include/gn/gnDefs.h File Reference

#include <limits.h>
#include <float.h>
#include "gn/gnSetup.h"

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Defines

#define BOOLEAN_MAX   1
#define BOOLEAN_MIN   0
#define CONTIG_SECTION_SIZE   3
#define FALSE   0
#define FLOAT32_DIGIT   FLT_DIG
#define FLOAT32_MAX   FLT_MAX
#define FLOAT32_MAX_10_EXP   FLT_MAX_10_EXP
#define FLOAT32_MAX_EXP   FLT_MAX_EXP
#define FLOAT32_MIN   FLT_MIN
#define FLOAT32_MIN_10_EXP   FLT_MIN_10_EXP
#define FLOAT32_MIN_EXP   FLT_MIN_EXP
#define FLOAT32_MIN_FRACTION   FLT_EPSILON
#define FLOAT32_RADIX   FLT_RADIX
#define FLOAT64_DIGIT   DBL_DIG
#define FLOAT64_MAX   DBL_MAX
#define FLOAT64_MAX_10_EXP   DBL_MAX_10_EXP
#define FLOAT64_MAX_EXP   DBL_MAX_EXP
#define FLOAT64_MIN   DBL_MIN
#define FLOAT64_MIN_10_EXP   DBL_MIN_10_EXP
#define FLOAT64_MIN_EXP   DBL_MIN_EXP
#define FLOAT64_MIN_FRACTION   DBL_EPSILON
#define FLOAT64_RADIX   DBL_RADIX
#define GNSEQC_MAX   INT8_MAX
#define GNSEQC_MIN   INT8_MIN
#define GNSEQC_NULL   0
#define GNSEQI_BEGIN   UINT64_MIN
#define GNSEQI_END   UINT32_MAX
#define GNSEQI_ERROR   UINT32_MAX
#define INT0_MIN   0
#define INT16_BIT_SIZE   16
#define INT16_BYTE_SIZE   2
#define INT16_MAX   SHRT_MAX
#define INT16_MIN   SHRT_MIN
#define INT1_MAX   1
#define INT32_BIT_SIZE   32
#define INT32_BYTE_SIZE   4
#define INT32_MAX   INT_MAX
#define INT32_MIN   INT_MIN
#define INT64_BIT_SIZE   64
#define INT64_BYTE_SIZE   8
#define INT64_MAX   LONG_MAX
#define INT64_MIN   LONG_MIN
#define INT8_BIT_SIZE   8
#define INT8_BYTE_SIZE   1
#define INT8_MAX   SCHAR_MAX
#define INT8_MIN   SCHAR_MIN
#define PI   3.1415926535897932384626433832795028
#define TRUE   1
#define UINT16_BIT_SIZE   16
#define UINT16_BYTE_SIZE   2
#define UINT16_MAX   USHRT_MAX
#define UINT16_MIN   0
#define UINT32_BIT_SIZE   32
#define UINT32_BYTE_SIZE   4
#define UINT32_MAX   UINT_MAX
#define UINT32_MIN   0
#define UINT64_BIT_SIZE   64
#define UINT64_BYTE_SIZE   8
#define UINT64_MAX   ULONG_MAX
#define UINT64_MIN   0
#define UINT8_BIT_SIZE   8
#define UINT8_BYTE_SIZE   1
#define UINT8_MAX   UCHAR_MAX
#define UINT8_MIN   0

Typedefs

typedef unsigned char boolean
typedef float float32
typedef double float64
typedef char gnSeqC
typedef uint64 gnSeqI
typedef unsigned char int1
typedef signed short int int16
typedef signed int int32
typedef signed long long int64
typedef signed char int8
typedef signed short int sint16
typedef signed int sint32
typedef signed long int sint64
typedef signed char sint8
typedef unsigned int uint
typedef unsigned short int uint16
typedef unsigned int uint32
typedef unsigned long long uint64
typedef unsigned char uint8

Enumerations

enum  gnContigSection { gnContigHeader = 0, gnContigAnnotation = 1, gnContigSequence = 2 }
enum  gnNewlineType { gnNewlineUnix = 0, gnNewlineWindows = 1, gnNewlineMac = 2 }

Variables

const uint32 ALL_CONTIGS = UINT32_MAX
const uint32 BUFFER_SIZE = 100000


Define Documentation

#define BOOLEAN_MAX   1
 

Definition at line 56 of file gnDefs.h.

