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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 +1,870 @@
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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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#include "json_reader.h"
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#include "json_value.h"
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#include "json_tool.h"
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#include <utility>
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#include <cstdio>
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#include <cassert>
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#include <cstring>
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#include <iostream>
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#include <stdexcept>
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#if _MSC_VER >= 1400 // VC++ 8.0
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#pragma warning( disable : 4996 ) // disable warning about strdup being deprecated.
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#endif
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namespace Json {
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// Implementation of class Features
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// ////////////////////////////////
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Features::Features()
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: allowComments_( true )
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, strictRoot_( false )
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{
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}
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Features
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Features::all()
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{
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return Features();
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}
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Features
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Features::strictMode()
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{
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Features features;
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features.allowComments_ = false;
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features.strictRoot_ = true;
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return features;
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}
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// Implementation of class Reader
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// ////////////////////////////////
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static inline bool
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in( Reader::Char c, Reader::Char c1, Reader::Char c2, Reader::Char c3, Reader::Char c4 )
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{
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return c == c1 || c == c2 || c == c3 || c == c4;
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}
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static inline bool
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in( Reader::Char c, Reader::Char c1, Reader::Char c2, Reader::Char c3, Reader::Char c4, Reader::Char c5 )
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{
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return c == c1 || c == c2 || c == c3 || c == c4 || c == c5;
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}
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static bool
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containsNewLine( Reader::Location begin,
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Reader::Location end )
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{
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for ( ;begin < end; ++begin )
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if ( *begin == '\n' || *begin == '\r' )
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return true;
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return false;
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}
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// Class Reader
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// //////////////////////////////////////////////////////////////////
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Reader::Reader()
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: features_( Features::all() )
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{
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}
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Reader::Reader( const Features &features )
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: features_( features )
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{
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}
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bool
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Reader::parse( const std::string &document,
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Value &root,
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bool collectComments )
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{
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document_ = document;
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const char *begin = document_.c_str();
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const char *end = begin + document_.length();
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return parse( begin, end, root, collectComments );
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}
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bool
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Reader::parse( std::istream& sin,
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Value &root,
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bool collectComments )
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{
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//std::istream_iterator<char> begin(sin);
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//std::istream_iterator<char> end;
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// Those would allow streamed input from a file, if parse() were a
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// template function.
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// Since std::string is reference-counted, this at least does not
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// create an extra copy.
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std::string doc;
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std::getline(sin, doc, (char)EOF);
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return parse( doc, root, collectComments );
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}
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bool
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Reader::parse( const char *beginDoc, const char *endDoc,
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Value &root,
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bool collectComments )
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{
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if ( !features_.allowComments_ )
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{
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collectComments = false;
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}
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begin_ = beginDoc;
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end_ = endDoc;
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collectComments_ = collectComments;
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current_ = begin_;
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lastValueEnd_ = 0;
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lastValue_ = 0;
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commentsBefore_ = "";
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errors_.clear();
