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contrafold_v2_02.patch
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contrafold_v2_02.patch
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diff -urN contrafold_v2_02.orig/src/InferenceEngine.hpp contrafold/src/InferenceEngine.hpp
--- contrafold_v2_02.orig/src/InferenceEngine.hpp 2008-08-14 09:08:31.000000000 +0900
+++ contrafold/src/InferenceEngine.hpp 2009-08-20 22:11:29.142650990 +0900
@@ -26,6 +26,7 @@
int is_complementary[M+1][M+1];
bool cache_initialized;
ParameterManager<RealT> *parameter_manager;
+ int max_bp_dist;
// dimensions
int L, SIZE;
@@ -223,11 +224,13 @@
// cache
std::pair<RealT,RealT> cache_score_single[C_MAX_SINGLE_LENGTH+1][C_MAX_SINGLE_LENGTH+1];
+#if ( PARAMS_HELIX_LENGTH || PARAMS_ISOLATED_BASE_PAIR ) && FAST_HELIX_LENGTHS
std::vector<std::pair<RealT,RealT> > cache_score_helix_sums;
+#endif
void FillScores(typename std::vector<std::pair<RealT, RealT> >::iterator begin, typename std::vector<std::pair<RealT, RealT> >::iterator end, RealT value);
void FillCounts(typename std::vector<std::pair<RealT, RealT> >::iterator begin, typename std::vector<std::pair<RealT, RealT> >::iterator end, RealT value);
- int ComputeRowOffset(int i, int N) const;
+ int ComputeRowOffset(int i, int N, int w) const;
bool IsComplementary(int i, int j) const;
RealT ScoreJunctionA(int i, int j) const;
@@ -262,7 +265,7 @@
public:
// constructor and destructor
- InferenceEngine(bool allow_noncomplementary);
+ InferenceEngine(bool allow_noncomplementary, int max_bp_dist=0);
~InferenceEngine();
// register params with the parameter manager
@@ -293,7 +296,10 @@
std::vector<RealT> ComputeFeatureCountExpectations();
void ComputePosterior();
std::vector<int> PredictPairingsPosterior(const RealT gamma) const;
+ std::vector<int> PredictPairingsStochasticTraceback() const;
RealT *GetPosterior(const RealT posterior_cutoff) const;
+ RealT *GetPosterior(const RealT posterior_cutoff, std::vector<RealT>& p) const;
+
};
#include "InferenceEngine.ipp"
diff -urN contrafold_v2_02.orig/src/InferenceEngine.ipp contrafold/src/InferenceEngine.ipp
--- contrafold_v2_02.orig/src/InferenceEngine.ipp 2008-08-14 09:08:31.000000000 +0900
+++ contrafold/src/InferenceEngine.ipp 2009-08-20 22:12:03.614594433 +0900
@@ -6,6 +6,11 @@
// Wrapper macros for certain model features.
//////////////////////////////////////////////////////////////////////
+#include <list>
+#include <utility>
+#include <cassert>
+#include <cstdlib>
+
// score for leaving s[i] unpaired
#if defined(HAMMING_LOSS)
@@ -166,13 +171,26 @@
//////////////////////////////////////////////////////////////////////
template<class RealT>
-int InferenceEngine<RealT>::ComputeRowOffset(int i, int N) const
+int InferenceEngine<RealT>::ComputeRowOffset(int i, int N, int w /*=0*/) const
{
Assert(i >= 0 && i <= N, "Index out-of-bounds.");
-
+#define USE_EFFICIENT_WINDOW
+#ifdef USE_EFFICIENT_WINDOW
+ if (w==0)
+ {
+ // equivalent to:
+ // return N*(N+1)/2 - (N-i)*(N-i+1)/2 - i;
+ return i*(N+N-i-1)/2;
+ }
+ else
+ {
+ return i*w - i;
+ }
+#else
// equivalent to:
// return N*(N+1)/2 - (N-i)*(N-i+1)/2 - i;
return i*(N+N-i-1)/2;
+#endif
}
//////////////////////////////////////////////////////////////////////
