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- data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/link.txt +1 -0
- data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/progress.make +5 -0
- data/ext/bamtools/src/utils/CMakeFiles/CMakeDirectoryInformation.cmake +23 -0
- data/ext/bamtools/src/utils/CMakeFiles/progress.marks +1 -0
- data/ext/bamtools/src/utils/CMakeLists.txt +30 -0
- data/ext/bamtools/src/utils/Makefile +290 -0
- data/ext/bamtools/src/utils/bamtools_fasta.cpp +632 -0
- data/ext/bamtools/src/utils/bamtools_fasta.h +47 -0
- data/ext/bamtools/src/utils/bamtools_filter_engine.h +552 -0
- data/ext/bamtools/src/utils/bamtools_filter_properties.h +195 -0
- data/ext/bamtools/src/utils/bamtools_filter_ruleparser.h +319 -0
- data/ext/bamtools/src/utils/bamtools_options.cpp +287 -0
- data/ext/bamtools/src/utils/bamtools_options.h +213 -0
- data/ext/bamtools/src/utils/bamtools_pileup_engine.cpp +327 -0
- data/ext/bamtools/src/utils/bamtools_pileup_engine.h +94 -0
- data/ext/bamtools/src/utils/bamtools_utilities.cpp +333 -0
- data/ext/bamtools/src/utils/bamtools_utilities.h +67 -0
- data/ext/bamtools/src/utils/bamtools_variant.h +128 -0
- data/ext/bamtools/src/utils/cmake_install.cmake +29 -0
- data/ext/bamtools/src/utils/utils_global.h +21 -0
- data/lib/ngs_server/version.rb +3 -0
- data/lib/ngs_server.rb +3 -0
- data/ngs_server.gemspec +23 -0
- metadata +339 -0
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// Copyright 2007-2010 Baptiste Lepilleur
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// Distributed under MIT license, or public domain if desired and
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// recognized in your jurisdiction.
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// See file LICENSE for detail or copy at http://jsoncpp.sourceforge.net/LICENSE
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// included by json_value.cpp
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// everything is within Json namespace
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// //////////////////////////////////////////////////////////////////
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// //////////////////////////////////////////////////////////////////
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// //////////////////////////////////////////////////////////////////
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// class ValueIteratorBase
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// //////////////////////////////////////////////////////////////////
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// //////////////////////////////////////////////////////////////////
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// //////////////////////////////////////////////////////////////////
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ValueIteratorBase::ValueIteratorBase()
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#ifndef JSON_VALUE_USE_INTERNAL_MAP
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: current_()
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, isNull_( true )
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{
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}
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#else
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: isArray_( true )
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, isNull_( true )
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{
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iterator_.array_ = ValueInternalArray::IteratorState();
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}
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#endif
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#ifndef JSON_VALUE_USE_INTERNAL_MAP
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ValueIteratorBase::ValueIteratorBase( const Value::ObjectValues::iterator ¤t )
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: current_( current )
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, isNull_( false )
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{
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}
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#else
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ValueIteratorBase::ValueIteratorBase( const ValueInternalArray::IteratorState &state )
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: isArray_( true )
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{
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iterator_.array_ = state;
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}
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ValueIteratorBase::ValueIteratorBase( const ValueInternalMap::IteratorState &state )
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: isArray_( false )
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{
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iterator_.map_ = state;
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}
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#endif
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Value &
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ValueIteratorBase::deref() const
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{
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#ifndef JSON_VALUE_USE_INTERNAL_MAP
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return current_->second;
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#else
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if ( isArray_ )
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return ValueInternalArray::dereference( iterator_.array_ );
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return ValueInternalMap::value( iterator_.map_ );
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#endif
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}
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void
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ValueIteratorBase::increment()
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{
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#ifndef JSON_VALUE_USE_INTERNAL_MAP
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++current_;
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#else
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if ( isArray_ )
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ValueInternalArray::increment( iterator_.array_ );
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ValueInternalMap::increment( iterator_.map_ );
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#endif
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}
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void
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ValueIteratorBase::decrement()
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{
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#ifndef JSON_VALUE_USE_INTERNAL_MAP
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--current_;
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#else
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if ( isArray_ )
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ValueInternalArray::decrement( iterator_.array_ );
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ValueInternalMap::decrement( iterator_.map_ );
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#endif
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}
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ValueIteratorBase::difference_type
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ValueIteratorBase::computeDistance( const SelfType &other ) const
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{
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#ifndef JSON_VALUE_USE_INTERNAL_MAP
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# ifdef JSON_USE_CPPTL_SMALLMAP
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return current_ - other.current_;
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# else
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// Iterator for null value are initialized using the default
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// constructor, which initialize current_ to the default
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// std::map::iterator. As begin() and end() are two instance
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// of the default std::map::iterator, they can not be compared.
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// To allow this, we handle this comparison specifically.
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if ( isNull_ && other.isNull_ )
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{
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return 0;
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}
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// Usage of std::distance is not portable (does not compile with Sun Studio 12 RogueWave STL,
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// which is the one used by default).