#define BOOLEAN_MIN   0
 

Definition at line 55 of file gnDefs.h.

#define CONTIG_SECTION_SIZE   3
 

Definition at line 132 of file gnDefs.h.

Referenced by gnFileContig::Clear(), gnFileContig::GetSectLength(), gnFileContig::GetSectStartEnd(), gnFileContig::gnFileContig(), main(), gnFileContig::SetSectEnd(), gnFileContig::SetSectStart(), and gnFileContig::SetSectStartEnd().

#define FALSE   0
 

Definition at line 49 of file gnDefs.h.

#define FLOAT32_DIGIT   FLT_DIG
 

Definition at line 106 of file gnDefs.h.

#define FLOAT32_MAX   FLT_MAX
 

Definition at line 101 of file gnDefs.h.

#define FLOAT32_MAX_10_EXP   FLT_MAX_10_EXP
 

Definition at line 105 of file gnDefs.h.

#define FLOAT32_MAX_EXP   FLT_MAX_EXP
 

Definition at line 103 of file gnDefs.h.

#define FLOAT32_MIN   FLT_MIN
 

Definition at line 100 of file gnDefs.h.

#define FLOAT32_MIN_10_EXP   FLT_MIN_10_EXP
 

Definition at line 104 of file gnDefs.h.

#define FLOAT32_MIN_EXP   FLT_MIN_EXP
 

Definition at line 102 of file gnDefs.h.

#define FLOAT32_MIN_FRACTION   FLT_EPSILON
 

Definition at line 108 of file gnDefs.h.

#define FLOAT32_RADIX   FLT_RADIX
 

Definition at line 107 of file gnDefs.h.

#define FLOAT64_DIGIT   DBL_DIG
 

Definition at line 116 of file gnDefs.h.

#define FLOAT64_MAX   DBL_MAX
 

Definition at line 111 of file gnDefs.h.

#define FLOAT64_MAX_10_EXP   DBL_MAX_10_EXP
 

Definition at line 115 of file gnDefs.h.

#define FLOAT64_MAX_EXP   DBL_MAX_EXP
 

Definition at line 113 of file gnDefs.h.

#define FLOAT64_MIN   DBL_MIN
 

Definition at line 110 of file gnDefs.h.

#define FLOAT64_MIN_10_EXP   DBL_MIN_10_EXP
 

Definition at line 114 of file gnDefs.h.

#define FLOAT64_MIN_EXP   DBL_MIN_EXP
 

Definition at line 112 of file gnDefs.h.

#define FLOAT64_MIN_FRACTION   DBL_EPSILON
 

Definition at line 118 of file gnDefs.h.

#define FLOAT64_RADIX   DBL_RADIX
 

Definition at line 117 of file gnDefs.h.

#define GNSEQC_MAX   INT8_MAX
 

Definition at line 129 of file gnDefs.h.

Referenced by gnCompare::gnCompare(), gnFilter::gnFilter(), and gnCompare::~gnCompare().

#define GNSEQC_MIN   INT8_MIN
 

Definition at line 128 of file gnDefs.h.

#define GNSEQC_NULL   0
 

Definition at line 127 of file gnDefs.h.

Referenced by gnSequence::GetSeqC().

#define GNSEQI_BEGIN   UINT64_MIN
 

Definition at line 126 of file gnDefs.h.

#define GNSEQI_END   UINT32_MAX
 

Definition at line 125 of file gnDefs.h.

