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Remove redundant feasibility checks from hot prediction paths #235

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12 changes: 3 additions & 9 deletions src/IntaRNA/HelixHandlerNoBulgeMax.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -58,9 +58,7 @@ fillHelix(const size_t i1min, const size_t i1max, const size_t i2min, const size
i2 = i2start+o;

// check if valid base pair
if( energy.isAccessible1( i1 )
&& energy.isAccessible2( i2 )
&& energy.areComplementary( i1, i2 ))
if (energy.areComplementary( i1, i2 ))
{
// start new canonical helix information
if (E_isINF(curHelixE)) {
Expand Down Expand Up @@ -232,9 +230,7 @@ fillHelixSeed(const size_t i1min, const size_t i1max, const size_t i2min, const
j1 = seedEnd1+trailingL;
j2 = seedEnd2+trailingL;
// check if trailing based pairs are possible, otherwise stop computation
if (!(energy.isAccessible1(j1)
&& energy.isAccessible2(j2)
&& energy.areComplementary(j1,j2)))
if (!energy.areComplementary(j1,j2))
{
break;
}
Expand All @@ -258,9 +254,7 @@ fillHelixSeed(const size_t i1min, const size_t i1max, const size_t i2min, const

// check if leading based pairs are possible, otherwise stop computation
if (leadingBP > 0
&&!(energy.isAccessible1(i1)
&& energy.isAccessible2(i2)
&& energy.areComplementary(i1,i2)))
&& !energy.areComplementary(i1,i2))
{
break;
}
Expand Down
8 changes: 2 additions & 6 deletions src/IntaRNA/PredictorMfe2d.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -131,9 +131,7 @@ fillHybridE( const size_t j1, const size_t j2
hybridE_pq(i1,i2) = E_INF;

// check if this cell is to be computed (!=E_INF)
if( energy.isAccessible1(i1)
&& energy.isAccessible2(i2)
&& energy.areComplementary(i1,i2)
if( energy.areComplementary(i1,i2)
)
{
// w2 = interaction width in seq2
Expand Down Expand Up @@ -162,9 +160,7 @@ fillHybridE( const size_t j1, const size_t j2
} else {
// no lp allowed
// check if right-side stacking of (i1,i2) is possible
if (energy.isAccessible1(i1+noLpShift)
&& energy.isAccessible2(i2+noLpShift)
&& energy.areComplementary(i1+noLpShift,i2+noLpShift))
if (energy.areComplementary(i1+noLpShift,i2+noLpShift))
{
// get stacking term to avoid recomputation
iStackE = energy.getE_interLeft(i1,i1+noLpShift,i2,i2+noLpShift);
Expand Down
4 changes: 1 addition & 3 deletions src/IntaRNA/PredictorMfe2dHelixBlockHeuristic.cpp
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Expand Up @@ -85,9 +85,7 @@ predict( const IndexRange & r1
for (i2=0; i2<hybridE.size2(); i2++) {

// check if positions can form interaction
if ( energy.isAccessible1(i1)
&& energy.isAccessible2(i2)
&& energy.areComplementary(i1,i2) )
if (energy.areComplementary(i1,i2) )
{
// set to interaction initiation with according boundary
hybridE(i1,i2) = BestInteractionE(energy.getE_init(), i1, i2);
Expand Down
4 changes: 1 addition & 3 deletions src/IntaRNA/PredictorMfe2dHelixBlockHeuristicSeed.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -94,9 +94,7 @@ predict( const IndexRange & r1
for (i2=0; i2<hybridE.size2(); i2++) {

// check if positions can form interaction
if ( energy.isAccessible1(i1)
&& energy.isAccessible2(i2)
&& energy.areComplementary(i1,i2) )
if (energy.areComplementary(i1,i2) )
{
// set to interaction initiation with according boundary
hybridE(i1,i2) = BestInteractionE(energy.getE_init(), i1, i2);
Expand Down
6 changes: 1 addition & 5 deletions src/IntaRNA/PredictorMfe2dHeuristic.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -102,17 +102,13 @@ fillHybridE()
curCellEtotal = E_INF;