@@ -210,10 +228,11 @@
//////////////////////////////////////////////////////////////////////
template<class RealT>
-InferenceEngine<RealT>::InferenceEngine(bool allow_noncomplementary) :
+InferenceEngine<RealT>::InferenceEngine(bool allow_noncomplementary, int max_bp_dist) :
allow_noncomplementary(allow_noncomplementary),
cache_initialized(false),
parameter_manager(NULL),
+ max_bp_dist(max_bp_dist),
L(0),
SIZE(0)
#if PROFILE
@@ -795,7 +814,14 @@
// compute dimensions
L = sstruct.GetLength();
+#ifdef USE_EFFICIENT_WINDOW
+ if (max_bp_dist==0)
+ SIZE = (L+1)*(L+2) / 2;
+ else
+ SIZE = (L+1)*max_bp_dist;
+#else
SIZE = (L+1)*(L+2) / 2;
+#endif
#if PROFILE
N = sstruct.GetNumSequences();
SIZE2 = (L+1)*(L+1);
@@ -864,7 +890,7 @@
#endif
-#if FAST_HELIX_LENGTHS
+#if ( PARAMS_HELIX_LENGTH || PARAMS_ISOLATED_BASE_PAIR ) && FAST_HELIX_LENGTHS
cache_score_helix_sums.clear(); cache_score_helix_sums.resize((2*L+1)*L);
#endif
@@ -895,7 +921,7 @@
// set the loss for each unpaired position to zero
for (int i = 0; i <= L; i++)
{
- offset[i] = ComputeRowOffset(i,L+1);
+ offset[i] = ComputeRowOffset(i,L+1,max_bp_dist);
allow_unpaired_position[i] = 1;
loss_unpaired_position[i] = RealT(0);
}
@@ -924,7 +950,8 @@
// for each pair of non-complementary letters in the sequence, disallow the pairing
for (int i = 1; i <= L; i++)
{
- for (int j = i+1; j <= L; j++)
+ int l = max_bp_dist==0 ? L : std::min(L,i+max_bp_dist);
+ for (int j = i+1; j <= l; j++)
{
if (!IsComplementary(i,j))
allow_paired[offset[i]+j] = 0;
@@ -1150,12 +1177,13 @@
#endif
-#if FAST_HELIX_LENGTHS
+#if ( PARAMS_HELIX_LENGTH || PARAMS_ISOLATED_BASE_PAIR ) && FAST_HELIX_LENGTHS
// precompute helix partial sums
FillScores(cache_score_helix_sums.begin(), cache_score_helix_sums.end(), RealT(0));
for (int i = L; i >= 1; i--)
{
- for (int j = i+3; j <= L; j++)
+ int l = max_bp_dist==0 ? L : std::min(L,i+max_bp_dist);
+ for (int j = i+3; j <= l; j++)
{
cache_score_helix_sums[(i+j)*L+j-i].first = cache_score_helix_sums[(i+j)*L+j-i-2].first;
if (allow_paired[offset[i+1]+j-1])
@@ -1291,7 +1319,7 @@
for (int l2 = 0; l2 <= C_MAX_SINGLE_LENGTH; l2++)
cache_score_single[l1][l2].second = RealT(0);
-#if FAST_HELIX_LENGTHS
+#if ( PARAMS_HELIX_LENGTH || PARAMS_ISOLATED_BASE_PAIR ) && FAST_HELIX_LENGTHS
FillCounts(cache_score_helix_sums.begin(), cache_score_helix_sums.end(), RealT(0));
#endif
@@ -1356,14 +1384,15 @@
template<class RealT>
void InferenceEngine<RealT>::FinalizeCounts()
{
-#if FAST_HELIX_LENGTHS
+#if ( PARAMS_HELIX_LENGTH || PARAMS_ISOLATED_BASE_PAIR ) && FAST_HELIX_LENGTHS
// reverse helix partial sums
std::vector<std::pair<RealT,RealT> > reverse_sums(cache_score_helix_sums);
for (int i = 1; i <= L; i++)
{
- for (int j = L; j >= i+3; j--)
+ int l = max_bp_dist==0 ? L : std::min(L,i+max_bp_dist);
+ for (int j = l; j >= i+3; j--)
{
// the "if" conditions here can be omitted
@@ -1682,7 +1711,8 @@
{
loss_unpaired[offset[i]+i] = RealT(0);
loss_paired[offset[i]+i] = RealT(NEG_INF);
- for (int j = i+1; j <= L; j++)
+ int l = max_bp_dist==0 ? L : std::min(L,i+max_bp_dist);
+ for (int j = i+1; j <= l; j++)
{
loss_unpaired[offset[i]+j] =
loss_unpaired[offset[i]+j-1] +
@@ -1720,7 +1750,8 @@
{
allow_unpaired[offset[i]+i] = 1;
allow_paired[offset[i]+i] = 0;
