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src/biu/RNAStructure.cc

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#include <biu/RNAStructure.hh>
#include <stack>
#include <biu/assertbiu.hh>

namespace biu
{
    const size_t RNAStructure::MIN_LOOP_LENGTH = 3;
    const size_t RNAStructure::INVALID_INDEX =
        std::numeric_limits<size_t>::max();
    const Alphabet RNAStructure::STRUCT_ALPH("().", 1);
    const Alphabet::AlphElem    RNAStructure::STRUCT_BND_OPEN = RNAStructure::STRUCT_ALPH.getElement("(");
    const Alphabet::AlphElem    RNAStructure::STRUCT_BND_CLOSE = RNAStructure::STRUCT_ALPH.getElement(")");
    const Alphabet::AlphElem    RNAStructure::STRUCT_UNBOUND = RNAStructure::STRUCT_ALPH.getElement(".");

// RNAStructure

    RNAStructure::RNAStructure( const std::string& rnaSeqStr,
                                const std::string& rnaStructBracketDotStr,
                                const AllowedBasePairs* const _bPair)
     :  rnaSeq(NULL),
        seqShared(false),
        rnaStructBracketDot(NULL),
        rnaBonds(),
        bPair(_bPair) 
    {
        assertbiu(bPair != NULL, "bPair is not allowed to be NULL.");
        assertbiu(bPair->getAlphabet()->isAlphabetString(rnaSeqStr),
         "RNA sequence contains characters which are not in the alphabet.");
        assertbiu(STRUCT_ALPH.isAlphabetString(rnaStructBracketDotStr),
         "RNA structure contains characters which are not in the alphabet.");

        
        rnaSeq = new Sequence(bPair->getAlphabet()->getSequence(rnaSeqStr));
        rnaStructBracketDot = new Structure(
         STRUCT_ALPH.getSequence(rnaStructBracketDotStr));

        assertbiu(rnaSeq->size() == rnaStructBracketDot->size(),
         "RNA sequence and structure have to have the same length.");
    
          // init bond data structure
        initBonds();
    }

    RNAStructure::RNAStructure( Sequence* rnaSeq_,
                                const Structure* const rnaStructBracketDot_,
                                const AllowedBasePairs* const bPair_,
                                const bool seqIsShared)
     :  rnaSeq(NULL),
        seqShared(seqIsShared),
        rnaStructBracketDot(NULL),
        bPair(bPair_) 
    {
        assertbiu(rnaSeq_ != NULL, "no RNA sequence given.");
        assertbiu(rnaStructBracketDot_ != NULL, "no RNA structure given.");
        assertbiu(bPair != NULL, "bPair is not allowed to be NULL.");
        assertbiu(bPair->getAlphabet()->isAlphabetSequence(*rnaSeq_),
         "RNA sequence contains characters which are not in the alphabet.");
        assertbiu(STRUCT_ALPH.isAlphabetSequence(*rnaStructBracketDot_),
         "RNA structure contains characters which are not in the alphabet.");
        assertbiu(rnaSeq_->size() == rnaStructBracketDot_->size(),
         "RNA sequence and structure have to have the same length.");

        
          // init sequence
        if (seqShared) {
            rnaSeq = rnaSeq_;
        } else {
            rnaSeq = new Sequence(*rnaSeq_);
        }
          // init structure
        rnaStructBracketDot = new Structure(*rnaStructBracketDot_);

          // init bond data structure
        initBonds();
    }

    RNAStructure::RNAStructure(const RNAStructure& rnaStruct)
     :  rnaSeq(rnaStruct.rnaSeq),
        seqShared(rnaStruct.seqShared),
        rnaStructBracketDot(new Structure(*(rnaStruct.rnaStructBracketDot))),
        rnaBonds(rnaStruct.rnaBonds), bPair(rnaStruct.bPair)
    {
        assertbiu(bPair != NULL, "bPair is not allowed to be NULL.");
        assertbiu(rnaSeq->size() == rnaStructBracketDot->size(),
         "RNA sequence and structure have to have the same length.");
        
        if (!seqShared) {
            rnaSeq = new Sequence(*(rnaStruct.rnaSeq));
        }
    }

    RNAStructure::~RNAStructure() {
        if(!seqShared && rnaSeq != NULL) {
            delete rnaSeq; rnaSeq = NULL;
        }
        if (rnaStructBracketDot != NULL) {
            delete rnaStructBracketDot; rnaStructBracketDot = NULL;
        }
    }

    bool        
    RNAStructure::isAllowedBasePair(    size_t first,
                                        size_t second)  const 
    {
        if (first == RNAStructure::INVALID_INDEX || second == RNAStructure::INVALID_INDEX)
            return false;
        assertbiu(first < rnaSeq->size() && second < rnaSeq->size(),
         "First or second is not a base position in the RNA sequence.");
        return bPair->allowedBasePair((*rnaSeq)[first], (*rnaSeq)[second]);
    }