Referenced by gnSequence::append(), gnGenomeSpec::CloneRange(), gnFragmentSpec::CloneRange(), gnSequence::erase(), gnBaseFeature::FirstIndexOfQualifier(), gnSequence::insert(), gnLocation::IsEndBoundShorter(), gnLocation::IsStartBoundShorter(), gnBaseFeature::LastIndexOfQualifier(), gnLocation::MovePositive(), gnSequence::operator+=(), gnDNXSource::ParseStream(), gnSequence::splitContig(), and gnSequence::ToArray().

#define GNSEQI_ERROR   UINT32_MAX
 

Definition at line 124 of file gnDefs.h.

Referenced by gnSequence::find(), gnSEQSource::GetContigSeqLength(), gnRAWSource::GetContigSeqLength(), gnGBKSource::GetContigSeqLength(), gnFASSource::GetContigSeqLength(), and gnABISource::GetContigSeqLength().

#define INT0_MIN   0
 

Definition at line 57 of file gnDefs.h.

#define INT16_BIT_SIZE   16
 

Definition at line 66 of file gnDefs.h.

#define INT16_BYTE_SIZE   2
 

Definition at line 61 of file gnDefs.h.

#define INT16_MAX   SHRT_MAX
 

Definition at line 84 of file gnDefs.h.

#define INT16_MIN   SHRT_MIN
 

Definition at line 83 of file gnDefs.h.

#define INT1_MAX   1
 

Definition at line 58 of file gnDefs.h.

#define INT32_BIT_SIZE   32
 

Definition at line 67 of file gnDefs.h.

#define INT32_BYTE_SIZE   4
 

Definition at line 62 of file gnDefs.h.

#define INT32_MAX   INT_MAX
 

Definition at line 86 of file gnDefs.h.

#define INT32_MIN   INT_MIN
 

Definition at line 85 of file gnDefs.h.

#define INT64_BIT_SIZE   64
 

Definition at line 68 of file gnDefs.h.

#define INT64_BYTE_SIZE   8
 

Definition at line 63 of file gnDefs.h.

#define INT64_MAX   LONG_MAX
 

Definition at line 88 of file gnDefs.h.

#define INT64_MIN   LONG_MIN
 

Definition at line 87 of file gnDefs.h.

#define INT8_BIT_SIZE   8
 

Definition at line 65 of file gnDefs.h.

#define INT8_BYTE_SIZE   1
 

Definition at line 60 of file gnDefs.h.

#define INT8_MAX   SCHAR_MAX
 

Definition at line 82 of file gnDefs.h.

#define INT8_MIN   SCHAR_MIN
 

Definition at line 81 of file gnDefs.h.

#define PI   3.1415926535897932384626433832795028
 

Definition at line 52 of file gnDefs.h.

#define TRUE   1
 

Definition at line 46 of file gnDefs.h.

#define UINT16_BIT_SIZE   16
 

Definition at line 76 of file gnDefs.h.

#define UINT16_BYTE_SIZE   2
 

Definition at line 71 of file gnDefs.h.

#define UINT16_MAX   USHRT_MAX
 

Definition at line 93 of file gnDefs.h.

#define UINT16_MIN   0
 

Definition at line 92 of file gnDefs.h.

#define UINT32_BIT_SIZE   32
 

Definition at line 77 of file gnDefs.h.

#define UINT32_BYTE_SIZE   4
 

Definition at line 72 of file gnDefs.h.

#define UINT32_MAX   UINT_MAX
 

Definition at line 95 of file gnDefs.h.

Referenced by gnMultiSpec< SubSpec >::AddHeader(), and gnMultiSpec< SubSpec >::AddSpec().

#define UINT32_MIN   0
 

Definition at line 94 of file gnDefs.h.

#define UINT64_BIT_SIZE   64
 

Definition at line 78 of file gnDefs.h.

#define UINT64_BYTE_SIZE   8
 

Definition at line 73 of file gnDefs.h.

