mpboot/pattern.cpp at fusing · magnified103/mpboot · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
//
// 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.h"

Pattern::Pattern()
        : string()
{
    frequency = 0;
    is_const = false;
}


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;
}


void Pattern::computeConst(int STATE_UNKNOWN) {
    char ch = STATE_UNKNOWN;
    is_const = true;
    for (iterator i = begin(); i != end(); i++) {
        if (ch != STATE_UNKNOWN && *i != STATE_UNKNOWN && *i != ch) {
            is_const = false;
            return;
        }
        if (*i != STATE_UNKNOWN) ch = *i;
    }
}