seqaln2gapos.cpp File Reference

#include <iostream>
#include <fstream>
#include <string>
#include <vector>
#include <utility>
#include <list>

Enumerations
enum	output_format { POSTGRES, TEXT }
Functions
pair< string, string >	split (const string &ln)
list< pair< int, int > >	listgap (const string &s)
void	outputgaparray (ostream &os, const string &seq)
void	printgaplist (ostream &os, const string &seq)
int	main (int argc, char *argv[])

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Enumeration Type Documentation

enum output_format

Enumerator:

POSTGRES
TEXT

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Function Documentation

list< pair< int, int > > listgap

(

const string &

s

)

convert the sequence string into a list of pair of (gap_pos, gap_len) -1 is before the first residue of the amino acid sequence. Should not list (-1,0) if no gap.

s is the input sequence string (including gaps).

int main	(	int	argc,
		char *	argv[]
	)

References ifstream(), name, outputgaparray(), POSTGRES, printgaplist(), split(), and TEXT.

void outputgaparray	(	ostream &	os,
		const string &	seq
	)

for postgres array format

References listgap().

Referenced by main().

void printgaplist	(	ostream &	os,
		const string &	seq
	)

text version, minimal space

References listgap().

Referenced by main().

pair<string, string> split

(

const string &

str

)

separate the line into name and sequence parts first=name, second=sequence string with gaps