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- data/ext/bamtools/src/utils/CMakeFiles/BamTools-utils.dir/flags.make +8 -0
- 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 ValueInternalArray
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// //////////////////////////////////////////////////////////////////
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// //////////////////////////////////////////////////////////////////
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// //////////////////////////////////////////////////////////////////
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ValueArrayAllocator::~ValueArrayAllocator()
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{
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}
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// //////////////////////////////////////////////////////////////////
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// class DefaultValueArrayAllocator
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// //////////////////////////////////////////////////////////////////
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#ifdef JSON_USE_SIMPLE_INTERNAL_ALLOCATOR
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class DefaultValueArrayAllocator : public ValueArrayAllocator
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{
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public: // overridden from ValueArrayAllocator
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virtual ~DefaultValueArrayAllocator()
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{
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}
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virtual ValueInternalArray *newArray()
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{
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return new ValueInternalArray();
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}
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virtual ValueInternalArray *newArrayCopy( const ValueInternalArray &other )
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{
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return new ValueInternalArray( other );
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}
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virtual void destructArray( ValueInternalArray *array )
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{
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delete array;
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}
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virtual void reallocateArrayPageIndex( Value **&indexes,
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ValueInternalArray::PageIndex &indexCount,
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ValueInternalArray::PageIndex minNewIndexCount )
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{
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ValueInternalArray::PageIndex newIndexCount = (indexCount*3)/2 + 1;
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if ( minNewIndexCount > newIndexCount )
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newIndexCount = minNewIndexCount;
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void *newIndexes = realloc( indexes, sizeof(Value*) * newIndexCount );
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if ( !newIndexes )
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throw std::bad_alloc();
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indexCount = newIndexCount;
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indexes = static_cast<Value **>( newIndexes );
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}
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virtual void releaseArrayPageIndex( Value **indexes,
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ValueInternalArray::PageIndex indexCount )
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{
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if ( indexes )
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free( indexes );
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}
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virtual Value *allocateArrayPage()
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{
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return static_cast<Value *>( malloc( sizeof(Value) * ValueInternalArray::itemsPerPage ) );
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}
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virtual void releaseArrayPage( Value *value )
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{
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if ( value )
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free( value );
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}
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};
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#else // #ifdef JSON_USE_SIMPLE_INTERNAL_ALLOCATOR
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/// @todo make this thread-safe (lock when accessign batch allocator)
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class DefaultValueArrayAllocator : public ValueArrayAllocator
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{
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public: // overridden from ValueArrayAllocator
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virtual ~DefaultValueArrayAllocator()
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{
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}
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virtual ValueInternalArray *newArray()
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{
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ValueInternalArray *array = arraysAllocator_.allocate();
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new (array) ValueInternalArray(); // placement new
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return array;
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}
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virtual ValueInternalArray *newArrayCopy( const ValueInternalArray &other )
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{
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ValueInternalArray *array = arraysAllocator_.allocate();
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new (array) ValueInternalArray( other ); // placement new
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return array;
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}
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virtual void destructArray( ValueInternalArray *array )
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{
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if ( array )
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{
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array->~ValueInternalArray();
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arraysAllocator_.release( array );
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}
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}
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virtual void reallocateArrayPageIndex( Value **&indexes,
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ValueInternalArray::PageIndex &indexCount,
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ValueInternalArray::PageIndex minNewIndexCount )
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{
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ValueInternalArray::PageIndex newIndexCount = (indexCount*3)/2 + 1;
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if ( minNewIndexCount > newIndexCount )
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newIndexCount = minNewIndexCount;
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void *newIndexes = realloc( indexes, sizeof(Value*) * newIndexCount );
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if ( !newIndexes )
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throw std::bad_alloc();
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indexCount = newIndexCount;
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indexes = static_cast<Value **>( newIndexes );
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}
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virtual void releaseArrayPageIndex( Value **indexes,
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ValueInternalArray::PageIndex indexCount )
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{
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if ( indexes )
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free( indexes );
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}
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virtual Value *allocateArrayPage()
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{
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return static_cast<Value *>( pagesAllocator_.allocate() );
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}
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virtual void releaseArrayPage( Value *value )
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{
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if ( value )
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pagesAllocator_.release( value );
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}
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private:
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BatchAllocator<ValueInternalArray,1> arraysAllocator_;
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BatchAllocator<Value,ValueInternalArray::itemsPerPage> pagesAllocator_;
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};
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#endif // #ifdef JSON_USE_SIMPLE_INTERNAL_ALLOCATOR
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static ValueArrayAllocator *&arrayAllocator()
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{
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static DefaultValueArrayAllocator defaultAllocator;
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static ValueArrayAllocator *arrayAllocator = &defaultAllocator;
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return arrayAllocator;
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}
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static struct DummyArrayAllocatorInitializer {
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DummyArrayAllocatorInitializer()
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{
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arrayAllocator(); // ensure arrayAllocator() statics are initialized before main().
