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// 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_NXSDISTANCESBLOCK_H
#define NCL_NXSDISTANCESBLOCK_H
class NxsDistanceDatum;
/*----------------------------------------------------------------------------------------------------------------------
| This class handles reading and storage for the NEXUS block DISTANCES. It overrides the member functions Read and
| Reset, which are abstract virtual functions in the base class NxsBlock. Below is a table showing the correspondence
| between the elements of a DISTANCES block and the variables and member functions that can be used to access each
| piece of information stored.
|>
| NEXUS command Command attribute Data Members Member Functions
| ------------------------------------------------------------------------
| DIMENSIONS NEWTAXA newtaxa
|
| NTAX ntax GetNtax
|
| NCHAR nchar GetNchar
|
| FORMAT TRIANGLE triangle GetTriangle
| IsUpperTriangular
| IsLowerTriangular
| IsRectangular
|
| [NO]DIAGONAL diagonal IsDiagonal
|
| [NO]LABELS labels IsLabels
|
| MISSING missing GetMissingSymbol
|
| INTERLEAVE interleave IsInterleave
|
| TAXLABELS (stored in the (access through
| NxsTaxaBlock data member taxa)
| object)
|
| MATRIX matrix GetDistance
| IsMissing
| SetMissing
| SetDistance
| ------------------------------------------------------------------------
|>
*/
class NxsDistancesBlock
: public NxsBlock
{
public:
NxsDistancesBlock(NxsTaxaBlock *t);
virtual ~NxsDistancesBlock();
double GetDistance(unsigned i, unsigned j);
char GetMissingSymbol();
unsigned GetNchar();
unsigned GetNtax();
unsigned GetTriangle();
bool IsRectangular();
bool IsDiagonal();
bool IsInterleave();
bool IsLabels();
bool IsLowerTriangular();
bool IsMissing(unsigned i, unsigned j);
bool IsUpperTriangular();
virtual void Report(std::ostream &out);
virtual void Reset();
void SetDistance(unsigned i, unsigned j, double d);
void SetMissing(unsigned i, unsigned j);
void SetNchar(unsigned i);
enum NxsDistancesBlockEnum /* used by data member triangle to determine which triangle(s) of the distance matrix is/are occupied */
{
upper = 1, /* matrix is upper-triangular */
lower = 2, /* matrix is lower-triangular */
both = 3 /* matrix is rectangular */
};
protected:
void HandleDimensionsCommand(NxsToken &token);
void HandleFormatCommand(NxsToken &token);
void HandleMatrixCommand(NxsToken &token);
bool HandleNextPass(NxsToken &token, unsigned &offset);
void HandleTaxlabelsCommand(NxsToken &token);
virtual void Read(NxsToken &token);
private:
NxsTaxaBlock *taxa; /* pointer to NxsTaxaBlock object that stores the taxon labels */
bool newtaxa; /* true if new taxa were named in this DISTANCES block */
unsigned ntax; /* number of taxa (determines dimensions of the matrix) */
unsigned nchar; /* the number of characters used in generating the pairwise distances */
bool diagonal; /* true if diagonal elements provided when reading in DISTANCES block */
bool interleave; /* true if interleave format used when reading in DISTANCES block */
bool labels; /* true if taxon labels were provided when reading in DISTANCES block */
int triangle; /* indicates whether matrix is upper triangular, lower triangular, or rectangular, taking on one of the elements of the NxsDistancesBlockEnum enumeration */
char missing; /* the symbol used to represent missing data (e.g. '?') */
NxsDistanceDatum **matrix; /* the structure used for storing the pairwise distance matrix */
unsigned *taxonPos; /* array holding 0-offset index into the NxsTaxaBlock list of taxon labels (used to ensure that order of taxa is same for each interleaved block) */
};
typedef NxsDistancesBlock DistancesBlock;
#define IsBoth IsRectangular
#endif
|
