Many resources are needed to download a project. Please understand that we have to compensate our server costs. Thank you in advance. Project price only 1 $
You can buy this project and download/modify it how often you want.
/*
* Copyright (c) 2012 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.
*/
package htsjdk.variant.variantcontext.writer;
import htsjdk.variant.bcf2.BCF2Type;
import htsjdk.variant.bcf2.BCF2Utils;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
/**
* See #BCFWriter for documentation on this classes role in encoding BCF2 files
*
* @author Mark DePristo
* @since 06/12
*/
public final class BCF2Encoder {
// TODO -- increase default size?
public static final int WRITE_BUFFER_INITIAL_SIZE = 16384;
private ByteArrayOutputStream encodeStream = new ByteArrayOutputStream(WRITE_BUFFER_INITIAL_SIZE);
// --------------------------------------------------------------------------------
//
// Functions to return the data being encoded here
//
// --------------------------------------------------------------------------------
public byte[] getRecordBytes() {
byte[] bytes = encodeStream.toByteArray();
encodeStream.reset();
return bytes;
}
// --------------------------------------------------------------------------------
//
// Writing typed values (have type byte)
//
// --------------------------------------------------------------------------------
public final void encodeTypedMissing(final BCF2Type type) throws IOException {
encodeType(0, type);
}
public final void encodeTyped(final Object value, final BCF2Type type) throws IOException {
if ( value == null )
encodeTypedMissing(type);
else {
switch ( type ) {
case INT8:
case INT16:
case INT32: encodeTypedInt((Integer)value, type); break;
case FLOAT: encodeTypedFloat((Double) value); break;
case CHAR: encodeTypedString((String) value); break;
default: throw new IllegalArgumentException("Illegal type encountered " + type);
}
}
}
public final void encodeTypedInt(final int v) throws IOException {
final BCF2Type type = BCF2Utils.determineIntegerType(v);
encodeTypedInt(v, type);
}
public final void encodeTypedInt(final int v, final BCF2Type type) throws IOException {
encodeType(1, type);
encodeRawInt(v, type);
}
public final void encodeTypedString(final String s) throws IOException {
encodeTypedString(s.getBytes());
}
public final void encodeTypedString(final byte[] s) throws IOException {
if ( s == null )
encodeType(0, BCF2Type.CHAR);
else {
encodeType(s.length, BCF2Type.CHAR);
for ( int i = 0; i < s.length; i++ ) {
encodeRawChar(s[i]);
}
}
}
public final void encodeTypedFloat(final double d) throws IOException {
encodeType(1, BCF2Type.FLOAT);
encodeRawFloat(d);
}
public final void encodeTyped(List v, final BCF2Type type) throws IOException {
if ( type == BCF2Type.CHAR && !v.isEmpty()) {
final String s = BCF2Utils.collapseStringList((List) v);
v = stringToBytes(s);
}
encodeType(v.size(), type);
encodeRawValues(v, type);
}
// --------------------------------------------------------------------------------
//
// Writing raw values (don't have a type byte)
//
// --------------------------------------------------------------------------------
public final void encodeRawValues(final Collection v, final BCF2Type type) throws IOException {
for ( final T v1 : v ) {
encodeRawValue(v1, type);
}
}
public final void encodeRawValue(final T value, final BCF2Type type) throws IOException {
try {
if ( value == type.getMissingJavaValue() )
encodeRawMissingValue(type);
else {
switch (type) {
case INT8:
case INT16:
case INT32: encodeRawBytes((Integer) value, type); break;
case FLOAT: encodeRawFloat((Double) value); break;
case CHAR: encodeRawChar((Byte) value); break;
default: throw new IllegalArgumentException("Illegal type encountered " + type);
}
}
} catch ( ClassCastException e ) {
throw new ClassCastException("BUG: invalid type cast to " + type + " from " + value);
}
}
public final void encodeRawMissingValue(final BCF2Type type) throws IOException {
encodeRawBytes(type.getMissingBytes(), type);
}
public final void encodeRawMissingValues(final int size, final BCF2Type type) throws IOException {
for ( int i = 0; i < size; i++ )
encodeRawMissingValue(type);
}
// --------------------------------------------------------------------------------
//
// low-level encoders
//
// --------------------------------------------------------------------------------
public final void encodeRawChar(final byte c) throws IOException {
encodeStream.write(c);
}
public final void encodeRawFloat(final double value) throws IOException {
encodeRawBytes(Float.floatToIntBits((float) value), BCF2Type.FLOAT);
}
public final void encodeType(final int size, final BCF2Type type) throws IOException {
if ( size <= BCF2Utils.MAX_INLINE_ELEMENTS ) {
final int typeByte = BCF2Utils.encodeTypeDescriptor(size, type);
encodeStream.write(typeByte);
} else {
final int typeByte = BCF2Utils.encodeTypeDescriptor(BCF2Utils.OVERFLOW_ELEMENT_MARKER, type);
encodeStream.write(typeByte);
// write in the overflow size
encodeTypedInt(size);
}
}
public final void encodeRawInt(final int value, final BCF2Type type) throws IOException {
type.write(value, encodeStream);
}
public final void encodeRawBytes(final int value, final BCF2Type type) throws IOException {
type.write(value, encodeStream);
}
// --------------------------------------------------------------------------------
//
// utility functions
//
// --------------------------------------------------------------------------------
public void encodeRawString(final String s, final int sizeToWrite) throws IOException {
final byte[] bytes = s.getBytes();
for ( int i = 0; i < sizeToWrite; i++ )
if ( i < bytes.length )
encodeRawChar(bytes[i]);
else
encodeRawMissingValue(BCF2Type.CHAR);
}
/**
* Totally generic encoder that examines o, determines the best way to encode it, and encodes it
*
* This method is incredibly slow, but it's only used for UnitTests so it doesn't matter
*
* @param o
* @return
*/
public final BCF2Type encode(final Object o) throws IOException {
if ( o == null ) throw new IllegalArgumentException("Generic encode cannot deal with null values");
if ( o instanceof List ) {
final BCF2Type type = determineBCFType(((List) o).get(0));
encodeTyped((List) o, type);
return type;
} else {
final BCF2Type type = determineBCFType(o);
encodeTyped(o, type);
return type;
}
}
private final BCF2Type determineBCFType(final Object arg) {
final Object toType = arg instanceof List ? ((List)arg).get(0) : arg;
if ( toType instanceof Integer )
return BCF2Utils.determineIntegerType((Integer) toType);
else if ( toType instanceof String )
return BCF2Type.CHAR;
else if ( toType instanceof Double )
return BCF2Type.FLOAT;
else
throw new IllegalArgumentException("No native encoding for Object of type " + arg.getClass().getSimpleName());
}
private final List stringToBytes(final String v) throws IOException {
if ( v == null || v.equals("") )
return Collections.emptyList();
else {
// TODO -- this needs to be optimized away for efficiency
final byte[] bytes = v.getBytes();
final List l = new ArrayList(bytes.length);
for ( int i = 0; i < bytes.length; i++) l.add(bytes[i]);
return l;
}
}
}