// check if positions can form interaction
if ( energy.isAccessible1(i1)
&& energy.isAccessible2(i2)
&& energy.areComplementary(i1,i2) )
if (energy.areComplementary(i1,i2) )
{
// no LP allowed
if (outConstraint.noLP) {
// check if right-side stacking of (i1,i2) is possible
if ( i1+noLpShift < energy.size1()
&& i2+noLpShift < energy.size2()
&& energy.isAccessible1(i1+noLpShift)
&& energy.isAccessible2(i2+noLpShift)
&& energy.areComplementary(i1+noLpShift,i2+noLpShift))
{
// get stacking term to avoid recomputation
Expand Down
6 changes: 1 addition & 5 deletions src/IntaRNA/PredictorMfe2dHeuristicSeed.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -119,18 +119,14 @@ fillHybridE()
curCellEtotal = E_INF;

// check if positions can form interaction
if ( energy.isAccessible1(i1)
&& energy.isAccessible2(i2)
&& energy.areComplementary(i1,i2) )
if (energy.areComplementary(i1,i2) )
{

// no lp allowed
if (noLpShift != 0) {
// check if right-side stacking of (i1,i2) is possible
if ( i1+noLpShift < energy.size1()
&& i2+noLpShift < energy.size2()
&& energy.isAccessible1(i1+noLpShift)
&& energy.isAccessible2(i2+noLpShift)
&& energy.areComplementary(i1+noLpShift,i2+noLpShift))
{
// get stacking term to avoid recomputation
Expand Down
16 changes: 4 additions & 12 deletions src/IntaRNA/PredictorMfe2dHeuristicSeedExtension.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -144,19 +144,15 @@ fillHybridE_right( const size_t sj1, const size_t sj2

// skip if not accessible
// check if complementary
if ( energy.isAccessible1(j1)
&& energy.isAccessible2(j2)
&& sj1<j1
if (sj1<j1
&& sj2<j2
&& energy.areComplementary(j1,j2) )
{

// left-stacking of j if no-LP
if (outConstraint.noLP) {
// skip if no stacking possible
if ( !energy.areComplementary(j1-noLpShift,j2-noLpShift)
| !energy.isAccessible1(j1-noLpShift)
| !energy.isAccessible2(j2-noLpShift))
if (!energy.areComplementary(j1-noLpShift,j2-noLpShift))
{
continue;
}
Expand Down Expand Up @@ -242,18 +238,14 @@ fillHybridE_left( const size_t si1, const size_t si2 )
curMinE = (i1==si1 && i2==si2) ? energy.getE_init() : E_INF;
// skip if not accessible
// check if complementary
if (energy.isAccessible1(i1)
&& energy.isAccessible2(i2)
&& i1<si1
if (i1<si1
&& i2<si2
&& energy.areComplementary(i1,i2) )
{
// left-stacking of j if no-LP
if (outConstraint.noLP) {
// skip if no stacking possible
if ( !energy.areComplementary(i1+noLpShift,i2+noLpShift)
| !energy.isAccessible1(i1+noLpShift)
| !energy.isAccessible2(i2+noLpShift))
if (!energy.areComplementary(i1+noLpShift,i2+noLpShift))
{
continue;
}
Expand Down
8 changes: 2 additions & 6 deletions src/IntaRNA/PredictorMfe2dSeed.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -153,9 +153,7 @@ fillHybridE( const size_t j1, const size_t j2
hybridE_pq_seed(i1,i2) = E_INF;

// check if this cell is to be computed (!=E_INF)
if( energy.isAccessible1(i1)
&& energy.isAccessible2(i2)
&& energy.areComplementary(i1,i2))
if( energy.areComplementary(i1,i2))
{