- for (int j = i+1; j <= L; j++)
+ int l = max_bp_dist==0 ? L : std::min(L,i+max_bp_dist);
+ for (int j = i+1; j <= l; j++)
{
allow_unpaired[offset[i]+j] =
allow_unpaired[offset[i]+j-1] &&
@@ -2042,7 +2073,7 @@
Assert(0 <= i && i + 2 * m <= j && j <= L, "Helix boundaries invalid.");
Assert(2 <= m && m <= D_MAX_HELIX_LENGTH, "Helix length invalid.");
-#if FAST_HELIX_LENGTHS
+#if ( PARAMS_HELIX_LENGTH || PARAMS_ISOLATED_BASE_PAIR ) && FAST_HELIX_LENGTHS
return
cache_score_helix_sums[(i+j+1)*L+j-i-1].first - cache_score_helix_sums[(i+j+1)*L+j-i-m-m+1].first
@@ -2073,7 +2104,7 @@
Assert(0 <= i && i + 2 * m <= j && j <= L, "Helix boundaries invalid.");
Assert(2 <= m && m <= D_MAX_HELIX_LENGTH, "Helix length invalid.");
-#if FAST_HELIX_LENGTHS
+#if ( PARAMS_HELIX_LENGTH || PARAMS_ISOLATED_BASE_PAIR ) && FAST_HELIX_LENGTHS
cache_score_helix_sums[(i+j+1)*L+j-i-1].second += value;
cache_score_helix_sums[(i+j+1)*L+j-i-m-m+1].second -= value;
@@ -2390,7 +2421,8 @@
candidates.clear();
#endif
- for (int j = i; j <= L; j++)
+ int L2 = max_bp_dist==0 ? L : std::min(L,i+max_bp_dist);
+ for (int j = i; j <= L2; j++)
{
// FM2[i,j] = MAX (i<k<j : FM1[i,k] + FM[k,j])
@@ -2403,34 +2435,41 @@
UPDATE_MAX(FM2v, FM2t, FM1v[offset[i]+k] + FMv[offset[k]+j], k);
#else
+ if (max_bp_dist==0)
+ {
#if !CANDIDATE_LIST
- if (i+2 <= j)
- {
- RealT *p1 = &(FM1v[offset[i]+i+1]);
- RealT *p2 = &(FMv[offset[i+1]+j]);
- for (register int k = i+1; k < j; k++)
+ if (i+2 <= j)
{
- UPDATE_MAX(FM2v, FM2t, (*p1) + (*p2), k);
- ++p1;
- p2 += L-k;
+ RealT *p1 = &(FM1v[offset[i]+i+1]);
+ RealT *p2 = &(FMv[offset[i+1]+j]);
+ for (register int k = i+1; k < j; k++)
+ {
+ UPDATE_MAX(FM2v, FM2t, (*p1) + (*p2), k);
+ ++p1;
+ p2 += L-k;
+ }
}
- }
#else
- for (register size_t kp = 0; kp < candidates.size(); kp++)
- {
- register const int k = candidates[kp];
- UPDATE_MAX(FM2v, FM2t, FM1v[offset[i]+k] + FMv[offset[k]+j], k);
- }
+ for (register size_t kp = 0; kp < candidates.size(); kp++)
+ {
+ register const int k = candidates[kp];
+ UPDATE_MAX(FM2v, FM2t, FM1v[offset[i]+k] + FMv[offset[k]+j], k);
+ }
- candidates_seen += (long long int) candidates.size();
- candidates_possible += (long long int) std::max(j-i-1,0);
+ candidates_seen += (long long int) candidates.size();
+ candidates_possible += (long long int) std::max(j-i-1,0);
#endif
-
+ }
+ else
+ {
+ for (int k = i+1; k < j; k++)
+ UPDATE_MAX(FM2v, FM2t, FM1v[offset[i]+k] + FMv[offset[k]+j], k);
+ }
#endif
#if PARAMS_HELIX_LENGTH || PARAMS_ISOLATED_BASE_PAIR
@@ -2607,7 +2646,7 @@
//
// Multi-branch loops are scored as [a + b * (# unpaired) + c * (# branches)]
- if (0 < i && j < L && allow_paired[offset[i]+j+1])
+ if (0 < i && j < L2 && allow_paired[offset[i]+j+1])
{
RealT best_v = RealT(NEG_INF);
@@ -2694,7 +2733,7 @@
//
// (assuming 0 < i < i+2 <= j < L)
- if (0 < i && i+2 <= j && j < L)
+ if (0 < i && i+2 <= j && j < L2)
{
RealT best_v = RealT(NEG_INF);
int best_t = -1;
@@ -2749,7 +2788,7 @@
//
// (assuming 0 < i < i+2 <= j < L)
- if (0 < i && i+2 <= j && j < L)
+ if (0 < i && i+2 <= j && j < L2)
{
RealT best_v = RealT(NEG_INF);
int best_t = -1;
@@ -2801,7 +2840,8 @@
// compute MAX (0<=k<j : F5[k] + FC[k+1,j-1] + ScoreExternalPaired() + ScoreBP(k+1,j) + ScoreJunctionA(j,k))
- for (int k = 0; k < j; k++)
