yinspire 0.1.0
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- data/README +24 -0
- data/bench/pq/Makefile +5 -0
- data/bench/pq/bench.cc +321 -0
- data/bench/pq/bench.rb +125 -0
- data/bench/pq/bench_binaryheap.h +46 -0
- data/bench/pq/bench_calendarqueue.h +58 -0
- data/bench/pq/bench_pairingheap.h +61 -0
- data/bench/pq/bench_stlpq.h +46 -0
- data/bench/pq/benchmark.h +225 -0
- data/bench/pq/distribution.h +93 -0
- data/bench/pq/make.rb +24 -0
- data/bin/yinspire +186 -0
- data/examples/nets/gereon2005.c.json +93723 -0
- data/examples/nets/gereon2005.yin +232650 -0
- data/examples/nets/skorpion.graphml +396 -0
- data/examples/nets/spiketrains_angle_180.txt +8 -0
- data/lib/Algorithms/Array.h +52 -0
- data/lib/Algorithms/BinaryHeap.h +265 -0
- data/lib/Algorithms/CalendarQueue.h +257 -0
- data/lib/Algorithms/IndexedBinaryHeap.h +90 -0
- data/lib/Algorithms/PairingHeap.h +169 -0
- data/lib/Allocators/ChunkedFreelistAllocator.h +96 -0
- data/lib/Allocators/MemoryAllocator.h +45 -0
- data/lib/Allocators/RubyMemoryAllocator.h +37 -0
- data/lib/Yinspire.rb +69 -0
- data/lib/Yinspire/All.rb +10 -0
- data/lib/Yinspire/Core/NeuralEntity.rb +133 -0
- data/lib/Yinspire/Core/Neuron.rb +162 -0
- data/lib/Yinspire/Core/Scheduling/NeuralEntity.rb +123 -0
- data/lib/Yinspire/Core/Scheduling/Simulator.rb +94 -0
- data/lib/Yinspire/Core/Simulator.rb +36 -0
- data/lib/Yinspire/Core/StimuliMixin.rb +103 -0
- data/lib/Yinspire/Core/Stimulus.rb +25 -0
- data/lib/Yinspire/Core/Synapse.rb +64 -0
- data/lib/Yinspire/Dumpers/Dumper.rb +19 -0
- data/lib/Yinspire/Dumpers/Dumper_Dot.rb +28 -0
- data/lib/Yinspire/Loaders/GraphML.rb +84 -0
- data/lib/Yinspire/Loaders/Loader.rb +31 -0
- data/lib/Yinspire/Loaders/Loader_GraphML.rb +97 -0
- data/lib/Yinspire/Loaders/Loader_JSON.rb +181 -0
- data/lib/Yinspire/Loaders/Loader_Spike.rb +42 -0
- data/lib/Yinspire/Loaders/Loader_Yin.rb +62 -0
- data/lib/Yinspire/Loaders/YinScanner.rb +247 -0
- data/lib/Yinspire/Models/Neuron_Base.rb +38 -0
- data/lib/Yinspire/Models/Neuron_Input.rb +12 -0
- data/lib/Yinspire/Models/Neuron_InputOutput.rb +39 -0
- data/lib/Yinspire/Models/Neuron_Output.rb +15 -0
- data/lib/Yinspire/Models/Neuron_SRM01.rb +50 -0
- data/lib/Yinspire/Models/Neuron_SRM02.rb +64 -0
- data/lib/Yinspire/Models/Synapse_Hebb.rb +67 -0
- data/pure_cpp/Makefile +22 -0
- data/pure_cpp/README +2 -0
- data/pure_cpp/src/algo/binary_heap.h +277 -0
- data/pure_cpp/src/algo/indexed_binary_heap.h +90 -0
- data/pure_cpp/src/json/json.cc +542 -0
- data/pure_cpp/src/json/json.h +182 -0
- data/pure_cpp/src/json/json_parser.cc +685 -0
- data/pure_cpp/src/json/json_parser.h +15 -0
- data/pure_cpp/src/json/json_parser.rl +213 -0
- data/pure_cpp/src/main.cc +49 -0
- data/pure_cpp/src/memory_allocator.h +45 -0
- data/pure_cpp/src/neural_entity.cc +208 -0
- data/pure_cpp/src/neural_entity.h +243 -0
- data/pure_cpp/src/neuron.cc +136 -0
- data/pure_cpp/src/neuron.h +70 -0
- data/pure_cpp/src/neuron_srm_01.cc +77 -0
- data/pure_cpp/src/neuron_srm_01.h +36 -0
- data/pure_cpp/src/simulator.cc +151 -0
- data/pure_cpp/src/simulator.h +116 -0
- data/pure_cpp/src/synapse.cc +117 -0
- data/pure_cpp/src/synapse.h +60 -0
- data/pure_cpp/src/types.h +18 -0
- data/run.rb +68 -0
- data/tools/conv_jsonc_to_yin.rb +165 -0
- data/tools/converter.rb +93 -0
- data/tools/json_writer.rb +122 -0
- data/yinspire.gemspec +20 -0
- metadata +156 -0
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/*
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* An Indexed Binary Heap
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*
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* Copyright (c) 2007, 2008 by Michael Neumann (mneumann@ntecs.de)
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*
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* The Indexed Binary Heap keeps track of the indices of it's elements
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* stored in the heap to allow efficient updating of their priorities.