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}
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} dummyArrayAllocatorInitializer;
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// //////////////////////////////////////////////////////////////////
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// class ValueInternalArray
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// //////////////////////////////////////////////////////////////////
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bool
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ValueInternalArray::equals( const IteratorState &x,
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const IteratorState &other )
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{
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return x.array_ == other.array_
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&& x.currentItemIndex_ == other.currentItemIndex_
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&& x.currentPageIndex_ == other.currentPageIndex_;
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}
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void
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ValueInternalArray::increment( IteratorState &it )
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{
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JSON_ASSERT_MESSAGE( it.array_ &&
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(it.currentPageIndex_ - it.array_->pages_)*itemsPerPage + it.currentItemIndex_
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!= it.array_->size_,
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"ValueInternalArray::increment(): moving iterator beyond end" );
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++(it.currentItemIndex_);
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if ( it.currentItemIndex_ == itemsPerPage )
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{
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it.currentItemIndex_ = 0;
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++(it.currentPageIndex_);
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}
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}
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void
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ValueInternalArray::decrement( IteratorState &it )
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{
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JSON_ASSERT_MESSAGE( it.array_ && it.currentPageIndex_ == it.array_->pages_
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&& it.currentItemIndex_ == 0,
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"ValueInternalArray::decrement(): moving iterator beyond end" );
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if ( it.currentItemIndex_ == 0 )
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{
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it.currentItemIndex_ = itemsPerPage-1;
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--(it.currentPageIndex_);
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}
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else
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{
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--(it.currentItemIndex_);
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}
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}
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Value &
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ValueInternalArray::unsafeDereference( const IteratorState &it )
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{
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return (*(it.currentPageIndex_))[it.currentItemIndex_];
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}
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Value &
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ValueInternalArray::dereference( const IteratorState &it )
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{
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JSON_ASSERT_MESSAGE( it.array_ &&
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(it.currentPageIndex_ - it.array_->pages_)*itemsPerPage + it.currentItemIndex_
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< it.array_->size_,
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"ValueInternalArray::dereference(): dereferencing invalid iterator" );
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return unsafeDereference( it );
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}
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void
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ValueInternalArray::makeBeginIterator( IteratorState &it ) const
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{
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it.array_ = const_cast<ValueInternalArray *>( this );
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it.currentItemIndex_ = 0;
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it.currentPageIndex_ = pages_;
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}
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void
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ValueInternalArray::makeIterator( IteratorState &it, ArrayIndex index ) const
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{
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it.array_ = const_cast<ValueInternalArray *>( this );
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it.currentItemIndex_ = index % itemsPerPage;
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it.currentPageIndex_ = pages_ + index / itemsPerPage;
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}
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void
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ValueInternalArray::makeEndIterator( IteratorState &it ) const
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{
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makeIterator( it, size_ );
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}
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ValueInternalArray::ValueInternalArray()
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: pages_( 0 )
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, size_( 0 )
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, pageCount_( 0 )
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{
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}
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ValueInternalArray::ValueInternalArray( const ValueInternalArray &other )
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: pages_( 0 )
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, pageCount_( 0 )
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, size_( other.size_ )
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{
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PageIndex minNewPages = other.size_ / itemsPerPage;
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arrayAllocator()->reallocateArrayPageIndex( pages_, pageCount_, minNewPages );
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JSON_ASSERT_MESSAGE( pageCount_ >= minNewPages,
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"ValueInternalArray::reserve(): bad reallocation" );
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IteratorState itOther;
