/** decode motion information for every PU block.
* \param pcCU
* \param uiAbsPartIdx
* \param uiDepth
* \param pcSubCU
* \returns Void
*/
Void TDecEntropy::decodePUWise( TComDataCU* pcCU, UInt uiAbsPartIdx, UInt uiDepth, TComDataCU* pcSubCU )
{
PartSize ePartSize = pcCU->getPartitionSize( uiAbsPartIdx );
UInt uiNumPU = ( ePartSize == SIZE_2Nx2N ? 1 : ( ePartSize == SIZE_NxN ? 4 : 2 ) );
UInt uiPUOffset = ( g_auiPUOffset[UInt( ePartSize )] << ( ( pcCU->getSlice()->getSPS()->getMaxCUDepth() - uiDepth ) << 1 ) ) >> 4;
TComMvField cMvFieldNeighbours[MRG_MAX_NUM_CANDS << 1]; // double length for mv of both lists
UChar uhInterDirNeighbours[MRG_MAX_NUM_CANDS];
for ( UInt ui = 0; ui < MRG_MAX_NUM_CANDS; ui++ )
{
uhInterDirNeighbours[ui] = 0;
}
Int numValidMergeCand = 0;
bool isMerged = false;
pcSubCU->copyInterPredInfoFrom( pcCU, uiAbsPartIdx, REF_PIC_LIST_0 );
pcSubCU->copyInterPredInfoFrom( pcCU, uiAbsPartIdx, REF_PIC_LIST_1 );
for ( UInt uiPartIdx = 0, uiSubPartIdx = uiAbsPartIdx; uiPartIdx < uiNumPU; uiPartIdx++, uiSubPartIdx += uiPUOffset )
{
decodeMergeFlag( pcCU, uiSubPartIdx, uiDepth, uiPartIdx );
if ( pcCU->getMergeFlag( uiSubPartIdx ) )
{
decodeMergeIndex( pcCU, uiPartIdx, uiSubPartIdx, ePartSize, uhInterDirNeighbours, cMvFieldNeighbours, uiDepth );
UInt uiMergeIndex = pcCU->getMergeIndex(uiSubPartIdx);
if ( pcCU->getSlice()->getPPS()->getLog2ParallelMergeLevelMinus2() && ePartSize != SIZE_2Nx2N && pcSubCU->getWidth( 0 ) <= 8 )
{
pcSubCU->setPartSizeSubParts( SIZE_2Nx2N, 0, uiDepth );
if ( !isMerged )
{
pcSubCU->getInterMergeCandidates( 0, 0, uiDepth, cMvFieldNeighbours, uhInterDirNeighbours, numValidMergeCand );
isMerged = true;
}
pcSubCU->setPartSizeSubParts( ePartSize, 0, uiDepth );
}
else
{
uiMergeIndex = pcCU->getMergeIndex(uiSubPartIdx);
pcSubCU->getInterMergeCandidates( uiSubPartIdx-uiAbsPartIdx, uiPartIdx, uiDepth, cMvFieldNeighbours, uhInterDirNeighbours, numValidMergeCand, uiMergeIndex );
}
pcCU->setInterDirSubParts( uhInterDirNeighbours[uiMergeIndex], uiSubPartIdx, uiPartIdx, uiDepth );
TComMv cTmpMv( 0, 0 );
for ( UInt uiRefListIdx = 0; uiRefListIdx < 2; uiRefListIdx++ )
{
if ( pcCU->getSlice()->getNumRefIdx( RefPicList( uiRefListIdx ) ) > 0 )
{
pcCU->setMVPIdxSubParts( 0, RefPicList( uiRefListIdx ), uiSubPartIdx, uiPartIdx, uiDepth);
pcCU->setMVPNumSubParts( 0, RefPicList( uiRefListIdx ), uiSubPartIdx, uiPartIdx, uiDepth);
pcCU->getCUMvField( RefPicList( uiRefListIdx ) )->setAllMvd( cTmpMv, ePartSize, uiSubPartIdx, uiDepth, uiPartIdx );
pcCU->getCUMvField( RefPicList( uiRefListIdx ) )->setAllMvField( cMvFieldNeighbours[ 2*uiMergeIndex + uiRefListIdx ], ePartSize, uiSubPartIdx, uiDepth, uiPartIdx );
}
}
}
else
{
decodeInterDirPU( pcCU, uiSubPartIdx, uiDepth, uiPartIdx );
for ( UInt uiRefListIdx = 0; uiRefListIdx < 2; uiRefListIdx++ )
{
if ( pcCU->getSlice()->getNumRefIdx( RefPicList( uiRefListIdx ) ) > 0 )
{
decodeRefFrmIdxPU( pcCU, uiSubPartIdx, uiDepth, uiPartIdx, RefPicList( uiRefListIdx ) );
decodeMvdPU ( pcCU, uiSubPartIdx, uiDepth, uiPartIdx, RefPicList( uiRefListIdx ) );
decodeMVPIdxPU ( pcSubCU, uiSubPartIdx-uiAbsPartIdx, uiDepth, uiPartIdx, RefPicList( uiRefListIdx ) );
}
}
}
if ( (pcCU->getInterDir(uiSubPartIdx) == 3) && pcSubCU->isBipredRestriction(uiPartIdx) )
{
pcCU->getCUMvField( REF_PIC_LIST_1 )->setAllMv( TComMv(0,0), ePartSize, uiSubPartIdx, uiDepth, uiPartIdx);
pcCU->getCUMvField( REF_PIC_LIST_1 )->setAllRefIdx( -1, ePartSize, uiSubPartIdx, uiDepth, uiPartIdx);
pcCU->setInterDirSubParts( 1, uiSubPartIdx, uiPartIdx, uiDepth);
}
}
return;
}
namespace Json {
// This is a walkaround to avoid the static initialization of Value::null.
// kNull must be word-aligned to avoid crashing on ARM. We use an alignment of
// 8 (instead of 4) as a bit of future-proofing.
#if defined(__ARMEL__)
#define ALIGNAS(byte_alignment) __attribute__((aligned(byte_alignment)))
#else
#define ALIGNAS(byte_alignment)
#endif
//static const unsigned char ALIGNAS(8) kNull[sizeof(Value)] = { 0 };
//const unsigned char& kNullRef = kNull[0];
//const Value& Value::null = reinterpret_cast<const Value&>(kNullRef);
//const Value& Value::nullRef = null;
// static
Value const& Value::nullSingleton()
{
static Value const nullStatic;
return nullStatic;
}
// for backwards compatibility, we'll leave these global references around, but DO NOT
// use them in JSONCPP library code any more!
Value const& Value::null = Value::nullSingleton();
Value const& Value::nullRef = Value::nullSingleton();
const Int Value::minInt = Int(~(UInt(-1) / 2));
const Int Value::maxInt = Int(UInt(-1) / 2);
const UInt Value::maxUInt = UInt(-1);
#if defined(JSON_HAS_INT64)
const Int64 Value::minInt64 = Int64(~(UInt64(-1) / 2));
const Int64 Value::maxInt64 = Int64(UInt64(-1) / 2);
const UInt64 Value::maxUInt64 = UInt64(-1);
// The constant is hard-coded because some compiler have trouble
// converting Value::maxUInt64 to a double correctly (AIX/xlC).
// Assumes that UInt64 is a 64 bits integer.
static const double maxUInt64AsDouble = 18446744073709551615.0;
#endif // defined(JSON_HAS_INT64)
const LargestInt Value::minLargestInt = LargestInt(~(LargestUInt(-1) / 2));
const LargestInt Value::maxLargestInt = LargestInt(LargestUInt(-1) / 2);
const LargestUInt Value::maxLargestUInt = LargestUInt(-1);
#if !defined(JSON_USE_INT64_DOUBLE_CONVERSION)
template <typename T, typename U>
static inline bool InRange(double d, T min, U max) {
// The casts can lose precision, but we are looking only for
// an approximate range. Might fail on edge cases though. ~cdunn
//return d >= static_cast<double>(min) && d <= static_cast<double>(max);
return d >= min && d <= max;
}
#else // if !defined(JSON_USE_INT64_DOUBLE_CONVERSION)
static inline double integerToDouble(Json::UInt64 value) {
return static_cast<double>(Int64(value / 2)) * 2.0 + static_cast<double>(Int64(value & 1));
}
template <typename T> static inline double integerToDouble(T value) {
return static_cast<double>(value);
}
template <typename T, typename U>
static inline bool InRange(double d, T min, U max) {
return d >= integerToDouble(min) && d <= integerToDouble(max);
}
#endif // if !defined(JSON_USE_INT64_DOUBLE_CONVERSION)
/** Duplicates the specified string value.
* @param value Pointer to the string to duplicate. Must be zero-terminated if
* length is "unknown".
* @param length Length of the value. if equals to unknown, then it will be
* computed using strlen(value).
* @return Pointer on the duplicate instance of string.
*/
static inline char* duplicateStringValue(const char* value,
size_t length)
{
// Avoid an integer overflow in the call to malloc below by limiting length
// to a sane value.
if (length >= static_cast<size_t>(Value::maxInt))
length = Value::maxInt - 1;
char* newString = static_cast<char*>(malloc(length + 1));
if (newString == NULL) {
throwRuntimeError(
"in Json::Value::duplicateStringValue(): "
"Failed to allocate string value buffer");
}
memcpy(newString, value, length);
newString[length] = 0;
return newString;
}
/* Record the length as a prefix.
*/
static inline char* duplicateAndPrefixStringValue(
const char* value,
unsigned int length)
{
// Avoid an integer overflow in the call to malloc below by limiting length
// to a sane value.
JSON_ASSERT_MESSAGE(length <= static_cast<unsigned>(Value::maxInt) - sizeof(unsigned) - 1U,
"in Json::Value::duplicateAndPrefixStringValue(): "
"length too big for prefixing");
unsigned actualLength = length + static_cast<unsigned>(sizeof(unsigned)) + 1U;
char* newString = static_cast<char*>(malloc(actualLength));
if (newString == 0) {
throwRuntimeError(
"in Json::Value::duplicateAndPrefixStringValue(): "
"Failed to allocate string value buffer");
}
*reinterpret_cast<unsigned*>(newString) = length;
memcpy(newString + sizeof(unsigned), value, length);
newString[actualLength - 1U] = 0; // to avoid buffer over-run accidents by users later
return newString;
}
inline static void decodePrefixedString(
bool isPrefixed, char const* prefixed,
unsigned* length, char const** value)
{
if (!isPrefixed) {
*length = static_cast<unsigned>(strlen(prefixed));
*value = prefixed;
} else {
*length = *reinterpret_cast<unsigned const*>(prefixed);
*value = prefixed + sizeof(unsigned);
}
}
/** Free the string duplicated by duplicateStringValue()/duplicateAndPrefixStringValue().