+ int l = max_bp_dist==0 ? 0 : std::max(0,j-max_bp_dist);
+ for (int k = l; k < j; k++)
{
if (allow_paired[offset[k+1]+j])
{
@@ -2952,7 +2992,7 @@
solution[j] = i+1;
traceback_queue.push(make_triple(&FCt[0], i+1, j-1));
}
- break;
+ break;
case TB_FM1_UNPAIRED:
{
traceback_queue.push(make_triple(&FM1t[0], i+1, j));
@@ -3199,7 +3239,8 @@
for (int i = L; i >= 0; i--)
{
- for (int j = i; j <= L; j++)
+ int L2 = max_bp_dist==0 ? L : std::min(L,i+max_bp_dist);
+ for (int j = i; j <= L2; j++)
{
// FM2[i,j] = SUM (i<k<j : FM1[i,k] + FM[k,j])
@@ -3212,19 +3253,25 @@
Fast_LogPlusEquals(FM2i, FM1i[offset[i]+k] + FMi[offset[k]+j]);
#else
-
- if (i+2 <= j)
+ if (max_bp_dist==0)
{
- const RealT *p1 = &(FM1i[offset[i]+i+1]);
- const RealT *p2 = &(FMi[offset[i+1]+j]);
- for (register int k = i+1; k < j; k++)
+ if (i+2 <= j)
{
- Fast_LogPlusEquals(FM2i, (*p1) + (*p2));
- ++p1;
- p2 += L-k;
+ const RealT *p1 = &(FM1i[offset[i]+i+1]);
+ const RealT *p2 = &(FMi[offset[i+1]+j]);
+ for (register int k = i+1; k < j; k++)
+ {
+ Fast_LogPlusEquals(FM2i, (*p1) + (*p2));
+ ++p1;
+ p2 += L-k;
+ }
}
}
-
+ else
+ {
+ for (int k = i+1; k < j; k++)
+ Fast_LogPlusEquals(FM2i, FM1i[offset[i]+k] + FMi[offset[k]+j]);
+ }
#endif
#if PARAMS_HELIX_LENGTH || PARAMS_ISOLATED_BASE_PAIR
@@ -3381,7 +3428,7 @@
//
// Multi-branch loops are scored as [a + b * (# unpaired) + c * (# branches)]
- if (0 < i && j < L && allow_paired[offset[i]+j+1])
+ if (0 < i && j < L2 && allow_paired[offset[i]+j+1])
{
RealT sum_i = RealT(NEG_INF);
@@ -3455,7 +3502,7 @@
//
// (assuming 0 < i < i+2 <= j < L)
- if (0 < i && i+2 <= j && j < L)
+ if (0 < i && i+2 <= j && j < L2)
{
RealT sum_i = RealT(NEG_INF);
@@ -3483,7 +3530,7 @@
//
// (assuming 0 < i < i+2 <= j < L)
- if (0 < i && i+2 <= j && j < L)
+ if (0 < i && i+2 <= j && j < L2)
{
RealT sum_i = RealT(NEG_INF);
@@ -3525,7 +3572,8 @@
// compute SUM (0<=k<j : F5[k] + FC[k+1,j-1] + ScoreExternalPaired() + ScoreBP(k+1,j) + ScoreJunctionA(j,k))
- for (int k = 0; k < j; k++)
+ int l = max_bp_dist==0 ? 0 : std::max(0,j-max_bp_dist);
+ for (int k = l; k < j; k++)
if (allow_paired[offset[k+1]+j])
Fast_LogPlusEquals(sum_i, F5i[k] + FCi[offset[k+1]+j-1] + ScoreExternalPaired() + ScoreBasePair(k+1,j) + ScoreJunctionA(j,k));
@@ -3582,7 +3630,8 @@
// compute SUM (0<=k<j : F5[k] + FC[k+1,j-1] + ScoreExternalPaired() + ScoreBP(k+1,j) + ScoreJunctionA(j,k))
{
- for (int k = 0; k < j; k++)
+ int l = max_bp_dist==0 ? 0 : std::max(0,j-max_bp_dist);
+ for (int k = l; k < j; k++)
{
if (allow_paired[offset[k+1]+j])
{
@@ -3596,7 +3645,8 @@
for (int i = 0; i <= L; i++)
{
- for (int j = L; j >= i; j--)
+ int L2 = max_bp_dist==0 ? L : std::min(L,i+max_bp_dist);
+ for (int j = L2; j >= i; j--)
{
RealT FM2o = RealT(NEG_INF);
@@ -3610,7 +3660,7 @@
//
// (assuming 0 < i < i+2 <= j < L)
- if (0 < i && i+2 <= j && j < L)
+ if (0 < i && i+2 <= j && j < L2)
{
// compute SUM (i<k<j : FM1[i,k] + FM[k,j])
@@ -3636,7 +3686,7 @@
//
// (assuming 0 < i < i+2 <= j < L)
- if (0 < i && i+2 <= j && j < L)
+ if (0 < i && i+2 <= j && j < L2)
{
// compute FC[i+1,j-1] + ScoreJunctionA(j,i) + c + ScoreBP(i+1,j)
@@ -3790,7 +3840,7 @@
//
// Multi-branch loops are scored as [a + b * (# unpaired) + c * (# branches)]
