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* AlignedSequenceLoader.h
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* Interface to Arb's DB.
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* This class loads aligned sequences from Arb's DB and allows the other
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* code in this package to access it in a standard way.
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* Created on: Feb 15, 2010
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* Institute of Microbiology (Technical University Munich)
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* http://www.arb-home.de/
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#ifndef ALIGNEDSEQUENCELOADER_H
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#define ALIGNEDSEQUENCELOADER_H
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class AlignedSequenceLoader : virtual Noncopyable {
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* The aligned sequences (see Cma.h for the definition of VecVecType).
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* The positions map between cleaned-up alignment and original one.
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vector<size_t> *position_map;
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* The length of the multiple sequence alignment.
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* Cleans-up the MSA, removing positions with no base occurrence.
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void cleanSeqs(size_t* occurrences, long len);
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* Returns the MSA length.
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* Returns the position map.
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vector<size_t> * getPositionMap();
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* Returns the aligned sequences.
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VecVecType* getSequences();
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AlignedSequenceLoader();
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virtual ~AlignedSequenceLoader();
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#error AlignedSequenceLoader.h included twice
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#endif // ALIGNEDSEQUENCELOADER_H