*/
#if JSONCPP_USING_SECURE_MEMORY
static inline void releasePrefixedStringValue(char* value) {
unsigned length = 0;
char const* valueDecoded;
decodePrefixedString(true, value, &length, &valueDecoded);
size_t const size = sizeof(unsigned) + length + 1U;
memset(value, 0, size);
free(value);
}
static inline void releaseStringValue(char* value, unsigned length) {
// length==0 => we allocated the strings memory
size_t size = (length==0) ? strlen(value) : length;
memset(value, 0, size);
free(value);
}
#else // !JSONCPP_USING_SECURE_MEMORY
static inline void releasePrefixedStringValue(char* value) {
free(value);
}
static inline void releaseStringValue(char* value, unsigned) {
free(value);
}
#endif // JSONCPP_USING_SECURE_MEMORY
} // namespace Json
namespace Json {
const Value Value::null;
const Int Value::minInt = Int( ~(UInt(-1)/2) );
const Int Value::maxInt = Int( UInt(-1)/2 );
const UInt Value::maxUInt = UInt(-1);
# if defined(JSON_HAS_INT64)
const Int64 Value::minInt64 = Int64( ~(UInt64(-1)/2) );
const Int64 Value::maxInt64 = Int64( UInt64(-1)/2 );
const UInt64 Value::maxUInt64 = UInt64(-1);
// The constant is hard-coded because some compiler have trouble
// converting Value::maxUInt64 to a double correctly (AIX/xlC).
// Assumes that UInt64 is a 64 bits integer.
static const double maxUInt64AsDouble = 18446744073709551615.0;
#endif // defined(JSON_HAS_INT64)
const LargestInt Value::minLargestInt = LargestInt( ~(LargestUInt(-1)/2) );
const LargestInt Value::maxLargestInt = LargestInt( LargestUInt(-1)/2 );
const LargestUInt Value::maxLargestUInt = LargestUInt(-1);
/// Unknown size marker
static const unsigned int unknown = (unsigned)-1;
#if !defined(JSON_USE_INT64_DOUBLE_CONVERSION)
template <typename T, typename U>
static inline bool InRange(double d, T min, U max) {
return d >= min && d <= max;
}
#else // if !defined(JSON_USE_INT64_DOUBLE_CONVERSION)
static inline double integerToDouble( Json::UInt64 value )
{
return static_cast<double>( Int64(value/2) ) * 2.0 + Int64(value & 1);
}
template<typename T>
static inline double integerToDouble( T value )
{
return static_cast<double>( value );
}
template <typename T, typename U>
static inline bool InRange(double d, T min, U max) {
return d >= integerToDouble(min) && d <= integerToDouble(max);
}
#endif // if !defined(JSON_USE_INT64_DOUBLE_CONVERSION)
/** Duplicates the specified string value.
* @param value Pointer to the string to duplicate. Must be zero-terminated if
* length is "unknown".
* @param length Length of the value. if equals to unknown, then it will be
* computed using strlen(value).
* @return Pointer on the duplicate instance of string.
*/
static inline char *
duplicateStringValue( const char *value,
unsigned int length = unknown )
{
if ( length == unknown )
length = (unsigned int)strlen(value);
// Avoid an integer overflow in the call to malloc below by limiting length
// to a sane value.
if (length >= (unsigned)Value::maxInt)
length = Value::maxInt - 1;
char *newString = static_cast<char *>( malloc( length + 1 ) );
JSON_ASSERT_MESSAGE( newString != 0, "Failed to allocate string value buffer" );
memcpy( newString, value, length );
newString[length] = 0;
return newString;
}
/** Free the string duplicated by duplicateStringValue().
*/
static inline void
releaseStringValue( char *value )
{
if ( value )
free( value );
}
} // namespace Json
ILboolean ReadLayerBlock(PspLoadState* state, ILuint BlockLen, ILimage* image)
{
BLOCKHEAD Block;
LAYERINFO_CHUNK LayerInfo;
LAYERBITMAP_CHUNK Bitmap;
ILuint ChunkSize, Padding, i, j;
ILushort NumChars;
(void)BlockLen;
// Layer sub-block header
if (image->io.read(&image->io, &Block, 1, sizeof(Block)) != sizeof(Block))
return IL_FALSE;
if (state->Header.MajorVersion == 3)
Block.BlockLen = GetLittleUInt(&image->io);
else
UInt(&Block.BlockLen);
if (Block.HeadID[0] != 0x7E || Block.HeadID[1] != 0x42 ||
Block.HeadID[2] != 0x4B || Block.HeadID[3] != 0x00) {
return IL_FALSE;
}
if (Block.BlockID != PSP_LAYER_BLOCK)
return IL_FALSE;
if (state->Header.MajorVersion == 3) {
image->io.seek(&image->io, 256, IL_SEEK_CUR); // We don't care about the name of the layer.
image->io.read(&image->io, &LayerInfo, sizeof(LayerInfo), 1);
if (image->io.read(&image->io, &Bitmap, sizeof(Bitmap), 1) != 1)
return IL_FALSE;
}
else { // Header.MajorVersion >= 4
ChunkSize = GetLittleUInt(&image->io);
NumChars = GetLittleUShort(&image->io);
image->io.seek(&image->io, NumChars, IL_SEEK_CUR); // We don't care about the layer's name.
ChunkSize -= (2 + 4 + NumChars);
if (image->io.read(&image->io, &LayerInfo, IL_MIN(sizeof(LayerInfo), ChunkSize), 1) != 1)
return IL_FALSE;
// Can have new entries in newer versions of the spec (5.0).
Padding = (ChunkSize) - sizeof(LayerInfo);
if (Padding > 0)
image->io.seek(&image->io, Padding, IL_SEEK_CUR);
ChunkSize = GetLittleUInt(&image->io);
if (image->io.read(&image->io, &Bitmap, sizeof(Bitmap), 1) != 1)
return IL_FALSE;
Padding = (ChunkSize - 4) - sizeof(Bitmap);
if (Padding > 0)
image->io.seek(&image->io, Padding, IL_SEEK_CUR);
}
state->Channels = (ILubyte**)ialloc(sizeof(ILubyte*) * Bitmap.NumChannels);
if (state->Channels == NULL) {
return IL_FALSE;
}
state->NumChannels = Bitmap.NumChannels;
for (i = 0; i < state->NumChannels; i++) {
state->Channels[i] = GetChannel(state, image);
if (state->Channels[i] == NULL) {
for (j = 0; j < i; j++)
ifree(state->Channels[j]);
return IL_FALSE;
}
}
return IL_TRUE;
}
ILboolean ReadAlphaBlock(PspLoadState* state, ILuint BlockLen, ILimage* image)
{
BLOCKHEAD Block;
ALPHAINFO_CHUNK AlphaInfo;
ALPHA_CHUNK AlphaChunk;
ILushort NumAlpha, StringSize;
ILuint ChunkSize, Padding;
if (state->Header.MajorVersion == 3) {
NumAlpha = GetLittleUShort(&image->io);
}
else {
ChunkSize = GetLittleUInt(&image->io);
NumAlpha = GetLittleUShort(&image->io);
Padding = (ChunkSize - 4 - 2);
if (Padding > 0)
image->io.seek(&image->io, Padding, IL_SEEK_CUR);
}
// Alpha channel header
if (image->io.read(&image->io, &Block, 1, sizeof(Block)) != sizeof(Block))
return IL_FALSE;
if (state->Header.MajorVersion == 3)
Block.BlockLen = GetLittleUInt(&image->io);
else
UInt(&Block.BlockLen);
if (Block.HeadID[0] != 0x7E || Block.HeadID[1] != 0x42 ||
Block.HeadID[2] != 0x4B || Block.HeadID[3] != 0x00) {
return IL_FALSE;
}
if (Block.BlockID != PSP_ALPHA_CHANNEL_BLOCK)
return IL_FALSE;
if (state->Header.MajorVersion >= 4) {
ChunkSize = GetLittleUInt(&image->io);
StringSize = GetLittleUShort(&image->io);
image->io.seek(&image->io, StringSize, IL_SEEK_CUR);
if (image->io.read(&image->io, &AlphaInfo, sizeof(AlphaInfo), 1) != 1)
return IL_FALSE;
Padding = (ChunkSize - 4 - 2 - StringSize - sizeof(AlphaInfo));
if (Padding > 0)
image->io.seek(&image->io, Padding, IL_SEEK_CUR);
ChunkSize = GetLittleUInt(&image->io);
if (image->io.read(&image->io, &AlphaChunk, sizeof(AlphaChunk), 1) != 1)
return IL_FALSE;
Padding = (ChunkSize - 4 - sizeof(AlphaChunk));
if (Padding > 0)
image->io.seek(&image->io, Padding, IL_SEEK_CUR);
}
else {
image->io.seek(&image->io, 256, IL_SEEK_CUR);
image->io.read(&image->io, &AlphaInfo, sizeof(AlphaInfo), 1);
if (image->io.read(&image->io, &AlphaChunk, sizeof(AlphaChunk), 1) != 1)
return IL_FALSE;
}
/*Alpha = (ILubyte*)ialloc(AlphaInfo.AlphaRect.x2 * AlphaInfo.AlphaRect.y2);
if (Alpha == NULL) {
return IL_FALSE;
}*/
state->Alpha = GetChannel(state, image);
if (state->Alpha == NULL)
return IL_FALSE;
return IL_TRUE;
}
namespace Json {
const Value Value::null;
const Int Value::minInt = Int( ~(UInt(-1)/2) );
const Int Value::maxInt = Int( UInt(-1)/2 );
const UInt Value::maxUInt = UInt(-1);
// A "safe" implementation of strdup. Allow null pointer to be passed.
// Also avoid warning on msvc80.