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other.makeBeginIterator( itOther );
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Value *value;
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for ( ArrayIndex index = 0; index < size_; ++index, increment(itOther) )
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{
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if ( index % itemsPerPage == 0 )
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{
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PageIndex pageIndex = index / itemsPerPage;
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value = arrayAllocator()->allocateArrayPage();
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pages_[pageIndex] = value;
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}
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new (value) Value( dereference( itOther ) );
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}
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}
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ValueInternalArray &
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ValueInternalArray::operator =( const ValueInternalArray &other )
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{
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ValueInternalArray temp( other );
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swap( temp );
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return *this;
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}
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ValueInternalArray::~ValueInternalArray()
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{
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// destroy all constructed items
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IteratorState it;
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IteratorState itEnd;
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makeBeginIterator( it);
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makeEndIterator( itEnd );
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for ( ; !equals(it,itEnd); increment(it) )
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{
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Value *value = &dereference(it);
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value->~Value();
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}
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// release all pages
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PageIndex lastPageIndex = size_ / itemsPerPage;
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for ( PageIndex pageIndex = 0; pageIndex < lastPageIndex; ++pageIndex )
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arrayAllocator()->releaseArrayPage( pages_[pageIndex] );
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// release pages index
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arrayAllocator()->releaseArrayPageIndex( pages_, pageCount_ );
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}
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void
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ValueInternalArray::swap( ValueInternalArray &other )
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{
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Value **tempPages = pages_;
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pages_ = other.pages_;
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other.pages_ = tempPages;
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ArrayIndex tempSize = size_;
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size_ = other.size_;
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other.size_ = tempSize;
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PageIndex tempPageCount = pageCount_;
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pageCount_ = other.pageCount_;
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other.pageCount_ = tempPageCount;
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}
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void
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ValueInternalArray::clear()
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{
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ValueInternalArray dummy;
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swap( dummy );
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}
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void
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ValueInternalArray::resize( ArrayIndex newSize )
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{
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if ( newSize == 0 )
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clear();
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else if ( newSize < size_ )
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{
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IteratorState it;
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IteratorState itEnd;
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makeIterator( it, newSize );
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makeIterator( itEnd, size_ );
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for ( ; !equals(it,itEnd); increment(it) )
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{
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Value *value = &dereference(it);
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value->~Value();
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}
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PageIndex pageIndex = (newSize + itemsPerPage - 1) / itemsPerPage;
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PageIndex lastPageIndex = size_ / itemsPerPage;
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for ( ; pageIndex < lastPageIndex; ++pageIndex )
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arrayAllocator()->releaseArrayPage( pages_[pageIndex] );
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size_ = newSize;
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}
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else if ( newSize > size_ )
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resolveReference( newSize );
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}
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void
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ValueInternalArray::makeIndexValid( ArrayIndex index )
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{
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// Need to enlarge page index ?
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if ( index >= pageCount_ * itemsPerPage )
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{
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PageIndex minNewPages = (index + 1) / itemsPerPage;
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arrayAllocator()->reallocateArrayPageIndex( pages_, pageCount_, minNewPages );
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JSON_ASSERT_MESSAGE( pageCount_ >= minNewPages, "ValueInternalArray::reserve(): bad reallocation" );
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}
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// Need to allocate new pages ?