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*
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* The requirement was to modify an elements priority. In a regular
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* implicit binary heap this is an inefficient operation as the element
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* has to be found prior to modifying it's priority. And finding an
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* element is O(n) in an implicit binary heap due to it's non sorted
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* nature (i.e. can't apply binary search). By keeping track of the
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* elements index and storing this value inside the elements structure,
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* the complexity of modifying an elements priority is reduced to
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* O(log n) in the worst-case!
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*
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* NOTE: Index 0 of the elements array is unused. It's the index that
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* should be used to denote that an element is NOT actually present in
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* the binary heap.
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*
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* See documentation of BinaryHeap as well.
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*
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* Example:
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*
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* struct E
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* {
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* float schedule_at;
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* unsigned int schedule_index;
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*
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* inline static bool less(const E& e1, const E& e2)
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* {
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* return e1.schedule_at < e2.schedule_at;
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* }
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*
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* inline static unsigned int& index(const E& e)
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* {
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* return e.schedule_index;
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* }
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* };
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*
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* IndexedBinaryHeap<E, MemoryAllocator> heap;
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* ...
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*
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*/
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#ifndef __YINSPIRE__INDEXED_BINARY_HEAP__
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#define __YINSPIRE__INDEXED_BINARY_HEAP__
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#include "binary_heap.h"
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template <typename E, class Acc=E>
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struct BinaryHeapIndexer
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{
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static inline void index_changed(E& e, unsigned int i)
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{
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Acc::index(e) = i;
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}
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};
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template <typename E, class Alloc, class Acc=E, unsigned int MIN_CAPA=1024>
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class IndexedBinaryHeap : public BinaryHeap<E, Alloc, Acc, BinaryHeapIndexer<E, Acc>, MIN_CAPA>
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{
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typedef unsigned int I; // index type
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typedef BinaryHeap<E, Alloc, Acc, BinaryHeapIndexer<E, Acc>, MIN_CAPA> super;
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typedef BinaryHeapIndexer<E, Acc> Idx;
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public:
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void
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update(const E& element)
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{
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I i = Acc::index(element);
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if (i == 0)
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{
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super::push(element);
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}
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else
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{
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// FIXME: use propagate up/down instead
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Idx::index_changed(this->elements[i], 0); // detach from heap
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I bubble = super::move_bubble_down(i);
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super::insert_and_bubble_up(bubble, element);
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}
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}
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};
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#endif
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#include "json.h"
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#include <string.h>
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#include <math.h>
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/* TODO:
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* output indentation
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* escape string (\0 characters in string?)
