockSize : 0;
if (lineSeparator != null) {
if (containsAlphabetOrPad(lineSeparator)) {
final String sep = new String(lineSeparator, StandardCharsets.UTF_8);
throw new IllegalArgumentException("lineSeparator must not contain base64 characters: [" + sep + "]");
}
if (lineLength > 0) { // null line-sep forces no chunking rather than throwing IAE
this.encodeSize = BYTES_PER_ENCODED_BLOCK + lineSeparator.length;
this.lineSeparator = new byte[lineSeparator.length];
System.arraycopy(lineSeparator, 0, this.lineSeparator, 0, lineSeparator.length);
} else {
this.encodeSize = BYTES_PER_ENCODED_BLOCK;
this.lineSeparator = null;
}
} else {
this.encodeSize = BYTES_PER_ENCODED_BLOCK;
this.lineSeparator = null;
}
this.decodeSize = this.encodeSize - 1;
this.encodeTable = urlSafe ? URL_SAFE_ENCODE_TABLE : STANDARD_ENCODE_TABLE;
}
/**
* Tests a given byte array to see if it contains only valid characters
* within the alphabet. The method optionally treats whitespace and pad as
* valid.
*
* @param arrayOctet byte array to test
* @param allowWSPad if {@code true}, then whitespace and PAD are also
* allowed
*
* @return {@code true} if all bytes are valid characters in the alphabet or
* if the byte array is empty; {@code false}, otherwise
*/
public boolean isInAlphabet(final byte[] arrayOctet, final boolean allowWSPad) {
for (int i = 0; i < arrayOctet.length; i++) {
if (!isInAlphabet(arrayOctet[i])
&& (!allowWSPad || (arrayOctet[i] != PAD) && !isWhiteSpace(arrayOctet[i]))) {
return false;
}
}
return true;
}
/**
* Returns whether or not the octet is in the Base64 alphabet.
*
* @param octet The value to test
* @return {@code true} if the value is defined in the the Base64 alphabet
* {@code false} otherwise.
*/
protected boolean isInAlphabet(final byte octet) {
return octet >= 0 && octet < decodeTable.length && decodeTable[octet] != -1;
}
/**
* Checks if a byte value is whitespace or not. Whitespace is taken to mean:
* space, tab, CR, LF
*
* @param byteToCheck the byte to check
* @return true if byte is whitespace, false otherwise
*/
protected static boolean isWhiteSpace(final byte byteToCheck) {
switch (byteToCheck) {
case ' ':
case '\n':
case '\r':
case '\t':
return true;
default:
return false;
}
}
/**
* Tests a given String to see if it contains only valid characters within
* the alphabet. The method treats whitespace and PAD as valid.
*
* @param basen String to test
* @return {@code true} if all characters in the String are valid characters
* in the alphabet or if the String is empty; {@code false}, otherwise
* @see #isInAlphabet(byte[], boolean)
*/
public boolean isInAlphabet(final String basen) {
return isInAlphabet(basen.getBytes(StandardCharsets.UTF_8), true);
}
/**
* Tests a given byte array to see if it contains any characters within the
* alphabet or PAD.
*
* Intended for use in checking line-ending arrays
*
* @param arrayOctet byte array to test
* @return {@code true} if any byte is a valid character in the alphabet or
* PAD; {@code false} otherwise
*/
protected boolean containsAlphabetOrPad(final byte[] arrayOctet) {
if (arrayOctet == null) {
return false;
}
for (final byte element : arrayOctet) {
if (PAD == element || isInAlphabet(element)) {
return true;
}
}
return false;
}
/**
* Returns our current encode mode. True if we're URL-SAFE, false otherwise.
*
* @return true if we're in URL-SAFE mode, false otherwise.
* @since 1.4
*/
public boolean isUrlSafe() {
return this.encodeTable == URL_SAFE_ENCODE_TABLE;
}
/**
* Get the default buffer size. Can be overridden.
*
* @return {@link #DEFAULT_BUFFER_SIZE}
*/
protected int getDefaultBufferSize() {
return DEFAULT_BUFFER_SIZE;
}
/**
* WARNING: this method has never been even tried, after conversion from Apache Commons
*
* Encodes all of the provided data, starting at inPos, for inAvail bytes.
* Must be called at least twice: once with the data to encode, and once
* with inAvail set to "-1" to alert encoder that EOF has been reached, to
* flush last remaining bytes (if not multiple of 3).
*
*
* Note: no padding is added when encoding using the URL-safe
* alphabet.
*
* Thanks to "commons" project in ws.apache.org for the bitwise operations,
* and general approach.
* http://svn.apache.org/repos/asf/webservices/commons/trunk/modules/util/
*
*
* @param in byte[] array of binary data to base64 encode.
* @param offset Position to start reading data from.
