Type and macro definitions from C toolkit that are not defined in C++ toolkit. More...

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <ctype.h>
#include <assert.h>
#include "blast_toolkit.h"
#include <algo/blast/core/blast_export.h>

Include dependency graph for ncbi_std.h:

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Go to the SVN repository for this file.

Classes
struct	ListNode
	A generic linked list node structure. More...

Macros
#define	NCBI_INLINE inline
	"inline" seems to work on our remaining in-house compilers (WorkShop, Compaq, ICC, MPW) More...

#define	TRUE 1
	bool replacment for C indicating true. More...

#define	FALSE 0
	bool replacment for C indicating false. More...

#define	ASSERT assert
	macro for assert. More...

#define	MIN(a, b) ((a)>(b)?(b):(a))
	returns smaller of a and b. More...

#define	MAX(a, b) ((a)>=(b)?(a):(b))
	returns larger of a and b. More...

#define	ABS(a) ((a)>=0?(a):-(a))
	returns absolute value of a (\|a\|) More...

#define	SIGN(a) ((a)>0?1:((a)<0?-1:0))
	return +1 for a > 0, -1 for a < 0 More...

#define	UINT4_MAX 4294967295U
	largest number represented by unsigned int. More...

#define	INT4_MAX 2147483647
	largest nubmer represented by signed int More...

#define	INT4_MIN (-2147483647-1)
	Smallest (most negative) number represented by signed int. More...

#define	NCBIMATH_LN2 0.69314718055994530941723212145818
	natural log of 2. More...

#define	INT2_MAX 32767
	largest number represented by signed (two byte) short More...

#define	INT2_MIN (-32768)
	smallest (most negative) number represented by signed (two byte) short More...

#define	INT1_MAX 127
	largest number represented by signed short (one byte) More...

#define	INT1_MIN (-128)
	smallest (most negative) number represented by signed short (one byte) More...

#define	DIM(A) (sizeof(A)/sizeof((A)[0]))
	dimension of an array. More...

#define	NULLB '\0'
	terminating byte of a char* string. More...

#define	NCBI_CONST_INT8(v) v##LL
	64-bit integers More...

#define	NCBI_CONST_UINT8(v) v##ULL

Typedefs
typedef Uint1	Boolean
	bool replacment for C More...

typedef struct ListNode	ListNode
	A generic linked list node structure. More...

Functions
void *	BlastMemDup (const void *orig, size_t size)
	Copies memory using memcpy and malloc. More...

ListNode *	ListNodeNew (ListNode *vnp)
	Create a new list node. More...

ListNode *	ListNodeAdd (ListNode **head)
	Add a node to the list. More...

ListNode *	ListNodeAddPointer (ListNode *head, Uint1 choice, void value)
	Add a node to the list with a given choice and data pointer. More...

ListNode *	ListNodeFree (ListNode *vnp)
	Free all list's nodes, does not attempt to free data. More...

ListNode *	ListNodeFreeData (ListNode *vnp)
	Free nodes as well as data (vnp->ptr) assuming it is one contiguous chunk. More...

ListNode *	ListNodeCopyStr (ListNode *head, Uint1 choice, const char str)
	Add a node to the list with a provided choice, and attached data pointing to a provided string. More...

Detailed Description

Type and macro definitions from C toolkit that are not defined in C++ toolkit.

Definition in file ncbi_std.h.

Macro Definition Documentation

◆ ABS

#define ABS ( a ) ((a)>=0?(a):-(a))

returns absolute value of a (|a|)

Definition at line 122 of file ncbi_std.h.

◆ ASSERT

#define ASSERT assert

macro for assert.

Definition at line 107 of file ncbi_std.h.

◆ DIM

#define DIM ( A ) (sizeof(A)/sizeof((A)[0]))

dimension of an array.

Definition at line 176 of file ncbi_std.h.

◆ FALSE

#define FALSE 0

bool replacment for C indicating false.

Definition at line 101 of file ncbi_std.h.

◆ INT1_MAX

#define INT1_MAX 127

largest number represented by signed short (one byte)

Definition at line 166 of file ncbi_std.h.