- if (0 < i && j < L && allow_paired[offset[i]+j+1])
+ if (0 < i && j < L2 && allow_paired[offset[i]+j+1])
{
// compute ScoreHairpin(i,j) -- do nothing
@@ -3857,23 +3907,33 @@
}
#else
- if (i+2 <= j)
+ if (max_bp_dist==0)
{
- RealT *p1i = &(FM1i[offset[i]+i+1]);
- RealT *p2i = &(FMi[offset[i+1]+j]);
- RealT *p1o = &(FM1o[offset[i]+i+1]);
- RealT *p2o = &(FMo[offset[i+1]+j]);
- for (register int k = i+1; k < j; k++)
+ if (i+2 <= j)
{
- Fast_LogPlusEquals(*p1o, FM2o + *p2i);
- Fast_LogPlusEquals(*p2o, FM2o + *p1i);
- ++p1i;
- ++p1o;
- p2i += L-k;
- p2o += L-k;
+ RealT *p1i = &(FM1i[offset[i]+i+1]);
+ RealT *p2i = &(FMi[offset[i+1]+j]);
+ RealT *p1o = &(FM1o[offset[i]+i+1]);
+ RealT *p2o = &(FMo[offset[i+1]+j]);
+ for (register int k = i+1; k < j; k++)
+ {
+ Fast_LogPlusEquals(*p1o, FM2o + *p2i);
+ Fast_LogPlusEquals(*p2o, FM2o + *p1i);
+ ++p1i;
+ ++p1o;
+ p2i += L-k;
+ p2o += L-k;
+ }
+ }
+ }
+ else
+ {
+ for (int k = i+1; k < j; k++)
+ {
+ Fast_LogPlusEquals(FM1o[offset[i]+k], FM2o + FMi[offset[k]+j]);
+ Fast_LogPlusEquals(FMo[offset[k]+j], FM2o + FM1i[offset[i]+k]);
}
}
-
#endif
}
}
@@ -3920,7 +3980,8 @@
for (int i = L; i >= 0; i--)
{
- for (int j = i; j <= L; j++)
+ int L2 = max_bp_dist==0 ? L : std::min(L,i+max_bp_dist);
+ for (int j = i; j <= L2; j++)
{
// FM2[i,j] = SUM (i<k<j : FM1[i,k] + FM[k,j])
@@ -3933,19 +3994,25 @@
Fast_LogPlusEquals(FM2i, FM1i[offset[i]+k] + FMi[offset[k]+j]);
#else
-
- if (i+2 <= j)
+ if (max_bp_dist==0)
{
- const RealT *p1 = &(FM1i[offset[i]+i+1]);
- const RealT *p2 = &(FMi[offset[i+1]+j]);
- for (register int k = i+1; k < j; k++)
+ if (i+2 <= j)
{
- Fast_LogPlusEquals(FM2i, (*p1) + (*p2));
- ++p1;
- p2 += L-k;
+ const RealT *p1 = &(FM1i[offset[i]+i+1]);
+ const RealT *p2 = &(FMi[offset[i+1]+j]);
+ for (register int k = i+1; k < j; k++)
+ {
+ Fast_LogPlusEquals(FM2i, (*p1) + (*p2));
+ ++p1;
+ p2 += L-k;
+ }
}
}
-
+ else
+ {
+ for (int k = i+1; k < j; k++)
+ Fast_LogPlusEquals(FM2i, FM1i[offset[i]+k] + FMi[offset[k]+j]);
+ }
#endif
#if PARAMS_HELIX_LENGTH || PARAMS_ISOLATED_BASE_PAIR
@@ -4104,7 +4171,7 @@
//
// Multi-branch loops are scored as [a + b * (# unpaired) + c * (# branches)]
- if (0 < i && j < L && allow_paired[offset[i]+j+1])
+ if (0 < i && j < L2 && allow_paired[offset[i]+j+1])
{
RealT outside = FCo[offset[i]+j] - Z;
@@ -4198,7 +4265,7 @@
//
// (assuming 0 < i < i+2 <= j < L)
- if (0 < i && i+2 <= j && j < L)
+ if (0 < i && i+2 <= j && j < L2)
{
// compute FC[i+1,j-1] + ScoreJunctionA(j,i) + c + ScoreBP(i+1,j)
@@ -4229,7 +4296,7 @@
//
// (assuming 0 < i < i+2 <= j < L)
- if (0 < i && i+2 <= j && j < L)
+ if (0 < i && i+2 <= j && j < L2)
{
// compute SUM (i<k<j : FM1[i,k] + FM[k,j]) -- do nothing
@@ -4262,7 +4329,8 @@
// compute SUM (0<=k<j : F5[k] + FC[k+1,j-1] + ScoreExternalPaired() + ScoreBP(k+1,j) + ScoreJunctionA(j,k))
- for (int k = 0; k < j; k++)
+ int l = max_bp_dist==0 ? 0 : std::max(0,j-max_bp_dist);
+ for (int k = l; k < j; k++)
{
if (allow_paired[offset[k+1]+j])
{
@@ -4302,9 +4370,11 @@
for (int i = L; i >= 0; i--)
{
- for (int j = i; j <= L; j++)
+ int L2 = max_bp_dist==0 ? L : std::min(L,i+max_bp_dist);
+ for (int j = i; j <= L2; j++)
{
-
+#if 0 // FM2 is not required
+
// FM2[i,j] = SUM (i<k<j : FM1[i,k] + FM[k,j])
RealT FM2i = RealT(NEG_INF);