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while ( !nodes_.empty() )
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nodes_.pop();
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nodes_.push( &root );
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bool successful = readValue();
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Token token;
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skipCommentTokens( token );
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if ( collectComments_ && !commentsBefore_.empty() )
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root.setComment( commentsBefore_, commentAfter );
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if ( features_.strictRoot_ )
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{
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if ( !root.isArray() && !root.isObject() )
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{
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// Set error location to start of doc, ideally should be first token found in doc
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token.type_ = tokenError;
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token.start_ = beginDoc;
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token.end_ = endDoc;
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addError( "A valid JSON document must be either an array or an object value.",
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token );
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return false;
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}
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}
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return successful;
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}
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bool
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Reader::readValue()
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{
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Token token;
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skipCommentTokens( token );
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bool successful = true;
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if ( collectComments_ && !commentsBefore_.empty() )
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{
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currentValue().setComment( commentsBefore_, commentBefore );
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commentsBefore_ = "";
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}
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switch ( token.type_ )
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{
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case tokenObjectBegin:
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successful = readObject( token );
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break;
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case tokenArrayBegin:
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successful = readArray( token );
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break;
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case tokenNumber:
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successful = decodeNumber( token );
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break;
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case tokenString:
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successful = decodeString( token );
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break;
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case tokenTrue:
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currentValue() = true;
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break;
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case tokenFalse:
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currentValue() = false;
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break;
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case tokenNull:
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currentValue() = Value();
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break;
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default:
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return addError( "Syntax error: value, object or array expected.", token );
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}
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if ( collectComments_ )
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{
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lastValueEnd_ = current_;
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lastValue_ = ¤tValue();
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}
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return successful;
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}
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void
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Reader::skipCommentTokens( Token &token )
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{
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if ( features_.allowComments_ )
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{
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do
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{
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readToken( token );
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}
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while ( token.type_ == tokenComment );
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}
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else
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{
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readToken( token );
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}
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}
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bool
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Reader::expectToken( TokenType type, Token &token, const char *message )
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{
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readToken( token );
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if ( token.type_ != type )
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return addError( message, token );
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return true;
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}
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bool
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Reader::readToken( Token &token )
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{
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skipSpaces();
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token.start_ = current_;
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Char c = getNextChar();
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bool ok = true;
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switch ( c )
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{
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case '{':
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token.type_ = tokenObjectBegin;
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break;
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case '}':
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token.type_ = tokenObjectEnd;
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break;
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case '[':
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token.type_ = tokenArrayBegin;
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break;
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case ']':
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token.type_ = tokenArrayEnd;
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break;
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case '"':
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token.type_ = tokenString;
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ok = readString();
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break;