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*/
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struct jsonArrayItem
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{
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jsonValue* value;
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jsonArrayItem* next;
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jsonArrayItem(jsonValue* value, jsonArrayItem* next=NULL)
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{
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this->value = value;
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this->next = next;
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this->value->ref_incr();
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}
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~jsonArrayItem()
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{
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this->value->ref_decr();
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}
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};
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struct jsonHashItem
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{
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jsonString* key;
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jsonValue* value;
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jsonHashItem* next;
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jsonHashItem(jsonString* key, jsonValue* value, jsonHashItem* next=NULL)
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{
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this->key = key;
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this->value = value;
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this->next = next;
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this->key->ref_incr();
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this->value->ref_incr();
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}
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~jsonHashItem()
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{
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this->key->ref_decr();
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this->value->ref_decr();
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}
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};
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jsonValue::jsonValue()
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{
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this->ref_count = 1;
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}
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jsonValue::~jsonValue()
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{
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}
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const char* jsonValue::type()
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{
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return "value";
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}
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bool jsonValue::is_type(const char* t)
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{
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return (strcmp(t, type()) == 0);
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}
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void jsonValue::ref_incr()
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{
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this->ref_count++;
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}
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void jsonValue::ref_decr()
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{
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if (--this->ref_count <= 0) delete this;
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}
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jsonNull* jsonValue::asNull()
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{
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return dynamic_cast<jsonNull*>(this);
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}
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jsonTrue* jsonValue::asTrue()
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{
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return dynamic_cast<jsonTrue*>(this);
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}
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jsonFalse* jsonValue::asFalse()
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{
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return dynamic_cast<jsonFalse*>(this);
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}
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jsonNumber* jsonValue::asNumber()
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{
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return dynamic_cast<jsonNumber*>(this);
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}
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jsonString* jsonValue::asString()
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{
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return dynamic_cast<jsonString*>(this);
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}
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jsonArray* jsonValue::asArray()
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{
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return dynamic_cast<jsonArray*>(this);
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}
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jsonHash* jsonValue::asHash()
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{
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return dynamic_cast<jsonHash*>(this);
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}
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void jsonNull::output(std::ostream& s)
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{
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s << "null";
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}
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const char* jsonNull::type()
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{
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return "null";
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}
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void jsonTrue::output(std::ostream& s)
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{
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s << "true";
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}
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const char* jsonTrue::type()
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{
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return "true";
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}
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void jsonFalse::output(std::ostream& s)
