/usr/include/ncl/nxstaxaassociationblock.h is in libncl-dev 2.1.18+dfsg-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 | // 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_NXSTAXAASSOCIATIONBLOCK_H
#define NCL_NXSTAXAASSOCIATIONBLOCK_H
#include "ncl/nxsdefs.h"
#include "ncl/nxstaxablock.h"
/*!
*/
class NxsTaxaAssociationBlockAPI
: public NxsBlock
{
public:
virtual NxsTaxaBlockAPI * GetFirstTaxaBlock() const = 0;
virtual NxsTaxaBlockAPI * GetSecondTaxaBlock() const = 0;
virtual std::set<unsigned> GetAssociatesForTaxonInFirstBlock(unsigned) const = 0;
virtual std::set<unsigned> GetAssociatesForTaxonInSecondBlock(unsigned) const = 0;
};
/*! The default implementation of the NxsTaxaBlockAPI that is used to parse TAXA blocks into a list of
unique (case-insensitive) labels.
*/
class NxsTaxaAssociationBlock
: public NxsTaxaAssociationBlockAPI
{
typedef std::map<unsigned, std::set<unsigned> > AssociationMap;
public:
NxsTaxaAssociationBlock();
virtual ~NxsTaxaAssociationBlock() {}
virtual void AddAssociation(unsigned firstIndex, const std::set<unsigned> & secIndices) {
std::set<unsigned> & former = this->firstToSecond[firstIndex];
for (std::set<unsigned>::const_iterator sIt = secIndices.begin(); sIt != secIndices.end(); ++sIt) {
const unsigned & secIndex = *sIt;
former.insert(secIndex);
this->secondToFirst[secIndex].insert(firstIndex);
}
}
virtual void SetFirstTaxaBlock(NxsTaxaBlockAPI *f) {
NxsTaxaBlockAPI * s = this->secondTaxaBlock;
this->Reset();
this->secondTaxaBlock = s;
this->firstTaxaBlock = f;
}
virtual NxsTaxaBlockAPI * GetFirstTaxaBlock() const {
return this->firstTaxaBlock;
}
virtual void SetSecondTaxaBlock(NxsTaxaBlockAPI *s) {
NxsTaxaBlockAPI * f = this->firstTaxaBlock;
this->Reset();
this->secondTaxaBlock = s;
this->firstTaxaBlock = f;
}
virtual NxsTaxaBlockAPI * GetSecondTaxaBlock() const {
return this->secondTaxaBlock;
}
virtual std::set<unsigned> GetAssociatesForTaxonInFirstBlock(unsigned i) const {
AssociationMap::const_iterator m = this->firstToSecond.find(i);
if (m == this->firstToSecond.end()) {
return std::set<unsigned>();
}
return m->second;
}
virtual std::set<unsigned> GetAssociatesForTaxonInSecondBlock(unsigned i) const {
AssociationMap::const_iterator m = this->secondToFirst.find(i);
if (m == this->secondToFirst.end()) {
return std::set<unsigned>();
}
return m->second;
}
virtual void Report(std::ostream &out) NCL_COULD_BE_CONST ; /*v2.1to2.2 1 */
virtual void Reset();
void WriteAsNexus(std::ostream &out) const;
NxsTaxaAssociationBlock &operator=(const NxsTaxaAssociationBlock &other)
{
Reset();
CopyBaseBlockContents(static_cast<const NxsBlock &>(other));
CopyTaxaAssociationContents(other);
return *this;
}
void CopyTaxaAssociationContents(const NxsTaxaAssociationBlock &other)
{
firstToSecond = other.firstToSecond;
secondToFirst = other.secondToFirst;
firstTaxaBlock = other.firstTaxaBlock;
secondTaxaBlock = other.secondTaxaBlock;
}
NxsTaxaAssociationBlock * Clone() const
{
NxsTaxaAssociationBlock *taxa = new NxsTaxaAssociationBlock();
*taxa = *this;
return taxa;
}
protected:
AssociationMap firstToSecond;
AssociationMap secondToFirst;
NxsTaxaBlockAPI * firstTaxaBlock;
NxsTaxaBlockAPI * secondTaxaBlock;
virtual void Read(NxsToken &token);
void HandleTaxaCommand(NxsToken &token);
void HandleAssociatesCommand(NxsToken &token);
NxsTaxaBlockAPI * ProcessTaxaBlockName(const NxsString & value, NxsToken &token) const;
};
class NxsTaxaAssociationBlockFactory
:public NxsBlockFactory
{
public:
virtual NxsTaxaAssociationBlock * GetBlockReaderForID(const std::string & NCL_BLOCKTYPE_ATTR_NAME, NxsReader *reader, NxsToken *token);
};
#endif
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