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/**
>HEADER
Copyright (c) 2013 Rob Patro robp@cs.cmu.edu
This file is part of Sailfish.
Sailfish 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 3 of the License, or
(at your option) any later version.
Sailfish 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 Sailfish. If not, see <http://www.gnu.org/licenses/>.
<HEADER
**/
#ifndef TRANSCRIPT_GENE_MAP_HPP
#define TRANSCRIPT_GENE_MAP_HPP
// Allows for the serialization of this class
#include <cereal/archives/binary.hpp>
#include <cereal/types/vector.hpp>
#include <cereal/types/string.hpp>
#include <algorithm>
#include <unordered_map>
#include <vector>
class TranscriptGeneMap {
using Index = size_t;
using Size = size_t;
using NameVector = std::vector<std::string>;
using IndexVector = std::vector<size_t>;
using IndexVectorList = std::vector<std::vector<size_t>>;
private:
NameVector _transcriptNames;
NameVector _geneNames;
IndexVector _transcriptsToGenes;
IndexVectorList _genesToTranscripts;
bool _haveReverseMap;
void _computeReverseMap() {
_genesToTranscripts.resize( _geneNames.size(), {});
Index transcriptID = 0;
size_t maxNumTrans = 0;
Index maxGene;
for ( transcriptID = 0; transcriptID < _transcriptsToGenes.size(); ++transcriptID ) {
_genesToTranscripts[ _transcriptsToGenes[transcriptID] ].push_back( transcriptID );
if ( maxNumTrans < _genesToTranscripts[ _transcriptsToGenes[transcriptID] ].size() ) {
maxNumTrans = _genesToTranscripts[ _transcriptsToGenes[transcriptID] ].size();
maxGene = _transcriptsToGenes[transcriptID];
}
}
std::cerr << "max # of transcripts in a gene was " << maxNumTrans << " in gene " << _geneNames[maxGene] << "\n";
}
friend class cereal::access;
template<class Archive>
void serialize(Archive & ar, const unsigned int version)
{
ar(_transcriptNames, _geneNames, _transcriptsToGenes,
_genesToTranscripts, _haveReverseMap);
}
public:
TranscriptGeneMap() :
_transcriptNames(NameVector()), _geneNames(NameVector()),
_transcriptsToGenes(IndexVector()), _haveReverseMap(false) {}
TranscriptGeneMap( const NameVector &transcriptNames,
const NameVector &geneNames,
const IndexVector &transcriptsToGenes ) :
_transcriptNames(transcriptNames), _geneNames(geneNames),
_transcriptsToGenes(transcriptsToGenes), _haveReverseMap(false) {}
TranscriptGeneMap(const TranscriptGeneMap& other) = default;
TranscriptGeneMap& operator=(const TranscriptGeneMap& other) = default;
Index INVALID { std::numeric_limits<Index>::max() };
Index findTranscriptID( const std::string &tname ) {
using std::distance;
using std::lower_bound;
auto it = lower_bound( _transcriptNames.begin(), _transcriptNames.end(), tname );
return ( it == _transcriptNames.end() ) ? INVALID : ( distance(_transcriptNames.begin(), it) );
}
Size numTranscripts() {
return _transcriptNames.size();
}
Size numGenes() {
return _geneNames.size();
}
bool needReverse() {
if ( _haveReverseMap ) {
return false;
} else {
_computeReverseMap();
return true;
}
}
const IndexVector &transcriptsForGene( Index geneID ) {
return _genesToTranscripts[geneID];
}
inline std::string nameFromGeneID( Index geneID ) {
return _geneNames[geneID];
}
inline Index gene( Index transcriptID ) {
return _transcriptsToGenes[transcriptID];
}
inline std::string geneName( Index transcriptID ) {
return _geneNames[_transcriptsToGenes[transcriptID]];
}
inline std::string geneName (const std::string& transcriptName,
bool complain=true) {
auto tid = findTranscriptID(transcriptName);
if (tid != INVALID) {
return geneName(tid);
} else {
std::cerr << "WARNING: couldn't find transcript named ["
<< transcriptName << "]; returning transcript "
<< " as it's own gene\n";
return transcriptName;
}
}
inline std::string transcriptName( Index transcriptID ) {
return _transcriptNames[transcriptID];
}
};
#endif // TRANSCRIPT_GENE_MAP_HPP
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