◆ INT1_MIN

#define INT1_MIN (-128)

smallest (most negative) number represented by signed short (one byte)

Definition at line 171 of file ncbi_std.h.

◆ INT2_MAX

#define INT2_MAX 32767

largest number represented by signed (two byte) short

Definition at line 156 of file ncbi_std.h.

◆ INT2_MIN

#define INT2_MIN (-32768)

smallest (most negative) number represented by signed (two byte) short

Definition at line 161 of file ncbi_std.h.

◆ INT4_MAX

#define INT4_MAX 2147483647

largest nubmer represented by signed int

Definition at line 141 of file ncbi_std.h.

◆ INT4_MIN

#define INT4_MIN (-2147483647-1)

Smallest (most negative) number represented by signed int.

Definition at line 146 of file ncbi_std.h.

◆ MAX

#define MAX	(	a,
		b
	)	((a)>=(b)?(a):(b))

returns larger of a and b.

Definition at line 117 of file ncbi_std.h.

◆ MIN

#define MIN	(	a,
		b
	)	((a)>(b)?(b):(a))

returns smaller of a and b.

Definition at line 112 of file ncbi_std.h.

◆ NCBI_CONST_INT8

#define NCBI_CONST_INT8 ( v ) v##LL

64-bit integers

Definition at line 195 of file ncbi_std.h.

◆ NCBI_CONST_UINT8

#define NCBI_CONST_UINT8 ( v ) v##ULL

Definition at line 196 of file ncbi_std.h.

◆ NCBI_INLINE

#define NCBI_INLINE inline

"inline" seems to work on our remaining in-house compilers (WorkShop, Compaq, ICC, MPW)

Definition at line 81 of file ncbi_std.h.

◆ NCBIMATH_LN2

#define NCBIMATH_LN2 0.69314718055994530941723212145818

natural log of 2.

Definition at line 151 of file ncbi_std.h.

◆ NULLB

#define NULLB '\0'

terminating byte of a char* string.

Definition at line 181 of file ncbi_std.h.

◆ SIGN

#define SIGN ( a ) ((a)>0?1:((a)<0?-1:0))

return +1 for a > 0, -1 for a < 0

Definition at line 127 of file ncbi_std.h.

◆ TRUE

#define TRUE 1

bool replacment for C indicating true.

Definition at line 97 of file ncbi_std.h.

◆ UINT4_MAX

#define UINT4_MAX 4294967295U

largest number represented by unsigned int.

Definition at line 136 of file ncbi_std.h.

Typedef Documentation

◆ Boolean

typedef Uint1 Boolean

bool replacment for C

Definition at line 94 of file ncbi_std.h.

◆ ListNode

typedef struct ListNode ListNode

A generic linked list node structure.

Function Documentation

◆ BlastMemDup()

void* BlastMemDup	(	const void *	orig,
		size_t	size
	)

Copies memory using memcpy and malloc.

Parameters

orig	memory to be copied [in]
size	amount to be copied [in]

Returns: pointer to newly allocated memory. NULL if orig NULL, size is zero, or allocation fails.

Definition at line 35 of file ncbi_std.c.

References copy(), malloc(), NULL, orig, and ncbi::grid::netcache::search::fields::size.

Referenced by Blast_HSPClone(), Blast_SetPHIPatternInfo(), Blast_TracebackFromHSPList(), BlastQueryInfoDup(), BlastScoringOptionsDup(), BlastSeqSrcCopy(), BlastSequenceBlkCopy(), BlastSetUp_MaskQuery(), BOOST_AUTO_TEST_CASE(), DynamicSGenCodeNodeArray_Append(), s_BlastHSPCopy(), s_GetNuclValuesArray(), s_PHIScoreBlkFill(), s_SetupSequencesForGappedReevaluateTest(), s_SetupSequencesForUngappedReevaluateNucl(), s_SetupSequencesForUngappedReevaluateTransl(), SPHIQueryInfoCopy(), CBlastOptionsLocal::x_Copy_CBlastDatabaseOptions(), CBlastOptionsLocal::x_Copy_CBlastEffectiveLengthsOptions(), CBlastOptionsLocal::x_Copy_CBlastExtensionOptions(), CBlastOptionsLocal::x_Copy_CBlastHitSavingOptions(), CBlastOptionsLocal::x_Copy_CBlastInitialWordOptions(), CBlastOptionsLocal::x_Copy_CLookupTableOptions(), CBlastOptionsLocal::x_Copy_CPSIBlastOptions(), and CBlastOptionsLocal::x_Copy_CQuerySetUpOptions().