//
//inline char *safeStringDup( const char *czstring )
//{
// if ( czstring )
// {
// const size_t length = (unsigned int)( strlen(czstring) + 1 );
// char *newString = static_cast<char *>( malloc( length ) );
// memcpy( newString, czstring, length );
// return newString;
// }
// return 0;
//}
//
//inline char *safeStringDup( const std::string &str )
//{
// if ( !str.empty() )
// {
// const size_t length = str.length();
// char *newString = static_cast<char *>( malloc( length + 1 ) );
// memcpy( newString, str.c_str(), length );
// newString[length] = 0;
// return newString;
// }
// return 0;
//}
ValueAllocator::~ValueAllocator()
{
}
class DefaultValueAllocator : public ValueAllocator
{
public:
virtual ~DefaultValueAllocator()
{
}
virtual char *makeMemberName( const char *memberName )
{
return duplicateStringValue( memberName );
}
virtual void releaseMemberName( char *memberName )
{
releaseStringValue( memberName );
}
virtual char *duplicateStringValue( const char *value,
unsigned int length = unknown )
{
//@todo invesgate this old optimization
//if ( !value || value[0] == 0 )
// return 0;
if ( length == unknown )
length = (unsigned int)strlen(value);
char *newString = static_cast<char *>( malloc( length + 1 ) );
memcpy( newString, value, length );
newString[length] = 0;
return newString;
}
virtual void releaseStringValue( char *value )
{
if ( value )
free( value );
}
};
static ValueAllocator *&valueAllocator()
{
static DefaultValueAllocator defaultAllocator;
static ValueAllocator *valueAllocator = &defaultAllocator;
return valueAllocator;
}
static struct DummyValueAllocatorInitializer {
DummyValueAllocatorInitializer()
{
valueAllocator(); // ensure valueAllocator() statics are initialized before main().
}
} dummyValueAllocatorInitializer;
// //////////////////////////////////////////////////////////////////
// //////////////////////////////////////////////////////////////////
// //////////////////////////////////////////////////////////////////
// ValueInternals...
// //////////////////////////////////////////////////////////////////
// //////////////////////////////////////////////////////////////////
// //////////////////////////////////////////////////////////////////
#ifdef JSON_VALUE_USE_INTERNAL_MAP
# include "json_internalarray.inl"
# include "json_internalmap.inl"
#endif // JSON_VALUE_USE_INTERNAL_MAP
# include "json_valueiterator.inl"
// //////////////////////////////////////////////////////////////////
// //////////////////////////////////////////////////////////////////
// //////////////////////////////////////////////////////////////////
// class Value::CommentInfo
// //////////////////////////////////////////////////////////////////
// //////////////////////////////////////////////////////////////////
// //////////////////////////////////////////////////////////////////
Value::CommentInfo::CommentInfo()
: comment_( 0 )
{
}
Value::CommentInfo::~CommentInfo()
{
if ( comment_ )
valueAllocator()->releaseStringValue( comment_ );
}
void
Value::CommentInfo::setComment( const char *text )
{
if ( comment_ )
valueAllocator()->releaseStringValue( comment_ );
//JSON_ASSERT( text );
//JSON_ASSERT_MESSAGE( text[0]=='\0' || text[0]=='/', "Comments must start with /");
// It seems that /**/ style comments are acceptable as well.
comment_ = valueAllocator()->duplicateStringValue( text );
}
// //////////////////////////////////////////////////////////////////
// //////////////////////////////////////////////////////////////////
// //////////////////////////////////////////////////////////////////
// class Value::CZString
// //////////////////////////////////////////////////////////////////
// //////////////////////////////////////////////////////////////////
// //////////////////////////////////////////////////////////////////
# ifndef JSON_VALUE_USE_INTERNAL_MAP
// Notes: index_ indicates if the string was allocated when
// a string is stored.
Value::CZString::CZString( int index )
: cstr_( 0 )
, index_( index )
{
}
Value::CZString::CZString( const char *cstr, DuplicationPolicy allocate )
: cstr_( allocate == duplicate ? valueAllocator()->makeMemberName(cstr)
: cstr )
, index_( allocate )
{
}
Value::CZString::CZString( const CZString &other )
: cstr_( other.index_ != noDuplication && other.cstr_ != 0
? valueAllocator()->makeMemberName( other.cstr_ )
: other.cstr_ )
, index_( other.cstr_ ? (other.index_ == noDuplication ? noDuplication : duplicate)
: other.index_ )
{
}
Value::CZString::~CZString()
{
if ( cstr_ && index_ == duplicate )
valueAllocator()->releaseMemberName( const_cast<char *>( cstr_ ) );
}
void
Value::CZString::swap( CZString &other )
{
std::swap( cstr_, other.cstr_ );
std::swap( index_, other.index_ );
}
Value::CZString &
Value::CZString::operator =( const CZString &other )
{
CZString temp( other );
swap( temp );
return *this;
}
bool
Value::CZString::operator<( const CZString &other ) const
{
if ( cstr_ )
return strcmp( cstr_, other.cstr_ ) < 0;
return index_ < other.index_;
}
bool
Value::CZString::operator==( const CZString &other ) const
{
if ( cstr_ )
return strcmp( cstr_, other.cstr_ ) == 0;
return index_ == other.index_;
}
int
Value::CZString::index() const
{
return index_;
}
const char *
Value::CZString::c_str() const
{
return cstr_;
}
bool
Value::CZString::isStaticString() const
{
return index_ == noDuplication;
}
#endif // ifndef JSON_VALUE_USE_INTERNAL_MAP
// //////////////////////////////////////////////////////////////////
// //////////////////////////////////////////////////////////////////
// //////////////////////////////////////////////////////////////////
// class Value::Value
// //////////////////////////////////////////////////////////////////
// //////////////////////////////////////////////////////////////////
// //////////////////////////////////////////////////////////////////
/*! \internal Default constructor initialization must be equivalent to:
* memset( this, 0, sizeof(Value) )
* This optimization is used in ValueInternalMap fast allocator.
*/
Value::Value( ValueType type )
: type_( type )
, allocated_( 0 )
, comments_( 0 )
# ifdef JSON_VALUE_USE_INTERNAL_MAP
, itemIsUsed_( 0 )
#endif
{
switch ( type )
{
case nullValue:
break;
case intValue:
case uintValue:
value_.int_ = 0;
break;
case realValue:
value_.real_ = 0.0;
break;
case stringValue:
value_.string_ = 0;
break;
#ifndef JSON_VALUE_USE_INTERNAL_MAP
case arrayValue:
case objectValue:
value_.map_ = new ObjectValues();
break;
#else
case arrayValue:
value_.array_ = arrayAllocator()->newArray();
break;
case objectValue:
value_.map_ = mapAllocator()->newMap();
break;
#endif
case booleanValue:
value_.bool_ = false;
break;
default:
JSON_ASSERT_UNREACHABLE;
}
}
Value::Value( Int value )
: type_( intValue )
, comments_( 0 )
# ifdef JSON_VALUE_USE_INTERNAL_MAP
, itemIsUsed_( 0 )
#endif
{
value_.int_ = value;
}
Value::Value( UInt value )
: type_( uintValue )
, comments_( 0 )
# ifdef JSON_VALUE_USE_INTERNAL_MAP
, itemIsUsed_( 0 )
#endif
{
value_.uint_ = value;
}
Value::Value( double value )
: type_( realValue )
, comments_( 0 )
# ifdef JSON_VALUE_USE_INTERNAL_MAP
, itemIsUsed_( 0 )
#endif
{
value_.real_ = value;
}
Value::Value( const char *value )
: type_( stringValue )
, allocated_( true )
, comments_( 0 )
# ifdef JSON_VALUE_USE_INTERNAL_MAP
, itemIsUsed_( 0 )
#endif
{
value_.string_ = valueAllocator()->duplicateStringValue( value );
}
Value::Value( const char *beginValue,
const char *endValue )
: type_( stringValue )
, allocated_( true )
, comments_( 0 )
# ifdef JSON_VALUE_USE_INTERNAL_MAP
, itemIsUsed_( 0 )
#endif
{
value_.string_ = valueAllocator()->duplicateStringValue( beginValue,
UInt(endValue - beginValue) );
}
Value::Value( const std::string &value )
: type_( stringValue )
, allocated_( true )
, comments_( 0 )
# ifdef JSON_VALUE_USE_INTERNAL_MAP
, itemIsUsed_( 0 )
#endif
{
value_.string_ = valueAllocator()->duplicateStringValue( value.c_str(),
(unsigned int)value.length() );
}
Value::Value( const StaticString &value )
: type_( stringValue )
, allocated_( false )
, comments_( 0 )
# ifdef JSON_VALUE_USE_INTERNAL_MAP
, itemIsUsed_( 0 )
#endif
{
value_.string_ = const_cast<char *>( value.c_str() );
}
# ifdef JSON_USE_CPPTL
Value::Value( const CppTL::ConstString &value )
: type_( stringValue )
, allocated_( true )
, comments_( 0 )
# ifdef JSON_VALUE_USE_INTERNAL_MAP
, itemIsUsed_( 0 )
#endif
{
value_.string_ = valueAllocator()->duplicateStringValue( value, value.length() );
}
# endif
Value::Value( bool value )
: type_( booleanValue )
, comments_( 0 )
# ifdef JSON_VALUE_USE_INTERNAL_MAP
, itemIsUsed_( 0 )
#endif
{
value_.bool_ = value;
}
Value::Value( const Value &other )
: type_( other.type_ )
, comments_( 0 )
# ifdef JSON_VALUE_USE_INTERNAL_MAP
, itemIsUsed_( 0 )
#endif
{
switch ( type_ )
{
case nullValue:
case intValue:
case uintValue:
case realValue:
case booleanValue:
value_ = other.value_;
break;
case stringValue:
if ( other.value_.string_ )
{
value_.string_ = valueAllocator()->duplicateStringValue( other.value_.string_ );
allocated_ = true;
}
else
value_.string_ = 0;
break;
#ifndef JSON_VALUE_USE_INTERNAL_MAP
case arrayValue:
case objectValue:
value_.map_ = new ObjectValues( *other.value_.map_ );
break;
#else
case arrayValue:
value_.array_ = arrayAllocator()->newArrayCopy( *other.value_.array_ );
break;
case objectValue:
value_.map_ = mapAllocator()->newMapCopy( *other.value_.map_ );
break;
#endif
default:
JSON_ASSERT_UNREACHABLE;
}
if ( other.comments_ )
{
comments_ = new CommentInfo[numberOfCommentPlacement];
for ( int comment =0; comment < numberOfCommentPlacement; ++comment )
{
const CommentInfo &otherComment = other.comments_[comment];
if ( otherComment.comment_ )
comments_[comment].setComment( otherComment.comment_ );
}
}
}
Value::~Value()
{
switch ( type_ )
{
case nullValue:
case intValue:
case uintValue:
case realValue:
case booleanValue:
break;
case stringValue:
if ( allocated_ )
valueAllocator()->releaseStringValue( value_.string_ );
break;
#ifndef JSON_VALUE_USE_INTERNAL_MAP
case arrayValue:
case objectValue:
delete value_.map_;
break;
#else
case arrayValue:
arrayAllocator()->destructArray( value_.array_ );
break;
case objectValue:
mapAllocator()->destructMap( value_.map_ );
break;
#endif
default:
JSON_ASSERT_UNREACHABLE;
}
if ( comments_ )
delete[] comments_;
}
Value &
Value::operator=( const Value &other )
{
Value temp( other );
swap( temp );
return *this;
}
void
Value::swap( Value &other )
{
ValueType temp = type_;
type_ = other.type_;
other.type_ = temp;
std::swap( value_, other.value_ );
int temp2 = allocated_;
allocated_ = other.allocated_;
other.allocated_ = temp2;
}
ValueType
Value::type() const
{
return type_;
}
int
Value::compare( const Value &other )
{
/*
int typeDelta = other.type_ - type_;
switch ( type_ )
{
case nullValue:
return other.type_ == type_;
case intValue:
if ( other.type_.isNumeric()
case uintValue:
case realValue:
case booleanValue:
break;
case stringValue,
break;
case arrayValue:
delete value_.array_;
break;
case objectValue:
delete value_.map_;
default:
JSON_ASSERT_UNREACHABLE;
}
*/
return 0; // unreachable
}
bool
Value::operator <( const Value &other ) const
{
int typeDelta = type_ - other.type_;
if ( typeDelta )
return typeDelta < 0 ? true : false;
switch ( type_ )
{
case nullValue:
return false;
case intValue:
return value_.int_ < other.value_.int_;
case uintValue:
return value_.uint_ < other.value_.uint_;
case realValue:
return value_.real_ < other.value_.real_;
case booleanValue:
return value_.bool_ < other.value_.bool_;
case stringValue:
return ( value_.string_ == 0 && other.value_.string_ )
|| ( other.value_.string_
&& value_.string_
&& strcmp( value_.string_, other.value_.string_ ) < 0 );
#ifndef JSON_VALUE_USE_INTERNAL_MAP
case arrayValue:
case objectValue:
{
int delta = int( value_.map_->size() - other.value_.map_->size() );
if ( delta )
return delta < 0;
return (*value_.map_) < (*other.value_.map_);
}
#else
case arrayValue:
return value_.array_->compare( *(other.value_.array_) ) < 0;
case objectValue:
return value_.map_->compare( *(other.value_.map_) ) < 0;
#endif
default:
JSON_ASSERT_UNREACHABLE;
}
return 0; // unreachable
}
bool
Value::operator <=( const Value &other ) const
{
return !(other > *this);
}
bool
Value::operator >=( const Value &other ) const
{
return !(*this < other);
}
bool
Value::operator >( const Value &other ) const
{
return other < *this;
}
bool
Value::operator ==( const Value &other ) const
{
//if ( type_ != other.type_ )
// GCC 2.95.3 says:
// attempt to take address of bit-field structure member `Json::Value::type_'
// Beats me, but a temp solves the problem.