* @param length Amount of bytes available from input for encoding.
* @param ctx the context to be used
*/
// void encodeImpl(final byte[] in, int offset, final int length, final Base64Context ctx)
// throws FileParsingException {
// try {
// if (ctx.eof) {
// return;
// }
// // inAvail < 0 is how we're informed of EOF in the underlying data we're encoding.
// if (length < 0) {
// ctx.eof = true;
// if (0 == ctx.modulus && lineLength == 0) {
// return; // no leftovers to process and not using chunking
// }
//
// int bytesToEncode = encodeSize;
// byte[] buffer = ctx.ensureBufferHasCapacityLeft(bytesToEncode);
// final int savedPos = ctx.pos;
// switch (ctx.modulus) { // 0-2
// case 0: // nothing to do here
// break;
// case 1: // 8 bits = 6 + 2
// // top 6 bits:
// buffer[ctx.pos++] = encodeTable[(ctx.ibitWorkArea >> 2) & MASK_6BITS];
// // remaining 2:
// buffer[ctx.pos++] = encodeTable[(ctx.ibitWorkArea << 4) & MASK_6BITS];
// // URL-SAFE skips the padding to further reduce size.
// if (encodeTable == STANDARD_ENCODE_TABLE) {
// buffer[ctx.pos++] = PAD;
// buffer[ctx.pos++] = PAD;
// }
// break;
//
// case 2: // 16 bits = 6 + 6 + 4
// buffer[ctx.pos++] = encodeTable[(ctx.ibitWorkArea >> 10) & MASK_6BITS];
// buffer[ctx.pos++] = encodeTable[(ctx.ibitWorkArea >> 4) & MASK_6BITS];
// buffer[ctx.pos++] = encodeTable[(ctx.ibitWorkArea << 2) & MASK_6BITS];
// // URL-SAFE skips the padding to further reduce size.
// if (encodeTable == STANDARD_ENCODE_TABLE) {
// buffer[ctx.pos++] = PAD;
// }
// break;
// default:
// throw new IllegalStateException("Impossible modulus " + ctx.modulus);
// }
// ctx.currentLinePos += ctx.pos - savedPos; // keep track of current line position
// // if currentPos == 0 we are at the start of a line, so don't add CRLF
// if (lineLength > 0 && ctx.currentLinePos > 0) {
// System.arraycopy(lineSeparator, 0, buffer, ctx.pos, lineSeparator.length);
// ctx.pos += lineSeparator.length;
// }
// } else {
// int bytesToEncode = encodeSize * length;
// byte[] buffer = ctx.ensureBufferHasCapacityLeft(bytesToEncode);
// for (int i = 0; i < length; i++) {
// //final byte[] buffer = ensureBufferSize(encodeSize, context);
// ctx.modulus = (ctx.modulus + 1) % BYTES_PER_UNENCODED_BLOCK;
// int b = in[offset++];
// if (b < 0) {
// b += 256;
// }
// ctx.ibitWorkArea = (ctx.ibitWorkArea << 8) + b; // BITS_PER_BYTE
// if (0 == ctx.modulus) { // 3 bytes = 24 bits = 4 * 6 bits to extract
// buffer[ctx.pos++] = encodeTable[(ctx.ibitWorkArea >> 18) & MASK_6BITS];
// buffer[ctx.pos++] = encodeTable[(ctx.ibitWorkArea >> 12) & MASK_6BITS];
// buffer[ctx.pos++] = encodeTable[(ctx.ibitWorkArea >> 6) & MASK_6BITS];
// buffer[ctx.pos++] = encodeTable[ctx.ibitWorkArea & MASK_6BITS];
// ctx.currentLinePos += BYTES_PER_ENCODED_BLOCK;
// if (lineLength > 0 && lineLength <= ctx.currentLinePos) {
// System.arraycopy(lineSeparator, 0, buffer, ctx.pos, lineSeparator.length);
// ctx.pos += lineSeparator.length;
// ctx.currentLinePos = 0;
// }
// }
// }
// }
// } finally {
// ctx.syncBufferPos();
// }
// }
/**
* Decodes a byte[] containing characters in the Base-N alphabet.
*
* @param pArray A byte array containing Base-N character data
* @param ctx
* @return a byte array containing binary data
* @throws umich.ms.fileio.exceptions.FileParsingException
*/
public Base64Context decode(final byte[] pArray, Base64Context ctx)
throws FileParsingException {
return decode(pArray, 0, pArray.length, ctx);
}
/**
* Decodes a byte[] containing characters in the Base-N alphabet.
