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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
@@ -0,0 +1,612 @@
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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 ValueInternalMap
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// //////////////////////////////////////////////////////////////////
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// //////////////////////////////////////////////////////////////////
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// //////////////////////////////////////////////////////////////////
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/** \internal MUST be safely initialized using memset( this, 0, sizeof(ValueInternalLink) );
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* This optimization is used by the fast allocator.
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*/
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ValueInternalLink::ValueInternalLink()
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: previous_( 0 )
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, next_( 0 )
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{
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}
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ValueInternalLink::~ValueInternalLink()
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{
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for ( int index =0; index < itemPerLink; ++index )
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{
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if ( !items_[index].isItemAvailable() )
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{
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if ( !items_[index].isMemberNameStatic() )
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free( keys_[index] );
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}
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else
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break;
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}
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}
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ValueMapAllocator::~ValueMapAllocator()
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{
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}
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#ifdef JSON_USE_SIMPLE_INTERNAL_ALLOCATOR
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class DefaultValueMapAllocator : public ValueMapAllocator
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{
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public: // overridden from ValueMapAllocator
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virtual ValueInternalMap *newMap()
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{
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return new ValueInternalMap();
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}
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virtual ValueInternalMap *newMapCopy( const ValueInternalMap &other )
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{
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return new ValueInternalMap( other );
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}
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virtual void destructMap( ValueInternalMap *map )
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{
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delete map;
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}
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virtual ValueInternalLink *allocateMapBuckets( unsigned int size )
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{
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return new ValueInternalLink[size];
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}
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virtual void releaseMapBuckets( ValueInternalLink *links )
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{
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delete [] links;
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}
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virtual ValueInternalLink *allocateMapLink()
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{
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return new ValueInternalLink();
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}
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virtual void releaseMapLink( ValueInternalLink *link )
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{
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delete link;
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}
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};
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#else
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/// @todo make this thread-safe (lock when accessign batch allocator)
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class DefaultValueMapAllocator : public ValueMapAllocator
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{
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public: // overridden from ValueMapAllocator
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virtual ValueInternalMap *newMap()
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{
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ValueInternalMap *map = mapsAllocator_.allocate();
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new (map) ValueInternalMap(); // placement new
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return map;
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}
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virtual ValueInternalMap *newMapCopy( const ValueInternalMap &other )
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{
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ValueInternalMap *map = mapsAllocator_.allocate();
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new (map) ValueInternalMap( other ); // placement new
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return map;
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}
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virtual void destructMap( ValueInternalMap *map )
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{
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if ( map )
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{
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map->~ValueInternalMap();
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mapsAllocator_.release( map );
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}
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}
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virtual ValueInternalLink *allocateMapBuckets( unsigned int size )
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{
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return new ValueInternalLink[size];
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}
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virtual void releaseMapBuckets( ValueInternalLink *links )
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{
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delete [] links;
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}
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virtual ValueInternalLink *allocateMapLink()
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{
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ValueInternalLink *link = linksAllocator_.allocate();
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memset( link, 0, sizeof(ValueInternalLink) );
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return link;
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}
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virtual void releaseMapLink( ValueInternalLink *link )
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{
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link->~ValueInternalLink();
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linksAllocator_.release( link );
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}
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private:
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BatchAllocator<ValueInternalMap,1> mapsAllocator_;
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BatchAllocator<ValueInternalLink,1> linksAllocator_;
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};
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#endif
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static ValueMapAllocator *&mapAllocator()
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{
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static DefaultValueMapAllocator defaultAllocator;
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static ValueMapAllocator *mapAllocator = &defaultAllocator;
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return mapAllocator;
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}
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static struct DummyMapAllocatorInitializer {
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DummyMapAllocatorInitializer()
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{
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mapAllocator(); // ensure mapAllocator() statics are initialized before main().
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}
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} dummyMapAllocatorInitializer;
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// h(K) = value * K >> w ; with w = 32 & K prime w.r.t. 2^32.
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/*
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use linked list hash map.
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buckets array is a container.