int temp = other.type_;
if ( type_ != temp )
return false;
switch ( type_ )
{
case nullValue:
return true;
case intValue:
return value_.int_ == other.value_.int_;
case uintValue:
return value_.uint_ == other.value_.uint_;
case realValue:
return value_.real_ == other.value_.real_;
case booleanValue:
return value_.bool_ == other.value_.bool_;
case stringValue:
return ( value_.string_ == other.value_.string_ )
|| ( other.value_.string_
&& value_.string_
&& strcmp( value_.string_, other.value_.string_ ) == 0 );
#ifndef JSON_VALUE_USE_INTERNAL_MAP
case arrayValue:
case objectValue:
return value_.map_->size() == other.value_.map_->size()
&& (*value_.map_) == (*other.value_.map_);
#else
case arrayValue:
return value_.array_->compare( *(other.value_.array_) ) == 0;
case objectValue:
return value_.map_->compare( *(other.value_.map_) ) == 0;
#endif
default:
JSON_ASSERT_UNREACHABLE;
}
return 0; // unreachable
}
bool
Value::operator !=( const Value &other ) const
{
return !( *this == other );
}
const char *
Value::asCString() const
{
JSON_ASSERT( type_ == stringValue );
return value_.string_;
}
std::string
Value::asString() const
{
switch ( type_ )
{
case nullValue:
return "";
case stringValue:
return value_.string_ ? value_.string_ : "";
case booleanValue:
return value_.bool_ ? "true" : "false";
case intValue:
case uintValue:
case realValue:
case arrayValue:
case objectValue:
//JSON_ASSERT_MESSAGE( false, "Type is not convertible to string" );
default:
JSON_ASSERT_UNREACHABLE;
}
return ""; // unreachable
}
# ifdef JSON_USE_CPPTL
CppTL::ConstString
Value::asConstString() const
{
return CppTL::ConstString( asString().c_str() );
}
# endif
Value::Int
Value::asInt() const
{
switch ( type_ )
{
case nullValue:
return 0;
case intValue:
return value_.int_;
case uintValue:
//JSON_ASSERT_MESSAGE( value_.uint_ < (unsigned)maxInt, "integer out of signed integer range" );
return value_.uint_;
case realValue:
//JSON_ASSERT_MESSAGE( value_.real_ >= minInt && value_.real_ <= maxInt, "Real out of signed integer range" );
return Int( value_.real_ );
case booleanValue:
return value_.bool_ ? 1 : 0;
case stringValue:
case arrayValue:
case objectValue:
//JSON_ASSERT_MESSAGE( false, "Type is not convertible to int" );
default:
JSON_ASSERT_UNREACHABLE;
}
return 0; // unreachable;
}
Value::UInt
Value::asUInt() const
{
switch ( type_ )
{
case nullValue:
return 0;
case intValue:
//JSON_ASSERT_MESSAGE( value_.int_ >= 0, "Negative integer can not be converted to unsigned integer" );
return value_.int_;
case uintValue:
return value_.uint_;
case realValue:
//JSON_ASSERT_MESSAGE( value_.real_ >= 0 && value_.real_ <= maxUInt, "Real out of unsigned integer range" );
return UInt( value_.real_ );
case booleanValue:
return value_.bool_ ? 1 : 0;
case stringValue:
case arrayValue:
case objectValue:
//JSON_ASSERT_MESSAGE( false, "Type is not convertible to uint" );
default:
JSON_ASSERT_UNREACHABLE;
}
return 0; // unreachable;
}
double
Value::asDouble() const
{
switch ( type_ )
{
case nullValue:
return 0.0;
case intValue:
return value_.int_;
case uintValue:
return value_.uint_;
case realValue:
return value_.real_;
case booleanValue:
return value_.bool_ ? 1.0 : 0.0;
case stringValue:
case arrayValue:
case objectValue:
//JSON_ASSERT_MESSAGE( false, "Type is not convertible to double" );
default:
JSON_ASSERT_UNREACHABLE;
}
return 0; // unreachable;
}
bool
Value::asBool() const
{
switch ( type_ )
{
case nullValue:
return false;
case intValue:
case uintValue:
return value_.int_ != 0;
case realValue:
return value_.real_ != 0.0;
case booleanValue:
return value_.bool_;
case stringValue:
return value_.string_ && value_.string_[0] != 0;
case arrayValue:
case objectValue:
return value_.map_->size() != 0;
default:
JSON_ASSERT_UNREACHABLE;
}
return false; // unreachable;
}
bool
Value::isConvertibleTo( ValueType other ) const
{
switch ( type_ )
{
case nullValue:
return true;
case intValue:
return ( other == nullValue && value_.int_ == 0 )
|| other == intValue
|| ( other == uintValue && value_.int_ >= 0 )
|| other == realValue
|| other == stringValue
|| other == booleanValue;
case uintValue:
return ( other == nullValue && value_.uint_ == 0 )
|| ( other == intValue && value_.uint_ <= (unsigned)maxInt )
|| other == uintValue
|| other == realValue
|| other == stringValue
|| other == booleanValue;
case realValue:
return ( other == nullValue && value_.real_ == 0.0 )
|| ( other == intValue && value_.real_ >= minInt && value_.real_ <= maxInt )
|| ( other == uintValue && value_.real_ >= 0 && value_.real_ <= maxUInt )
|| other == realValue
|| other == stringValue
|| other == booleanValue;
case booleanValue:
return ( other == nullValue && value_.bool_ == false )
|| other == intValue
|| other == uintValue
|| other == realValue
|| other == stringValue
|| other == booleanValue;
case stringValue:
return other == stringValue
|| ( other == nullValue && (!value_.string_ || value_.string_[0] == 0) );
case arrayValue:
return other == arrayValue
|| ( other == nullValue && value_.map_->size() == 0 );
case objectValue:
return other == objectValue
|| ( other == nullValue && value_.map_->size() == 0 );
default:
JSON_ASSERT_UNREACHABLE;
}
return false; // unreachable;
}
/// Number of values in array or object
Value::UInt
Value::size() const
{
switch ( type_ )
{
case nullValue:
case intValue:
case uintValue:
case realValue:
case booleanValue:
case stringValue:
return 0;
#ifndef JSON_VALUE_USE_INTERNAL_MAP
case arrayValue: // size of the array is highest index + 1
if ( !value_.map_->empty() )
{
ObjectValues::const_iterator itLast = value_.map_->end();
--itLast;
return (*itLast).first.index()+1;
}
return 0;
case objectValue:
return Int( value_.map_->size() );
#else
case arrayValue:
return Int( value_.array_->size() );
case objectValue:
return Int( value_.map_->size() );
#endif
default:
JSON_ASSERT_UNREACHABLE;
}
return 0; // unreachable;
}
bool
Value::empty() const
{
if ( isNull() || isArray() || isObject() )
return size() == 0u;
else
return false;
}
bool
Value::operator!() const
{
return isNull();
}
void
Value::clear()
{
JSON_ASSERT( type_ == nullValue || type_ == arrayValue || type_ == objectValue );
switch ( type_ )
{
#ifndef JSON_VALUE_USE_INTERNAL_MAP
case arrayValue:
case objectValue:
value_.map_->clear();
break;
#else
case arrayValue:
value_.array_->clear();
break;
case objectValue:
value_.map_->clear();
break;
#endif
default:
break;
}
}
void
Value::resize( UInt newSize )
{
JSON_ASSERT( type_ == nullValue || type_ == arrayValue );
if ( type_ == nullValue )
*this = Value( arrayValue );
#ifndef JSON_VALUE_USE_INTERNAL_MAP
UInt oldSize = size();
if ( newSize == 0 )
clear();
else if ( newSize > oldSize )
(*this)[ newSize - 1 ];
else
{
for ( UInt index = newSize; index < oldSize; ++index )
value_.map_->erase( index );
assert( size() == newSize );
}
#else
value_.array_->resize( newSize );
#endif
}
Value &
Value::operator[]( UInt index )
{
JSON_ASSERT( type_ == nullValue || type_ == arrayValue );
if ( type_ == nullValue )
*this = Value( arrayValue );
#ifndef JSON_VALUE_USE_INTERNAL_MAP
CZString key( index );
ObjectValues::iterator it = value_.map_->lower_bound( key );
if ( it != value_.map_->end() && (*it).first == key )
return (*it).second;
ObjectValues::value_type defaultValue( key, null );
it = value_.map_->insert( it, defaultValue );
return (*it).second;
#else
return value_.array_->resolveReference( index );
#endif
}
const Value &
Value::operator[]( UInt index ) const
{
JSON_ASSERT( type_ == nullValue || type_ == arrayValue );
if ( type_ == nullValue )
return null;
#ifndef JSON_VALUE_USE_INTERNAL_MAP
CZString key( index );
ObjectValues::const_iterator it = value_.map_->find( key );
if ( it == value_.map_->end() )
return null;
return (*it).second;
#else
Value *value = value_.array_->find( index );
return value ? *value : null;
#endif
}
Value &
Value::operator[]( const char *key )
{
return resolveReference( key, false );
}
Value &
Value::resolveReference( const char *key,
bool isStatic )
{
JSON_ASSERT( type_ == nullValue || type_ == objectValue );
if ( type_ == nullValue )
*this = Value( objectValue );
#ifndef JSON_VALUE_USE_INTERNAL_MAP
CZString actualKey( key, isStatic ? CZString::noDuplication
: CZString::duplicateOnCopy );
ObjectValues::iterator it = value_.map_->lower_bound( actualKey );
if ( it != value_.map_->end() && (*it).first == actualKey )
return (*it).second;
ObjectValues::value_type defaultValue( actualKey, null );
it = value_.map_->insert( it, defaultValue );
Value &value = (*it).second;
return value;
#else
return value_.map_->resolveReference( key, isStatic );
#endif
}
Value
Value::get( UInt index,
const Value &defaultValue ) const
{
const Value *value = &((*this)[index]);
return value == &null ? defaultValue : *value;
}
bool
Value::isValidIndex( UInt index ) const
{
return index < size();
}
const Value &
Value::operator[]( const char *key ) const
{
JSON_ASSERT( type_ == nullValue || type_ == objectValue );
if ( type_ == nullValue )
return null;
#ifndef JSON_VALUE_USE_INTERNAL_MAP
CZString actualKey( key, CZString::noDuplication );
ObjectValues::const_iterator it = value_.map_->find( actualKey );
if ( it == value_.map_->end() )
return null;