*
* @param pArray A byte array containing Base-N character data
* @param offset
* @param length
* @param ctx
* @return a byte array containing binary data
* @throws umich.ms.fileio.exceptions.FileParsingException
*/
public Base64Context decode(final byte[] pArray, int offset, int length, Base64Context ctx)
throws FileParsingException {
if (pArray == null || pArray.length == 0) {
return null;
}
decodeImpl(pArray, offset, length, ctx);
decodeImpl(pArray, 0, EOF, ctx); // Notify decoder of EOF.
return ctx;
}
/**
*
* Decodes all of the provided data, starting at inPos, for inAvail bytes.
* Should be called at least twice: once with the data to decode, and once
* with inAvail set to "-1" to alert decoder that EOF has been reached. The
* "-1" call is not necessary when decoding, but it doesn't hurt, either.
*
*
* Ignores all non-base64 characters. This is how chunked (e.g. 76
* character) data is handled, since CR and LF are silently ignored, but has
* implications for other bytes, too. This method subscribes to the
* garbage-in, garbage-out philosophy: it will not check the provided data
* for validity.
*
*
* Thanks to "commons" project in ws.apache.org for the bitwise operations,
* and general approach.
* http://svn.apache.org/repos/asf/webservices/commons/trunk/modules/util/
*
*
* @param bytes byte[] array of ascii data to base64 decode.
* @param offset Position to start reading data from.
* @param length Amount of bytes available from input for dencoding.
* @param ctx the context to be used
*/
void decodeImpl(byte[] bytes, int offset, int length, Base64Context ctx)
throws FileParsingException {
try {
if (ctx.eof) {
return;
}
byte[] buffer = null;
if (length < 0) {
ctx.eof = true;
} else {
// in general the resulting decoded array should be 3/4 the
// length of the input. We just leave it at 'length' to be on the safe side.
buffer = ctx.ensureBufferHasCapacityLeft(length);
}
int readPos = offset;
byte b;
for (int i = 0; i < length; i++) {
// I don't know why in Apache impl this has been checked on every iteration
//final byte[] buffer = ensureBufferSize(decodeSize, context);
b = bytes[readPos++];
if (b == PAD) {
// We're done.
ctx.eof = true;
break;
} else {
try {
if (b >= 0 && b < DECODE_TABLE.length) {
final int result = DECODE_TABLE[b];
if (result >= 0) {
ctx.modulus = (ctx.modulus + 1) % BYTES_PER_ENCODED_BLOCK;
ctx.ibitWorkArea = (ctx.ibitWorkArea << BITS_PER_ENCODED_BYTE) + result;
if (ctx.modulus == 0) {
buffer[ctx.pos] = (byte) ((ctx.ibitWorkArea >> 16) & MASK_8BITS);
ctx.pos++;
buffer[ctx.pos] = (byte) ((ctx.ibitWorkArea >> 8) & MASK_8BITS);
ctx.pos++;
buffer[ctx.pos] = (byte) (ctx.ibitWorkArea & MASK_8BITS);
ctx.pos++;
}
}
}
} catch (ArrayIndexOutOfBoundsException e) {
throw new FileParsingException("Something went wrong in Base64 decoder, got out of array bounds", e);
}
}
}
// Two forms of EOF as far as base64 decoder is concerned: actual
// EOF (-1) and first time '=' character is encountered in stream.
// This approach makes the '=' padding characters completely optional.
if (ctx.eof && ctx.modulus != 0) {
buffer = ctx.ensureBufferHasCapacityLeft(decodeSize);
// We have some spare bits remaining
// Output all whole multiples of 8 bits and ignore the rest
switch (ctx.modulus) {
//case 0 : // impossible, as excluded above
case 1: // 6 bits - ignore entirely
// TODO not currently tested; perhaps it is impossible?
break;
case 2: // 12 bits = 8 + 4
ctx.ibitWorkArea = ctx.ibitWorkArea >> 4; // dump the extra 4 bits
buffer[ctx.pos++] = (byte) ((ctx.ibitWorkArea) & MASK_8BITS);
break;
case 3: // 18 bits = 8 + 8 + 2
ctx.ibitWorkArea = ctx.ibitWorkArea >> 2; // dump 2 bits
buffer[ctx.pos++] = (byte) ((ctx.ibitWorkArea >> 8) & MASK_8BITS);
buffer[ctx.pos++] = (byte) ((ctx.ibitWorkArea) & MASK_8BITS);
break;
default:
throw new IllegalStateException("Impossible modulus " + ctx.modulus);
}
}
} finally {
ctx.syncBufferPos();
}
}
/**
* Decodes a char[] containing characters in the Base-N alphabet.
*
* @param pArray A byte array containing Base-N character data
* @param ctx
* @return a byte array containing binary data
* @throws umich.ms.fileio.exceptions.FileParsingException
*/
public Base64Context decode(final char[] pArray, Base64Context ctx)
throws FileParsingException {
return decode(pArray, 0, pArray.length, ctx);
}
/**
* Decodes a char[] containing characters in the Base-N alphabet.