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// Using a portable hand-made version for non random iterator instead:
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// return difference_type( std::distance( current_, other.current_ ) );
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difference_type myDistance = 0;
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for ( Value::ObjectValues::iterator it = current_; it != other.current_; ++it )
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{
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++myDistance;
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}
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return myDistance;
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# endif
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#else
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if ( isArray_ )
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return ValueInternalArray::distance( iterator_.array_, other.iterator_.array_ );
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return ValueInternalMap::distance( iterator_.map_, other.iterator_.map_ );
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#endif
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}
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bool
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ValueIteratorBase::isEqual( const SelfType &other ) const
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{
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#ifndef JSON_VALUE_USE_INTERNAL_MAP
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if ( isNull_ )
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{
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return other.isNull_;
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}
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return current_ == other.current_;
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#else
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if ( isArray_ )
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return ValueInternalArray::equals( iterator_.array_, other.iterator_.array_ );
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return ValueInternalMap::equals( iterator_.map_, other.iterator_.map_ );
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#endif
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}
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void
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ValueIteratorBase::copy( const SelfType &other )
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{
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#ifndef JSON_VALUE_USE_INTERNAL_MAP
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current_ = other.current_;
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#else
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if ( isArray_ )
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iterator_.array_ = other.iterator_.array_;
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iterator_.map_ = other.iterator_.map_;
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#endif
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}
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Value
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ValueIteratorBase::key() const
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{
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#ifndef JSON_VALUE_USE_INTERNAL_MAP
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const Value::CZString czstring = (*current_).first;
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if ( czstring.c_str() )
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{
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if ( czstring.isStaticString() )
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return Value( StaticString( czstring.c_str() ) );
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return Value( czstring.c_str() );
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}
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return Value( czstring.index() );
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#else
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if ( isArray_ )
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return Value( ValueInternalArray::indexOf( iterator_.array_ ) );
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bool isStatic;
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const char *memberName = ValueInternalMap::key( iterator_.map_, isStatic );
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if ( isStatic )
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return Value( StaticString( memberName ) );
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return Value( memberName );
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#endif
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}
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UInt
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ValueIteratorBase::index() const
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{
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#ifndef JSON_VALUE_USE_INTERNAL_MAP
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const Value::CZString czstring = (*current_).first;
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if ( !czstring.c_str() )
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return czstring.index();
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return Value::UInt( -1 );
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#else
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if ( isArray_ )
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return Value::UInt( ValueInternalArray::indexOf( iterator_.array_ ) );
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return Value::UInt( -1 );
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#endif
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}
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const char *
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ValueIteratorBase::memberName() const
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{
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#ifndef JSON_VALUE_USE_INTERNAL_MAP
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const char *name = (*current_).first.c_str();
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return name ? name : "";
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#else
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if ( !isArray_ )
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return ValueInternalMap::key( iterator_.map_ );
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return "";
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#endif
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}
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// //////////////////////////////////////////////////////////////////
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// //////////////////////////////////////////////////////////////////
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// //////////////////////////////////////////////////////////////////
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// class ValueConstIterator
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// //////////////////////////////////////////////////////////////////
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// //////////////////////////////////////////////////////////////////
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// //////////////////////////////////////////////////////////////////
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ValueConstIterator::ValueConstIterator()
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{
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}
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#ifndef JSON_VALUE_USE_INTERNAL_MAP
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ValueConstIterator::ValueConstIterator( const Value::ObjectValues::iterator ¤t )
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: ValueIteratorBase( current )
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{
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}
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#else
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ValueConstIterator::ValueConstIterator( const ValueInternalArray::IteratorState &state )
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: ValueIteratorBase( state )
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{
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}
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ValueConstIterator::ValueConstIterator( const ValueInternalMap::IteratorState &state )
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: ValueIteratorBase( state )
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{
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}
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#endif
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ValueConstIterator &
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ValueConstIterator::operator =( const ValueIteratorBase &other )
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{
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copy( other );
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return *this;
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}
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// //////////////////////////////////////////////////////////////////
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// //////////////////////////////////////////////////////////////////
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// //////////////////////////////////////////////////////////////////
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// class ValueIterator
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// //////////////////////////////////////////////////////////////////
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// //////////////////////////////////////////////////////////////////
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// //////////////////////////////////////////////////////////////////
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ValueIterator::ValueIterator()
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{
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}
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#ifndef JSON_VALUE_USE_INTERNAL_MAP
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ValueIterator::ValueIterator( const Value::ObjectValues::iterator ¤t )
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: ValueIteratorBase( current )
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{
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}
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#else
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ValueIterator::ValueIterator( const ValueInternalArray::IteratorState &state )
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: ValueIteratorBase( state )
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{
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}
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ValueIterator::ValueIterator( const ValueInternalMap::IteratorState &state )
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: ValueIteratorBase( state )
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{
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}
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#endif
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ValueIterator::ValueIterator( const ValueConstIterator &other )
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: ValueIteratorBase( other )
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{
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}
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ValueIterator::ValueIterator( const ValueIterator &other )
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: ValueIteratorBase( other )
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{
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}
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ValueIterator &
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ValueIterator::operator =( const SelfType &other )
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{
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copy( other );
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return *this;
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}
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