return (*it).second;
#else
const Value *value = value_.map_->find( key );
return value ? *value : null;
#endif
}
Value &
Value::operator[]( const std::string &key )
{
return (*this)[ key.c_str() ];
}
const Value &
Value::operator[]( const std::string &key ) const
{
return (*this)[ key.c_str() ];
}
Value &
Value::operator[]( const StaticString &key )
{
return resolveReference( key, true );
}
# ifdef JSON_USE_CPPTL
Value &
Value::operator[]( const CppTL::ConstString &key )
{
return (*this)[ key.c_str() ];
}
const Value &
Value::operator[]( const CppTL::ConstString &key ) const
{
return (*this)[ key.c_str() ];
}
# endif
Value &
Value::append( const Value &value )
{
return (*this)[size()] = value;
}
Value
Value::get( const char *key,
const Value &defaultValue ) const
{
const Value *value = &((*this)[key]);
return value == &null ? defaultValue : *value;
}
Value
Value::get( const std::string &key,
const Value &defaultValue ) const
{
return get( key.c_str(), defaultValue );
}
Value
Value::removeMember( const char* key )
{
JSON_ASSERT( type_ == nullValue || type_ == objectValue );
if ( type_ == nullValue )
return null;
#ifndef JSON_VALUE_USE_INTERNAL_MAP
CZString actualKey( key, CZString::noDuplication );
ObjectValues::iterator it = value_.map_->find( actualKey );
if ( it == value_.map_->end() )
return null;
Value old(it->second);
value_.map_->erase(it);
return old;
#else
Value *value = value_.map_->find( key );
if (value){
Value old(*value);
value_.map_.remove( key );
return old;
} else {
return null;
}
#endif
}
Value
Value::removeMember( const std::string &key )
{
return removeMember( key.c_str() );
}
# ifdef JSON_USE_CPPTL
Value
Value::get( const CppTL::ConstString &key,
const Value &defaultValue ) const
{
return get( key.c_str(), defaultValue );
}
# endif
bool
Value::isMember( const char *key ) const
{
const Value *value = &((*this)[key]);
return value != &null;
}
bool
Value::isMember( const std::string &key ) const
{
return isMember( key.c_str() );
}
# ifdef JSON_USE_CPPTL
bool
Value::isMember( const CppTL::ConstString &key ) const
{
return isMember( key.c_str() );
}
#endif
Value::Members
Value::getMemberNames() const
{
JSON_ASSERT( type_ == nullValue || type_ == objectValue );
if ( type_ == nullValue )
return Value::Members();
Members members;
members.reserve( value_.map_->size() );
#ifndef JSON_VALUE_USE_INTERNAL_MAP
ObjectValues::const_iterator it = value_.map_->begin();
ObjectValues::const_iterator itEnd = value_.map_->end();
for ( ; it != itEnd; ++it )
members.push_back( std::string( (*it).first.c_str() ) );
#else
ValueInternalMap::IteratorState it;
ValueInternalMap::IteratorState itEnd;
value_.map_->makeBeginIterator( it );
value_.map_->makeEndIterator( itEnd );
for ( ; !ValueInternalMap::equals( it, itEnd ); ValueInternalMap::increment(it) )
members.push_back( std::string( ValueInternalMap::key( it ) ) );
#endif
return members;
}
//
//# ifdef JSON_USE_CPPTL
//EnumMemberNames
//Value::enumMemberNames() const
//{
// if ( type_ == objectValue )
// {
// return CppTL::Enum::any( CppTL::Enum::transform(
// CppTL::Enum::keys( *(value_.map_), CppTL::Type<const CZString &>() ),
// MemberNamesTransform() ) );
// }
// return EnumMemberNames();
//}
//
//
//EnumValues
//Value::enumValues() const
//{
// if ( type_ == objectValue || type_ == arrayValue )
// return CppTL::Enum::anyValues( *(value_.map_),
// CppTL::Type<const Value &>() );
// return EnumValues();
//}
//
//# endif
bool
Value::isNull() const
{
return type_ == nullValue;
}
bool
Value::isBool() const
{
return type_ == booleanValue;
}
bool
Value::isInt() const
{
return type_ == intValue;
}
bool
Value::isUInt() const
{
return type_ == uintValue;
}
bool
Value::isIntegral() const
{
return type_ == intValue
|| type_ == uintValue
|| type_ == booleanValue;
}
bool
Value::isDouble() const
{
return type_ == realValue;
}
bool
Value::isNumeric() const
{
return isIntegral() || isDouble();
}
bool
Value::isString() const
{
return type_ == stringValue;
}
bool
Value::isArray() const
{
return type_ == nullValue || type_ == arrayValue;
}
bool
Value::isObject() const
{
return type_ == nullValue || type_ == objectValue;
}
void
Value::setComment( const char *comment,
CommentPlacement placement )
{
if ( !comments_ )
comments_ = new CommentInfo[numberOfCommentPlacement];
comments_[placement].setComment( comment );
}
void
Value::setComment( const std::string &comment,
CommentPlacement placement )
{
setComment( comment.c_str(), placement );
}
bool
Value::hasComment( CommentPlacement placement ) const
{
return comments_ != 0 && comments_[placement].comment_ != 0;
}
std::string
Value::getComment( CommentPlacement placement ) const
{
if ( hasComment(placement) )
return comments_[placement].comment_;
return "";
}
std::string
Value::toStyledString() const
{
StyledWriter writer;
return writer.write( *this );
}
Value::const_iterator
Value::begin() const
{
switch ( type_ )
{
#ifdef JSON_VALUE_USE_INTERNAL_MAP
case arrayValue:
if ( value_.array_ )
{
ValueInternalArray::IteratorState it;
value_.array_->makeBeginIterator( it );
return const_iterator( it );
}
break;
case objectValue:
if ( value_.map_ )
{
ValueInternalMap::IteratorState it;
value_.map_->makeBeginIterator( it );
return const_iterator( it );
}
break;
#else
case arrayValue:
case objectValue:
if ( value_.map_ )
return const_iterator( value_.map_->begin() );
break;
#endif
default:
break;
}
return const_iterator();
}
Value::const_iterator
Value::end() const
{
switch ( type_ )
{
#ifdef JSON_VALUE_USE_INTERNAL_MAP
case arrayValue:
if ( value_.array_ )
{
ValueInternalArray::IteratorState it;
value_.array_->makeEndIterator( it );
return const_iterator( it );
}
break;
case objectValue:
if ( value_.map_ )
{
ValueInternalMap::IteratorState it;
value_.map_->makeEndIterator( it );
return const_iterator( it );
}
break;
#else
case arrayValue:
case objectValue:
if ( value_.map_ )
return const_iterator( value_.map_->end() );
break;
#endif
default:
break;
}
return const_iterator();
}
Value::iterator
Value::begin()
{
switch ( type_ )
{
#ifdef JSON_VALUE_USE_INTERNAL_MAP
case arrayValue:
if ( value_.array_ )
{
ValueInternalArray::IteratorState it;
value_.array_->makeBeginIterator( it );
return iterator( it );
}
break;
case objectValue:
if ( value_.map_ )
{
ValueInternalMap::IteratorState it;
value_.map_->makeBeginIterator( it );
return iterator( it );
}
break;
#else
case arrayValue:
case objectValue:
if ( value_.map_ )
return iterator( value_.map_->begin() );
break;
#endif
default:
break;
}
return iterator();
}
Value::iterator
Value::end()
{
switch ( type_ )
{
#ifdef JSON_VALUE_USE_INTERNAL_MAP
case arrayValue:
if ( value_.array_ )
{
ValueInternalArray::IteratorState it;
value_.array_->makeEndIterator( it );
return iterator( it );
}
break;
case objectValue:
if ( value_.map_ )
{
ValueInternalMap::IteratorState it;
value_.map_->makeEndIterator( it );
return iterator( it );
}
break;
#else
case arrayValue:
case objectValue:
if ( value_.map_ )
return iterator( value_.map_->end() );
break;
#endif
default:
break;
}
return iterator();
}
// class PathArgument
// //////////////////////////////////////////////////////////////////
PathArgument::PathArgument()
: kind_( kindNone )
{
}
PathArgument::PathArgument( Value::UInt index )
: index_( index )
, kind_( kindIndex )
{
}
PathArgument::PathArgument( const char *key )
: key_( key )
, kind_( kindKey )
{
}
PathArgument::PathArgument( const std::string &key )
: key_( key.c_str() )
, kind_( kindKey )
{
}
// class Path
// //////////////////////////////////////////////////////////////////
Path::Path( const std::string &path,
const PathArgument &a1,
const PathArgument &a2,
const PathArgument &a3,
const PathArgument &a4,
const PathArgument &a5 )
{
InArgs in;
in.push_back( &a1 );
in.push_back( &a2 );
in.push_back( &a3 );
in.push_back( &a4 );
in.push_back( &a5 );
makePath( path, in );
}
void
Path::makePath( const std::string &path,
const InArgs &in )
{
const char *current = path.c_str();
const char *end = current + path.length();
InArgs::const_iterator itInArg = in.begin();
while ( current != end )
{
if ( *current == '[' )
{
++current;
if ( *current == '%' )
addPathInArg( path, in, itInArg, PathArgument::kindIndex );
else
{
Value::UInt index = 0;
for ( ; current != end && *current >= '0' && *current <= '9'; ++current )
index = index * 10 + Value::UInt(*current - '0');
args_.push_back( index );
}
if ( current == end || *current++ != ']' )
invalidPath( path, int(current - path.c_str()) );
}
else if ( *current == '%' )
{
addPathInArg( path, in, itInArg, PathArgument::kindKey );
++current;
}
else if ( *current == '.' )
{
++current;
}
else
{
const char *beginName = current;
while ( current != end && !strchr( "[.", *current ) )
++current;
args_.push_back( std::string( beginName, current ) );
}
}
}
void
Path::addPathInArg( const std::string &path,
const InArgs &in,
InArgs::const_iterator &itInArg,
PathArgument::Kind kind )
{
if ( itInArg == in.end() )
{
// Error: missing argument %d
}
else if ( (*itInArg)->kind_ != kind )
{
// Error: bad argument type
}
else
{
args_.push_back( **itInArg );
}
}
void
Path::invalidPath( const std::string &path,
int location )
{
// Error: invalid path.
