spliced_hits.h File Reference

#include <algo/blast/core/blast_hits.h>

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Classes
struct	HSPContainer
struct	HSPChain
	A chain of HSPs: spliced alignment. More...
struct	BlastMappingResults
	Structure that contains BLAST mapping results. More...

Typedefs
typedef struct HSPContainer	HSPContainer
typedef struct HSPChain	HSPChain
	A chain of HSPs: spliced alignment. More...
typedef struct BlastMappingResults	BlastMappingResults
	Structure that contains BLAST mapping results. More...

Functions
HSPContainer *	HSPContainerNew (BlastHSP **hsp)
	Create HSPContainer and take ownership of the HSP. More...
HSPContainer *	HSPContainerFree (HSPContainer *hc)
	Free the list of HSPs, along with the stored HSPs. More...
HSPContainer *	HSPContainerDup (HSPContainer *inh)
	Clone a list of HSP containers. More...
HSPChain *	HSPChainFree (HSPChain *chain_list)
	Deallocate a chain or list of chains. More...
HSPChain *	HSPChainNew (Int4 context)
	Allocate a chain. More...
HSPChain *	CloneChain (const HSPChain *chain)
	Clone a single HSP chain. More...
BlastMappingResults *	Blast_MappingResultsNew (void)
	Initialize BlastMappingResults structure. More...
BlastMappingResults *	Blast_MappingResultsFree (BlastMappingResults *results)
	Free BlastMappingResults structure. More...

Typedef Documentation

BlastMappingResults

typedef struct BlastMappingResults BlastMappingResults

Structure that contains BLAST mapping results.

HSPChain

typedef struct HSPChain HSPChain

A chain of HSPs: spliced alignment.

HSPContainer

typedef struct HSPContainer HSPContainer

Function Documentation

Blast_MappingResultsFree()

BlastMappingResults* Blast_MappingResultsFree

(

BlastMappingResults *

results

)

Free BlastMappingResults structure.

Definition at line 170 of file spliced_hits.c.

References HSPChainFree(), i, NULL, results, and sfree.

Referenced by CMagicBlast::Run(), and CMagicBlast::RunEx().

Blast_MappingResultsNew()

BlastMappingResults* Blast_MappingResultsNew

(

void

)

Initialize BlastMappingResults structure.

Definition at line 164 of file spliced_hits.c.

References calloc().

Referenced by CMagicBlast::Run(), and CMagicBlast::RunEx().

CloneChain()

HSPChain* CloneChain

(

const HSPChain *

chain

)

Clone a single HSP chain.

Definition at line 139 of file spliced_hits.c.

References HSPChain::adapter, HSPChain::context, HSPChainFree(), HSPChainNew(), HSPContainerDup(), HSPChain::hsps, NULL, HSPChain::oid, HSPChain::polyA, and HSPChain::score.

Referenced by FindPartialyCoveredQueries(), and s_FindBestPairs().

HSPChainFree()

HSPChain* HSPChainFree

(

HSPChain *

chain_list

)

Deallocate a chain or list of chains.

Definition at line 109 of file spliced_hits.c.

References ASSERT, HSPContainerFree(), HSPChain::hsps, HSPChain::next, next(), NULL, HSPChain::pair, and sfree.

Referenced by Blast_MappingResultsFree(), CloneChain(), DoAnchoredSearch(), HSPChainListInsert(), HSPChainListTrim(), s_FilterChains(), s_FindBestPath(), s_HSPChainListInsertOne(), s_HSPChainListInsertOne_OLD(), s_PruneChains(), and s_SetAdapter().

HSPChainNew()

HSPChain* HSPChainNew

(

Int4

context

)

Allocate a chain.

Definition at line 126 of file spliced_hits.c.

References HSPChain::adapter, calloc(), HSPChain::context, context, and NULL.

Referenced by CloneChain(), s_FindBestPath(), and s_RemoveOverlaps().

HSPContainerDup()

HSPContainer* HSPContainerDup

(

HSPContainer *

inh

)

Clone a list of HSP containers.

Definition at line 68 of file spliced_hits.c.

References Blast_HSPClone(), Blast_HSPFree(), HSPContainer::hsp, HSPContainerFree(), HSPContainerNew(), HSPContainer::next, and NULL.

Referenced by CloneChain().

HSPContainerFree()

HSPContainer* HSPContainerFree

(

HSPContainer *

hc

)

Free the list of HSPs, along with the stored HSPs.

Definition at line 51 of file spliced_hits.c.

References Blast_HSPFree(), HSPContainer::hsp, HSPContainer::next, next(), NULL, and sfree.

Referenced by HSPChainFree(), HSPContainerDup(), s_FindSpliceJunctions(), s_IntronToGap(), s_SetAdapter(), s_TrimChainEndToSubjPos(), and s_TrimChainStartToSubjPos().

HSPContainerNew()

HSPContainer* HSPContainerNew

(

BlastHSP **

hsp

)

Create HSPContainer and take ownership of the HSP.

Definition at line 37 of file spliced_hits.c.

References calloc(), HSPContainer::hsp, and NULL.

Referenced by HSPContainerDup(), and s_FindBestPath().