#define UINT64_MAX   ULONG_MAX
 

Definition at line 97 of file gnDefs.h.

#define UINT64_MIN   0
 

Definition at line 96 of file gnDefs.h.

#define UINT8_BIT_SIZE   8
 

Definition at line 75 of file gnDefs.h.

#define UINT8_BYTE_SIZE   1
 

Definition at line 70 of file gnDefs.h.

#define UINT8_MAX   UCHAR_MAX
 

Definition at line 91 of file gnDefs.h.

#define UINT8_MIN   0
 

Definition at line 90 of file gnDefs.h.


Typedef Documentation

typedef unsigned char boolean
 

Definition at line 23 of file gnDefs.h.

typedef float float32
 

Definition at line 41 of file gnDefs.h.

typedef double float64
 

Definition at line 42 of file gnDefs.h.

typedef char gnSeqC
 

Definition at line 121 of file gnDefs.h.

Referenced by gnCompare::AddArrayEntry(), gnCompare::Contains(), gnCompare::DelArrayEntry(), gnTranslator::Filter(), gnPosSpecificTranslator::Filter(), gnFastTranslator::Filter(), gnFilter::Filter(), gnTranslator::GetDefaultChar(), gnFilter::GetDefaultChar(), gnFastTranslator::GetDefaultChar(), gnFilter::GetRDefaultChar(), gnSequence::GetSeqC(), gnCompare::gnCompare(), gnDNASequence::gnDNASequence(), gnFilter::gnFilter(), gnProteinSequence::gnProteinSequence(), gnRNASequence::gnRNASequence(), gnSequence::gnSequence(), gnSequence::insert(), gnFilter::IsValid(), gnCompare::LessThan(), main(), gnFilter::MakeValid(), gnSequence::operator[](), gnStringSpec::Read(), gnSourceSpec::Read(), gnCompare::RemoveContained(), gnFilter::RemovePair(), gnCompare::RemovePair(), gnFilter::RemoveSingle(), gnCompare::RemoveSingle(), gnFilter::ReverseFilter(), gnSEQSource::SeqRead(), gnGBKSource::SeqRead(), gnFASSource::SeqRead(), gnContigSpec::SeqRead(), gnMultiSpec< SubSpec >::SeqRead(), gnCompare::SetContained(), gnTranslator::SetDefaultChar(), gnFilter::SetDefaultChar(), gnFastTranslator::SetDefaultChar(), gnFilter::SetPair(), gnCompare::SetPair(), gnFilter::SetSingle(), gnCompare::SetSingle(), gnSequence::ToArray(), gnRAWSource::Write(), gnGBKSource::Write(), gnFASSource::Write(), and gnCompare::~gnCompare().

typedef uint64 gnSeqI
 

Definition at line 122 of file gnDefs.h.