@@ -4329,6 +4399,7 @@
}
#endif
+#endif
#if PARAMS_HELIX_LENGTH || PARAMS_ISOLATED_BASE_PAIR
@@ -4476,16 +4547,15 @@
//
// Multi-branch loops are scored as [a + b * (# unpaired) + c * (# branches)]
- if (0 < i && j < L && allow_paired[offset[i]+j+1])
+ if (0 < i && j < L2 && allow_paired[offset[i]+j+1])
{
-
RealT outside = FCo[offset[i]+j] - Z;
-
+#if 0
// compute ScoreHairpin(i,j)
-
if (allow_unpaired[offset[i]+j] && j-i >= C_MIN_HAIRPIN_LENGTH)
CountHairpin(i,j,Fast_Exp(outside + ScoreHairpin(i,j)));
-
+#endif
+
// compute SUM (i<=p<p+2<=q<=j : ScoreSingle(i,j,p,q) + FC[p+1,q-1])
#if !FAST_SINGLE_BRANCH_LOOPS
@@ -4551,7 +4621,6 @@
// FM1[i+1,j] + b if i+2<=j]
//
// (assuming 0 < i < i+2 <= j < L)
-
if (0 < i && i+2 <= j && j < L)
{
@@ -4581,7 +4650,7 @@
// Compute FM1[i,j] -- do nothing
}
}
-
+
for (int j = 1; j <= L; j++)
{
@@ -4597,7 +4666,8 @@
// compute SUM (0<=k<j : F5[k] + FC[k+1,j-1] + ScoreExternalPaired() + ScoreBP(k+1,j) + ScoreJunctionA(j,k))
- for (int k = 0; k < j; k++)
+ int l = max_bp_dist==0 ? 0 : std::max(0,j-max_bp_dist);
+ for (int k = l; k < j; k++)
{
if (allow_paired[offset[k+1]+j])
posterior[offset[k+1]+j] += Fast_Exp(outside + F5i[k] + FCi[offset[k+1]+j-1] + ScoreExternalPaired() + ScoreBasePair(k+1,j) + ScoreJunctionA(j,k));
@@ -4606,7 +4676,8 @@
for (int i = 1; i <= L; i++)
{
- for (int j = i+1; j <= L; j++)
+ int l = max_bp_dist==0 ? L : std::min(L,i+max_bp_dist);
+ for (int j = i+1; j <= l; j++)
{
posterior[offset[i]+j] = Clip(posterior[offset[i]+j], RealT(0), RealT(1));
}
@@ -4627,9 +4698,9 @@
#if SHOW_TIMINGS
double starting_time = GetSystemTime();
#endif
- RealT* unpaired_posterior = new RealT[L+1];
- RealT* score = new RealT[SIZE];
- int* traceback = new int[SIZE];
+ std::vector<RealT> unpaired_posterior(L+1);
+ std::vector<RealT> score(SIZE);
+ std::vector<int> traceback(SIZE);
// compute the scores for unpaired nucleotides
@@ -4644,8 +4715,8 @@
// initialize matrices
- std::fill(score, score+SIZE, RealT(-1.0));
- std::fill(traceback, traceback+SIZE, -1);
+ std::fill(score.begin(), score.end(), RealT(-1.0));
+ std::fill(traceback.begin(), traceback.end(), -1);
// dynamic programming
@@ -4677,16 +4748,22 @@
UPDATE_MAX(this_score, this_traceback, score[offset[i]+k] + score[offset[k]+j], k+4);
#else
-
- RealT *p1 = &(score[offset[i]+i+1]);
- RealT *p2 = &(score[offset[i+1]+j]);
- for (register int k = i+1; k < j; k++)
+ if (max_bp_dist==0)
{
- UPDATE_MAX(this_score, this_traceback, (*p1) + (*p2), k+4);
- ++p1;
- p2 += L-k;
+ RealT *p1 = &(score[offset[i]+i+1]);
+ RealT *p2 = &(score[offset[i+1]+j]);
+ for (register int k = i+1; k < j; k++)
+ {
+ UPDATE_MAX(this_score, this_traceback, (*p1) + (*p2), k+4);
+ ++p1;
+ p2 += L-k;
+ }
+ }
+ else
+ {
+ for (int k = i+1; k < j; k++)
+ UPDATE_MAX(this_score, this_traceback, score[offset[i]+k] + score[offset[k]+j], k+4);
}
-
#endif
}
}
@@ -4743,6 +4820,325 @@
return solution;
}
+double rand01()
+{
+ return rand()/(RAND_MAX+1.0);
+}
+
+template < class T, class RealT >
+class Roulette
+{
+public:
+ Roulette()
+ : t_(), sum_(0)
+ { }
+
+ void add(T t, RealT v)
+ {
+ t_.push_back(std::make_pair(t, v));
+ sum_ += v;
+ }
+
+ T choose() const
+ {
+ RealT r = rand01() * sum_;
+ RealT s = 0.0;
