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
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
|
/*
* TreeLib
* A library for manipulating phylogenetic trees.
* Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
*
* This library is free software; you can redistribute it and/or
* modify it under the terms of the GNU Library General Public
* License as published by the Free Software Foundation; either
* version 2 of the License, or (at your option) any later version.
*
* This library is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* Library General Public License for more details.
*
* You should have received a copy of the GNU Library General Public
* License along with this library; if not, write to the Free
* Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
* MA 02111-1307, USA.
*/
// $Id: quartet.h,v 1.2 2005/09/08 12:58:29 rdmp1c Exp $
/**
* @file quartet.h
*
* Compute quartet distance between two trees. Algorithm is based on
* Doucette, C. R. 1985. An efficient algorithm to
* compute quartet dissimilarity measures. Unpubl.
* BSc(Hons) dissertation, Dept. Computer Science,
* Memorial University of Newfoundland.
*
*
*/
#ifndef QUARTETH
#define QUARTETH
#ifdef __BORLANDC__
// Undefine __MINMAX_DEFINED so that min and max are correctly defined
#ifdef __MINMAX_DEFINED
#undef __MINMAX_DEFINED
#endif
// Ignore "Cannot create precompiled header: code in header" message
// generated when compiling string.cc
#pragma warn -pch
#endif
#include <vector>
#include "ntree.h"
// Values
typedef struct {
int u; // unresolved in T1 and T2
int d; // resolved but different
int s; // resolved and same
int r1; // resolved in T1 but not T2
int r2; // resolved in T2 but not T1
int x1; // total resolved in T1
int n; // maximum no. of quartets/triplets
float SD; // symmetric difference
float EA; // explicitly agree
float SJA; // strict joint assertions
float DC; // do not conflict
}QTValues;
void SummaryStats (QTValues &QR);
void ShowHeader (std::ostream &s);
void ShowQTRecord (std::ostream &s, QTValues &QR);
void CompareQuartets (NTree &t1, NTree &t2, QTValues &QR);
void CompareTriplets (NTree &t1, NTree &t2, QTValues &QR);
#if __BORLANDC__
// Redefine __MINMAX_DEFINED so Windows header files compile
#ifndef __MINMAX_DEFINED
#define __MINMAX_DEFINED
#endif
#endif
#endif
|