}
const Value &
Path::resolve( const Value &root ) const
{
const Value *node = &root;
for ( Args::const_iterator it = args_.begin(); it != args_.end(); ++it )
{
const PathArgument &arg = *it;
if ( arg.kind_ == PathArgument::kindIndex )
{
if ( !node->isArray() || node->isValidIndex( arg.index_ ) )
{
// Error: unable to resolve path (array value expected at position...
}
node = &((*node)[arg.index_]);
}
else if ( arg.kind_ == PathArgument::kindKey )
{
if ( !node->isObject() )
{
// Error: unable to resolve path (object value expected at position...)
}
node = &((*node)[arg.key_]);
if ( node == &Value::null )
{
// Error: unable to resolve path (object has no member named '' at position...)
}
}
}
return *node;
}
Value
Path::resolve( const Value &root,
const Value &defaultValue ) const
{
const Value *node = &root;
for ( Args::const_iterator it = args_.begin(); it != args_.end(); ++it )
{
const PathArgument &arg = *it;
if ( arg.kind_ == PathArgument::kindIndex )
{
if ( !node->isArray() || node->isValidIndex( arg.index_ ) )
return defaultValue;
node = &((*node)[arg.index_]);
}
else if ( arg.kind_ == PathArgument::kindKey )
{
if ( !node->isObject() )
return defaultValue;
node = &((*node)[arg.key_]);
if ( node == &Value::null )
return defaultValue;
}
}
return *node;
}
Value &
Path::make( Value &root ) const
{
Value *node = &root;
for ( Args::const_iterator it = args_.begin(); it != args_.end(); ++it )
{
const PathArgument &arg = *it;
if ( arg.kind_ == PathArgument::kindIndex )
{
if ( !node->isArray() )
{
// Error: node is not an array at position ...
}
node = &((*node)[arg.index_]);
}
else if ( arg.kind_ == PathArgument::kindKey )
{
if ( !node->isObject() )
{
// Error: node is not an object at position...
}
node = &((*node)[arg.key_]);
}
}
return *node;
}
} // namespace Json
ILubyte *GetChannel(PspLoadState* state, ILimage* image)
{
BLOCKHEAD Block;
CHANNEL_CHUNK Channel;
ILubyte *CompData, *Data;
ILuint ChunkSize, Padding;
if (image->io.read(&image->io, &Block, 1, sizeof(Block)) != sizeof(Block))
return NULL;
if (state->Header.MajorVersion == 3)
Block.BlockLen = GetLittleUInt(&image->io);
else
UInt(&Block.BlockLen);
if (Block.HeadID[0] != 0x7E || Block.HeadID[1] != 0x42 ||
Block.HeadID[2] != 0x4B || Block.HeadID[3] != 0x00) {
il2SetError(IL_ILLEGAL_FILE_VALUE);
return NULL;
}
if (Block.BlockID != PSP_CHANNEL_BLOCK) {
il2SetError(IL_ILLEGAL_FILE_VALUE);
return NULL;
}
if (state->Header.MajorVersion >= 4) {
ChunkSize = GetLittleUInt(&image->io);
if (image->io.read(&image->io, &Channel, sizeof(Channel), 1) != 1)
return NULL;
Padding = (ChunkSize - 4) - sizeof(Channel);
if (Padding > 0)
image->io.seek(&image->io, Padding, IL_SEEK_CUR);
}
else {
if (image->io.read(&image->io, &Channel, sizeof(Channel), 1) != 1)
return NULL;
}
CompData = (ILubyte*)ialloc(Channel.CompLen);
Data = (ILubyte*)ialloc(state->AttChunk.Width * state->AttChunk.Height);
if (CompData == NULL || Data == NULL) {
ifree(Data);
ifree(CompData);
return NULL;
}
if (image->io.read(&image->io, CompData, 1, Channel.CompLen) != Channel.CompLen) {
ifree(CompData);
ifree(Data);
return NULL;
}
switch (state->AttChunk.Compression)
{
case PSP_COMP_NONE:
ifree(Data);
return CompData;
break;
case PSP_COMP_RLE:
if (!UncompRLE(CompData, Data, Channel.CompLen)) {
ifree(CompData);
ifree(Data);
return IL_FALSE;
}
break;
default:
ifree(CompData);
ifree(Data);
il2SetError(IL_INVALID_FILE_HEADER);
return NULL;
}
ifree(CompData);
return Data;
}
Expr const_true(int w) {
return make_one(UInt(1, w));
}
Expr const_false(int w) {
return make_zero(UInt(1, w));
}
Expr make_bool(bool val, int w) {
return make_const(UInt(1, w), val);
}
//-----------------------------------------------------------------------------------
void NetTranspondPacketProcesser::broadcastClientTranspondPackToFrontServer(
NetTranspondSendDataBufferPtr& dataPtr, Int dataSize, SRegionObjectBase* region)
{
#if 0
//---------------------------------------------------------------------
if (NULL == region)
{
DYNAMIC_EEXCEPT_LOG("NetTranspondPacketProcesser::broadcastClientTranspondPackToFrontServer : not find region!");
return;
}
//---------------------------------------------------------------------
// 转换成标准包格式
GameNetPacketData* packet = (GameNetPacketData*) dataPtr.mDataPtr->getLogicData();
if (NULL == packet)
{
DYNAMIC_ASSERT(0);
return;
}
// 设置标签
packet->channel = GNPC_NET_TRANSPOND;
packet->type = PT_NETTRANPOND_M2F_GROUP_TO_CLIENT;
// 转换转发包结构
PT_NETTRANPOND_CLIENT_GROUP_DATA* clientGroupData = ( PT_NETTRANPOND_CLIENT_GROUP_DATA* )packet->data;
if (NULL == clientGroupData)
{
DYNAMIC_ASSERT(0);
return;
}
// 初始化逻辑数据大小
clientGroupData->dataSize = dataSize;
clientGroupData->clientNetInfoCount = 0;
// 得到发送数据头大小
I32 sendDataHeadSize = GameNetPacketData_INFO::headSize + PT_NETTRANPOND_CLIENT_GROUP_DATA_INFO::headSize + dataSize;
ClientNetInfo* clientNetInfoArray = (ClientNetInfo*)( dataPtr.getTranspondData() + dataSize );
ClientNetInfo* clientNetInfo = NULL;
// 当前发送数据大小
I32 sendDataSize = sendDataHeadSize;
// 准备发送数据大小
I32 prepareSendDataSize = 0;
//---------------------------------------------------------------------
// 玩家对象
SPlayer* player = NULL;
// frontSvr网络编号
NetIdType frontServerID = 0;
// 玩家列表
std::map<AccountIdType, Player*>* playerList = NULL;
// 玩家列表iterator
std::map<AccountIdType, Player*>::iterator playerIter;
// 遍历玩家列表根据FrontServerSlot划分
std::vector<NetIdType> netList;
ServerManager::getInstance().getFrontServerList( netList );
for ( UInt i=0; i<netList.size(); i++ )
{
// frontSvr网络编号
frontServerID = netList[i];
// 获得玩家列表
playerList = region->getPlayerListByFronServerId(frontServerID);
// 如果为空则跳出
if ( playerList == NULL )
{
continue;
}
if ( playerList->size() == 0 )
{
continue;
}
// 遍历玩家列表
for ( playerIter = playerList->begin(); playerIter != playerList->end(); ++playerIter )
{
//---------------------------------------------------------------------
// 获得玩家对象
player = (SPlayer*)playerIter->second;
//---------------------------------------------------------------------
if ( dataPtr.mDataPtr.isNull() == false )
{
// 递增一个玩家准备发送数据大小到发送数据缓存大小
prepareSendDataSize = sendDataSize + PT_NETTRANPOND_CLIENT_GROUP_DATA_INFO::clientNetInfoSize;
// 如果准备发送数据大于缓存最大容量则发送
if ( prepareSendDataSize >= dataPtr.mDataPtr->getLogicDataMaxSize() )
{
MapServerMain::getInstance().getServerLauncher()->sendServer( dataPtr.mDataPtr, sendDataSize, frontServerID );
//------------------------------------------------------------------------------------
//Clone
{
// clone
MapServerMain::getInstance().getServerLauncher()->cloneSendDataBuffer( dataPtr.mDataPtr, dataPtr.mDataPtr, UInt(sendDataHeadSize) );
// 转换成标准包格式
packet = (GameNetPacketData*) dataPtr.mDataPtr->getLogicData();
if (NULL == packet)
{
DYNAMIC_ASSERT(0);
return;
}
// 设置标签
packet->channel = GNPC_NET_TRANSPOND;
packet->type = PT_NETTRANPOND_M2F_GROUP_TO_CLIENT;
// 转换转发包结构
clientGroupData = ( PT_NETTRANPOND_CLIENT_GROUP_DATA* )packet->data;
if (NULL == clientGroupData)
{
DYNAMIC_ASSERT(0);
return;
}
// 初始化逻辑数据大小
clientGroupData->dataSize = dataSize;
clientGroupData->clientNetInfoCount = 0;
// 得到发送数据头大小
clientNetInfoArray = (ClientNetInfo*)( dataPtr.getTranspondData() + dataSize );
// 当前发送数据大小
sendDataSize = sendDataHeadSize;
}
}
}
//---------------------------------------------------------------------
// 增加玩家记录
clientNetInfo = clientNetInfoArray + clientGroupData->clientNetInfoCount;
clientNetInfo->account_id = player->getAccountId();
