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macrostateCenter.gap
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714 lines (543 loc) · 22.9 KB
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import rna
import "Extensions/singlefold.hh" //necessary to redefine the meaning of the filter "basepair". In singlefold this filter directly calles the build-in "basepairing" filter, in alignmentfold it gets hard codes parameters and returns true or false with dependance to the number of gaps in the rows
import "Extensions/probabilities.hh"
input rna
type answer_macrostate_pfunc = extern
type answer_macrostate_mfe = extern
type mfeanswer_dbg = (int energy, Subsequence firstStem, Subsequence lastStem, string rep)
type mfeanswer_v2 = (int energy, Subsequence firstStem, Subsequence lastStem, Subsequence subword, string rep)
type shape_t = shape
type base_t = extern
type Rope = extern
signature sig_foldrna(alphabet,answer) {
answer sadd(Subsequence,answer);
answer cadd(answer,answer);
answer cadd_Pr(answer,answer);
answer cadd_Pr_Pr(answer,answer);
answer cadd_Pr_Pr_Pr(answer,answer);
answer ambd(answer,Subsequence,answer);
answer ambd_Pr(answer,Subsequence,answer);
answer nil(Subsequence);
answer edl(Subsequence,answer,Subsequence);
answer edr(Subsequence,answer,Subsequence);
answer edlr(Subsequence,answer,Subsequence);
answer drem(Subsequence,answer,Subsequence);
answer sr(Subsequence,answer,Subsequence);
answer hl(Subsequence,Subsequence,Subsequence);
answer hlTag(Subsequence,Subsequence,Subsequence);
answer bl(Subsequence, Subsequence, answer, Subsequence);
answer br(Subsequence, answer, Subsequence, Subsequence);
answer il(Subsequence, Subsequence, answer, Subsequence, Subsequence);
answer ml(Subsequence,answer,Subsequence);
answer mldr(Subsequence,answer,Subsequence,Subsequence);
answer mladr(Subsequence,answer,Subsequence,Subsequence);
answer mldlr(Subsequence,Subsequence,answer,Subsequence,Subsequence);
answer mladlr(Subsequence,Subsequence,answer,Subsequence,Subsequence);
answer mldladr(Subsequence,Subsequence,answer,Subsequence,Subsequence);
answer mladldr(Subsequence,Subsequence,answer,Subsequence,Subsequence);
answer mldl(Subsequence,Subsequence,answer,Subsequence);
answer mladl(Subsequence,Subsequence,answer,Subsequence);
answer addss(answer,Subsequence);
answer ssadd(Subsequence,answer);
answer trafo(answer);
answer incl(answer);
answer combine(answer,answer);
answer acomb(answer,Subsequence,answer);
choice [answer] h([answer]);
}
algebra alg_pfunc_macrostate implements sig_foldrna(alphabet = char, answer = answer_macrostate_pfunc) {
answer_macrostate_pfunc sadd(Subsequence lb,answer_macrostate_pfunc e) {
answer_macrostate_pfunc res = e;
res.pf.q1 = scale(1) * e.pf.q1 * mk_pf(sbase_energy());
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc cadd(answer_macrostate_pfunc le,answer_macrostate_pfunc re) {
answer_macrostate_pfunc res = le;
res.pf.q1 = le.pf.q1 * re.pf.q1;
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc cadd_Pr(answer_macrostate_pfunc le,answer_macrostate_pfunc re) {
answer_macrostate_pfunc res = le;
res.pf.q1 = le.pf.q1 * sum_elems(re.pf);
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc cadd_Pr_Pr(answer_macrostate_pfunc le,answer_macrostate_pfunc re) {
answer_macrostate_pfunc res = le;
res.pf = mk_tuple(le.firststem, le.pf.q1 * re.pf.q1);
return res;
}
answer_macrostate_pfunc cadd_Pr_Pr_Pr(answer_macrostate_pfunc le,answer_macrostate_pfunc re) {
answer_macrostate_pfunc res = le;
res.pf = mk_tuple(le.firststem, le.pf.q1 * sum_elems(re.pf));
return res;
