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//
// C++ Interface: pattern
//
// Description:
//
//
// Author: BUI Quang Minh, Steffen Klaere, Arndt von Haeseler <minh.bui@univie.ac.at>, (C) 2008
//
// Copyright: See COPYING file that comes with this distribution
//
//
#ifndef PATTERN_H
#define PATTERN_H
#include <iostream>
#include <string>
#include <vector>
#include <stdint.h>
using namespace std;
const int PAT_CONST = 1; // const site pattern, e.g. AAAAAA, CC-C-CCCC
const int PAT_INVARIANT = 2; // invariant site pattern, including const patterns and e.g., GS--G-GGG (S = G/C)
const int PAT_INFORMATIVE = 4; // parsimony informative sites
const int PAT_VARIANT = 8; // variant site pattern
typedef uint32_t StateType;
/**
Site-patterns in a multiple sequence alignment
@author BUI Quang Minh, Steffen Klaere, Arndt von Haeseler <minh.bui@univie.ac.at>
*/
class Pattern : public vector<StateType>
{
public:
/**
constructor
*/
Pattern();
Pattern(const Pattern &pat);
/**
@param num_states number of states of the model
@return the number of ambiguous character incl. gaps
*/
int computeAmbiguousChar(int num_states);
/**
@param num_states number of states of the model
@return the number of gaps
*/
int computeGapChar(int num_states, int STATE_UNKNOWN);
// Pattern &operator= (Pattern pat);
/**
destructor
*/
virtual ~Pattern();
inline bool isConst() {
return (flag & PAT_CONST) != 0;
}
inline bool isInvariant() {
return (flag & PAT_INVARIANT) != 0;
}
inline bool isInformative() {
return (flag & PAT_INFORMATIVE) != 0;
}
/**
frequency appearance of the pattern
*/
int frequency;
/**
true if this is a constant pattern
2015-03-04: is_const will also be true for pattern like "AA-A--AAA"
*/
// bool is_const;
/** true if pattern is informative, false otherwise */
// bool is_informative;
int flag;
/** 2015-03-04: if is_const is true, this will store the const character for the pattern */
char const_char;
/** number of different character states */
int num_chars;
};
#endif
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