Postprocessing utilities header. More...

#include "alignment.h"
#include "chain.h"
#include "db_alignment.h"
#include "scorer.h"

Include dependency graph for post_proc.h:

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Macros
#define	SW_OUT_PAIR 0
	Pairwise alignment pair output format. More...

#define	SW_OUT_PLOT 1
	Pairwise alignment plotting output format. More...

#define	SW_OUT_STAT 2
	Pairwise alignment stat output format. More...

#define	SW_OUT_STAT_PAIR 3
	Pairwise alignment stat-pair output format. More...

#define	SW_OUT_DUMP 4
	Pairwise alignment binary output format. More...

#define	SW_OUT_DB_BLASTM0 0
	Database alignment blast m1-like output format. More...

#define	SW_OUT_DB_BLASTM8 1
	Database alignment blast m8-like output format. More...

#define	SW_OUT_DB_BLASTM9 2
	Database alignment blast m9-like output format. More...

#define	SW_OUT_DB_LIGHT 3
	Database alignment light output format. More...

Functions
int	checkAlignment (Alignment *alignment)
	Checks if the alignment is correct. More...

Alignment *	readAlignment (char *path)
	Reads the alignment object from the binary file. More...

void	outputAlignment (Alignment alignment, char path, int type)
	Pairwise alignment output function. More...

void	outputScore (int score, Chain query, Chain target, Scorer scorer, char path)
	Score only output function. More...

void	outputDatabase (DbAlignment *dbAlignments, int dbAlignmentsLen, char path, int type)
	Database alignment output function. More...

void	outputShotgunDatabase (DbAlignment **dbAlignments, int dbAlignmentsLens, int dbAlignmentsLen, char *path, int type)
	Shotgun database alignment output function. More...

void	dumpFastaChains (Chain *chains, int chainsLen, char path)
	Database serialization function. More...

void	deleteFastaChains (Chain **chains, int chainsLen)
	Chain array delete utility. More...

void	deleteDatabase (DbAlignment **dbAlignments, int dbAlignmentsLen)
	Database delete utility. More...

void	deleteShotgunDatabase (DbAlignment **dbAlignments, int dbAlignmentsLens, int dbAlignmentsLen)
	Shotgun database delete utility. More...

Detailed Description

Postprocessing utilities header.

Macro Definition Documentation

#define SW_OUT_DB_BLASTM0 0

Database alignment blast m1-like output format.

Blast m1 output example: http://www.compbio.ox.ac.uk/analysis_tools/BLAST/BLAST_blastall/blastall_examples.shtml#m_0

#define SW_OUT_DB_BLASTM8 1

Database alignment blast m8-like output format.

Blast m8 output example: http://www.compbio.ox.ac.uk/analysis_tools/BLAST/BLAST_blastall/blastall_examples.shtml#m_8

#define SW_OUT_DB_BLASTM9 2

Database alignment blast m9-like output format.

Blast m9 output example: http://www.compbio.ox.ac.uk/analysis_tools/BLAST/BLAST_blastall/blastall_examples.shtml#m_9

#define SW_OUT_DB_LIGHT 3

Database alignment light output format.

Format outputs only the scores and the names of the output alignments.

#define SW_OUT_DUMP 4

Pairwise alignment binary output format.

This output can be read with the readAlignment().

#define SW_OUT_PAIR 0

Pairwise alignment pair output format.

Format is equal to the emboss pair output without the header. Emboss output example: http://emboss.sourceforge.net/docs/themes/alnformats/align.pair

#define SW_OUT_PLOT 1

Pairwise alignment plotting output format.

This output format is used as the input file for plotting with gnuplot.

#define SW_OUT_STAT 2

Pairwise alignment stat output format.

Format is equal to the emboss pair output header. Emboss output example: http://emboss.sourceforge.net/docs/themes/alnformats/align.pair

#define SW_OUT_STAT_PAIR 3

Pairwise alignment stat-pair output format.