}
answer_macrostate_pfunc ambd(answer_macrostate_pfunc le,Subsequence b,answer_macrostate_pfunc re) {
answer_macrostate_pfunc res = le;
res.pf.q1 = scale(1) * check_tuple(le.pf.q1, le.firststem, re.firststem, b, re.pf);
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc ambd_Pr(answer_macrostate_pfunc le,Subsequence b,answer_macrostate_pfunc re) {
answer_macrostate_pfunc res = le;
res.pf = mk_tuple(le.firststem, scale(1) * check_tuple(le.pf.q1, le.firststem, re.firststem, b, re.pf));
return res;
}
answer_macrostate_pfunc nil(Subsequence loc) {
answer_macrostate_pfunc res;
res.pf.q1 = 1.0;
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
res.firststem.i = seq_size(loc);
res.firststem.j = seq_size(loc);
res.firststem.seq = loc.seq;
return res;
}
answer_macrostate_pfunc edl(Subsequence lb,answer_macrostate_pfunc e, Subsequence rloc) {
answer_macrostate_pfunc res = e;
res.pf.q1 = scale(1) * e.pf.q1 * mk_pf(dl_energy(e.firststem, e.firststem) + termau_energy(e.firststem, e.firststem));
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc edr(Subsequence lloc, answer_macrostate_pfunc e,Subsequence rb) {
answer_macrostate_pfunc res = e;
res.pf.q1 = scale(1) * e.pf.q1 * mk_pf(dr_energy(e.firststem, e.firststem) + termau_energy(e.firststem, e.firststem));
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc edlr(Subsequence lb,answer_macrostate_pfunc e,Subsequence rb) {
answer_macrostate_pfunc res = e;
//this minimization is necessary since Turner2004 parameters introduced the ext_mismatch_energy table. It now might happen, that dangling from one side only is better than dangling from both sides.
int help = min(min(ext_mismatch_energy(e.firststem, e.firststem), dl_energy(e.firststem, e.firststem)), dr_energy(e.firststem, e.firststem));
res.pf.q1 = scale(2) * e.pf.q1 * mk_pf(help + termau_energy(e.firststem, e.firststem));
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc drem(Subsequence lloc, answer_macrostate_pfunc e, Subsequence rloc) {
answer_macrostate_pfunc res = e;
res.pf.q1 = e.pf.q1 * mk_pf(termau_energy(e.firststem, e.firststem));
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc sr(Subsequence lb,answer_macrostate_pfunc e,Subsequence rb) {
answer_macrostate_pfunc res = e;
res.firststem.i = lb.i;
res.firststem.j = rb.j;
res.pf.q1 = scale(2) * e.pf.q1 * mk_pf(sr_energy(res.firststem,res.firststem));
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc hl(Subsequence lb,Subsequence region,Subsequence rb) {
answer_macrostate_pfunc res;
res.firststem.seq = lb.seq;
res.firststem.i = lb.i;
res.firststem.j = rb.j;
res.pf.q1 = scale(region.j - region.i + 2) * mk_pf(hl_energy(region));
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc hlTag(Subsequence lb,Subsequence region,Subsequence rb) {
answer_macrostate_pfunc res;
res.firststem.seq = lb.seq;
res.firststem.i = lb.i;
res.firststem.j = rb.j;
res.pf.q1 = scale(region.j - region.i + 2) * mk_pf(hl_energy(region));
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc bl(Subsequence lb,Subsequence lregion,answer_macrostate_pfunc e,Subsequence rb) {
answer_macrostate_pfunc res = e;
res.firststem.i = lb.i;
res.firststem.j = rb.j;
res.pf.q1 = scale(lregion.j - lregion.i + 2) * e.pf.q1 * mk_pf(bl_energy(lregion,rb));
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc br(Subsequence lb,answer_macrostate_pfunc e,Subsequence rregion,Subsequence rb) {
answer_macrostate_pfunc res = e;
res.firststem.i = lb.i;
res.firststem.j = rb.j;
res.pf.q1 = scale(rregion.j - rregion.i + 2) * e.pf.q1 * mk_pf(br_energy(lb, rregion));