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ArrayIndex nextPageIndex =
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|
+
(size_ % itemsPerPage) != 0 ? size_ - (size_%itemsPerPage) + itemsPerPage
|
376
|
+
: size_;
|
377
|
+
if ( nextPageIndex <= index )
|
378
|
+
{
|
379
|
+
PageIndex pageIndex = nextPageIndex / itemsPerPage;
|
380
|
+
PageIndex pageToAllocate = (index - nextPageIndex) / itemsPerPage + 1;
|
381
|
+
for ( ; pageToAllocate-- > 0; ++pageIndex )
|
382
|
+
pages_[pageIndex] = arrayAllocator()->allocateArrayPage();
|
383
|
+
}
|
384
|
+
|
385
|
+
// Initialize all new entries
|
386
|
+
IteratorState it;
|
387
|
+
IteratorState itEnd;
|
388
|
+
makeIterator( it, size_ );
|
389
|
+
size_ = index + 1;
|
390
|
+
makeIterator( itEnd, size_ );
|
391
|
+
for ( ; !equals(it,itEnd); increment(it) )
|
392
|
+
{
|
393
|
+
Value *value = &dereference(it);
|
394
|
+
new (value) Value(); // Construct a default value using placement new
|
395
|
+
}
|
396
|
+
}
|
397
|
+
|
398
|
+
Value &
|
399
|
+
ValueInternalArray::resolveReference( ArrayIndex index )
|
400
|
+
{
|
401
|
+
if ( index >= size_ )
|
402
|
+
makeIndexValid( index );
|
403
|
+
return pages_[index/itemsPerPage][index%itemsPerPage];
|
404
|
+
}
|
405
|
+
|
406
|
+
Value *
|
407
|
+
ValueInternalArray::find( ArrayIndex index ) const
|
408
|
+
{
|
409
|
+
if ( index >= size_ )
|
410
|
+
return 0;
|
411
|
+
return &(pages_[index/itemsPerPage][index%itemsPerPage]);
|
412
|
+
}
|
413
|
+
|
414
|
+
ValueInternalArray::ArrayIndex
|
415
|
+
ValueInternalArray::size() const
|
416
|
+
{
|
417
|
+
return size_;
|
418
|
+
}
|
419
|
+
|
420
|
+
int
|
421
|
+
ValueInternalArray::distance( const IteratorState &x, const IteratorState &y )
|
422
|
+
{
|
423
|
+
return indexOf(y) - indexOf(x);
|
424
|
+
}
|
425
|
+
|
426
|
+
|
427
|
+
ValueInternalArray::ArrayIndex
|
428
|
+
ValueInternalArray::indexOf( const IteratorState &iterator )
|
429
|
+
{
|
430
|
+
if ( !iterator.array_ )
|
431
|
+
return ArrayIndex(-1);
|
432
|
+
return ArrayIndex(
|
433
|
+
(iterator.currentPageIndex_ - iterator.array_->pages_) * itemsPerPage
|
434
|
+
+ iterator.currentItemIndex_ );
|
435
|
+
}
|
436
|
+
|
437
|
+
|
438
|
+
int
|
439
|
+
ValueInternalArray::compare( const ValueInternalArray &other ) const
|
440
|
+
{
|
441
|
+
int sizeDiff( size_ - other.size_ );
|
442
|
+
if ( sizeDiff != 0 )
|
443
|
+
return sizeDiff;
|
444
|
+
|
445
|
+
for ( ArrayIndex index =0; index < size_; ++index )
|
446
|
+
{
|
447
|
+
int diff = pages_[index/itemsPerPage][index%itemsPerPage].compare(
|
448
|
+
other.pages_[index/itemsPerPage][index%itemsPerPage] );
|
449
|
+
if ( diff != 0 )
|
450
|
+
return diff;
|
451
|
+
}
|
452
|
+
return 0;
|
453
|
+
}
|