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linked list element contains 6 key/values. (memory = (16+4) * 6 + 4 = 124)
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value have extra state: valid, available, deleted
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*/
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ValueInternalMap::ValueInternalMap()
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: buckets_( 0 )
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, tailLink_( 0 )
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, bucketsSize_( 0 )
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, itemCount_( 0 )
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{
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}
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ValueInternalMap::ValueInternalMap( const ValueInternalMap &other )
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: buckets_( 0 )
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, tailLink_( 0 )
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, bucketsSize_( 0 )
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, itemCount_( 0 )
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{
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reserve( other.itemCount_ );
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IteratorState it;
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IteratorState itEnd;
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other.makeBeginIterator( it );
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other.makeEndIterator( itEnd );
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for ( ; !equals(it,itEnd); increment(it) )
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{
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bool isStatic;
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const char *memberName = key( it, isStatic );
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const Value &aValue = value( it );
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resolveReference(memberName, isStatic) = aValue;
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}
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}
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ValueInternalMap &
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ValueInternalMap::operator =( const ValueInternalMap &other )
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{
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ValueInternalMap dummy( other );
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swap( dummy );
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return *this;
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}
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ValueInternalMap::~ValueInternalMap()
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{
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if ( buckets_ )
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{
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for ( BucketIndex bucketIndex =0; bucketIndex < bucketsSize_; ++bucketIndex )
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{
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ValueInternalLink *link = buckets_[bucketIndex].next_;
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while ( link )
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{
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ValueInternalLink *linkToRelease = link;
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link = link->next_;
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mapAllocator()->releaseMapLink( linkToRelease );
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}
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}
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mapAllocator()->releaseMapBuckets( buckets_ );
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}
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}
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void
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ValueInternalMap::swap( ValueInternalMap &other )
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{
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ValueInternalLink *tempBuckets = buckets_;
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buckets_ = other.buckets_;
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other.buckets_ = tempBuckets;
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ValueInternalLink *tempTailLink = tailLink_;
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tailLink_ = other.tailLink_;
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other.tailLink_ = tempTailLink;
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BucketIndex tempBucketsSize = bucketsSize_;
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bucketsSize_ = other.bucketsSize_;
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other.bucketsSize_ = tempBucketsSize;
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BucketIndex tempItemCount = itemCount_;
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itemCount_ = other.itemCount_;
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other.itemCount_ = tempItemCount;
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}
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void
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ValueInternalMap::clear()
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{
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ValueInternalMap dummy;
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swap( dummy );
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}
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ValueInternalMap::BucketIndex
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ValueInternalMap::size() const
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{
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return itemCount_;
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}
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bool
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ValueInternalMap::reserveDelta( BucketIndex growth )
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{
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return reserve( itemCount_ + growth );
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}
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bool
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ValueInternalMap::reserve( BucketIndex newItemCount )
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{
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if ( !buckets_ && newItemCount > 0 )
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{
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buckets_ = mapAllocator()->allocateMapBuckets( 1 );
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bucketsSize_ = 1;
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tailLink_ = &buckets_[0];
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}
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// BucketIndex idealBucketCount = (newItemCount + ValueInternalLink::itemPerLink) / ValueInternalLink::itemPerLink;
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return true;
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}
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const Value *
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ValueInternalMap::find( const char *key ) const
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{
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if ( !bucketsSize_ )
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return 0;
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HashKey hashedKey = hash( key );
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BucketIndex bucketIndex = hashedKey % bucketsSize_;
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for ( const ValueInternalLink *current = &buckets_[bucketIndex];
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current != 0;
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current = current->next_ )
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{
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for ( BucketIndex index=0; index < ValueInternalLink::itemPerLink; ++index )
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{
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if ( current->items_[index].isItemAvailable() )
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return 0;
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if ( strcmp( key, current->keys_[index] ) == 0 )
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return ¤t->items_[index];
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}
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}
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return 0;
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}
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Value *
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ValueInternalMap::find( const char *key )
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{
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const ValueInternalMap *constThis = this;
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return const_cast<Value *>( constThis->find( key ) );
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}
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Value &
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ValueInternalMap::resolveReference( const char *key,
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bool isStatic )
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{
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HashKey hashedKey = hash( key );
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if ( bucketsSize_ )
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{
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BucketIndex bucketIndex = hashedKey % bucketsSize_;
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ValueInternalLink **previous = 0;
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BucketIndex index;
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for ( ValueInternalLink *current = &buckets_[bucketIndex];
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current != 0;
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previous = ¤t->next_, current = current->next_ )
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{
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for ( index=0; index < ValueInternalLink::itemPerLink; ++index )
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{
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if ( current->items_[index].isItemAvailable() )
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return setNewItem( key, isStatic, current, index );
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if ( strcmp( key, current->keys_[index] ) == 0 )
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return current->items_[index];
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}
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}
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}
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reserveDelta( 1 );
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return unsafeAdd( key, isStatic, hashedKey );
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}
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void
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ValueInternalMap::remove( const char *key )
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{
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HashKey hashedKey = hash( key );
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if ( !bucketsSize_ )
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return;
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BucketIndex bucketIndex = hashedKey % bucketsSize_;
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for ( ValueInternalLink *link = &buckets_[bucketIndex];
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link != 0;
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link = link->next_ )
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{
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BucketIndex index;
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for ( index =0; index < ValueInternalLink::itemPerLink; ++index )
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{
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if ( link->items_[index].isItemAvailable() )
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return;
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if ( strcmp( key, link->keys_[index] ) == 0 )
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{
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doActualRemove( link, index, bucketIndex );
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return;
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}
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}
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}
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}
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void
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ValueInternalMap::doActualRemove( ValueInternalLink *link,
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BucketIndex index,
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BucketIndex bucketIndex )
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{
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// find last item of the bucket and swap it with the 'removed' one.