clientNetInfo->client_net_id = player->getClientNetIdInFrontServer();
// 递增参数
sendDataSize += PT_NETTRANPOND_CLIENT_GROUP_DATA_INFO::clientNetInfoSize;
clientGroupData->clientNetInfoCount++;
}
//---------------------------------------------------------------------
// 如果有剩余则发送
if ( dataPtr.mDataPtr.isNull() == false )
{
if ( clientGroupData->clientNetInfoCount > 0 )
{
MapServerMain::getInstance().getServerLauncher()->sendServer(
dataPtr.mDataPtr,
sendDataSize,
frontServerID );
dataPtr.mDataPtr.setNull();
}
}
}
#endif
}
//-----------------------------------------------------------------------------------
void NetTranspondPacketProcesser::gridsBroadcastClientTranspondPackToFrontServer(
SSceneGrid* currSceneGrid,
SSceneGrid* lastSceneGrid,
NetTranspondSendDataBufferPtr& dataPtr,
Int dataSize,
PlayerIdType ignorePlayerId,
GridsBroadcastType broadcastType )
{
#if 0
//-----------------------------------------------------------------------------------
// 通过pos得到所在网格(一个)
// 通过这个网格得到需要广播的玩家列表(根据FrontServer分组)
//-----------------------------------------------------------------------------------
if (NULL == currSceneGrid && broadcastType == GBT_CURR)
{
/*DYNAMIC_ASSERT(0);*/
return;
}
//-----------------------------------------------------------------------------------
// 转换成标准包格式
GameNetPacketData* packet = (GameNetPacketData*) dataPtr.mDataPtr->getLogicData();
if (NULL == packet)
{
DYNAMIC_ASSERT(0);
return;
}
// 设置标签
packet->channel = GNPC_NET_TRANSPOND;
packet->type = PT_NETTRANPOND_M2F_GROUP_TO_CLIENT;
// 转换转发包结构
PT_NETTRANPOND_CLIENT_GROUP_DATA* clientGroupData = ( PT_NETTRANPOND_CLIENT_GROUP_DATA* )packet->data;
if (NULL == clientGroupData)
{
DYNAMIC_ASSERT(0);
return;
}
// 初始化逻辑数据大小
clientGroupData->dataSize = dataSize;
clientGroupData->clientNetInfoCount = 0;
// 得到发送数据头大小
I32 sendDataHeadSize = GameNetPacketData_INFO::headSize + PT_NETTRANPOND_CLIENT_GROUP_DATA_INFO::headSize + dataSize;
ClientNetInfo* clientNetInfoArray = (ClientNetInfo*)( dataPtr.getTranspondData() + dataSize );
ClientNetInfo* clientNetInfo = 0;
// 当前发送数据大小
I32 sendDataSize = sendDataHeadSize;
// 准备发送数据大小
I32 prepareSendDataSize = 0;
//-----------------------------------------------------------------------------------
// 玩家对象
SPlayer* player = NULL;
// frontSvr网络编号
NetIdType frontServerID = 0;
// 玩家列表
std::map<PlayerIdType, SPlayer*>* playerList = NULL;
// 玩家列表iterator
std::map<PlayerIdType, SPlayer*>::iterator playerIter;
// 是否克隆新的发送数据对象
std::map<NetIdType, std::map<PlayerIdType, SPlayer*>> newPlayerListList;
//-----------------------------------------------------------------------------------
if(broadcastType == GBT_CURR || !lastSceneGrid)
{
std::map<NetIdType, PlayerListInGrid*>* currPlayerListList = 0;//currSceneGrid->getPlayerInteractionListList();
PlayerListInGrid* currGridPlayerList = NULL;
for(std::map<NetIdType, PlayerListInGrid*>::iterator currListIt = currPlayerListList->begin(); currListIt != currPlayerListList->end(); ++currListIt)
{
currGridPlayerList = currListIt->second;
for(std::map<PlayerIdType, PlayerInGrid*>::iterator currIt = currGridPlayerList->mPlayerList.begin(); currIt != currGridPlayerList->mPlayerList.end(); ++currIt)
{
newPlayerListList[currListIt->first][currIt->first] = currIt->second->player;
}
}
}
else if((broadcastType == GBT_LAST))
{
std::map<NetIdType, PlayerListInGrid*>* lastPlayerListList = lastSceneGrid->getPlayerInteractionListList();
PlayerListInGrid* lastGridPlayerList = NULL;
for(std::map<NetIdType, PlayerListInGrid*>::iterator lastListIt = lastPlayerListList->begin(); lastListIt != lastPlayerListList->end(); ++lastListIt)
{
lastGridPlayerList = lastListIt->second;
for(std::map<PlayerIdType, PlayerInGrid*>::iterator lastIt = lastGridPlayerList->mPlayerList.begin(); lastIt != lastGridPlayerList->mPlayerList.end(); ++lastIt)
{
newPlayerListList[lastListIt->first][lastIt->first] = lastIt->second->player;
}
}
}
else if(broadcastType == GBT_FILTER_LAST)
{
subSceneGridsPlayerList(lastSceneGrid, currSceneGrid, newPlayerListList);
}
else if(broadcastType == GBT_FILTER_CURR)
{
subSceneGridsPlayerList(currSceneGrid, lastSceneGrid, newPlayerListList);
}
else
{
return;
}
//-----------------------------------------------------------------------------------
for (std::map<NetIdType, std::map<PlayerIdType, SPlayer*>>::iterator playerListIt = newPlayerListList.begin();
playerListIt != newPlayerListList.end();
++playerListIt)
{
// 获得玩家列表
playerList = &(playerListIt->second);
// 如果为空则跳出
if ( playerList == NULL )
{
continue;
}
if ( playerList->size() == 0 )
{
continue;
}
frontServerID = playerListIt->first;
// 遍历玩家列表
for ( playerIter = playerList->begin(); playerIter != playerList->end(); ++playerIter )
{
//-----------------------------------------------------------------------------------
// 获得玩家对象
player = playerIter->second;
if ( player->getAccountId() != (U64)playerIter->first )
{
//DYNAMIC_EEXCEPT_LOG("player->getAccountID != playerIter->first");
//DYNAMIC_ASSERT(false);
continue;
}
if(ignorePlayerId == player->getAccountId())
{
continue;
}
//-----------------------------------------------------------------------------------
if ( dataPtr.mDataPtr.isNull() == false )
{
// 递增一个玩家准备发送数据大小到发送数据缓存大小
prepareSendDataSize = sendDataSize + PT_NETTRANPOND_CLIENT_GROUP_DATA_INFO::clientNetInfoSize;
// 如果准备发送数据大于缓存最大容量则发送
if ( prepareSendDataSize >= dataPtr.mDataPtr->getLogicDataMaxSize() )
{
MapServerMain::getInstance().getServerLauncher()->sendServer( dataPtr.mDataPtr, sendDataSize, frontServerID );
//------------------------------------------------------------------------------------
// Clone
{
MapServerMain::getInstance().getServerLauncher()->cloneSendDataBuffer( dataPtr.mDataPtr , dataPtr.mDataPtr, UInt(sendDataHeadSize) );
// 转换成标准包格式
packet = (GameNetPacketData*) dataPtr.mDataPtr->getLogicData();
if (NULL == packet)
{
DYNAMIC_ASSERT(0);
return;
}
// 设置标签
packet->channel = GNPC_NET_TRANSPOND;
packet->type = PT_NETTRANPOND_M2F_GROUP_TO_CLIENT;
// 转换转发包结构
clientGroupData = ( PT_NETTRANPOND_CLIENT_GROUP_DATA* )packet->data;
if (NULL == clientGroupData)
{
DYNAMIC_ASSERT(0);
return;
}
// 初始化逻辑数据大小
clientGroupData->dataSize = dataSize;
clientGroupData->clientNetInfoCount = 0;
// 客户端信息
clientNetInfoArray = (ClientNetInfo*)( dataPtr.getTranspondData() + dataSize );
// 当前发送数据大小
sendDataSize = sendDataHeadSize;
}
}
}
//-----------------------------------------------------------------------------------
// 增加玩家记录
clientNetInfo = clientNetInfoArray + clientGroupData->clientNetInfoCount;
clientNetInfo->account_id = player->getAccountId();
clientNetInfo->client_net_id = player->getClientNetIdInFrontServer();
// 递增参数
sendDataSize += PT_NETTRANPOND_CLIENT_GROUP_DATA_INFO::clientNetInfoSize;
clientGroupData->clientNetInfoCount++;
}
// 如果有剩余则发送
if ( dataPtr.mDataPtr.isNull() == false )
{
if ( clientGroupData->clientNetInfoCount > 0 )
{
MapServerMain::getInstance().getServerLauncher()->sendServer(
dataPtr.mDataPtr,
sendDataSize,
frontServerID );
dataPtr.mDataPtr.setNull();
}
}
}
#endif
}
UInt getDecimalWidth(const Double value)
{
return (value == 0) ? 1 : (UInt(floor(log10(fabs(value)))) + ((value < 0) ? 2 : 1));
//for the minus sign
}
int main(int argc, char* argv[]) {
#ifdef USE_GOOGLE_PROFILER
char *profileFileName = getenv("CPUPROFILE");
if (profileFileName != NULL) {
ProfilerStart(profileFileName);
}
else {
ProfilerStart("google_profile.txt");
}
#endif
// Register inputs and outputs.