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc il(Subsequence lb,Subsequence lregion,answer_macrostate_pfunc e,Subsequence rregion,Subsequence rb) {
answer_macrostate_pfunc res = e;
res.firststem.i = lb.i;
res.firststem.j = rb.j;
res.pf.q1 = scale((lregion.j - lregion.i) + (rregion.j - rregion.i) + 2) * e.pf.q1 * mk_pf(il_energy(lregion, rregion));
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc ml(Subsequence lb,answer_macrostate_pfunc e,Subsequence rb) {
answer_macrostate_pfunc res = e;
res.firststem.i = lb.i;
res.firststem.j = rb.j;
res.pf.q1 = scale(2) * sum_elems(e.pf) * mk_pf(ml_energy() + ul_energy() + termau_energy(res.firststem,res.firststem));
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc mldr(Subsequence lb,answer_macrostate_pfunc e,Subsequence dr,Subsequence rb) {
answer_macrostate_pfunc res = e;
res.firststem.i = lb.i;
res.firststem.j = rb.j;
res.pf.q1 = scale(3) * sum_elems(e.pf) * mk_pf(ml_energy() + ul_energy() + dri_energy(res.firststem,res.firststem) + termau_energy(res.firststem,res.firststem));
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc mladr(Subsequence lb,answer_macrostate_pfunc e,Subsequence dr,Subsequence rb) {
answer_macrostate_pfunc res = e;
res.firststem.i = lb.i;
res.firststem.j = rb.j;
base_t rightdanglingBase = base_t(dr[dr.i]);
base_t rightmostBaselastStem = base_t(e.firststem[dr.i-1]);
float amdangle;
amdangle = (e.pf.q1 + e.pf.q3) * mk_pf(min(dr_dangle_dg( wc_comp(rightmostBaselastStem), rightmostBaselastStem, rightdanglingBase), dri_energy(res.firststem,res.firststem))) +
(e.pf.q2 + e.pf.q4) * mk_pf(min(dr_dangle_dg(wob_comp(rightmostBaselastStem), rightmostBaselastStem, rightdanglingBase), dri_energy(res.firststem,res.firststem)));
res.pf.q1 = scale(3) * amdangle * mk_pf(ml_energy() + ul_energy() + termau_energy(res.firststem,res.firststem));
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc mldlr(Subsequence lb,Subsequence dl,answer_macrostate_pfunc e,Subsequence dr,Subsequence rb) {
answer_macrostate_pfunc res = e;
res.firststem.i = lb.i;
res.firststem.j = rb.j;
//this minimization is necessary since Turner2004 parameters introduced the ml_mismatch_energy table. It now might happen, that dangling from one side only is better than dangling from both sides.
int help = min(min(ml_mismatch_energy(res.firststem,res.firststem), dli_energy(res.firststem,res.firststem)), dri_energy(res.firststem,res.firststem));
res.pf.q1 = scale(4) * sum_elems(e.pf) * mk_pf(ml_energy() + ul_energy() + help + termau_energy(res.firststem,res.firststem));
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc mladlr(Subsequence lb,Subsequence dl,answer_macrostate_pfunc e,Subsequence dr,Subsequence rb) {
answer_macrostate_pfunc res = e;
res.firststem.i = lb.i;
res.firststem.j = rb.j;
base_t leftdanglingBase = base_t(dl[dl.i]);
base_t rightdanglingBase = base_t(dr[dr.i]);
base_t leftmostBasefirstStem = base_t(e.firststem[dl.i+1]);
base_t rightmostBaselastStem = base_t(e.firststem[dr.i-1]);
float amdangle;
amdangle = e.pf.q1 * mk_pf(min(dl_dangle_dg(leftdanglingBase, leftmostBasefirstStem, wc_comp(leftmostBasefirstStem)), dli_energy(res.firststem,res.firststem)) + min(dr_dangle_dg( wc_comp(rightmostBaselastStem), rightmostBaselastStem, rightdanglingBase), dri_energy(res.firststem,res.firststem))) +
e.pf.q2 * mk_pf(min(dl_dangle_dg(leftdanglingBase, leftmostBasefirstStem, wc_comp(leftmostBasefirstStem)), dli_energy(res.firststem,res.firststem)) + min(dr_dangle_dg(wob_comp(rightmostBaselastStem), rightmostBaselastStem, rightdanglingBase), dri_energy(res.firststem,res.firststem))) +