Referenced by gnFileContig::AddToSeqLength(), BaseCount(), gnSEQSource::BaseCount(), gnFastTranslator::CacheTranslator(), gnStringSpec::CloneRange(), gnSourceSpec::CloneRange(), gnGenomeSpec::CloneRange(), gnFragmentSpec::CloneRange(), gnSequence::compare(), gnCompare::Contains(), gnBaseFeature::Contains(), gnSequence::contigByBase(), gnSequence::contigIndexByBase(), gnSequence::contigLength(), gnSequence::contigListLength(), gnSequence::contigListSize(), gnSequence::contigStart(), gnLocation::CropEnd(), gnFragmentSpec::CropEnd(), gnContigSpec::CropEnd(), gnBaseFeature::CropEnd(), gnMultiSpec< SubSpec >::CropEnd(), gnLocation::CropStart(), gnFragmentSpec::CropStart(), gnContigSpec::CropStart(), gnBaseFeature::CropStart(), gnMultiSpec< SubSpec >::CropStart(), gnLocation::CropTo(), gnSequence::erase(), gnTranslator::Filter(), gnPosSpecificTranslator::Filter(), gnFilter::Filter(), gnFastTranslator::Filter(), gnSequence::find(), gnLocation::GetBounds(), gnGenomeSpec::GetBrokenFeatures(), gnGenomeSpec::GetContainedFeatures(), gnSEQSource::GetContigSeqLength(), gnRAWSource::GetContigSeqLength(), gnGBKSource::GetContigSeqLength(), gnFASSource::GetContigSeqLength(), gnDNXSource::GetContigSeqLength(), gnABISource::GetContigSeqLength(), gnLocation::GetEnd(), gnLocation::GetEndLength(), gnLocation::GetFirst(), gnSourceHeader::GetHeader(), gnGenomeSpec::GetIntersectingFeatures(), gnLocation::GetLast(), gnMultiSpec< SubSpec >::GetLength(), gnContigSpec::GetLength(), gnSequence::GetSeqC(), gnFileContig::GetSeqLength(), gnStringSpec::GetSourceLength(), gnSourceSpec::GetSourceLength(), gnMultiSpec< SubSpec >::GetSpecByBase(), gnMultiSpec< SubSpec >::GetSpecEndBase(), gnMultiSpec< SubSpec >::GetSpecIndexByBase(), gnMultiSpec< SubSpec >::GetSpecStartBase(), gnLocation::GetStart(), gnContigSpec::GetStart(), gnLocation::GetStartLength(), gnSourceQualifier::GetValue(), gnSequence::globalToLocal(), gnSequence::globalToSource(), gnDNASequence::gnDNASequence(), gnLocation::gnLocation(), gnProteinSequence::gnProteinSequence(), gnRNASequence::gnRNASequence(), gnSequence::gnSequence(), gnSourceSpec::gnSourceSpec(), gnStringSpec::gnStringSpec(), gnSequence::insert(), gnSequence::length(), gnCompare::LessThan(), load_map_file(), gnSequence::localToGlobal(), gnSequence::localToSource(), main(), map_coordinates(), map_list_coordinates(), gnSequence::merge(), gnLocation::MoveNegative(), gnBaseFeature::MoveNegative(), gnLocation::MovePositive(), gnBaseFeature::MovePositive(), gnLocation::MoveTo(), gnSequence::operator[](), gnSEQSource::ParseStream(), gnRAWSource::ParseStream(), gnGBKSource::ParseStream(), gnFileSource::Read(), gnStringSpec::Read(), gnSourceSpec::Read(), gnFilter::ReverseFilter(), gnSEQSource::SeqRead(), gnRAWSource::SeqRead(), gnGBKSource::SeqRead(), gnFASSource::SeqRead(), gnContigSpec::SeqRead(), gnABISource::SeqRead(), gnMultiSpec< SubSpec >::SeqRead(), gnDNXSource::SeqRead(), gnSEQSource::SeqSeek(), gnGBKSource::SeqSeek(), gnFASSource::SeqSeek(), gnABISource::SeqSeek(), gnSEQSource::SeqStartPos(), gnGBKSource::SeqStartPos(), gnFASSource::SeqStartPos(), gnABISource::SeqStartPos(), gnLocation::SetBounds(), gnLocation::SetEnd(), gnLocation::SetEndLength(), gnContigSpec::SetLength(), gnFileContig::SetSeqLength(), gnLocation::SetStart(), gnContigSpec::SetStart(), gnLocation::SetStartLength(), gnSequence::size(), gnSequence::splitContig(), gnSequence::subseq(), gnSequence::ToArray(), gnSequence::ToString(), gnRAWSource::Write(), gnGBKSource::Write(), and gnFASSource::Write().

typedef unsigned char int1
 

Definition at line 24 of file gnDefs.h.

typedef signed short int int16
 

Definition at line 27 of file gnDefs.h.

typedef signed int int32
 

Definition at line 28 of file gnDefs.h.

Referenced by main(), gnSEQSource::ParseStream(), and gnGBKSource::ParseStream().

typedef signed long long int64
 

Definition at line 29 of file gnDefs.h.