+ typename std::list< std::pair<T,RealT> >::const_iterator x;
+ for (x=t_.begin(); x!=t_.end(); ++x)
+ {
+ s += x->second;
+ if (r<s) return x->first;
+ }
+ return t_.back().first;
+ }
+
+private:
+ std::list<std::pair<T,RealT> > t_;
+ RealT sum_;
+};
+
+
+// stochastic traceback algorithm
+template<class RealT>
+std::vector<int> InferenceEngine<RealT>::PredictPairingsStochasticTraceback() const
+{
+ enum { ST_FC, ST_F5, ST_FM, ST_FM1, ST_FE, ST_FN };
+
+ std::vector<int> solution(L+1,SStruct::UNPAIRED);
+ solution[0] = SStruct::UNKNOWN;
+
+ std::queue<triple<int,int,int> > traceback_queue;
+ traceback_queue.push(make_triple(int(ST_F5), 0, L));
+
+ while (!traceback_queue.empty())
+ {
+ triple<int,int,int> t = traceback_queue.front();
+ traceback_queue.pop();
+ const int i = t.second;
+ const int j = t.third;
+ int L2 = max_bp_dist==0 ? L : std::min(L,i+max_bp_dist);
+ const RealT Z = ComputeLogPartitionCoefficient();
+
+ switch (t.first)
+ {
+#if PARAMS_HELIX_LENGTH || PARAMS_ISOLATED_BASE_PAIR
+ case ST_FC:
+ break;
+ case ST_FE:
+ break;
+ case ST_FN:
+ break;
+#else
+ case ST_FC:
+ {
+ if (0 < i && j < L2 && allow_paired[offset[i]+j+1]) // ???
+ {
+ Roulette<int,RealT> roulette;
+ RealT outside = FCo[offset[i]+j] - Z;
+
+ // compute ScoreHairpin(i,j)
+ if (allow_unpaired[offset[i]+j] && j-i >= C_MIN_HAIRPIN_LENGTH)
+ roulette.add(EncodeTraceback(TB_FC_HAIRPIN,0), Fast_Exp(outside + ScoreHairpin(i,j)));
+
+ // compute SUM (i<=p<p+2<=q<=j : ScoreSingle(i,j,p,q) + FC[p+1,q-1])
+#if 1 //!FAST_SINGLE_BRANCH_LOOPS
+ for (int p = i; p <= std::min(i+C_MAX_SINGLE_LENGTH,j); p++)
+ {
+ if (p > i && !allow_unpaired_position[p]) break;
+ int q_min = std::max(p+2,p-i+j-C_MAX_SINGLE_LENGTH);
+ for (int q = j; q >= q_min; q--)
+ {
+ if (q < j && !allow_unpaired_position[q+1]) break;
+ if (!allow_paired[offset[p+1]+q]) continue;
+
+ if (p == i && q == j)
+ {
+ roulette.add(EncodeTraceback(TB_FC_SINGLE,(p-i)*(C_MAX_SINGLE_LENGTH+1)+j-q),
+ Fast_Exp(outside + ScoreBasePair(i+1,j) + ScoreHelixStacking(i,j+1) +
+ FCi[offset[p+1]+q-1]));
+ }
+ else
+ {
+ roulette.add(EncodeTraceback(TB_FC_SINGLE,(p-i)*(C_MAX_SINGLE_LENGTH+1)+j-q),
+ Fast_Exp(outside + ScoreSingle(i,j,p,q) + FCi[offset[p+1]+q-1]));
+ }
+ }
+ }
+#else
+ {
+ RealT score_helix = (i+2 <= j ? outside + ScoreBasePair(i+1,j) + ScoreHelixStacking(i,j+1) : 0);
+ RealT score_other = outside + ScoreJunctionB(i,j);
+
+ for (int p = i; p <= std::min(i+C_MAX_SINGLE_LENGTH,j); p++)
+ {
+ if (p > i && !allow_unpaired_position[p]) break;
+ int q_min = std::max(p+2,p-i+j-C_MAX_SINGLE_LENGTH);
+ const RealT *FCptr = &(FCi[offset[p+1]-1]);
+ for (int q = j; q >= q_min; q--)
+ {
+ if (q < j && !allow_unpaired_position[q+1]) break;
+ if (!allow_paired[offset[p+1]+q]) continue;
+
+ if (p == i && q == j)
+ {
+ RealT value = Fast_Exp(score_helix + FCptr[q]);
+ cache_score_single[0][0].second += value;
+ roulette.add(EncodeTraceback(TB_FC_SINGLE,(p-i)*(C_MAX_SINGLE_LENGTH+1)+j-q), value);
+ }
+ else
+ {
+ RealT value = Fast_Exp(score_other + cache_score_single[p-i][j-q].first +
+ FCptr[q] + ScoreBasePair(p+1,q) +
+ ScoreJunctionB(q,p) + ScoreSingleNucleotides(i,j,p,q));
+ cache_score_single[p-i][j-q].second += value;
+ roulette.add(EncodeTraceback(TB_FC_SINGLE,(p-i)*(C_MAX_SINGLE_LENGTH+1)+j-q), value);