// w2 = interaction width in seq2
Expand Down Expand Up @@ -184,9 +182,7 @@ fillHybridE( const size_t j1, const size_t j2
} else {
// no lp allowed
// check if right-side stacking of (i1,i2) is possible
if (energy.isAccessible1(i1+noLpShift)
&& energy.isAccessible2(i2+noLpShift)
&& energy.areComplementary(i1+noLpShift,i2+noLpShift))
if (energy.areComplementary(i1+noLpShift,i2+noLpShift))
{
// get stacking term to avoid recomputation
iStackE = energy.getE_interLeft(i1,i1+noLpShift,i2,i2+noLpShift);
Expand Down
16 changes: 4 additions & 12 deletions src/IntaRNA/PredictorMfe2dSeedExtension.cpp
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Expand Up @@ -158,19 +158,15 @@ fillHybridE_left( const size_t si1, const size_t si2 )
curE = (i1==si1 && i2==si2) ? energy.getE_init() : E_INF;
// skip if not accessible
// check if complementary
if (energy.isAccessible1(i1)
&& energy.isAccessible2(i2)
&& i1<si1
if (i1<si1
&& i2<si2
&& energy.areComplementary(i1,i2) )
{

// right-stacking of i if no-LP
if (outConstraint.noLP) {
// skip if no stacking possible
if ( !energy.areComplementary(i1+noLpShift,i2+noLpShift)
| !energy.isAccessible1(i1+noLpShift)
| !energy.isAccessible2(i2+noLpShift))
if (!energy.areComplementary(i1+noLpShift,i2+noLpShift))
{
continue;
}
Expand Down Expand Up @@ -238,19 +234,15 @@ fillHybridE_right( const size_t sj1, const size_t sj2 )

// skip if not accessible
// check if complementary
if (energy.isAccessible1(j1)
&& energy.isAccessible2(j2)
&& sj1<j1
if (sj1<j1
&& sj2<j2
&& energy.areComplementary(j1,j2) )
{

// left-stacking of j if no-LP
if (outConstraint.noLP) {
// skip if no stacking possible
if (!energy.areComplementary(j1-noLpShift,j2-noLpShift)
| !energy.isAccessible1(j1-noLpShift)
| !energy.isAccessible2(j2-noLpShift))
if (!energy.areComplementary(j1-noLpShift,j2-noLpShift))
{
continue;
}
Expand Down
12 changes: 2 additions & 10 deletions src/IntaRNA/PredictorMfe2dSeedExtensionRIblast.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -164,9 +164,7 @@ parallelExtension( PredictorMfe2dSeedExtensionRIblast::ExtendedSeed & seed
// extend left
while (seed.i1 > 1 && seed.i2 > 1) {
// todo acc1/acc2 maxLength() termination
if (energy.isAccessible1(seed.i1-1)
&& energy.isAccessible2(seed.i2-1)
&& energy.areComplementary(seed.i1-1,seed.i2-1))
if (energy.areComplementary(seed.i1-1,seed.i2-1))
{
E_type newEnergy = seed.energy + energy.getE_interLeft(seed.i1-1,i1min,seed.i2-1,i2min);
if (newEnergy < seed.energy) {
Expand All @@ -190,9 +188,7 @@ parallelExtension( PredictorMfe2dSeedExtensionRIblast::ExtendedSeed & seed
// extend right
while (seed.j1 < max_extension1-1 && seed.j2 < max_extension2-1) {
// todo acc1/acc2 maxLength() termination
if (energy.isAccessible1(seed.j1+1)
&& energy.isAccessible2(seed.j2+1)
&& energy.areComplementary(seed.j1+1,seed.j2+1))
if (energy.areComplementary(seed.j1+1,seed.j2+1))
{
E_type newEnergy = seed.energy + energy.getE_interLeft(j1min,seed.j1+1,j2min,seed.j2+1);
if (newEnergy < seed.energy) {
Expand Down Expand Up @@ -238,8 +234,6 @@ fillHybridE_left( const size_t j1, const size_t j2 )
// check if complementary
if( i1>0
&& i2>0
&& energy.isAccessible1(j1-i1)
&& energy.isAccessible2(j2-i2)
&& energy.areComplementary(j1-i1,j2-i2) )
{
curMinE = E_INF;
Expand Down Expand Up @@ -299,8 +293,6 @@ fillHybridE_right( const size_t i1, const size_t i2 )
// check if complementary
if( j1>i1
&& j2>i2
&& energy.isAccessible1(i1+j1)
&& energy.isAccessible2(i2+j2)
&& energy.areComplementary(i1+j1,i2+j2) )
{
curMinE = E_INF;
Expand Down
8 changes: 2 additions & 6 deletions src/IntaRNA/PredictorMfeEns2d.cpp
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Expand Up @@ -128,9 +128,7 @@ fillHybridZ( const size_t j1, const size_t j2
hybridZ(i1,i2) = Z_type(0.0);