Referenced by gnSequence::contigStart(), main(), gnSEQSource::ParseStream(), IntervalSequenceTree< Key, Allocator >::propogateChanges(), and gnGBKSource::Write().

typedef signed char int8
 

Definition at line 26 of file gnDefs.h.

typedef signed short int sint16
 

Definition at line 31 of file gnDefs.h.

typedef signed int sint32
 

Definition at line 32 of file gnDefs.h.

typedef signed long int sint64
 

Definition at line 33 of file gnDefs.h.

typedef signed char sint8
 

Definition at line 30 of file gnDefs.h.

typedef unsigned int uint
 

Definition at line 39 of file gnDefs.h.

Referenced by gnFilter::Filter(), gnFilter::IsValid(), main(), gnFilter::MakeValid(), gnFilter::RemovePair(), gnFilter::RemoveSingle(), gnFilter::SetPair(), and gnFilter::SetSingle().

typedef unsigned short int uint16
 

Definition at line 36 of file gnDefs.h.

typedef unsigned int uint32
 

Definition at line 37 of file gnDefs.h.

Referenced by gnCompare::AddArrayEntry(), gnGenomeSpec::AddFeature(), gnSequence::addFeature(), gnFragmentSpec::AddFeature(), gnSequence::addHeader(), gnMultiSpec< SubSpec >::AddHeader(), gnBaseFeature::AddLocation(), gnMultiSpec< SubSpec >::AddSpec(), BaseCount(), gnSEQSource::BaseCount(), gnGenomeSpec::Clear(), gnFragmentSpec::Clear(), gnFileContig::Clear(), gnMultiSpec< SubSpec >::Clear(), gnGenomeSpec::CloneRange(), gnFragmentSpec::CloneRange(), ComplementLocation(), gnCompare::Contains(), gnBaseFeature::Contains(), gnSequence::contig(), gnSequence::contigByName(), gnSequence::contigIndexByBase(), gnSequence::contigIndexByName(), gnSequence::contigLength(), gnSequence::contigName(), gnSequence::contigStart(), gnFragmentSpec::CropEnd(), gnBaseFeature::CropEnd(), gnMultiSpec< SubSpec >::CropEnd(), gnFragmentSpec::CropStart(), gnBaseFeature::CropStart(), gnMultiSpec< SubSpec >::CropStart(), gnCompare::DelArrayEntry(), gnSourceFactory::DelPath(), gnSourceFactory::DelSource(), gnSequence::erase(), gnTranslator::Filter(), gnFilter::Filter(), gnFastTranslator::Filter(), gnBaseFeature::FirstIndexOfQualifier(), gnSEQSource::FormatString(), gnGBKSource::FormatString(), gnGenomeSpec::GetBrokenFeatures(), gnFragmentSpec::GetBrokenFeatures(), gnGenomeSpec::GetContainedFeatures(), gnFragmentSpec::GetContainedFeatures(), gnFASSource::GetContig(), gnSEQSource::GetContigID(), gnRAWSource::GetContigID(), gnGBKSource::GetContigID(), gnFASSource::GetContigID(), gnDNXSource::GetContigID(), gnABISource::GetContigID(), gnSEQSource::GetContigListLength(), gnRAWSource::GetContigListLength(), gnGBKSource::GetContigListLength(), gnFASSource::GetContigListLength(), gnDNXSource::GetContigListLength(), gnABISource::GetContigListLength(), gnSEQSource::GetContigName(), gnRAWSource::GetContigName(), gnGBKSource::GetContigName(), gnFASSource::GetContigName(), gnDNXSource::GetContigName(), gnABISource::GetContigName(), gnSEQSource::GetContigSeqLength(), gnRAWSource::GetContigSeqLength(), gnGBKSource::GetContigSeqLength(), gnFASSource::GetContigSeqLength(), gnDNXSource::GetContigSeqLength(), gnABISource::GetContigSeqLength(), gnTranslator::GetDefaultInputWidth(), gnGenomeSpec::GetFeature(), gnSequence::getFeature(), gnFragmentSpec::GetFeature(), gnGenomeSpec::GetFeatureListLength(), gnSequence::getFeatureListLength(), gnFragmentSpec::GetFeatureListLength(), gnSEQSource::GetFileContig(), gnRAWSource::GetFileContig(), gnGBKSource::GetFileContig(), gnFASSource::GetFileContig(), gnDNXSource::GetFileContig(), gnABISource::GetFileContig(), gnSequence::getHeader(), gnMultiSpec< SubSpec >::GetHeader(), gnSequence::getHeaderListLength(), gnMultiSpec< SubSpec >::GetHeaderListLength(), gnSourceHeader::GetHeaderStart(), gnBaseFeature::GetID(), gnExceptionCode::GetInt(), gnGenomeSpec::GetIntersectingFeatures(), gnFragmentSpec::GetIntersectingFeatures(), gnStringHeader::GetLength(), gnSourceHeader::GetLength(), gnMultiSpec< SubSpec >::GetLength(), gnBaseFeature::GetLocation(), gnBaseFeature::GetLocationListLength(), gnStringQualifier::GetNameLength(), gnSourceQualifier::GetNameLength(), GetNewExceptionCode(), gnSourceFactory::GetPath(), gnSourceFactory::GetPathListSize(), gnBaseFeature::GetQualifier(), gnBaseFeature::GetQualifierListLength(), gnBaseFeature::GetQualifierName(), gnBaseFeature::GetQualifierValue(), gnFileContig::GetSectLength(), gnFileContig::GetSectStartEnd(), gnSourceFactory::GetSource(), gnSourceFactory::GetSourceClassListSize(), gnContigSpec::GetSourceContigIndex(), gnSourceFactory::GetSourceListSize(), gnFASSource::GetSpec(), gnMultiSpec< SubSpec >::GetSpec(), gnMultiSpec< SubSpec >::GetSpecEndBase(), gnMultiSpec< SubSpec >::GetSpecIndexByBase(), gnMultiSpec< SubSpec >::GetSpecIndexByName(), gnMultiSpec< SubSpec >::GetSpecListLength(), gnMultiSpec< SubSpec >::GetSpecStartBase(), gnSourceFactory::GetURL(), gnStringQualifier::GetValueLength(), gnSourceQualifier::GetValueLength(), gnSourceQualifier::GetValueStart(), gnSequence::globalToLocal(), gnSequence::globalToSource(), gnBaseFeature::gnBaseFeature(), gnExceptionCode::gnExceptionCode(), gnFeature::gnFeature(), gnFileContig::gnFileContig(), gnFragmentSpec::gnFragmentSpec(), gnGenomeSpec::gnGenomeSpec(), gnSourceHeader::gnSourceHeader(), gnSourceQualifier::gnSourceQualifier(), gnSourceSpec::gnSourceSpec(), gnSEQSource::HasContig(), gnGBKSource::HasContig(), gnFASSource::HasContig(), gnDNXSource::HasContig(), gnSourceFactory::HasPath(), gnBaseFeature::HasQualifier(), gnSequence::insert(), gnSourceFactory::InsPath(), gnBaseFeature::Intersects(), gnBaseFeature::IsContainedBy(), gnSequence::isReverseComplement(), gnFilter::IsValid(), gnBaseFeature::LastIndexOfQualifier(), gnCompare::LessThan(), loc_binary_search(), gnSequence::localToGlobal(), gnSequence::localToSource(), main(), gnFilter::MakeValid(), map_coordinates(), gnSequence::mergeContigs(), gnGenomeSpec::MergeFragments(), gnBaseFeature::MoveNegative(), gnBaseFeature::MovePositive(), gnSEQSource::ParseStream(), gnRAWSource::ParseStream(), gnGBKSource::ParseStream(), gnFASSource::ParseStream(), gnDNXSource::ParseStream(), print_feature(), gnGenomeSpec::RemoveFeature(), gnSequence::removeFeature(), gnFragmentSpec::RemoveFeature(), gnSequence::removeHeader(), gnMultiSpec< SubSpec >::RemoveHeader(), gnBaseFeature::RemoveLocation(), gnTranslator::RemovePair(), gnBaseFeature::RemoveQualifier(), gnMultiSpec< SubSpec >::RemoveSpec(), gnFilter::ReverseFilter(), gnSEQSource::SeqRead(), gnRAWSource::SeqRead(), gnGBKSource::SeqRead(), gnFASSource::SeqRead(), gnContigSpec::SeqRead(), gnABISource::SeqRead(), gnMultiSpec< SubSpec >::SeqRead(), gnDNXSource::SeqRead(), gnSEQSource::SeqSeek(), gnGBKSource::SeqSeek(), gnFASSource::SeqSeek(), gnABISource::SeqSeek(), gnSEQSource::SeqStartPos(), gnGBKSource::SeqStartPos(), gnFASSource::SeqStartPos(), gnSequence::setContigName(), gnTranslator::SetDefaultInputWidth(), gnSourceHeader::SetHeaderLength(), gnSourceHeader::SetHeaderStart(), gnBaseFeature::SetID(), gnBaseFeature::SetLocation(), gnBaseFeature::SetQualifier(), gnBaseFeature::SetQualifierName(), gnBaseFeature::SetQualifierValue(), gnSequence::setReverseComplement(), gnGenomeSpec::SetReverseComplement(), gnFragmentSpec::SetReverseComplement(), gnFileContig::SetSectEnd(), gnFileContig::SetSectStart(), gnFileContig::SetSectStartEnd(), gnContigSpec::SetSourceContigIndex(), gnSourceQualifier::SetValueLength(), gnSourceQualifier::SetValueStart(), gnSequence::splitContig(), gnGBKSource::Write(), gnFASSource::Write(), gnDNXSource::Write(), WriteData(), WriteHeader(), and gnBaseFeature::~gnBaseFeature().