string samFileName, refFileName, outFileName;
CommandLineParser clp;
clp.RegisterStringOption("file.sam", &samFileName,
"Input SAM file.");
clp.RegisterStringOption("reference.fasta", &refFileName,
"Reference used to generate reads.");
clp.RegisterStringOption("out.sam", &outFileName,
"Output SAM file.");
clp.RegisterPreviousFlagsAsHidden();
// Register filter criteria options.
int minAlnLength = 50;
float minPctSimilarity = 70, minPctAccuracy = 70;
string hitPolicyStr = "randombest";
bool useScoreCutoff = false;
int scoreCutoff = INF_INT;
int scoreSignInt = -1;
RegisterFilterOptions(clp, minAlnLength, minPctSimilarity,
minPctAccuracy, hitPolicyStr, useScoreCutoff,
scoreSignInt, scoreCutoff);
int seed = 1;
clp.RegisterIntOption("seed", &seed,
"(1) Seed for random number generator.\n"
"If seed is 0, then use current time as seed.",
CommandLineParser::Integer);
string holeNumberStr;
Ranges holeNumberRanges;
clp.RegisterStringOption("holeNumbers", &holeNumberStr,
"A string of comma-delimited hole number ranges to output hits, "
"such as '1,2,10-12'. "
"This requires hit titles to be in SMRT read title format.");
bool parseSmrtTitle = false;
clp.RegisterFlagOption("smrtTitle", &parseSmrtTitle,
"Use this option when filtering alignments generated by "
"programs other than blasr, e.g. bwa-sw or gmap. "
" Parse read coordinates from the SMRT read title. "
"The title is in the format /name/hole/coordinates, where"
" coordinates are in the format \\d+_\\d+, and represent "
"the interval of the read that was aligned.");
/* This experimental option can be useful for metagenomics, in which case
* there are hundreds of sequences in the target, of which many titles are
* long and may contain white spaces (e.g., ' ', '\t').
* In order to save disc space and avoid the (possibly) none unique mapping
* between full and short reference names, one may call blasr with
* -titleTable option to represent all target sequences in the output
* by their indices in the title table.*/
string titleTableName = "";
clp.RegisterStringOption("titleTable", &titleTableName,
"Use this experimental option when filtering alignments generated by "
"blasr with -titleTable titleTableName, in which case "
"reference titles in SAM are represented by their "
"indices (e.g., 0, 1, 2, ...) in the title table.");
string adapterGffFileName = "";
clp.RegisterStringOption("filterAdapterOnly", &adapterGffFileName,
"Use this option to remove reads which can only map to adapters "
"specified in the GFF file.");
bool verbose = false;
clp.RegisterFlagOption("v", &verbose, "Be verbose.");
clp.SetExamples(
"Because SAM has optional tags that have different meanings"
" in different programs, careful usage is required in order "
"to have proper output. The \"xs\" tag in bwa-sw is used to "
"show the suboptimal score, but in PacBio SAM (blasr) it is "
"defined as the start in the query sequence of the alignment.\n"
"When \"-smrtTitle\" is specified, the xs tag is ignored, but "
"when it is not specified, the coordinates given by the xs and "
"xe tags are used to define the interval of a read that is "
"aligned. The CIGAR string is relative to this interval.");
clp.ParseCommandLine(argc, argv);
// Set random number seed.
if (seed == 0) {
srand(time(NULL));
} else {
srand(seed);
}
scoreSign = (scoreSignInt == -1)?ScoreSign::NEGATIVE:ScoreSign::POSITIVE;
Score s(static_cast<float>(scoreCutoff), scoreSign);
FilterCriteria filterCriteria(minAlnLength, minPctSimilarity,
minPctAccuracy, true, s);
filterCriteria.Verbose(verbose);
HitPolicy hitPolicy(hitPolicyStr, scoreSign);
string errMsg;
if (not filterCriteria.MakeSane(errMsg)) {
cout << errMsg << endl;
exit(1);
}
// Parse hole number ranges.
if (holeNumberStr.size() != 0) {
if (not holeNumberRanges.setRanges(holeNumberStr)) {
cout << "Could not parse hole number ranges: "
<< holeNumberStr << "." << endl;
exit(1);
}
}
// Open output file.
ostream * outFilePtr = &cout;
ofstream outFileStrm;
if (outFileName != "") {
CrucialOpen(outFileName, outFileStrm, std::ios::out);
outFilePtr = &outFileStrm;
}
GFFFile adapterGffFile;
if (adapterGffFileName != "")
adapterGffFile.ReadAll(adapterGffFileName);
SAMReader<SAMFullReferenceSequence, SAMReadGroup, SAMAlignment> samReader;
FASTAReader fastaReader;
//
// Initialize samReader and fastaReader.
//
samReader.Initialize(samFileName);
fastaReader.Initialize(refFileName);
//
// Configure the file log.
//
string command;
CommandLineParser::CommandLineToString(argc, argv, command);
string log = "Filter sam hits.";
string program = "samFilter";
string versionString = VERSION;
AppendPerforceChangelist(PERFORCE_VERSION_STRING, versionString);
//
// Read necessary input.
//
vector<FASTASequence> references;
fastaReader.ReadAllSequences(references);
// If the SAM file is generated by blasr with -titleTable,
// then references in the SAM are represented by
// their corresponding indices in the title table.
// In that case, we need to convert reference titles in fasta file
// to their corresponding indices in the title table, such that
// references in both SAM and fasta files are represented
// by title table indices and therefore can match.
if (titleTableName != "") {
ConvertTitlesToTitleTableIndices(references, titleTableName);
}
AlignmentSet<SAMFullReferenceSequence, SAMReadGroup, SAMAlignment> alignmentSet;
vector<string> allHeaders = samReader.ReadHeader(alignmentSet);
// Process SAM Header.
string commandLineString;
clp.CommandLineToString(argc, argv, commandLineString);
allHeaders.push_back("@PG\tID:SAMFILTER\tVN:" + versionString + \
"\tCL:" + program + " " + commandLineString);
for (int i = 0; i < allHeaders.size(); i++) {
outFileStrm << allHeaders[i] << endl;
}
//
// The order of references in vector<FASTASequence> references and
// AlignmentSet<, , >alignmentSet.references can be different.
// Rearrange alignmentSet.references such that they are ordered in
// exactly the same way as vector<FASTASequence> references.
//
alignmentSet.RearrangeReferences(references);
// Map reference name obtained from SAM file to indices
map<string, int> refNameToIndex;
for (int i = 0; i < references.size(); i++) {
string refName = alignmentSet.references[i].GetSequenceName();
refNameToIndex[refName] = i;
}
//
// Store the alignments.
//
SAMAlignment samAlignment;
int alignIndex = 0;
//
// For 150K, each chip produces about 300M sequences
// (not including quality values and etc.).
// Let's assume that the sam file and reference data can
// fit in the memory.
// Need to scale for larger sequal data in the future.
//
vector<SAMAlignment> allSAMAlignments;
while (samReader.GetNextAlignment(samAlignment)) {
if (samAlignment.rName == "*") {
continue;
}
if (parseSmrtTitle and holeNumberStr.size() != 0) {
string movieName;
int thisHoleNumber;
if (not ParsePBIReadName(samAlignment.qName,
movieName,
thisHoleNumber)) {
cout << "ERROR, could not parse SMRT title: "
<< samAlignment.qName << "." << endl;
exit(1);
}
if (not holeNumberRanges.contains(UInt(thisHoleNumber))) {
if (verbose)
cout << thisHoleNumber << " is not in range." << endl;
continue;
}
}
if (samAlignment.cigar.find('P') != string::npos) {
cout << "WARNING. Could not process SAM record with 'P' in "
<< "its cigar string." << endl;
continue;
}
vector<AlignmentCandidate<> > convertedAlignments;
SAMAlignmentsToCandidates(samAlignment,
references, refNameToIndex,
convertedAlignments, parseSmrtTitle, false);
if (convertedAlignments.size() > 1) {
cout << "WARNING. Ignore multiple segments." << endl;
continue;
}
for (int i = 0; i < 1; i++) {
AlignmentCandidate<> & alignment = convertedAlignments[i];
//score func does not matter
DistanceMatrixScoreFunction<DNASequence, DNASequence> distFunc;
ComputeAlignmentStats(alignment, alignment.qAlignedSeq.seq,
alignment.tAlignedSeq.seq, distFunc);
// Check whether this alignment can only map to adapters in
// the adapter GFF file.
if (adapterGffFileName != "" and
CheckAdapterOnly(adapterGffFile, alignment, refNameToIndex)) {
if (verbose)
cout << alignment.qName << " filter adapter only."
<< endl;
continue;
}
// Assign score to samAlignment.
samAlignment.score = samAlignment.as;
if (not filterCriteria.Satisfy(static_cast<AlignmentCandidate<> *>(&alignment))) {
continue;
}
allSAMAlignments.push_back( samAlignment );
alignment.FreeSubsequences();
}
++alignIndex;
}
// Sort all SAM alignments by qName, score and target position.
sort(allSAMAlignments.begin(), allSAMAlignments.end(),
byQNameScoreTStart);
unsigned int groupBegin = 0;
unsigned int groupEnd = -1;
vector<SAMAlignment> filteredSAMAlignments;
while(groupBegin < allSAMAlignments.size()) {
// Get the next group of SAM alignments which have the same qName
// from allSAMAlignments[groupBegin ... groupEnd)
GetNextSAMAlignmentGroup(allSAMAlignments, groupBegin, groupEnd);
vector<unsigned int> hitIndices = ApplyHitPolicy(
hitPolicy, allSAMAlignments, groupBegin, groupEnd);
for(unsigned int i = 0; i < hitIndices.size(); i++) {
filteredSAMAlignments.push_back(allSAMAlignments[hitIndices[i]]);
}
groupBegin = groupEnd;
}
// Sort all SAM alignments by reference name and query name
sort(filteredSAMAlignments.begin(), filteredSAMAlignments.end(),
byRNameQName);
for(unsigned int i = 0; i < filteredSAMAlignments.size(); i++) {
filteredSAMAlignments[i].PrintSAMAlignment(outFileStrm);
}
if (outFileName != "") {
outFileStrm.close();
}
#ifdef USE_GOOGLE_PROFILER
ProfilerStop();
#endif
return 0;
}
