alignment.h File Reference

#include <iostream>
#include <string>
#include <vector>

Go to the source code of this file.

Classes
class	alignpos
class	alignment
Enumerations
enum	quality {   best, good, partial_good, ok,   bad, good, bad, modify }
enum	alnmethod { clustal, dialign }
Functions
list< pair< int, int > >	listgap (const string &s, const char gapChar='-')

---

Enumeration Type Documentation

enum alnmethod

Enumerator:

clustal
dialign

enum quality

Enumerator:

best
good
partial_good
ok
bad
good
bad
modify

---

Function Documentation

list<pair<int, int> > listgap	(	const string &	s,
		const char	gapChar = '-'
	)

helper functons given the aligned sequence string it will return the list of gap position and gap length pair The default gap character is '-'

Referenced by main(), operator<<(), outputgaparray(), and printgaplist().