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{
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s << "false";
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}
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const char* jsonFalse::type()
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{
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return "false";
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}
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jsonNumber::jsonNumber(double value)
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{
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this->value = value;
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}
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void jsonNumber::output(std::ostream& s) {
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if (isinf(value))
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{
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if (value < 0.0)
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{
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s << "-Infinity";
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}
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else
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{
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s << "Infinity";
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}
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}
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else
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{
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s << value;
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}
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}
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const char* jsonNumber::type()
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{
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return "number";
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}
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jsonString::jsonString(std::string& value)
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{
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this->value = value;
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}
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jsonString::jsonString(const char* value)
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{
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this->value = value;
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}
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jsonString::jsonString(const char* _value, int len) : value(_value, len)
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{
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}
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void jsonString::output(std::ostream& s)
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{
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s << '"' << value << '"';
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}
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const char* jsonString::type()
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{
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return "string";
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}
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jsonArrayIterator::jsonArrayIterator(jsonArray *array)
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{
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this->array = array;
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this->array->ref_incr();
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this->pos = this->array->head;
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}
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jsonArrayIterator::~jsonArrayIterator()
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{
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this->array->ref_decr();
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}
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void jsonArrayIterator::next()
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{
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if (this->pos != NULL)
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{
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this->pos = this->pos->next;
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}
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}
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jsonValue *jsonArrayIterator::current()
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{
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if (this->pos != NULL)
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{
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return this->pos->value;
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}
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else
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{
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return NULL;
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}
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}
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jsonHashIterator::jsonHashIterator(jsonHash *hash)
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{
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this->hash = hash;
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this->hash->ref_incr();
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this->pos = this->hash->head;
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}
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jsonHashIterator::~jsonHashIterator()
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{
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this->hash->ref_decr();
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}
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void jsonHashIterator::next()
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{
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if (this->pos != NULL)
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{
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this->pos = this->pos->next;
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}
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}
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jsonString *jsonHashIterator::current_key()
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{
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if (this->pos != NULL)
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{
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return this->pos->key;
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}
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else
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{
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return NULL;
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}