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case '/':
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token.type_ = tokenComment;
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ok = readComment();
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break;
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case '0':
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case '1':
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case '2':
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case '3':
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case '4':
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case '5':
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case '6':
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case '7':
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case '8':
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case '9':
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case '-':
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token.type_ = tokenNumber;
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readNumber();
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break;
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case 't':
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token.type_ = tokenTrue;
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ok = match( "rue", 3 );
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break;
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case 'f':
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token.type_ = tokenFalse;
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ok = match( "alse", 4 );
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break;
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case 'n':
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token.type_ = tokenNull;
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ok = match( "ull", 3 );
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break;
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case ',':
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token.type_ = tokenArraySeparator;
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break;
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case ':':
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token.type_ = tokenMemberSeparator;
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break;
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case 0:
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token.type_ = tokenEndOfStream;
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break;
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default:
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ok = false;
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break;
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}
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if ( !ok )
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token.type_ = tokenError;
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token.end_ = current_;
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return true;
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}
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void
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Reader::skipSpaces()
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{
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while ( current_ != end_ )
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{
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Char c = *current_;
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if ( c == ' ' || c == '\t' || c == '\r' || c == '\n' )
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++current_;
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else
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break;
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}
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}
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bool
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Reader::match( Location pattern,
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int patternLength )
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{
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if ( end_ - current_ < patternLength )
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return false;
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int index = patternLength;
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while ( index-- )
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340
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if ( current_[index] != pattern[index] )
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return false;
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current_ += patternLength;
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return true;
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}
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345
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bool
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348
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Reader::readComment()
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349
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{
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Location commentBegin = current_ - 1;
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Char c = getNextChar();
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bool successful = false;
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if ( c == '*' )
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successful = readCStyleComment();
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else if ( c == '/' )
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successful = readCppStyleComment();
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357
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if ( !successful )
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return false;
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360
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if ( collectComments_ )
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361
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{
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362
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CommentPlacement placement = commentBefore;
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363
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if ( lastValueEnd_ && !containsNewLine( lastValueEnd_, commentBegin ) )
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364
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{
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365
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if ( c != '*' || !containsNewLine( commentBegin, current_ ) )
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placement = commentAfterOnSameLine;
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367
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}
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368
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369
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addComment( commentBegin, current_, placement );
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}
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return true;
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372
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}
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374
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375
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void
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376
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Reader::addComment( Location begin,
|
377
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Location end,
|
378
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CommentPlacement placement )
|
379
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{
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380
