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# gnDefs.h File Reference

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

Go to the source code of this file.

## Compounds
class | Array
| Class used to ensure correct deallocation of arrays. More...
## Defines
#define | TRUE 1
#define | FALSE 0
#define | PI 3.1415926535897932384626433832795028
#define | BOOLEAN_MIN 0
#define | BOOLEAN_MAX 1
#define | INT0_MIN 0
#define | INT1_MAX 1
#define | INT8_BYTE_SIZE 1
#define | INT16_BYTE_SIZE 2
#define | INT32_BYTE_SIZE 4
#define | INT64_BYTE_SIZE 8
#define | INT8_BIT_SIZE 8
#define | INT16_BIT_SIZE 16
#define | INT32_BIT_SIZE 32
#define | INT64_BIT_SIZE 64
#define | UINT8_BYTE_SIZE 1
#define | UINT16_BYTE_SIZE 2
#define | UINT32_BYTE_SIZE 4
#define | UINT64_BYTE_SIZE 8
#define | UINT8_BIT_SIZE 8
#define | UINT16_BIT_SIZE 16
#define | UINT32_BIT_SIZE 32
#define | UINT64_BIT_SIZE 64
#define | INT8_MIN SCHAR_MIN
#define | INT8_MAX SCHAR_MAX
#define | INT16_MIN SHRT_MIN
#define | INT16_MAX SHRT_MAX
#define | INT32_MIN INT_MIN
#define | INT32_MAX INT_MAX
#define | INT64_MIN LONG_MIN
#define | INT64_MAX LONG_MAX
#define | UINT8_MIN 0
#define | UINT8_MAX UCHAR_MAX
#define | UINT16_MIN 0
#define | UINT16_MAX USHRT_MAX
#define | UINT32_MIN 0
#define | UINT32_MAX UINT_MAX
#define | UINT64_MIN 0
#define | UINT64_MAX ULONG_MAX
#define | FLOAT32_MIN FLT_MIN
#define | FLOAT32_MAX FLT_MAX
#define | FLOAT32_MIN_EXP FLT_MIN_EXP
#define | FLOAT32_MAX_EXP FLT_MAX_EXP
#define | FLOAT32_MIN_10_EXP FLT_MIN_10_EXP
#define | FLOAT32_MAX_10_EXP FLT_MAX_10_EXP
#define | FLOAT32_DIGIT FLT_DIG
#define | FLOAT32_RADIX FLT_RADIX
#define | FLOAT32_MIN_FRACTION FLT_EPSILON
#define | FLOAT64_MIN DBL_MIN
#define | FLOAT64_MAX DBL_MAX
#define | FLOAT64_MIN_EXP DBL_MIN_EXP
#define | FLOAT64_MAX_EXP DBL_MAX_EXP
#define | FLOAT64_MIN_10_EXP DBL_MIN_10_EXP
#define | FLOAT64_MAX_10_EXP DBL_MAX_10_EXP
#define | FLOAT64_DIGIT DBL_DIG
#define | FLOAT64_RADIX DBL_RADIX
#define | FLOAT64_MIN_FRACTION DBL_EPSILON
#define | GNSEQI_ERROR UINT32_MAX
#define | GNSEQI_END UINT32_MAX
#define | GNSEQI_BEGIN UINT32_MIN
#define | GNSEQC_NULL 0
#define | GNSEQC_MIN INT8_MIN
#define | GNSEQC_MAX INT8_MAX
#define | CONTIG_SECTION_SIZE 3
## Typedefs
typedef unsigned char | boolean
typedef unsigned char | int1
typedef signed char | int8
typedef signed short int | int16
typedef signed int | int32
typedef signed long long | int64
typedef signed char | sint8
typedef signed short int | sint16
typedef signed int | sint32
typedef signed long int | sint64
typedef unsigned char | uint8
typedef unsigned short int | uint16
typedef unsigned int | uint32
typedef unsigned long long | uint64
typedef unsigned int | uint
typedef float | float32
typedef double | float64
typedef char | gnSeqC
typedef uint32 | gnSeqI
## 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(), 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 UINT32_MIN

| Definition at line 126 of file gnDefs.h.