+ }
+ }
+ }
+ }
+#endif
+ // compute SUM (i<k<j : FM1[i,k] + FM[k,j] + ScoreJunctionA(i,j) + a + c)
+ for (int k=i+1; k < j; k++)
+ {
+ RealT FM2i = FM1i[offset[i]+k] + FMi[offset[k]+j];
+ RealT val = Fast_Exp(outside + FM2i + ScoreJunctionA(i,j) + ScoreMultiPaired() + ScoreMultiBase());
+ roulette.add(EncodeTraceback(TB_FC_BIFURCATION, k), val);
+ }
+
+ // choose
+ std::pair<int,int> traceback = DecodeTraceback(roulette.choose());
+ switch (traceback.first)
+ {
+ case TB_FC_HAIRPIN:
+ break;
+ case TB_FC_SINGLE:
+ {
+ const int p = i + traceback.second / (C_MAX_SINGLE_LENGTH+1);
+ const int q = j - traceback.second % (C_MAX_SINGLE_LENGTH+1);
+ solution[p+1] = q;
+ solution[q] = p+1;
+ traceback_queue.push(make_triple(int(ST_FC), p+1, q-1));
+ }
+ break;
+ case TB_FC_BIFURCATION:
+ {
+ const int k = traceback.second;
+ traceback_queue.push(make_triple(int(ST_FM1), i, k));
+ traceback_queue.push(make_triple(int(ST_FM), k, j));
+ }
+ break;
+ }
+ } else { assert(!"unreachable"); }
+ }
+ break;
+#endif
+
+ case ST_FM:
+ if (0 < i && i+2 <= j && j < L2) // ???
+ {
+ RealT outside = FMo[offset[i]+j] - Z;
+ Roulette<int,RealT> roulette;
+
+ // compute SUM (i<k<j : FM1[i,k] + FM[k,j])
+ for (int k=i+1; k < j; k++)
+ {
+ RealT FM2i = FM1i[offset[i]+k] + FMi[offset[k]+j];
+ roulette.add(EncodeTraceback(TB_FM_BIFURCATION, k), Fast_Exp(outside + FM2i));
+ }
+
+ // compute FM[i,j-1] + b
+ if (allow_unpaired_position[j])
+ {
+ roulette.add(EncodeTraceback(TB_FM_UNPAIRED,0),
+ Fast_Exp(outside + FMi[offset[i]+j-1] + ScoreMultiUnpaired(j)));
+ }
+
+ // compute FM1[i,j]
+ roulette.add(EncodeTraceback(TB_FM_FM1,0), Fast_Exp(outside + FM1i[offset[i]+j]));
+
+ // choose
+ std::pair<int,int> traceback = DecodeTraceback(roulette.choose());
+ switch (traceback.first)
+ {
+ case TB_FM_BIFURCATION:
+ {
+ const int k = traceback.second;
+ traceback_queue.push(make_triple(int(ST_FM1), i, k));
+ traceback_queue.push(make_triple(int(ST_FM), k, j));
+ }
+ break;
+ case TB_FM_UNPAIRED:
+ {
+ traceback_queue.push(make_triple(int(ST_FM), i, j-1));
+ }
+ break;
+ case TB_FM_FM1:
+ {
+ traceback_queue.push(make_triple(int(ST_FM1), i, j));
+ }
+ break;
+ }
+
+ } else { assert(!"unreachable"); }
+ break;
+
+ case ST_FM1:
+ if (0 < i && i+2 <= j && j < L2) // ???
+ {
+ Roulette<int,RealT> roulette;
+
+ // compute FC[i+1,j-1] + ScoreJunctionA(j,i) + c + ScoreBP(i+1,j)
+ if (allow_paired[offset[i+1]+j])
+ {
+ RealT value = Fast_Exp(FM1o[offset[i]+j] + FCi[offset[i+1]+j-1] + ScoreJunctionA(j,i) +
+ ScoreMultiPaired() + ScoreBasePair(i+1,j) - Z);
+ roulette.add(EncodeTraceback(TB_FM1_PAIRED, 0), value);
+ }
+
+ // compute FM1[i+1,j] + b
+ if (allow_unpaired_position[i+1])
+ {
+ roulette.add(EncodeTraceback(TB_FM1_UNPAIRED,0),
+ Fast_Exp(FM1o[offset[i]+j] + FM1i[offset[i+1]+j] + ScoreMultiUnpaired(i+1) - Z));
+ }
+
+ // choose
+ std::pair<int,int> traceback = DecodeTraceback(roulette.choose());
+ switch (traceback.first)
+ {
+ case TB_FM1_PAIRED:
+ {
+ solution[i+1] = j;
+ solution[j] = i+1;
+ traceback_queue.push(make_triple(int(ST_FC), i+1, j-1));
+ }
+ break;
+ case TB_FM1_UNPAIRED:
+ {
+ traceback_queue.push(make_triple(int(ST_FM1), i+1, j));
+ }
+ break;
+ }
+ } else { assert(!"unreachable"); }
+ break;