typedef unsigned long long uint64
 

Definition at line 38 of file gnDefs.h.

Referenced by gnFileContig::GetFileLength(), gnFileContig::GetSectLength(), gnFileContig::gnFileContig(), gnSEQSource::ParseStream(), gnRAWSource::ParseStream(), gnGBKSource::ParseStream(), gnFASSource::ParseStream(), gnDNXSource::ParseStream(), gnFileSource::Read(), gnSEQSource::SeqRead(), gnGBKSource::SeqRead(), gnFASSource::SeqRead(), gnSEQSource::SeqSeek(), gnGBKSource::SeqSeek(), gnFASSource::SeqSeek(), gnABISource::SeqSeek(), gnSEQSource::SeqStartPos(), gnGBKSource::SeqStartPos(), gnFASSource::SeqStartPos(), gnABISource::SeqStartPos(), gnFileContig::SetFileEnd(), gnFileContig::SetFileStart(), gnFileContig::SetRepeatGapSize(), gnFileContig::SetRepeatSeqSize(), gnFileContig::SetSectEnd(), and gnFileContig::SetSectStart().

typedef unsigned char uint8
 

Definition at line 35 of file gnDefs.h.


Enumeration Type Documentation

enum gnContigSection
 

Enumeration values:
gnContigHeader 
gnContigAnnotation 
gnContigSequence 

Definition at line 133 of file gnDefs.h.

Referenced by main().

enum gnNewlineType
 

Enumeration values:
gnNewlineUnix 
gnNewlineWindows 
gnNewlineMac 

Definition at line 139 of file gnDefs.h.


Variable Documentation

const uint32 ALL_CONTIGS = UINT32_MAX [static]
 

Definition at line 145 of file gnDefs.h.

const uint32 BUFFER_SIZE = 100000 [static]
 

Definition at line 146 of file gnDefs.h.


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