/usr/include/ncl/nxssetreader.h is in libncl-dev 2.1.18+dfsg-2build1.
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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 91 92 93 94 95 96 97 98 99 100 101 102 103 104 | // 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_NXSSETREADER_H
#define NCL_NXSSETREADER_H
#include <sstream>
#include "ncl/nxstoken.h"
#include "ncl/nxsblock.h"
/*!
A class for reading NEXUS set objects and storing them in a set of int values. The NxsUnsignedSet `nxsset' will be
cleared, and `nxsset' will be built up as the set is read, with each element in the list storing a
member of the set (ranges are stored as individual elements). This class handles set descriptions of the following
form:
>
4-7 15 20-.\3;
>
The above set includes every number from 4 to 7 (inclusive), 15 and every third number from 20 to max, where `max'
would ordinarily be set to either the last character (if `settype' is `NxsSetReaderEnum::charset') or the last
taxon (if `settype' is `NxsSetReaderEnum::taxset'). If `max' equaled 30, the example above would be stored as
follows (remember that internally the numbers are stored with offset 0, even though in the NEXUS data file the
numbers always start at 1.
>
3, 4, 5, 6, 14, 19, 22, 25, 28
>
The following example of how NxsSetReader is used comes from the NxsCharactersBlock::HandleEliminate function:
>
NxsSetReader(token, ncharTotal, eliminated, *this, NxsSetReader::charset).Run();
>
This reads in a set of eliminated characters from a NEXUS data file, storing the resulting set in the data member
`eliminated'. In this case `max' is set to `ncharTotal' (the total number of characters), and the block reference
is set to the NxsCharactersBlock object, which provides a
*/
class NxsSetReader
{
static unsigned InterpretTokenAsIndices(NxsToken &t,
const NxsLabelToIndicesMapper &,
const char * setType,
const char * cmd,
NxsUnsignedSet * destination);
static void AddRangeToSet(unsigned first, unsigned last, unsigned stride, NxsUnsignedSet * destination, const NxsUnsignedSet * taboo, NxsToken &t);
public:
static void ReadSetDefinition(NxsToken &t,
const NxsLabelToIndicesMapper &,
const char * setType,
const char * cmd,
NxsUnsignedSet * destination,
const NxsUnsignedSet * taboo = NULL);
static void WriteSetAsNexusValue(const NxsUnsignedSet &, std::ostream & out);
static std::string GetSetAsNexusString(const NxsUnsignedSet &s)
{
std::stringstream os;
NxsSetReader::WriteSetAsNexusValue(s, os);
//os << ' ';
return os.str();
}
static std::vector<unsigned> GetSetAsVector(const NxsUnsignedSet &s);
enum NxsSetReaderEnum /* For use with the variable `settype' */
{
generic = 1, /* means expect a generic set (say, characters weights) */
charset, /* means expect a character set */
taxset /* means expect a taxon set */
};
NxsSetReader(NxsToken &t, unsigned maxValue, NxsUnsignedSet &iset, NxsBlock &nxsblk, unsigned type);
bool Run();
void WriteAsNexusValue(std::ostream & out) const
{
WriteSetAsNexusValue(nxsset, out);
}
protected:
bool AddRange(unsigned first, unsigned last, unsigned modulus = 0);
private:
unsigned GetTokenValue();
NxsBlock █ /* reference to the block object used for looking up labels */
NxsToken &token; /* reference to the token being used to parse the NEXUS data file */
NxsUnsignedSet &nxsset; /* reference to the NxsUnsignedSet set being read */
unsigned max; /* maximum number of elements in the set */
unsigned settype; /* the type of set being read (see the NxsSetReaderEnum enumeration) */
};
typedef NxsSetReader SetReader;
#endif
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