// check if this cell is to be computed (!=E_INF)
if( energy.isAccessible1(i1)
&& energy.isAccessible2(i2)
&& energy.areComplementary(i1,i2)
if( energy.areComplementary(i1,i2)
)
{
// w2 = interaction width in seq2
Expand Down Expand Up @@ -159,9 +157,7 @@ fillHybridZ( const size_t j1, const size_t j2
} else {
// no lp allowed
// check if right-side stacking of (i1,i2) is possible
if (energy.isAccessible1(i1+noLpShift)
&& energy.isAccessible2(i2+noLpShift)
&& energy.areComplementary(i1+noLpShift,i2+noLpShift))
if (energy.areComplementary(i1+noLpShift,i2+noLpShift))
{
// get stacking term to avoid recomputation
iStackZ = energy.getBoltzmannWeight(energy.getE_interLeft(i1,i1+noLpShift,i2,i2+noLpShift));
Expand Down
6 changes: 1 addition & 5 deletions src/IntaRNA/PredictorMfeEns2dHeuristic.cpp
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Expand Up @@ -104,17 +104,13 @@ fillHybridZ()
curCellEtotal = E_INF;

// check if positions can form interaction
if ( energy.isAccessible1(i1)
&& energy.isAccessible2(i2)
&& energy.areComplementary(i1,i2) )
if (energy.areComplementary(i1,i2) )
{
// no lp allowed
if (noLpShift != 0) {
// check if right-side stacking of (i1,i2) is possible
if ( i1+noLpShift < energy.size1()
&& i2+noLpShift < energy.size2()
&& energy.isAccessible1(i1+noLpShift)
&& energy.isAccessible2(i2+noLpShift)
&& energy.areComplementary(i1+noLpShift,i2+noLpShift))
{
// get stacking term to avoid recomputation
Expand Down
12 changes: 2 additions & 10 deletions src/IntaRNA/PredictorMfeEns2dSeedExtension.cpp
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Expand Up @@ -213,17 +213,13 @@ fillHybridZ_left( const size_t si1, const size_t si2 )
// check if complementary (use global sequence indexing)
if( i1<si1
&& i2<si2
&& energy.isAccessible1(i1)
&& energy.isAccessible2(i2)
&& energy.areComplementary(i1,i2) )
{

// right-stacking of i if no-LP
if (outConstraint.noLP) {
// skip if no stacking possible
if (!energy.areComplementary(i1+noLpShift,i2+noLpShift)
| !energy.isAccessible1(i1+noLpShift)
| !energy.isAccessible2(i2+noLpShift) )
if (!energy.areComplementary(i1+noLpShift,i2+noLpShift))
{
continue;
}
Expand Down Expand Up @@ -376,17 +372,13 @@ fillHybridZ_right( const size_t sj1, const size_t sj2 )
// check if complementary free base pair
if( sj1<j1
&& sj2<j2
&& energy.isAccessible1(j1)
&& energy.isAccessible2(j2)
&& energy.areComplementary(j1,j2) )
{

// left-stacking of j if no-LP
if (outConstraint.noLP) {
// skip if no stacking possible
if (!energy.areComplementary(j1-noLpShift,j2-noLpShift)
| !energy.isAccessible1(j1-noLpShift)
| !energy.isAccessible2(j2-noLpShift) )
if (!energy.areComplementary(j1-noLpShift,j2-noLpShift))
{
continue;
}
Expand Down
2 changes: 0 additions & 2 deletions src/IntaRNA/SeedHandler.cpp
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Expand Up @@ -13,8 +13,6 @@ isFeasibleSeedBasePair( const size_t i1, const size_t i2, const bool atEndOfSeed
{

return i1 < energy.size1() && i2 < energy.size2()
&& energy.isAccessible1(i1)
&& energy.isAccessible2(i2)
&& energy.areComplementary(i1,i2)
&& seedConstraint.getMaxED() >= energy.getED1( i1,i1 )
&& seedConstraint.getMaxED() >= energy.getED2( i2,i2 )
Expand Down
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