◆ ListNodeAdd()

ListNode* ListNodeAdd ( ListNode ** head )

Add a node to the list.

Parameters

head	Pointer to the start of the list, if *head is NULL will be Pointer to new node. [in] [out]

Returns: New node

Definition at line 77 of file ncbi_std.c.

References head, ListNodeNew(), and NULL.

Referenced by ListNodeAddPointer(), and ListNodeCopyStr().

◆ ListNodeAddPointer()

ListNode* ListNodeAddPointer	(	ListNode **	head,
		Uint1	choice,
		void *	value
	)

Add a node to the list with a given choice and data pointer.

Parameters

head	Pointer to the start of the list, if *head is NULL will be Pointer to new node. [in] [out]
choice	Choice value for the new node. [in]
value	Data pointer for the new node. [in]

Returns: New node

Definition at line 99 of file ncbi_std.c.

References ListNode::choice, head, ListNodeAdd(), NULL, ListNode::ptr, and rapidjson::value.

Referenced by BlastLoadMatrixValues().

◆ ListNodeCopyStr()

ListNode* ListNodeCopyStr	(	ListNode **	head,
		Uint1	choice,
		const char *	str
	)

Add a node to the list with a provided choice, and attached data pointing to a provided string.

Parameters

head	Pointer to the start of the list, if *head is NULL will be Pointer to new node. [in] [out]
choice	sets the "choice" field in ListNode [in]
str	char* buffer to be copied [in]

Returns: newly allocated node

Definition at line 124 of file ncbi_std.c.

References ListNode::choice, head, ListNodeAdd(), NULL, ListNode::ptr, str(), and strdup.

Referenced by BlastScoreBlkNucleotideMatrixRead(), and BlastScoreBlkProteinMatrixRead().

◆ ListNodeFree()

ListNode* ListNodeFree ( ListNode * vnp )

Free all list's nodes, does not attempt to free data.

Parameters

vnp	objects to be freed [in]

Returns: NULL

Definition at line 148 of file ncbi_std.c.

References ListNode::next, next(), NULL, and sfree.

Referenced by BlastMatrixValuesDestruct().

◆ ListNodeFreeData()

ListNode* ListNodeFreeData ( ListNode * vnp )

Free nodes as well as data (vnp->ptr) assuming it is one contiguous chunk.

Parameters

vnp	objects to be freed [in]

Returns: NULL

Definition at line 169 of file ncbi_std.c.

References ListNode::next, next(), NULL, ListNode::ptr, and sfree.

Referenced by BlastScoreBlkFree().

◆ ListNodeNew()

ListNode* ListNodeNew ( ListNode * vnp )

Create a new list node.

Parameters

vnp	Pointer to the start of the list, may be NULL [in]

Returns: newly allocated node

Definition at line 55 of file ncbi_std.c.

References calloc(), ListNode::next, and NULL.

Referenced by ListNodeAdd().

Classes

Macros

Typedefs

Functions

Detailed Description

Macro Definition Documentation

◆ ABS

◆ ASSERT

◆ DIM

◆ FALSE

◆ INT1_MAX

◆ INT1_MIN

◆ INT2_MAX

◆ INT2_MIN

◆ INT4_MAX

◆ INT4_MIN

◆ MAX

◆ MIN

◆ NCBI_CONST_INT8

◆ NCBI_CONST_UINT8

◆ NCBI_INLINE

◆ NCBIMATH_LN2

◆ NULLB

◆ SIGN

◆ TRUE

◆ UINT4_MAX

Typedef Documentation

◆ Boolean

◆ ListNode

Function Documentation

◆ BlastMemDup()

◆ ListNodeAdd()

◆ ListNodeAddPointer()

◆ ListNodeCopyStr()

◆ ListNodeFree()

◆ ListNodeFreeData()

◆ ListNodeNew()