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assert( collectComments_ );
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381
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if ( placement == commentAfterOnSameLine )
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382
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{
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383
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assert( lastValue_ != 0 );
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lastValue_->setComment( std::string( begin, end ), placement );
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385
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}
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386
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else
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387
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{
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388
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if ( !commentsBefore_.empty() )
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389
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commentsBefore_ += "\n";
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commentsBefore_ += std::string( begin, end );
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391
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+
}
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392
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}
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393
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+
|
394
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+
|
395
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bool
|
396
|
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Reader::readCStyleComment()
|
397
|
+
{
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398
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while ( current_ != end_ )
|
399
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{
|
400
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Char c = getNextChar();
|
401
|
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if ( c == '*' && *current_ == '/' )
|
402
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break;
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403
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}
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404
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return getNextChar() == '/';
|
405
|
+
}
|
406
|
+
|
407
|
+
|
408
|
+
bool
|
409
|
+
Reader::readCppStyleComment()
|
410
|
+
{
|
411
|
+
while ( current_ != end_ )
|
412
|
+
{
|
413
|
+
Char c = getNextChar();
|
414
|
+
if ( c == '\r' || c == '\n' )
|
415
|
+
break;
|
416
|
+
}
|
417
|
+
return true;
|
418
|
+
}
|
419
|
+
|
420
|
+
|
421
|
+
void
|
422
|
+
Reader::readNumber()
|
423
|
+
{
|
424
|
+
while ( current_ != end_ )
|
425
|
+
{
|
426
|
+
if ( !(*current_ >= '0' && *current_ <= '9') &&
|
427
|
+
!in( *current_, '.', 'e', 'E', '+', '-' ) )
|
428
|
+
break;
|
429
|
+
++current_;
|
430
|
+
}
|
431
|
+
}
|
432
|
+
|
433
|
+
bool
|
434
|
+
Reader::readString()
|
435
|
+
{
|
436
|
+
Char c = 0;
|
437
|
+
while ( current_ != end_ )
|
438
|
+
{
|
439
|
+
c = getNextChar();
|
440
|
+
if ( c == '\\' )
|
441
|
+
getNextChar();
|
442
|
+
else if ( c == '"' )
|
443
|
+
break;
|
444
|
+
}
|
445
|
+
return c == '"';
|
446
|
+
}
|
447
|
+
|
448
|
+
|
449
|
+
bool
|
450
|
+
Reader::readObject( Token &tokenStart )
|
451
|
+
{
|
452
|
+
Token tokenName;
|
453
|
+
std::string name;
|
454
|
+
currentValue() = Value( objectValue );
|
455
|
+
while ( readToken( tokenName ) )
|
456
|
+
{
|
457
|
+
bool initialTokenOk = true;
|
458
|
+
while ( tokenName.type_ == tokenComment && initialTokenOk )
|
459
|
+
initialTokenOk = readToken( tokenName );
|
460
|
+
if ( !initialTokenOk )
|
461
|
+
break;
|
462
|
+
if ( tokenName.type_ == tokenObjectEnd && name.empty() ) // empty object
|
463
|
+
return true;
|
464
|
+
if ( tokenName.type_ != tokenString )
|
465
|
+
break;
|
466
|
+
|
467
|
+
name = "";
|
468
|
+
if ( !decodeString( tokenName, name ) )
|
469
|
+
return recoverFromError( tokenObjectEnd );
|
470
|
+
|
471
|
+
Token colon;
|
472
|
+
if ( !readToken( colon ) || colon.type_ != tokenMemberSeparator )
|
473
|
+
{
|
474
|
+
return addErrorAndRecover( "Missing ':' after object member name",
|
475
|
+
colon,
|
476
|
+
tokenObjectEnd );
|
477
|
+
}
|
478
|
+
Value &value = currentValue()[ name ];
|
479
|
+
nodes_.push( &value );
|
480
|
+
bool ok = readValue();
|
481
|
+
nodes_.pop();
|
482
|
+
if ( !ok ) // error already set
|
483
|
+
return recoverFromError( tokenObjectEnd );
|
484
|
+
|
485
|
+
Token comma;
|
486
|
+
if ( !readToken( comma )
|
487
|
+
|| ( comma.type_ != tokenObjectEnd &&
|
488
|
+
comma.type_ != tokenArraySeparator &&
|
489
|
+
comma.type_ != tokenComment ) )
|
490
|
+
{
|
491
|
+
return addErrorAndRecover( "Missing ',' or '}' in object declaration",
|
492
|
+
comma,
|
493
|
+
tokenObjectEnd );
|
494
|
+
}
|
495
|
+
bool finalizeTokenOk = true;
|
496
|
+
while ( comma.type_ == tokenComment &&
|
497
|
+
finalizeTokenOk )
|
498
|
+
finalizeTokenOk = readToken( comma );
|
499
|
+
if ( comma.type_ == tokenObjectEnd )
|
500
|
+
return true;
|
501
|
+
}
|
502
|
+
return addErrorAndRecover( "Missing '}' or object member name",
|
503
|
+
tokenName,
|
504
|
+
tokenObjectEnd );
|
505
|
+
}
|
506
|
+
|
507
|
+
|
508
|
+
bool
|
509
|
+
Reader::readArray( Token &tokenStart )
|
510
|
+
{
|
511
|
+
currentValue() = Value( arrayValue );
|
512
|
+
skipSpaces();
|
513
|
+
if ( *current_ == ']' ) // empty array
|
514
|
+
{
|
515
|
+
Token endArray;
|
516
|
+
readToken( endArray );
|
517
|
+
return true;
|
518
|
+
}
|
519
|
+
int index = 0;
|
520
|
+
while ( true )
|
521
|
+
{
|
522
|
+
Value &value = currentValue()[ index++ ];
|
523
|
+
nodes_.push( &value );
|
524
|
+
bool ok = readValue();
|
525
|
+
nodes_.pop();
|
526
|
+
if ( !ok ) // error already set
|
527
|
+
return recoverFromError( tokenArrayEnd );
|
528
|
+
|
529
|
+
Token token;
|
530
|
+
// Accept Comment after last item in the array.
|
531
|
+
ok = readToken( token );
|
532
|
+
while ( token.type_ == tokenComment && ok )
|
533
|
+
{
|
534
|
+
ok = readToken( token );
|
535
|
+
}
|
536
|
+
bool badTokenType = ( token.type_ == tokenArraySeparator &&
|
537
|
+
token.type_ == tokenArrayEnd );
|
538
|
+
if ( !ok || badTokenType )
|
539
|
+
{
|
540
|
+
return addErrorAndRecover( "Missing ',' or ']' in array declaration",
|
541
|
+
token,
|
542
|
+
tokenArrayEnd );
|
543
|
+
}
|
544
|
+
if ( token.type_ == tokenArrayEnd )
|
545
|
+
break;
|
546
|
+
}
|
547
|
+
return true;
|
548
|
+
}
|
549
|
+
|
550
|
+
|
551
|
+
bool
|
552
|
+
Reader::decodeNumber( Token &token )
|
553
|
+
{
|
554
|
+
bool isDouble = false;
|
555
|
+
for ( Location inspect = token.start_; inspect != token.end_; ++inspect )
|
556
|
+
{
|
557
|
+
isDouble = isDouble
|
558
|
+
|| in( *inspect, '.', 'e', 'E', '+' )
|
559
|
+
|| ( *inspect == '-' && inspect != token.start_ );
|
560
|
+
}
|
561
|
+
if ( isDouble )
|
562
|
+
return decodeDouble( token );
|
563
|
+
// Attempts to parse the number as an integer. If the number is
|
564
|
+
// larger than the maximum supported value of an integer then
|
565
|
+
// we decode the number as a double.
|
566
|
+
Location current = token.start_;
|
567
|
+
bool isNegative = *current == '-';
|
568
|
+
if ( isNegative )
|
569
|
+
++current;
|
570
|
+
Value::UInt maxIntegerValue = isNegative ? Value::UInt(-Value::minInt)
|
571
|
+
: Value::maxUInt;
|
572
|
+
Value::UInt threshold = maxIntegerValue / 10;
|
573
|
+
Value::UInt lastDigitThreshold = maxIntegerValue % 10;
|
574
|
+
assert( lastDigitThreshold >=0 && lastDigitThreshold <= 9 );
|
575
|
+
Value::UInt value = 0;
|
576
|
+
while ( current < token.end_ )
|
577
|
+
{
|
578
|
+
Char c = *current++;
|
579
|
+
if ( c < '0' || c > '9' )
|
580
|
+
return addError( "'" + std::string( token.start_, token.end_ ) + "' is not a number.", token );
|
581
|
+
Value::UInt digit(c - '0');
|
582
|
+
if ( value >= threshold )
|
583
|
+
{
|
584
|
+
// If the current digit is not the last one, or if it is
|
585
|
+
// greater than the last digit of the maximum integer value,
|
586
|
+
// the parse the number as a double.