*
* @param pArray A byte array containing Base-N character data
* @param offset offset in the input array where the data starts
* @param length length of the data, starting at offset in the input array
* @param ctx {@link Base64Context} or {@link Base64ContextPooled}, pooled
* version is preferred
* @return a byte array containing binary data
* @throws umich.ms.fileio.exceptions.FileParsingException
*/
public Base64Context decode(final char[] pArray, final int offset, final int length, Base64Context ctx)
throws FileParsingException {
if (pArray == null || pArray.length == 0) {
return null;
}
decodeImpl(pArray, offset, length, ctx);
decodeImpl(pArray, 0, EOF, ctx); // Notify decoder of EOF.
return ctx;
}
/**
*
* Decodes all of the provided data, starting at inPos, for inAvail bytes.
* Should be called at least twice: once with the data to decode, and once
* with inAvail set to "-1" to alert decoder that EOF has been reached. The
* "-1" call is not necessary when decoding, but it doesn't hurt, either.
*
*
* Ignores all non-base64 characters. This is how chunked (e.g. 76
* character) data is handled, since CR and LF are silently ignored, but has
* implications for other bytes, too. This method subscribes to the
* garbage-in, garbage-out philosophy: it will not check the provided data
* for validity.
*
*
* Thanks to "commons" project in ws.apache.org for the bitwise operations,
* and general approach.
* http://svn.apache.org/repos/asf/webservices/commons/trunk/modules/util/
*
*
* @param chars char[] array of ascii data to base64 decode.
* @param offset offset in the input array where the data starts
* @param length length of the data, starting at offset in the input array
* @param ctx the context to be used
*/
void decodeImpl(final char[] chars, final int offset, final int length, Base64Context ctx)
throws FileParsingException {
try {
if (ctx.eof) {
return;
}
byte[] buffer = null;
if (length < 0) {
ctx.eof = true;
} else {
// in general the resulting decoded array should be 3/4 the
// length of the input. We double that amount, as consequent scans
// might have longer base64 strings
buffer = ctx.ensureBufferHasCapacityLeft(length * 2);
}
int readPos = offset;
byte b;
for (int i = 0; i < length; i++) {
// I don't know why in Apache impl this has been checked on every iteration
//final byte[] buffer = ensureBufferSize(decodeSize, context);
b = (byte) chars[readPos++];
if (b == PAD) {
// We're done.
ctx.eof = true;
break;
} else {
try {
if (b >= 0 && b < DECODE_TABLE.length) {
final int result = DECODE_TABLE[b];
if (result >= 0) {
ctx.modulus = (ctx.modulus + 1) % BYTES_PER_ENCODED_BLOCK;
ctx.ibitWorkArea = (ctx.ibitWorkArea << BITS_PER_ENCODED_BYTE) + result;
if (ctx.modulus == 0) {
buffer[ctx.pos] = (byte) ((ctx.ibitWorkArea >> 16) & MASK_8BITS);
ctx.pos++;
buffer[ctx.pos] = (byte) ((ctx.ibitWorkArea >> 8) & MASK_8BITS);
ctx.pos++;
buffer[ctx.pos] = (byte) (ctx.ibitWorkArea & MASK_8BITS);
ctx.pos++;
}
}
}
} catch (ArrayIndexOutOfBoundsException e) {
throw new FileParsingException("Something went wrong in Base64 decoder, got out of array bounds", e);
}
}
}
// Two forms of EOF as far as base64 decoder is concerned: actual
// EOF (-1) and first time '=' character is encountered in stream.
// This approach makes the '=' padding characters completely optional.
if (ctx.eof && ctx.modulus != 0) {
buffer = ctx.ensureBufferHasCapacityLeft(decodeSize);
// We have some spare bits remaining
// Output all whole multiples of 8 bits and ignore the rest
switch (ctx.modulus) {
//case 0 : // impossible, as excluded above
case 1: // 6 bits - ignore entirely
// TODO not currently tested; perhaps it is impossible?
break;
case 2: // 12 bits = 8 + 4
ctx.ibitWorkArea = ctx.ibitWorkArea >> 4; // dump the extra 4 bits
buffer[ctx.pos++] = (byte) ((ctx.ibitWorkArea) & MASK_8BITS);
break;
case 3: // 18 bits = 8 + 8 + 2
ctx.ibitWorkArea = ctx.ibitWorkArea >> 2; // dump 2 bits
buffer[ctx.pos++] = (byte) ((ctx.ibitWorkArea >> 8) & MASK_8BITS);
buffer[ctx.pos++] = (byte) ((ctx.ibitWorkArea) & MASK_8BITS);
break;
default:
throw new IllegalStateException("Impossible modulus " + ctx.modulus);
}
}
} finally {
ctx.syncBufferPos();
}
}
}
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