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//
// C++ Implementation: 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
//
//
#include "pattern.h"
#include "alignment/alignment.h"
Pattern::Pattern()
: vector<StateType>()
{
frequency = 0;
// is_const = false;
// is_informative = false;
flag = 0;
const_char = 255;
num_chars = 0;
}
Pattern::Pattern(const Pattern &pat)
: vector<StateType>(pat)
{
frequency = pat.frequency;
// is_const = pat.is_const;
// is_informative = pat.is_informative;
flag = pat.flag;
const_char = pat.const_char;
num_chars = pat.num_chars;
}
Pattern::~Pattern()
{
}
int Pattern::computeAmbiguousChar(int num_states) {
int num = 0;
for (iterator i = begin(); i != end(); i++)
if (*i >= num_states) num++;
return num;
}
int Pattern::computeGapChar(int num_states, int STATE_UNKNOWN) {
int num = 0;
for (iterator i = begin(); i != end(); i++)
if (*i == STATE_UNKNOWN) num++;
return num;
}
//Pattern &Pattern::operator= (Pattern pat) {
// assign(pat);
// frequency = pat.frequency;
// is_const = pat.is_const;
// const_char = pat.const_char;
// return *this;
//}
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