|
587
|
+
if ( current != token.end_ || digit > lastDigitThreshold )
|
588
|
+
{
|
589
|
+
return decodeDouble( token );
|
590
|
+
}
|
591
|
+
}
|
592
|
+
value = value * 10 + digit;
|
593
|
+
}
|
594
|
+
if ( isNegative )
|
595
|
+
currentValue() = -Value::Int( value );
|
596
|
+
else if ( value <= Value::UInt(Value::maxInt) )
|
597
|
+
currentValue() = Value::Int( value );
|
598
|
+
else
|
599
|
+
currentValue() = value;
|
600
|
+
return true;
|
601
|
+
}
|
602
|
+
|
603
|
+
|
604
|
+
bool
|
605
|
+
Reader::decodeDouble( Token &token )
|
606
|
+
{
|
607
|
+
double value = 0;
|
608
|
+
const int bufferSize = 32;
|
609
|
+
int count;
|
610
|
+
int length = int(token.end_ - token.start_);
|
611
|
+
if ( length <= bufferSize )
|
612
|
+
{
|
613
|
+
Char buffer[bufferSize];
|
614
|
+
memcpy( buffer, token.start_, length );
|
615
|
+
buffer[length] = 0;
|
616
|
+
count = sscanf( buffer, "%lf", &value );
|
617
|
+
}
|
618
|
+
else
|
619
|
+
{
|
620
|
+
std::string buffer( token.start_, token.end_ );
|
621
|
+
count = sscanf( buffer.c_str(), "%lf", &value );
|
622
|
+
}
|
623
|
+
|
624
|
+
if ( count != 1 )
|
625
|
+
return addError( "'" + std::string( token.start_, token.end_ ) + "' is not a number.", token );
|
626
|
+
currentValue() = value;
|
627
|
+
return true;
|
628
|
+
}
|
629
|
+
|
630
|
+
|
631
|
+
bool
|
632
|
+
Reader::decodeString( Token &token )
|
633
|
+
{
|
634
|
+
std::string decoded;
|
635
|
+
if ( !decodeString( token, decoded ) )
|
636
|
+
return false;
|
637
|
+
currentValue() = decoded;
|
638
|
+
return true;
|
639
|
+
}
|
640
|
+
|
641
|
+
|
642
|
+
bool
|
643
|
+
Reader::decodeString( Token &token, std::string &decoded )
|
644
|
+
{
|
645
|
+
decoded.reserve( token.end_ - token.start_ - 2 );
|
646
|
+
Location current = token.start_ + 1; // skip '"'
|
647
|
+
Location end = token.end_ - 1; // do not include '"'
|
648
|
+
while ( current != end )
|
649
|
+
{
|
650
|
+
Char c = *current++;
|
651
|
+
if ( c == '"' )
|
652
|
+
break;
|
653
|
+
else if ( c == '\\' )
|
654
|
+
{
|
655
|
+
if ( current == end )
|
656
|
+
return addError( "Empty escape sequence in string", token, current );
|
657
|
+
Char escape = *current++;
|
658
|
+
switch ( escape )
|
659
|
+
{
|
660
|
+
case '"': decoded += '"'; break;
|
661
|
+
case '/': decoded += '/'; break;
|
662
|
+
case '\\': decoded += '\\'; break;
|
663
|
+
case 'b': decoded += '\b'; break;
|
664
|
+
case 'f': decoded += '\f'; break;
|
665
|
+
case 'n': decoded += '\n'; break;
|
666
|
+
case 'r': decoded += '\r'; break;
|
667
|
+
case 't': decoded += '\t'; break;
|
668
|
+
case 'u':
|
669
|
+
{
|
670
|
+
unsigned int unicode;
|
671
|
+
if ( !decodeUnicodeCodePoint( token, current, end, unicode ) )
|
672
|
+
return false;
|
673
|
+
decoded += codePointToUTF8(unicode);
|
674
|
+
}
|
675
|
+
break;
|
676
|
+
default:
|
677
|
+