#define GNSEQI_END UINT32_MAX

| Definition at line 125 of file gnDefs.h. Referenced by gnGenomeSpec::CloneRange(), gnFragmentSpec::CloneRange(), gnBaseFeature::FirstIndexOfQualifier(), gnSequence::insert(), gnBaseFeature::LastIndexOfQualifier(), gnLocation::MovePositive(), gnDNXSource::ParseStream(), 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::AddHeader(), gnGenomeSpec::AddSpec(), and gnFragmentSpec::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(), gnFilter::Filter(), gnFastTranslator::Filter(), gnTranslator::GetDefaultChar(), gnFilter::GetDefaultChar(), gnFastTranslator::GetDefaultChar(), gnFilter::GetRDefaultChar(), gnSequence::GetSeqC(), gnCompare::gnCompare(), gnFilter::gnFilter(), gnCompare::LessThan(), gnFilter::MakeValid(), gnSequence::operator[](), gnFilter::ReverseFilter(), gnSEQSource::SeqRead(), gnGBKSource::SeqRead(), gnFASSource::SeqRead(), gnSequence::ToArray(), gnRAWSource::Write(), gnGBKSource::Write(), gnFASSource::Write(), and gnCompare::~gnCompare().

typedef uint32 gnSeqI

| Definition at line 122 of file gnDefs.h. Referenced by gnFastTranslator::CacheTranslator(), gnGenomeSpec::CloneRange(), gnFragmentSpec::CloneRange(), gnSequence::compare(), gnCompare::Contains(), gnSequence::contigLength(), gnSequence::contigListLength(), gnSequence::contigListSize(), gnSequence::contigStart(), gnMultiSpec::CropEnd(), gnLocation::CropEnd(), gnMultiSpec::CropStart(), gnLocation::CropStart(), gnLocation::CropTo(), gnSequence::erase(), gnFilter::Filter(), gnSequence::find(), gnGenomeSpec::GetBrokenFeatures(), gnGenomeSpec::GetContainedFeatures(), gnSEQSource::GetContigSeqLength(), gnRAWSource::GetContigSeqLength(), gnGBKSource::GetContigSeqLength(), gnFASSource::GetContigSeqLength(), gnDNXSource::GetContigSeqLength(), gnABISource::GetContigSeqLength(), gnLocation::GetEnd(), gnLocation::GetEndLength(), gnLocation::GetFirst(), gnGenomeSpec::GetIntersectingFeatures(), gnLocation::GetLast(), gnMultiSpec::GetLength(), gnContigSpec::GetLength(), gnSequence::GetSeqC(), gnFileContig::GetSeqLength(), gnStringSpec::GetSourceLength(), gnSourceSpec::GetSourceLength(), gnMultiSpec::GetSpecEndBase(), gnMultiSpec::GetSpecIndexByBase(), gnMultiSpec::GetSpecStartBase(), gnLocation::GetStart(), gnContigSpec::GetStart(), gnLocation::GetStartLength(), gnSequence::globalToSource(), gnSourceSpec::gnSourceSpec(), gnStringSpec::gnStringSpec(), gnSequence::insert(), gnSequence::length(), gnCompare::LessThan(), gnSEQSource::ParseStream(), gnRAWSource::ParseStream(), gnGBKSource::ParseStream(), gnSEQSource::SeqRead(), gnMultiSpec::SeqRead(), gnGBKSource::SeqRead(), gnFASSource::SeqRead(), gnContigSpec::SeqRead(), gnSEQSource::SeqSeek(), gnGBKSource::SeqSeek(), gnFASSource::SeqSeek(), gnSequence::size(), gnSequence::splitContig(), 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 gnSEQSource::ParseStream(), and gnGBKSource::ParseStream().

typedef signed long long int64

| Definition at line 29 of file gnDefs.h. Referenced by gnSequence::contigStart(), gnSEQSource::ParseStream(), 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.