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// set removed items flags to 'available'.
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// if last page only contains 'available' items, then desallocate it (it's empty)
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ValueInternalLink *&lastLink = getLastLinkInBucket( index );
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BucketIndex lastItemIndex = 1; // a link can never be empty, so start at 1
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for ( ;
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lastItemIndex < ValueInternalLink::itemPerLink;
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++lastItemIndex ) // may be optimized with dicotomic search
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{
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if ( lastLink->items_[lastItemIndex].isItemAvailable() )
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break;
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}
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BucketIndex lastUsedIndex = lastItemIndex - 1;
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Value *valueToDelete = &link->items_[index];
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Value *valueToPreserve = &lastLink->items_[lastUsedIndex];
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if ( valueToDelete != valueToPreserve )
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|
+
valueToDelete->swap( *valueToPreserve );
|
385
|
+
if ( lastUsedIndex == 0 ) // page is now empty
|
386
|
+
{ // remove it from bucket linked list and delete it.
|
387
|
+
ValueInternalLink *linkPreviousToLast = lastLink->previous_;
|
388
|
+
if ( linkPreviousToLast != 0 ) // can not deleted bucket link.
|
389
|
+
{
|
390
|
+
mapAllocator()->releaseMapLink( lastLink );
|
391
|
+
linkPreviousToLast->next_ = 0;
|
392
|
+
lastLink = linkPreviousToLast;
|
393
|
+
}
|
394
|
+
}
|
395
|
+
else
|
396
|
+
{
|
397
|
+
Value dummy;
|
398
|
+
valueToPreserve->swap( dummy ); // restore deleted to default Value.
|
399
|
+
valueToPreserve->setItemUsed( false );
|
400
|
+
}
|
401
|
+
--itemCount_;
|
402
|
+
}
|
403
|
+
|
404
|
+
|
405
|
+
ValueInternalLink *&
|
406
|
+
ValueInternalMap::getLastLinkInBucket( BucketIndex bucketIndex )
|
407
|
+
{
|
408
|
+
if ( bucketIndex == bucketsSize_ - 1 )
|
409
|
+
return tailLink_;
|
410
|
+
ValueInternalLink *&previous = buckets_[bucketIndex+1].previous_;
|
411
|
+
if ( !previous )
|
412
|
+
previous = &buckets_[bucketIndex];
|
413
|
+
return previous;
|
414
|
+
}
|
415
|
+
|
416
|
+
|
417
|
+
Value &
|
418
|
+
ValueInternalMap::setNewItem( const char *key,
|
419
|
+
bool isStatic,
|
420
|
+
ValueInternalLink *link,
|
421
|
+
BucketIndex index )
|
422
|
+
{
|
423
|
+
char *duplicatedKey = makeMemberName( key );
|
424
|
+
++itemCount_;
|
425
|
+
link->keys_[index] = duplicatedKey;
|
426
|
+
link->items_[index].setItemUsed();
|
427
|
+
link->items_[index].setMemberNameIsStatic( isStatic );
|
428
|
+
return link->items_[index]; // items already default constructed.
