std::string
Interaction::
dotBracket( const Interaction & i, const char symOpen, const char symClose, const bool fullLength )
{
#if INTARNA_IN_DEBUG_MODE
if (!i.isValid())
throw std::runtime_error("Interaction::dotBracket("+toString(i)+") not valid!");
#endif
if (fullLength) {
// compile dot-bracket representation for full sequence lengths
return std::string(i.basePairs.begin()->first, '.' ) // leading unpaired s1
+ dotSomething(i.basePairs.begin(), i.basePairs.end(), true, symOpen) // s1 structure
+ std::string(i.s1->size() - i.basePairs.rbegin()->first -1, '.' ) // trailing unpaired s1
+"&"
+ std::string(i.s2->size() - i.basePairs.rbegin()->second -1, '.' ) // leading unpaired s2
+ dotSomething(i.basePairs.rbegin(), i.basePairs.rend(), false, symClose) // s2 structure
+ std::string(i.basePairs.rbegin()->second, '.' ) // trailing unpaired s2
;
} else {
// compile dot-bracket representation for interacting subsequences only
return dotSomething(i.basePairs.begin(), i.basePairs.end(), true, symOpen)
+"&"
+ dotSomething(i.basePairs.rbegin(), i.basePairs.rend(), false, symClose)
;
}
}
std::string
Interaction::
dotBar( const Interaction & i, const bool fullLength )
{
#if INTARNA_IN_DEBUG_MODE
if (!i.isValid())
throw std::runtime_error("Interaction::dotBar("+toString(i)+") not valid!");
#endif
// check whether to do full length output
if (fullLength) {
// compile dot-bar representation for full sequences
return "1"
+ std::string(i.basePairs.begin()->first, '.' ) // leading unpaired s1
+ dotSomething(i.basePairs.begin(), i.basePairs.end(), true, '|') // s1 structure
+ std::string(i.s1->size() - i.basePairs.rbegin()->first -1, '.' ) // trailing unpaired s1
+ "&"
+ "1"
+ std::string(i.basePairs.rbegin()->second, '.' ) // trailing unpaired s2
+ dotSomething(i.basePairs.rbegin(), i.basePairs.rend(), false, '|') // s2 structure
+ std::string( i.s2->size() - i.basePairs.begin()->second -1, '.' ) // leading unpaired s2
;
} else {
// compile dot-bar representation for interacting subsequences only
return toString(i.basePairs.begin()->first +1)
+ dotSomething(i.basePairs.begin(), i.basePairs.end(), true, '|')
+"&"
+toString(i.basePairs.rbegin()->second +1)
+ dotSomething(i.basePairs.rbegin(), i.basePairs.rend(), false, '|')
;
}
}
void
PredictorMfe2dHeuristic::
traceBack( Interaction & interaction, const OutputConstraint & outConstraint )
{
// check if something to trace
if (interaction.basePairs.size() < 2) {
return;
}
#if INTARNA_IN_DEBUG_MODE
// sanity checks
if ( interaction.basePairs.size() != 2 ) {
throw std::runtime_error("PredictorMfe2dHeuristic::traceBack() : given interaction does not contain boundaries only");
}
#endif
// check for single interaction
if (interaction.basePairs.at(0).first == interaction.basePairs.at(1).first) {
// delete second boundary (identical to first)
interaction.basePairs.resize(1);
// update done
return;
}
#if INTARNA_IN_DEBUG_MODE
// sanity checks
if ( ! interaction.isValid() ) {
throw std::runtime_error("PredictorMfe2dHeuristic::traceBack() : given interaction not valid : "+toString(interaction));
}
#endif
// ensure sorting
interaction.sort();
// get indices in hybridE for boundary base pairs
size_t i1 = energy.getIndex1(interaction.basePairs.at(0)),
i2 = energy.getIndex2(interaction.basePairs.at(0));
const size_t j1 = energy.getIndex1(interaction.basePairs.at(1));
const size_t j2 = energy.getIndex2(interaction.basePairs.at(1));
// the currently traced value for i1-j1, i2-j2
E_type curE = hybridE(i1,i2).E;
assert( hybridE(i1,i2).j1 == j1 );
assert( hybridE(i1,i2).j2 == j2 );
assert( i1 <= j1 );
assert( i2 <= j2 );
assert( j1 < hybridE.size1() );
assert( j2 < hybridE.size2() );
// trace back
// temp variables
size_t k1,k2;
// check all possible splits of the interval (i1,i2)-(j1,j2)
// only reasonable, if there is an enclosed position k1 between i1-j1
while( (j1-i1) > 1 ) {
const BestInteraction * curCell = NULL;
bool traceNotFound = true;
// check all combinations of decompositions into (i1,i2)..(k1,k2)-(j1,j2)
for (k1=std::min(j1,i1+energy.getMaxInternalLoopSize1()+1); traceNotFound && k1>i1; k1--) {
for (k2=std::min(j2,i2+energy.getMaxInternalLoopSize2()+1); traceNotFound && k2>i2; k2--) {
// temp access to current cell
curCell = &(hybridE(k1,k2));
// check if right boundary is equal (part of the heuristic)
if ( curCell->j1 == j1 && curCell->j2 == j2 &&
// and energy is the source of curE
E_equal( curE, (energy.getE_interLeft(i1,k1,i2,k2) + curCell->E ) ) )
{
// stop searching
traceNotFound = false;
// store splitting base pair if not last one of interaction range
if ( k1 < j1 ) {
interaction.basePairs.push_back( energy.getBasePair(k1,k2) );
}
// trace right part of split
i1=k1;
i2=k2;
curE = curCell->E;
}
}
}
assert( !traceNotFound );
}
// sort final interaction (to make valid) (faster than calling sort())
if (interaction.basePairs.size() > 2) {
Interaction::PairingVec & bps = interaction.basePairs;
// shift all added base pairs to the front
for (size_t i=2; i<bps.size(); i++) {
bps.at(i-1).first = bps.at(i).first;
bps.at(i-1).second = bps.at(i).second;
}
// set last to j1-j2
(*bps.rbegin()) = energy.getBasePair( j1, j2 );
}
}
