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martin-radenmartin-raden
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+ support for length-corrected E optimization and output
1 parent f8e7f6e commit 1a82b34

6 files changed

Lines changed: 95 additions & 3 deletions

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‎src/IntaRNA/Makefile.am‎

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@@ -42,6 +42,7 @@ libIntaRNA_a_HEADERS = \
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InteractionEnergyVrna.h \
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InteractionRange.h \
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NussinovHandler.h \
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ObjectiveHandler.h \
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OutputConstraint.h \
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OutputStreamHandler.h \
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OutputStreamHandlerSortedCsv.h \
@@ -107,6 +108,7 @@ libIntaRNA_a_SOURCES = \
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InteractionEnergyVrna.cpp \
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InteractionRange.cpp \
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NussinovHandler.cpp \
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ObjectiveHandler.cpp \
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OutputConstraint.cpp \
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OutputStreamHandlerSortedCsv.cpp \
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OutputHandler.cpp \

‎src/IntaRNA/ObjectiveHandler.cpp‎

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#include "IntaRNA/ObjectiveHandler.h"
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namespace IntaRNA
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{
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ObjectiveHandler::ObjectiveHandler()
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{
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}
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ObjectiveHandler::~ObjectiveHandler()
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{
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}
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E_type
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ObjectiveHandler::
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getLcE( const Interaction & i, const InteractionEnergy & energy )
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{
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const size_t curLength = std::max(
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( 1 + i.basePairs.rbegin()->first - i.basePairs.begin()->first )
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, ( 1 + i.basePairs.begin()->second - i.basePairs.rbegin()->second )
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);
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return getLcE( curLength, i.energy, energy);
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}
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E_type
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ObjectiveHandler::
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getLcE( const size_t & curLength, const E_type & fullE, const InteractionEnergy & energy )
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{
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// const size_t maxLength = std::max( std::min(energy.getAccessibility1().getSequence().size(), energy.getAccessibility1().getMaxLength())
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// , std::min(energy.getAccessibility2().getSequence().size(), energy.getAccessibility2().getMaxLength()) );
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LOG_IF(curLength<1, DEBUG) <<"curLength < 1";
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return (E_type)( (double)(fullE) / std::log2(1+(double)curLength) );
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// return (E_type)( (double)(fullE) / std::log(5+(double)curLength) );
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// return (E_type)( (double)(fullE) / std::log(2.0*(double)curLength) );
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// return (fullE) / (E_type)curLength;
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// return (fullE * maxLength) / curLength;
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}
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} /* namespace IntaRNA */

‎src/IntaRNA/ObjectiveHandler.h‎

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#ifndef INTARNA_OBJECTIVEHANDLER_H_
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#define INTARNA_OBJECTIVEHANDLER_H_
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#include "IntaRNA/Interaction.h"
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#include "IntaRNA/InteractionEnergy.h"
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namespace IntaRNA
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{
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/**
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* Defines the optimization objective of Predictor instances
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*/
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class ObjectiveHandler
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{
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public:
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ObjectiveHandler();
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virtual ~ObjectiveHandler();
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static
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E_type
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getLcE( const Interaction & i, const InteractionEnergy & energy );
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static
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E_type
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getLcE( const size_t & curLength, const E_type & fullE, const InteractionEnergy & energy );
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};
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} /* namespace IntaRNA */
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#endif /* INTARNA_OBJECTIVEHANDLER_H_ */

‎src/IntaRNA/OutputHandlerCsv.cpp‎

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@@ -1,5 +1,6 @@
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#include "IntaRNA/OutputHandlerCsv.h"
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#include "IntaRNA/ObjectiveHandler.h"
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#if INTARNA_MULITHREADING
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#include <omp.h>
@@ -22,7 +23,7 @@ const std::string OutputHandlerCsv::notAvailable = "NAN";
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const OutputHandlerCsv::ColTypeList OutputHandlerCsv::colTypeNumericSort(
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OutputHandlerCsv::string2list(
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"start1,end1,start2,end2"
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",E,ED1,ED2,Pu1,Pu2,E_init,E_loops,E_dangleL,E_dangleR,E_endL,E_endR,E_hybrid,E_norm,E_hybridNorm,E_add"
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",E,ED1,ED2,Pu1,Pu2,E_init,E_loops,E_dangleL,E_dangleR,E_endL,E_endR,E_hybrid,E_norm,E_hybridNorm,E_add,lcE"
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",seedStart1,seedEnd1,seedStart2,seedEnd2,seedE,seedED1,seedED2,seedPu1,seedPu2"
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",Eall,Zall,P_E"
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));
@@ -242,6 +243,10 @@ add( const Interaction & i, const OutputConstraint & outConstraint )
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outTmp <<E_2_Ekcal(contr.energyAdd);
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break;
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case lcE:
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outTmp <<E_2_Ekcal(ObjectiveHandler::getLcE(i,energy));
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break;
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case seedStart1:
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if (i.seed == NULL) {
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outTmp <<notAvailable;

‎src/IntaRNA/OutputHandlerCsv.h‎

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@@ -61,6 +61,7 @@ class OutputHandlerCsv : public OutputHandler
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E_norm, //!< length normalized energy = E/ln(length(seq1)*length(seq2))
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E_hybridNorm, //!< length normalized energy of hybridization only = E_hybrid / ln(length(seq1)*length(seq2))
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E_add, //!< user provided energy shift
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lcE, //!< length normalized interaction energy = E*maxLength/curMaxLength
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seedStart1, //!< start index of the seed in seq1
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seedEnd1, //!< end index of the seed in seq1
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seedStart2, //!< start index of the seed in seq2
@@ -134,6 +135,7 @@ class OutputHandlerCsv : public OutputHandler
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colType2string[E_norm] = "E_norm";
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colType2string[E_hybridNorm] = "E_hybridNorm";
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colType2string[E_add] = "E_add";
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colType2string[lcE] = "lcE";
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colType2string[seedStart1] = "seedStart1";
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colType2string[seedEnd1] = "seedEnd1";
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colType2string[seedStart2] = "seedStart2";

‎src/IntaRNA/PredictorMfe.cpp‎

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@@ -1,5 +1,6 @@
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#include "IntaRNA/PredictorMfe.h"
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#include "IntaRNA/ObjectiveHandler.h"
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#include <iostream>
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#include <algorithm>
@@ -114,7 +115,10 @@ updateOptima( const size_t i1, const size_t j1
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// check if we have to care about insertion (curE <= worst E in list)
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if (curE > mfeInteractions.rbegin()->energy ) {
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// if (curE > mfeInteractions.rbegin()->energy ) {
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if (ObjectiveHandler::getLcE( std::max(1+j1-i1,1+j2-i2), curE, energy)
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> ObjectiveHandler::getLcE( *(mfeInteractions.rbegin()), energy) )
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{
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return;
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}
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@@ -136,7 +140,10 @@ updateOptima( const size_t i1, const size_t j1
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} else {
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// check for insertion position
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InteractionList::iterator insertPos = std::find_if_not( mfeInteractions.begin(), mfeInteractions.end(), [&](Interaction & i){return i < tmp;});
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InteractionList::iterator insertPos = std::find_if_not( mfeInteractions.begin(), mfeInteractions.end(), [&](Interaction & i){
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return ObjectiveHandler::getLcE(i,energy) < ObjectiveHandler::getLcE(tmp,energy);
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// return i < tmp;
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});
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if ( insertPos != mfeInteractions.end() && !( tmp == *insertPos )) {
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