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
86
87
88
89
90
|
// Copyright (C) 1999-2003 Paul O. Lewis
//
// This file is part of NCL (Nexus Class Library) version 2.0.
//
// NCL is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation; either version 2 of the License, or
// (at your option) any later version.
//
// NCL 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 General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with NCL; if not, write to the Free Software Foundation, Inc.,
// 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
//
#ifndef NCL_NXSDISCRETEMATRIX_H
#define NCL_NXSDISCRETEMATRIX_H
#include <limits.h>
/*----------------------------------------------------------------------------------------------------------------------
| Class providing storage for the discrete data types (dna, rna, nucleotide, standard, and protein) inside a DATA or
| CHARACTERS block. This class is also used to store the data for an ALLELES block. Maintains a matrix in which each
| cell is an object of the class NxsDiscreteDatum. NxsDiscreteDatum stores the state for a particular combination of
| taxon and character as an integer. Ordinarily, there will be a single state recorded for each taxon-character
| combination, but exceptions exist if there is polymorphism for a taxon-character combination, or if there is
| uncertainty about the state (e.g., in dna data, the data file might have contained an R or Y entry). Please consult
| the documentation for the NxsDiscreteDatum class for the details about how states are stored. For data stored in an
| ALLELES block, rows of the matrix correspond to individuals and columns to loci. Each NxsDiscreteDatum must
| therefore store information about both genes at a single locus for a single individual in the case of diploid data.
| To do this, two macros HIWORD and LOWORD are used to divide up the unsigned value into two words. A maximum of 255
| distinct allelic forms can be accommodated by this scheme, assuming at minimum a 32-bit architecture. Because it is
| not known in advance how many rows are going to be necessary, The NxsDiscreteMatrix class provides the AddRows
| method, which expands the number of rows allocated for the matrix while preserving data already stored.
*/
class NxsDiscreteMatrix
{
friend class NxsCharactersBlock;
friend class NxsAllelesBlock;
public:
NxsDiscreteMatrix(unsigned rows, unsigned cols);
virtual ~NxsDiscreteMatrix();
void AddRows(unsigned nAddRows);
void AddState(unsigned i, unsigned j, unsigned value);
void CopyStatesFromFirstTaxon(unsigned i, unsigned j);
void DebugSaveMatrix(ostream &out, unsigned colwidth = 12);
unsigned DuplicateRow(unsigned row, unsigned count, unsigned startCol = 0, unsigned endCol = UINT_MAX);
void Flush();
unsigned GetState(unsigned i, unsigned j, unsigned k = 0);
unsigned GetNumStates(unsigned i, unsigned j);
unsigned GetObsNumStates(unsigned j);
bool IsGap(unsigned i, unsigned j);
bool IsMissing(unsigned i, unsigned j);
bool IsPolymorphic(unsigned i, unsigned j);
void Reset(unsigned rows, unsigned cols);
void SetGap(unsigned i, unsigned j);
void SetMissing(unsigned i, unsigned j);
void SetPolymorphic(unsigned i, unsigned j, unsigned value = 1);
void SetState(unsigned i, unsigned j, unsigned value);
private:
unsigned nrows; /* number of rows (taxa) in the data matrix */
unsigned ncols; /* number of columns (characters) in the data matrix */
NxsDiscreteDatum **data; /* storage for the data */
void AddState(NxsDiscreteDatum &d, unsigned value);
bool IsGap(NxsDiscreteDatum &d);
bool IsMissing(NxsDiscreteDatum &d);
bool IsPolymorphic(NxsDiscreteDatum &d);
NxsDiscreteDatum &GetDiscreteDatum(unsigned i, unsigned j);
unsigned GetNumStates(NxsDiscreteDatum &d);
unsigned GetState(NxsDiscreteDatum &d, unsigned k = 0);
void SetGap(NxsDiscreteDatum &d);
void SetMissing(NxsDiscreteDatum &d);
void SetPolymorphic(NxsDiscreteDatum &d, unsigned value);
void SetState(NxsDiscreteDatum &d, unsigned value);
};
typedef NxsDiscreteMatrix DiscreteMatrix;
#endif
|