return addError( "Bad escape sequence in string", token, current );
|
678
|
+
}
|
679
|
+
}
|
680
|
+
else
|
681
|
+
{
|
682
|
+
decoded += c;
|
683
|
+
}
|
684
|
+
}
|
685
|
+
return true;
|
686
|
+
}
|
687
|
+
|
688
|
+
bool
|
689
|
+
Reader::decodeUnicodeCodePoint( Token &token,
|
690
|
+
Location ¤t,
|
691
|
+
Location end,
|
692
|
+
unsigned int &unicode )
|
693
|
+
{
|
694
|
+
|
695
|
+
if ( !decodeUnicodeEscapeSequence( token, current, end, unicode ) )
|
696
|
+
return false;
|
697
|
+
if (unicode >= 0xD800 && unicode <= 0xDBFF)
|
698
|
+
{
|
699
|
+
// surrogate pairs
|
700
|
+
if (end - current < 6)
|
701
|
+
return addError( "additional six characters expected to parse unicode surrogate pair.", token, current );
|
702
|
+
unsigned int surrogatePair;
|
703
|
+
if (*(current++) == '\\' && *(current++)== 'u')
|
704
|
+
{
|
705
|
+
if (decodeUnicodeEscapeSequence( token, current, end, surrogatePair ))
|
706
|
+
{
|
707
|
+
unicode = 0x10000 + ((unicode & 0x3FF) << 10) + (surrogatePair & 0x3FF);
|
708
|
+
}
|
709
|
+
else
|
710
|
+
return false;
|
711
|
+
}
|
712
|
+
else
|
713
|
+
return addError( "expecting another \\u token to begin the second half of a unicode surrogate pair", token, current );
|
714
|
+
}
|
715
|
+
return true;
|
716
|
+
}
|
717
|
+
|
718
|
+
bool
|
719
|
+
Reader::decodeUnicodeEscapeSequence( Token &token,
|
720
|
+
Location ¤t,
|
721
|
+
Location end,
|
722
|
+
unsigned int &unicode )
|
723
|
+
{
|
724
|
+
if ( end - current < 4 )
|
725
|
+
return addError( "Bad unicode escape sequence in string: four digits expected.", token, current );
|
726
|
+
unicode = 0;
|
727
|
+
for ( int index =0; index < 4; ++index )
|
728
|
+
{
|
729
|
+
Char c = *current++;
|
730
|
+
unicode *= 16;
|
731
|
+
if ( c >= '0' && c <= '9' )
|
732
|
+
unicode += c - '0';
|
733
|
+
else if ( c >= 'a' && c <= 'f' )
|
734
|
+
unicode += c - 'a' + 10;
|
735
|
+
else if ( c >= 'A' && c <= 'F' )
|
736
|
+
unicode += c - 'A' + 10;
|
737
|
+
else
|
738
|
+
return addError( "Bad unicode escape sequence in string: hexadecimal digit expected.", token, current );
|
739
|
+
}
|
740
|
+
return true;
|
741
|
+
}
|
742
|
+
|
743
|
+
|
744
|
+
bool
|
745
|
+
Reader::addError( const std::string &message,
|
746
|
+
Token &token,
|
747
|
+
Location extra )
|
748
|
+
{
|
749
|
+
ErrorInfo info;
|
750
|
+
info.token_ = token;
|
751
|
+
info.message_ = message;
|
752
|
+
info.extra_ = extra;
|
753
|
+
errors_.push_back( info );
|
754
|
+
return false;
|
755
|
+
}
|
756
|
+
|
757
|
+
|
758
|
+
bool
|
759
|
+
Reader::recoverFromError( TokenType skipUntilToken )
|
760
|
+
{
|
761
|
+
int errorCount = int(errors_.size());
|
762
|
+
Token skip;
|
763
|
+
while ( true )
|
764
|
+
{
|
765
|
+
if ( !readToken(skip) )
|
766
|
+
errors_.resize( errorCount ); // discard errors caused by recovery
|
767
|
+
if ( skip.type_ == skipUntilToken || skip.type_ == tokenEndOfStream )
