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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_NXSDISCRETEDATUM_H
#define NCL_NXSDISCRETEDATUM_H
/*----------------------------------------------------------------------------------------------------------------------
| Class for holding discrete states in a matrix. Note that there is no way to access the variables of this class
| since they are all private and there are no public access functions. This class is designed to be manipulated by
| the class NxsDiscreteMatrix, which is the only class that has been designated a friend of NxsDiscreteDatum.
| The variable `states' is NULL if there is missing data, and non-NULL for any other state. If `states' is non-NULL,
| the first cell is used to store the number of states. This will be 0 if the state is the gap state, 1 if the state
| is unambiguous and nonpolymorphic (and not the gap state of course), and 2 or higher if there is either
| polymorphism or uncertainty. If polymorphism or uncertainty apply, it becomes necessary to store information about
| which of these two situations holds. Thus, the last cell in the array is set to either 1 (polymorphism) or 0
| (uncertainty). While a little complicated, this scheme has the following benefits:
|~
| o if the state is missing, the only memory allocated is for a pointer (`states')
| o if the state is unambiguous and not polymorphic, no storage is used for keeping track of whether polymorphism or
| uncertainty holds
| o it allows for a virtually unlimited number of states, which is important if it is to be general enough to store
| microsatellite data for a NxsAllelesBlock object, for example.
|~
| Supposing the gap symbol is '-', the missing data symbol is '?', and the symbols list is "ACGT", the following
| table shows the status of the states variable under several different possible data matrix entries:
|>
| Matrix entry states array
| --------------------------------
| ? NULL
| - [0]
| G [1][2]
| (AG) polymorphic [2][0][2][1]
| {AG} ambiguous [2][0][2][0]
| --------------------------------
|>
*/
class NxsDiscreteDatum
{
friend class NxsDiscreteMatrix;
public:
NxsDiscreteDatum();
virtual ~NxsDiscreteDatum();
void CopyFrom(const NxsDiscreteDatum &other);
private:
unsigned *states; /* holds information about state for a single taxon-character combination */
};
typedef NxsDiscreteDatum DiscreteDatum;
#endif
|