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(), gnSequence::addFeature(), gnGenomeSpec::AddFeature(), gnFragmentSpec::AddFeature(), gnMultiSpec::AddHeader(), gnGenomeSpec::AddSpec(), gnFragmentSpec::AddSpec(), BaseCount(), gnSEQSource::BaseCount(), gnMultiSpec::Clear(), gnGenomeSpec::Clear(), gnFragmentSpec::Clear(), gnFileContig::Clear(), gnGenomeSpec::CloneRange(), gnFragmentSpec::CloneRange(), gnCompare::Contains(), gnBaseFeature::Contains(), gnSequence::contigByName(), gnSequence::contigIndexByBase(), gnSequence::contigIndexByName(), gnMultiSpec::CropEnd(), gnFragmentSpec::CropEnd(), gnBaseFeature::CropEnd(), gnMultiSpec::CropStart(), gnFragmentSpec::CropStart(), gnBaseFeature::CropStart(), gnCompare::DelArrayEntry(), gnSequence::erase(), gnTranslator::Filter(), gnFilter::Filter(), gnFastTranslator::Filter(), gnBaseFeature::FirstIndexOfQualifier(), gnSEQSource::FormatString(), gnGBKSource::FormatString(), gnGenomeSpec::GetBrokenFeatures(), gnFragmentSpec::GetBrokenFeatures(), gnGenomeSpec::GetContainedFeatures(), gnFragmentSpec::GetContainedFeatures(), gnSEQSource::GetContigID(), gnRAWSource::GetContigID(), gnGBKSource::GetContigID(), gnFASSource::GetContigID(), gnDNXSource::GetContigID(), gnABISource::GetContigID(), gnSEQSource::GetContigListLength(), gnRAWSource::GetContigListLength(), gnGBKSource::GetContigListLength(), gnFASSource::GetContigListLength(), gnDNXSource::GetContigListLength(), gnABISource::GetContigListLength(), gnFASSource::GetContigSeqLength(), gnTranslator::GetDefaultInputWidth(), gnGenomeSpec::GetFeature(), gnSequence::getFeatureListLength(), gnGenomeSpec::GetFeatureListLength(), gnFragmentSpec::GetFeatureListLength(), gnSourceHeader::GetHeader(), gnSequence::getHeaderListLength(), gnMultiSpec::GetHeaderListLength(), gnSourceHeader::GetHeaderStart(), gnBaseFeature::GetID(), gnExceptionCode::GetInt(), gnGenomeSpec::GetIntersectingFeatures(), gnFragmentSpec::GetIntersectingFeatures(), gnStringHeader::GetLength(), gnSourceHeader::GetLength(), gnMultiSpec::GetLength(), gnBaseFeature::GetLocationListLength(), gnStringQualifier::GetNameLength(), gnSourceQualifier::GetNameLength(), GetNewExceptionCode(), gnSourceFactory::GetPathListSize(), gnBaseFeature::GetQualifierListLength(), gnSourceFactory::GetSourceClassListSize(), gnContigSpec::GetSourceContigIndex(), gnSourceFactory::GetSourceListSize(), gnFASSource::GetSpec(), gnMultiSpec::GetSpecEndBase(), gnMultiSpec::GetSpecIndexByBase(), gnMultiSpec::GetSpecIndexByName(), gnGenomeSpec::GetSpecListLength(), gnFragmentSpec::GetSpecListLength(), gnMultiSpec::GetSpecStartBase(), gnSourceFactory::GetURL(), gnSourceQualifier::GetValue(), gnStringQualifier::GetValueLength(), gnSourceQualifier::GetValueLength(), gnSourceQualifier::GetValueStart(), gnFeature::gnFeature(), gnFileContig::gnFileContig(), gnFragmentSpec::gnFragmentSpec(), gnGenomeSpec::gnGenomeSpec(), gnSEQSource::HasContig(), gnGBKSource::HasContig(), gnFASSource::HasContig(), gnDNXSource::HasContig(), gnSourceFactory::HasPath(), gnBaseFeature::HasQualifier(), gnSequence::insert(), gnBaseFeature::Intersects(), gnBaseFeature::IsContainedBy(), gnFilter::IsValid(), gnBaseFeature::LastIndexOfQualifier(), gnCompare::LessThan(), gnFilter::MakeValid(), gnGenomeSpec::MergeFragments(), gnBaseFeature::MoveNegative(), gnBaseFeature::MovePositive(), gnSEQSource::ParseStream(), gnRAWSource::ParseStream(), gnGBKSource::ParseStream(), gnFASSource::ParseStream(), gnDNXSource::ParseStream(), gnGenomeSpec::RemoveFeature(), gnTranslator::RemovePair(), gnFilter::ReverseFilter(), gnSEQSource::SeqRead(), gnMultiSpec::SeqRead(), gnGBKSource::SeqRead(), gnFASSource::SeqRead(), gnSEQSource::SeqStartPos(), gnGBKSource::SeqStartPos(), gnFASSource::SeqStartPos(), gnGenomeSpec::SetReverseComplement(), gnFragmentSpec::SetReverseComplement(), gnGBKSource::Write(), gnFASSource::Write(), gnDNXSource::Write(), gnGBKSource::WriteHeader(), and gnBaseFeature::~gnBaseFeature().

typedef unsigned long long uint64

| Definition at line 38 of file gnDefs.h. Referenced by gnFileContig::GetFileLength(), gnFileContig::GetSectLength(), gnSEQSource::ParseStream(), gnRAWSource::ParseStream(), gnGBKSource::ParseStream(), gnFASSource::ParseStream(), gnDNXSource::ParseStream(), gnSEQSource::SeqRead(), gnGBKSource::SeqRead(), gnFASSource::SeqRead(), gnSEQSource::SeqSeek(), gnGBKSource::SeqSeek(), gnFASSource::SeqSeek(), gnSEQSource::SeqStartPos(), and gnGBKSource::SeqStartPos().

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.

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.