Format is equal to the emboss pair output. Emboss output example: http://emboss.sourceforge.net/docs/themes/alnformats/align.pair

Function Documentation

int checkAlignment ( Alignment * alignment )

Checks if the alignment is correct.

Parameters

alignment alignment object

Returns: 1 if the alignment is correct, 0 otherwise

void deleteDatabase	(	DbAlignment **	dbAlignments,
		int	dbAlignmentsLen
	)

Database delete utility.

Function calls dbAlignmentDelete() function on every dbAlignment object in dbAlignments array and then deletes the array.

Parameters

dbAlignments	database alignments array
dbAlignmentsLen	database alignments array length

void deleteFastaChains	(	Chain **	chains,
		int	chainsLen
	)

Chain array delete utility.

Function calls chainDelete() function on every chain and then deletes the array.

Parameters

chains	chain array object
chainsLen	chain array length

void deleteShotgunDatabase	(	DbAlignment ***	dbAlignments,
		int *	dbAlignmentsLens,
		int	dbAlignmentsLen
	)

Shotgun database delete utility.

Function calls dbAlignmentDelete() function on every dbAlignment object in dbAlignments, deletes dbAlignments structure and then deletes dbAlignmentsLens array.

Parameters

dbAlignments	database alignments array of arrays
dbAlignmentsLens	database alignments arrays lengths
dbAlignmentsLen	database alignments array of arrays length

void dumpFastaChains	(	Chain **	chains,
		int	chainsLen,
		char *	path
	)

Database serialization function.

Function creates a file named path.swsharp which represents the serialized version of the chain database which was read from the given path. Since reading of the serialized version of the database is much faster than reading the original one, this function is used for caching the databases for future usage.

Parameters

chains	database chains
chainsLen	database length
path	original chain database file path

void outputAlignment	(	Alignment *	alignment,
		char *	path,
		int	type
	)

Pairwise alignment output function.

Parameters

alignment	alignment object
path	output file path, if NULL output goes to standard output
type	output format type, can be SW_OUT_PAIR, SW_OUT_PLOT, SW_OUT_STAT, SW_OUT_STAT_PAIR or SW_OUT_DUMP

void outputDatabase	(	DbAlignment **	dbAlignments,
		int	dbAlignmentsLen,
		char *	path,
		int	type
	)

Database alignment output function.

Parameters

dbAlignments	database alignments array
dbAlignmentsLen	database alignments array length
path	output file path, if NULL output goes to standard output
type	output format type, can be SW_OUT_DB_BLASTM0 , SW_OUT_DB_BLASTM8, SW_OUT_DB_BLASTM9 or SW_OUT_DB_LIGHT

void outputScore	(	int	score,
		Chain *	query,
		Chain *	target,
		Scorer *	scorer,
		char *	path
	)

Score only output function.

Parameters

score	alignment score
query	query chain
target	target chain
scorer	scorer object used for alignment
path	output file path, if NULL output goes to standard output

void outputShotgunDatabase	(	DbAlignment ***	dbAlignments,
		int *	dbAlignmentsLens,
		int	dbAlignmentsLen,
		char *	path,
		int	type
	)

Shotgun database alignment output function.

Parameters

dbAlignments	database alignments array of arrays
dbAlignmentsLens	database alignments arrays lengths
dbAlignmentsLen	database alignments array of arrays length
path	output file path, if NULL output goes to standard output
type	output format type, can be SW_OUT_DB_BLASTM0 , SW_OUT_DB_BLASTM8, SW_OUT_DB_BLASTM9 or SW_OUT_DB_LIGHT

Alignment* readAlignment ( char * path )

Reads the alignment object from the binary file.

The binary file must previously be created with the outputAlignment() function with the SW_OUT_DUMP type.

Parameters

path	input binary file path

Returns: alignment object

Macros

Functions

Detailed Description

Macro Definition Documentation

Function Documentation