    RNAStructure&   
    RNAStructure::operator= (const RNAStructure& rnaStruct2) {
        assertbiu(  seqShared == rnaStruct2.seqShared, 
                    "sequence of both has to be shared or not");
        if (this != &rnaStruct2) {
              // copy seq
            if (seqShared) { // copy only pointer
                rnaSeq = rnaStruct2.rnaSeq;
            } else { // copy
                rnaSeq->resize(rnaStruct2.rnaSeq->size());
                std::copy(  rnaStruct2.rnaSeq->begin(),
                            rnaStruct2.rnaSeq->end(),
                            rnaSeq->begin());
            }
              // copy structure
            rnaStructBracketDot->resize(rnaStruct2.rnaStructBracketDot->size());
            std::copy(  rnaStruct2.rnaStructBracketDot->begin(),
                        rnaStruct2.rnaStructBracketDot->end(),
                        rnaStructBracketDot->begin());
              // copy remaining data
            bPair = rnaStruct2.bPair;
            rnaBonds = rnaStruct2.rnaBonds;
        }
        return *this;
    }

    bool        
    RNAStructure::operator== (const RNAStructure& rnaStruct2)
             const {
        return (rnaSeq == rnaStruct2.rnaSeq || *rnaSeq == *(rnaStruct2.rnaSeq))
            && *rnaStructBracketDot == *(rnaStruct2.rnaStructBracketDot)
            && rnaBonds == rnaStruct2.rnaBonds
            && *bPair == *(rnaStruct2.bPair);
    }

    bool        
    RNAStructure::operator!= (const RNAStructure& rnaStruct2)
             const {
        return (rnaSeq != rnaStruct2.rnaSeq && *rnaSeq != *(rnaStruct2.rnaSeq))
            || *rnaStructBracketDot != *(rnaStruct2.rnaStructBracketDot)
            || rnaBonds != rnaStruct2.rnaBonds
            || *bPair != *(rnaStruct2.bPair);
    }

    bool        
    RNAStructure::hasValidStructure() const {
        int count = 0;  // counter for open bonds
        // each opening bracket has to have a closing bracket
        for (size_t i=0; i < rnaStructBracketDot->size(); i++) {
            if ((*rnaStructBracketDot)[i] == STRUCT_BND_OPEN ) {
                count++;
            }
            else if ((*rnaStructBracketDot)[i] == STRUCT_BND_CLOSE) {
                count--;
            }
            if (count < 0) {
                return false;
            }
        }
        return (count == 0);
    }

    bool        
    RNAStructure::hasValidBasePairs() const{
        for (size_t i=0; i < rnaBonds.size(); i++) {
            // existing bond has to be an allowed base pair
            if (rnaBonds[i] != RNAStructure::INVALID_INDEX
                && !isAllowedBasePair(i, rnaBonds[i])) {
                return false;
            }
        }
        return true;
    }   

    bool        
    RNAStructure::hasMinLoopLength() const {
        for (size_t i=0; i < rnaBonds.size(); i++) {
            // existing bond has to have at least MIN_LENGTH_LOOP
            if (rnaBonds[i] != RNAStructure::INVALID_INDEX
                && (rnaBonds[i]-i) <= RNAStructure::MIN_LOOP_LENGTH) {
                return false;
            }
        }
        return true;
    }


    bool        
    RNAStructure::isValid() const{
        assertbiu(rnaSeq->size() == rnaStructBracketDot->size(),
                 "RNA sequence and structure have to have the same length.");
        return (    hasValidStructure() && hasMinLoopLength()
                    && hasValidBasePairs() );
    }

    std::string 
    RNAStructure::getStringRepresentation() const {
        return ( getStructureString() + "(" + getSequenceString() + ")" );
    }
    
    void
    RNAStructure::initBonds() {
          // resize and initialise bonds vector
        rnaBonds = std::vector<size_t>
               (rnaStructBracketDot->size(), RNAStructure::INVALID_INDEX);

          // do initialization only if structure is valid 
        if (!hasValidStructure()) {
            return;
        }
          // std::stack openingBonds contains opening bonds to create
          // vector rnaBonds during intitialisation
        std::stack<size_t>  openingBonds;
        
          // do update for real initialisation
        for (size_t i=0; i <  rnaStructBracketDot->size(); i++) {
            if ( (*rnaStructBracketDot)[i] == STRUCT_BND_OPEN ) {
                openingBonds.push(i);
            }
            else if ( (*rnaStructBracketDot)[i] == STRUCT_BND_CLOSE ) {
                assertbiu(!openingBonds.empty(),
                 "Closing without opening bond.");
                // check whether pairing of bases allowed   
                rnaBonds[openingBonds.top()] = i;
                openingBonds.pop();
            }
        }
        assertbiu(openingBonds.empty(), "Opening without closing bond.");
    }

} // namespace biu