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}
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jsonValue *jsonHashIterator::current_value()
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{
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if (this->pos != NULL)
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{
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return this->pos->value;
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}
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else
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{
|
268
|
+
return NULL;
|
269
|
+
}
|
270
|
+
}
|
271
|
+
|
272
|
+
jsonArray::jsonArray()
|
273
|
+
{
|
274
|
+
head = tail = NULL;
|
275
|
+
}
|
276
|
+
|
277
|
+
jsonArray::~jsonArray()
|
278
|
+
{
|
279
|
+
jsonArrayItem* j;
|
280
|
+
for (jsonArrayItem* i=head; i != NULL; )
|
281
|
+
{
|
282
|
+
j = i->next;
|
283
|
+
delete i;
|
284
|
+
i = j;
|
285
|
+
}
|
286
|
+
}
|
287
|
+
|
288
|
+
void jsonArray::output(std::ostream& s)
|
289
|
+
{
|
290
|
+
s << "[";
|
291
|
+
for (jsonArrayItem* i=head; i != NULL; i=i->next)
|
292
|
+
{
|
293
|
+
if (i != head) s << ", ";
|
294
|
+
i->value->output(s);
|
295
|
+
}
|
296
|
+
s << "]";
|
297
|
+
}
|
298
|
+
|
299
|
+
void jsonArray::push(jsonValue* value)
|
300
|
+
{
|
301
|
+
jsonArrayItem* i = new jsonArrayItem(value);
|
302
|
+
|
303
|
+
if (head == NULL)
|
304
|
+
{
|
305
|
+
head = tail = i;
|
306
|
+
}
|
307
|
+
else
|
308
|
+
{
|
309
|
+
tail->next = i;
|
310
|
+
tail = i;
|
311
|
+
}
|
312
|
+
}
|
313
|
+
|
314
|
+
/*void jsonArray::each(void (*iter)(jsonValue*, void*), void* data)
|
315
|
+
{
|
316
|
+
for (jsonArrayItem* i=head; i != NULL; i=i->next)
|
317
|
+
{
|
318
|
+
iter(i->value, data);
|
319
|
+
}
|
320
|
+
}
|
321
|
+
*/
|
322
|
+
|
323
|
+
jsonValue* jsonArray::get(int index)
|
324
|
+
{
|
325
|
+
for (jsonArrayItem* i=head; i != NULL; i=i->next, index--)
|
326
|
+
{
|
327
|
+
if (index == 0)
|
328
|
+
return i->value;
|
329
|
+
}
|
330
|
+
return NULL;
|
331
|
+
}
|
332
|
+
|
333
|
+
const char* jsonArray::type()
|
334
|
+
{
|
335
|
+
return "array";
|
336
|
+
}
|
337
|
+
|
338
|
+
jsonHash::jsonHash()
|
339
|
+
{
|
340
|
+
head = tail = NULL;
|
341
|
+
}
|
342
|
+
|
343
|
+
jsonHash::~jsonHash()
|
344
|
+
{
|
345
|
+
jsonHashItem* j;
|
346
|
+
for (jsonHashItem* i=head; i != NULL; )
|
347
|
+
{
|
348
|
+
j = i->next;
|
349
|
+
delete i;
|
350
|
+
i = j;
|
351
|
+
}
|
352
|
+
}
|
353
|
+
|
354
|
+
void jsonHash::output(std::ostream& s)
|
355
|
+
{
|
356
|
+
s << "{";
|
357
|
+
for (jsonHashItem* i=head; i != NULL; i=i->next)
|
358
|
+
{
|
359
|
+
if (i != head) s << ", " << std::endl;
|
360
|
+
i->key->output(s);
|
361
|
+
s << ": ";
|
362
|
+
i->value->output(s);
|
363
|
+
}
|
364
|
+
s << "}";
|
365
|
+
}
|
366
|
+
|
367
|
+
/*void jsonHash::each(void (*iter)(jsonString*, jsonValue*, void*), void* data)
|
368
|
+
{
|
369
|
+
for (jsonHashItem* i=head; i != NULL; i=i->next)
|
370
|
+
{
|
371
|
+
iter(i->key, i->value, data);
|
372
|
+
}
|
373
|
+
}
|
374
|
+
*/
|
375
|
+
|
376
|
+
jsonValue* jsonHash::get(const char* key)
|
377
|
+
{
|
378
|
+
for (jsonHashItem* i=head; i != NULL; i=i->next)
|
379
|
+
{
|
380
|
+
if (i->key->value == key)
|
381
|
+
{
|
382
|
+
return i->value;
|
383
|
+
}
|
384
|
+
}
|
385
|
+
return NULL;
|
386
|
+
}
|
387
|
+
|
388
|
+
jsonValue* jsonHash::get(std::string& key)
|
389
|
+
{
|
390
|
+
return get(key.c_str());
|
391
|
+
}
|
392
|
+
|
393
|
+
jsonValue* jsonHash::get(jsonString* key)
|
394
|
+
{
|
395
|
+
return get(key->value);
|
396
|
+
}
|
397
|
+
|
398
|
+
bool jsonHash::has_key(const char* key)
|
399
|
+
{
|
400
|
+
return (get(key) != NULL);
|
401
|
+
}
|
402
|
+
|
403
|
+
bool jsonHash::has_key(std::string& key)
|
404
|
+
{
|
405
|
+
return (get(key.c_str()) != NULL);
|
406
|
+
}
|
407
|
+
|
408
|
+
bool jsonHash::has_key(jsonString* key)
|
409
|
+
{
|
410
|
+
return (get(key) != NULL);
|
411
|
+
}
|
412
|
+
|
413
|
+
bool jsonHash::get_bool(const char* key, bool default_value)
|
414
|
+
{
|
415
|
+
jsonValue* v = get(key);
|
416
|
+
if (v != NULL)
|
417
|
+
{
|
418
|
+
if (v->is_type("true"))
|
419
|
+
{
|
420
|
+
return true;
|
421
|
+
}
|
422
|
+
else if (v->is_type("false"))
|
423
|
+
{
|
424
|
+
return false;
|
425
|
+
}
|
426
|
+
else
|
427
|
+
{
|
428
|
+
throw "invalid type cast";
|
429
|
+
}
|
430
|
+
}
|
431
|
+
else
|
432
|
+
{
|
433
|
+
return default_value;
|
434
|
+
}
|
435
|
+
}
|
436
|
+
|
437
|
+
double jsonHash::get_number(const char* key, double default_value)
|
438
|
+
{
|
439
|
+
jsonValue* v = get(key);
|
440
|
+
if (v != NULL)
|
441
|
+
{
|
442
|
+
if (v->is_type("number"))
|
443
|
+
{
|
444
|
+
return ((jsonNumber*)v)->value;
|
445
|
+
}
|
446
|
+
else
|
447
|
+
{
|
448
|
+
throw "invalid type cast";
|
449
|
+
}
|
450
|
+
}
|
451
|
+
else
|
452
|
+
{
|
453
|
+
return default_value;
|
454
|
+
}
|
455
|
+
}
|
456
|
+
|
457
|
+
std::string& jsonHash::get_string(const char* key)
|
458
|
+
{
|
459
|
+
jsonValue* v = get(key);
|
460
|
+
if (v != NULL)
|
461
|
+
{
|
462
|
+
if (v->is_type("string"))
|
463
|
+
{
|
464
|
+
return ((jsonString*)v)->value;
|
465
|
+
}
|
466
|
+
else
|
467
|
+
{
|
468
|
+
throw "invalid type cast";
|
469
|
+
}
|
470
|
+
}
|
471
|
+
else
|
472
|
+
{
|
473
|
+
throw "key not found";
|
474
|
+
}
|
475
|
+
}
|
476
|
+
|
477
|
+
void jsonHash::set(const char* key, jsonValue* value)
|
478
|
+
{
|
479
|
+
set(new jsonString(key), value);
|
480
|
+
}
|
481
|
+
|
482
|
+
void jsonHash::set(const char* key, double value)
|
483
|
+
{
|
484
|
+
set(new jsonString(key), new jsonNumber(value));
|
485
|
+
}
|
486
|
+
|
487
|
+
void jsonHash::set(const char* key, int value)
|
488
|
+
{
|
489
|
+
set(new jsonString(key), new jsonNumber(value));
|
490
|
+
}
|
491
|
+
|
492
|
+
void jsonHash::set(const char* key, bool value)
|
493
|
+
{
|
494
|
+
set(new jsonString(key), value ? (jsonValue*)new jsonTrue() : (jsonValue*)new jsonFalse());
|
495
|
+
}
|
496
|
+
|
497
|
+
void jsonHash::set(const char* key, const char* value)
|
498
|
+
{
|
499
|
+
set(new jsonString(key), new jsonString(value));
|
500
|
+
}
|
501
|
+
|
502
|
+
void jsonHash::set(const char* key, std::string& value)
|
503
|
+
{
|
504
|
+
set(new jsonString(key), new jsonString(value));
|
505
|
+
}
|
506
|
+
|
507
|
+
void jsonHash::set(jsonString* key, jsonValue* value)
|
508
|
+
{
|
509
|
+
if (head == NULL)
|
510
|
+
{
|
511
|
+
head = tail = new jsonHashItem(key, value);
|
512
|
+
}
|
513
|
+
else
|
514
|
+
{
|
515
|
+
bool duplicate = false;
|
516
|
+
|
517
|
+
for (jsonHashItem* i=head; i != NULL; i=i->next)
|
518
|
+
{
|
519
|
+
if (i->key->value == key->value)
|
520
|
+
{
|
521
|
+
i->key->ref_decr();
|
522
|
+
i->value->ref_decr();
|
523
|
+
i->key = key;
|
524
|
+
i->value = value;
|
525
|
+
duplicate = true;
|
526
|
+
break;
|
527
|
+
}
|
528
|
+
}
|
529
|
+
|
530
|
+
if (!duplicate)
|
531
|
+
{
|
532
|
+
jsonHashItem* t = new jsonHashItem(key, value);
|
533
|
+
tail->next = t;
|
534
|
+
tail = t;
|
535
|
+
}
|
536
|
+
}
|
537
|
+
}
|
538
|
+
|
539
|
+
const char* jsonHash::type()
|
540
|
+
{
|
541
|
+
return "hash";
|
542
|
+
}
|