|
768
|
+
break;
|
769
|
+
}
|
770
|
+
errors_.resize( errorCount );
|
771
|
+
return false;
|
772
|
+
}
|
773
|
+
|
774
|
+
|
775
|
+
bool
|
776
|
+
Reader::addErrorAndRecover( const std::string &message,
|
777
|
+
Token &token,
|
778
|
+
TokenType skipUntilToken )
|
779
|
+
{
|
780
|
+
addError( message, token );
|
781
|
+
return recoverFromError( skipUntilToken );
|
782
|
+
}
|
783
|
+
|
784
|
+
|
785
|
+
Value &
|
786
|
+
Reader::currentValue()
|
787
|
+
{
|
788
|
+
return *(nodes_.top());
|
789
|
+
}
|
790
|
+
|
791
|
+
|
792
|
+
Reader::Char
|
793
|
+
Reader::getNextChar()
|
794
|
+
{
|
795
|
+
if ( current_ == end_ )
|
796
|
+
return 0;
|
797
|
+
return *current_++;
|
798
|
+
}
|
799
|
+
|
800
|
+
|
801
|
+
void
|
802
|
+
Reader::getLocationLineAndColumn( Location location,
|
803
|
+
int &line,
|
804
|
+
int &column ) const
|
805
|
+
{
|
806
|
+
Location current = begin_;
|
807
|
+
Location lastLineStart = current;
|
808
|
+
line = 0;
|
809
|
+
while ( current < location && current != end_ )
|
810
|
+
{
|
811
|
+
Char c = *current++;
|
812
|
+
if ( c == '\r' )
|
813
|
+
{
|
814
|
+
if ( *current == '\n' )
|
815
|
+
++current;
|
816
|
+
lastLineStart = current;
|
817
|
+
++line;
|
818
|
+
}
|
819
|
+
else if ( c == '\n' )
|
820
|
+
{
|
821
|
+
lastLineStart = current;
|
822
|
+
++line;
|
823
|
+
}
|
824
|
+
}
|
825
|
+
// column & line start at 1
|
826
|
+
column = int(location - lastLineStart) + 1;
|
827
|
+
++line;
|
828
|
+
}
|
829
|
+
|
830
|
+
|
831
|
+
std::string
|
832
|
+
Reader::getLocationLineAndColumn( Location location ) const
|
833
|
+
{
|
834
|
+
int line, column;
|
835
|
+
getLocationLineAndColumn( location, line, column );
|
836
|
+
char buffer[18+16+16+1];
|
837
|
+
sprintf( buffer, "Line %d, Column %d", line, column );
|
838
|
+
return buffer;
|
839
|
+
}
|
840
|
+
|
841
|
+
|
842
|
+
std::string
|
843
|
+
Reader::getFormatedErrorMessages() const
|
844
|
+
{
|
845
|
+
std::string formattedMessage;
|
846
|
+
for ( Errors::const_iterator itError = errors_.begin();
|
847
|
+
itError != errors_.end();
|
848
|
+
++itError )
|
849
|
+
{
|
850
|
+
const ErrorInfo &error = *itError;
|
851
|
+
formattedMessage += "* " + getLocationLineAndColumn( error.token_.start_ ) + "\n";
|
852
|
+
formattedMessage += " " + error.message_ + "\n";
|
853
|
+
if ( error.extra_ )
|
854
|
+
formattedMessage += "See " + getLocationLineAndColumn( error.extra_ ) + " for detail.\n";
|
855
|
+
}
|
856
|
+
return formattedMessage;
|
857
|
+
}
|
858
|
+
|
859
|
+
|
860
|
+
std::istream& operator>>( std::istream &sin, Value &root )
|
861
|
+
{
|
862
|
+
Json::Reader reader;
|
863
|
+
bool ok = reader.parse(sin, root, true);
|
864
|
+
//JSON_ASSERT( ok );
|
865
|
+
if (!ok) throw std::runtime_error(reader.getFormatedErrorMessages());
|
866
|
+
return sin;
|
867
|
+
}
|
868
|
+
|
869
|
+
|
870
|
+
} // namespace Json
|