|
429
|
+
}
|
430
|
+
|
431
|
+
|
432
|
+
Value &
|
433
|
+
ValueInternalMap::unsafeAdd( const char *key,
|
434
|
+
bool isStatic,
|
435
|
+
HashKey hashedKey )
|
436
|
+
{
|
437
|
+
JSON_ASSERT_MESSAGE( bucketsSize_ > 0, "ValueInternalMap::unsafeAdd(): internal logic error." );
|
438
|
+
BucketIndex bucketIndex = hashedKey % bucketsSize_;
|
439
|
+
ValueInternalLink *&previousLink = getLastLinkInBucket( bucketIndex );
|
440
|
+
ValueInternalLink *link = previousLink;
|
441
|
+
BucketIndex index;
|
442
|
+
for ( index =0; index < ValueInternalLink::itemPerLink; ++index )
|
443
|
+
{
|
444
|
+
if ( link->items_[index].isItemAvailable() )
|
445
|
+
break;
|
446
|
+
}
|
447
|
+
if ( index == ValueInternalLink::itemPerLink ) // need to add a new page
|
448
|
+
{
|
449
|
+
ValueInternalLink *newLink = mapAllocator()->allocateMapLink();
|
450
|
+
index = 0;
|
451
|
+
link->next_ = newLink;
|
452
|
+
previousLink = newLink;
|
453
|
+
link = newLink;
|
454
|
+
}
|
455
|
+
return setNewItem( key, isStatic, link, index );
|
456
|
+
}
|
457
|
+
|
458
|
+
|
459
|
+
ValueInternalMap::HashKey
|
460
|
+
ValueInternalMap::hash( const char *key ) const
|
461
|
+
{
|
462
|
+
HashKey hash = 0;
|
463
|
+
while ( *key )
|
464
|
+
hash += *key++ * 37;
|
465
|
+
return hash;
|
466
|
+
}
|
467
|
+
|
468
|
+
|
469
|
+
int
|
470
|
+
ValueInternalMap::compare( const ValueInternalMap &other ) const
|
471
|
+
{
|
472
|
+
int sizeDiff( itemCount_ - other.itemCount_ );
|
473
|
+
if ( sizeDiff != 0 )
|
474
|
+
return sizeDiff;
|
475
|
+
// Strict order guaranty is required. Compare all keys FIRST, then compare values.
|
476
|
+
IteratorState it;
|
477
|
+
IteratorState itEnd;
|
478
|
+
makeBeginIterator( it );
|
479
|
+
makeEndIterator( itEnd );
|
480
|
+
for ( ; !equals(it,itEnd); increment(it) )
|
481
|
+
{
|
482
|
+
if ( !other.find( key( it ) ) )
|
483
|
+
return 1;
|
484
|
+
}
|
485
|
+
|
486
|
+
// All keys are equals, let's compare values
|
487
|
+
makeBeginIterator( it );
|
488
|
+
for ( ; !equals(it,itEnd); increment(it) )
|
489
|
+
{
|
490
|
+
const Value *otherValue = other.find( key( it ) );
|
491
|
+
int valueDiff = value(it).compare( *otherValue );
|
492
|
+
if ( valueDiff != 0 )
|
493
|
+
return valueDiff;
|
494
|
+
}
|
495
|
+
return 0;
|
496
|
+
}
|
497
|
+
|
498
|
+
|
499
|
+
void
|
500
|
+
ValueInternalMap::makeBeginIterator( IteratorState &it ) const
|
501
|
+
{
|
502
|
+
it.map_ = const_cast<ValueInternalMap *>( this );
|
503
|
+
it.bucketIndex_ = 0;
|
504
|
+
it.itemIndex_ = 0;
|
505
|
+
it.link_ = buckets_;
|
506
|
+
}
|
507
|
+
|
508
|
+
|
509
|
+
void
|
510
|
+
ValueInternalMap::makeEndIterator( IteratorState &it ) const
|
511
|
+
{
|
512
|
+
it.map_ = const_cast<ValueInternalMap *>( this );
|
513
|
+
it.bucketIndex_ = bucketsSize_;
|
514
|
+
it.itemIndex_ = 0;
|
515
|
+
it.link_ = 0;
|
516
|
+
}
|
517
|
+
|
518
|
+
|
519
|
+
bool
|
520
|
+
ValueInternalMap::equals( const IteratorState &x, const IteratorState &other )
|
521
|
+
{
|
522
|
+
return x.map_ == other.map_
|
523
|
+
&& x.bucketIndex_ == other.bucketIndex_
|
524
|
+
&& x.link_ == other.link_
|
525
|
+
&& x.itemIndex_ == other.itemIndex_;
|
526
|
+
}
|
527
|
+
|
528
|
+
|
529
|
+
void
|
530
|
+
ValueInternalMap::incrementBucket( IteratorState &iterator )
|
531
|
+
{
|
532
|
+
++iterator.bucketIndex_;
|
533
|
+
JSON_ASSERT_MESSAGE( iterator.bucketIndex_ <= iterator.map_->bucketsSize_,
|
534
|
+
"ValueInternalMap::increment(): attempting to iterate beyond end." );
|
535
|
+
if ( iterator.bucketIndex_ == iterator.map_->bucketsSize_ )
|
536
|
+
iterator.link_ = 0;
|
537
|
+
else
|
538
|
+
iterator.link_ = &(iterator.map_->buckets_[iterator.bucketIndex_]);
|
539
|
+
iterator.itemIndex_ = 0;
|
540
|
+
}
|
541
|
+
|
542
|
+
|
543
|
+
void
|
544
|
+
ValueInternalMap::increment( IteratorState &iterator )
|
545
|
+
{
|
546
|
+
JSON_ASSERT_MESSAGE( iterator.map_, "Attempting to iterator using invalid iterator." );
|
547
|
+
++iterator.itemIndex_;
|
548
|
+
if ( iterator.itemIndex_ == ValueInternalLink::itemPerLink )
|
549
|
+
{
|
550
|
+
JSON_ASSERT_MESSAGE( iterator.link_ != 0,
|
551
|
+
"ValueInternalMap::increment(): attempting to iterate beyond end." );
|
552
|
+
iterator.link_ = iterator.link_->next_;
|
553
|
+
if ( iterator.link_ == 0 )
|
554
|
+
incrementBucket( iterator );
|
555
|
+
}
|
556
|
+
else if ( iterator.link_->items_[iterator.itemIndex_].isItemAvailable() )
|
557
|
+
{
|
558
|
+
incrementBucket( iterator );
|
559
|
+
}
|
560
|
+
}
|
561
|
+
|
562
|
+
|
563
|
+
void
|
564
|
+
ValueInternalMap::decrement( IteratorState &iterator )
|
565
|
+
{
|
566
|
+
if ( iterator.itemIndex_ == 0 )
|
567
|
+
{
|
568
|
+
JSON_ASSERT_MESSAGE( iterator.map_, "Attempting to iterate using invalid iterator." );
|
569
|
+
if ( iterator.link_ == &iterator.map_->buckets_[iterator.bucketIndex_] )
|
570
|
+
{
|
571
|
+
JSON_ASSERT_MESSAGE( iterator.bucketIndex_ > 0, "Attempting to iterate beyond beginning." );
|
572
|
+
--(iterator.bucketIndex_);
|
573
|
+
}
|
574
|
+
iterator.link_ = iterator.link_->previous_;
|
575
|
+
iterator.itemIndex_ = ValueInternalLink::itemPerLink - 1;
|
576
|
+
}
|
577
|
+
}
|
578
|
+
|
579
|
+
|
580
|
+
const char *
|
581
|
+
ValueInternalMap::key( const IteratorState &iterator )
|
582
|
+
{
|
583
|
+
JSON_ASSERT_MESSAGE( iterator.link_, "Attempting to iterate using invalid iterator." );
|
584
|
+
return iterator.link_->keys_[iterator.itemIndex_];
|
585
|
+
}
|
586
|
+
|
587
|
+
const char *
|
588
|
+
ValueInternalMap::key( const IteratorState &iterator, bool &isStatic )
|
589
|
+
{
|
590
|
+
JSON_ASSERT_MESSAGE( iterator.link_, "Attempting to iterate using invalid iterator." );
|
591
|
+
isStatic = iterator.link_->items_[iterator.itemIndex_].isMemberNameStatic();
|
592
|
+
return iterator.link_->keys_[iterator.itemIndex_];
|
593
|
+
}
|
594
|
+
|
595
|
+
|
596
|
+
Value &
|
597
|
+
ValueInternalMap::value( const IteratorState &iterator )
|
598
|
+
{
|
599
|
+
JSON_ASSERT_MESSAGE( iterator.link_, "Attempting to iterate using invalid iterator." );
|
600
|
+
return iterator.link_->items_[iterator.itemIndex_];
|
601
|
+
}
|
602
|
+
|
603
|
+
|
604
|
+
int
|
605
|
+
ValueInternalMap::distance( const IteratorState &x, const IteratorState &y )
|
606
|
+
{
|
607
|
+
int offset = 0;
|
608
|
+
IteratorState it = x;
|
609
|
+
while ( !equals( it, y ) )
|
610
|
+
increment( it );
|
611
|
+
return offset;
|
612
|
+
}
|