e.pf.q3 * mk_pf(min(dl_dangle_dg(leftdanglingBase, leftmostBasefirstStem, wob_comp(leftmostBasefirstStem)), dli_energy(res.firststem,res.firststem)) + min(dr_dangle_dg( wc_comp(rightmostBaselastStem), rightmostBaselastStem, rightdanglingBase), dri_energy(res.firststem,res.firststem))) +
e.pf.q4 * mk_pf(min(dl_dangle_dg(leftdanglingBase, leftmostBasefirstStem, wob_comp(leftmostBasefirstStem)), dli_energy(res.firststem,res.firststem)) + min(dr_dangle_dg(wob_comp(rightmostBaselastStem), rightmostBaselastStem, rightdanglingBase), dri_energy(res.firststem,res.firststem)));
res.pf.q1 = scale(4) * amdangle * mk_pf(ml_energy() + ul_energy() + termau_energy(res.firststem,res.firststem));
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc mldladr(Subsequence lb,Subsequence dl,answer_macrostate_pfunc e,Subsequence dr,Subsequence rb) {
answer_macrostate_pfunc res = e;
res.firststem.i = lb.i;
res.firststem.j = rb.j;
base_t rightdanglingBase = base_t(dr[dr.i]);
base_t rightmostBaselastStem = base_t(e.firststem[dr.i-1]);
double amdangle;
amdangle = (e.pf.q1 * mk_pf(dli_energy(res.firststem,res.firststem)) + e.pf.q3) * mk_pf(min(dr_dangle_dg(wc_comp(rightmostBaselastStem), rightmostBaselastStem, rightdanglingBase), dri_energy(res.firststem,res.firststem))) +
(e.pf.q2 + e.pf.q4) * mk_pf(min(dr_dangle_dg(wob_comp(rightmostBaselastStem), rightmostBaselastStem, rightdanglingBase), dri_energy(res.firststem,res.firststem)));
res.pf.q1 = scale(4) * amdangle * mk_pf(ml_energy() + ul_energy() + termau_energy(res.firststem,res.firststem));
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc mladldr(Subsequence lb,Subsequence dl,answer_macrostate_pfunc e,Subsequence dr,Subsequence rb) {
answer_macrostate_pfunc res = e;
res.firststem.i = lb.i;
res.firststem.j = rb.j;
base_t leftdanglingBase = base_t(dl[dl.i]);
base_t leftmostBasefirstStem = base_t(e.firststem[dl.i+1]);
float amdangle;
amdangle = (e.pf.q1 + e.pf.q2) * mk_pf(min(dl_dangle_dg(leftdanglingBase, leftmostBasefirstStem, wc_comp(leftmostBasefirstStem)), dli_energy(res.firststem,res.firststem))) +
(e.pf.q3 + e.pf.q4 * mk_pf(dri_energy(res.firststem,res.firststem))) * mk_pf(min(dl_dangle_dg(leftdanglingBase, leftmostBasefirstStem, wob_comp(leftmostBasefirstStem)), dli_energy(res.firststem,res.firststem)));
res.pf.q1 = scale(4) * amdangle * mk_pf(ml_energy() + ul_energy() + termau_energy(res.firststem,res.firststem));
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc mldl(Subsequence lb,Subsequence dl,answer_macrostate_pfunc e,Subsequence rb) {
answer_macrostate_pfunc res = e;
res.firststem.i = lb.i;
res.firststem.j = rb.j;
res.pf.q1 = scale(3) * sum_elems(e.pf) * mk_pf(ml_energy() + ul_energy() + dli_energy(res.firststem,res.firststem) + termau_energy(res.firststem,res.firststem));
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc mladl(Subsequence lb,Subsequence dl,answer_macrostate_pfunc e,Subsequence rb) {
answer_macrostate_pfunc res = e;
res.firststem.i = lb.i;
res.firststem.j = rb.j;
base_t leftdanglingBase = base_t(dl[dl.i]);
base_t leftmostBasefirstStem = base_t(e.firststem[dl.i+1]);
float amdangle;
amdangle = (e.pf.q1 + e.pf.q2) * mk_pf(min(dl_dangle_dg(leftdanglingBase, leftmostBasefirstStem, wc_comp(leftmostBasefirstStem)), dli_energy(res.firststem,res.firststem))) +
(e.pf.q3 + e.pf.q4) * mk_pf(min(dl_dangle_dg(leftdanglingBase, leftmostBasefirstStem, wob_comp(leftmostBasefirstStem)), dli_energy(res.firststem,res.firststem)));
res.pf.q1 = scale(3) * amdangle * mk_pf(ml_energy() + ul_energy() + termau_energy(res.firststem,res.firststem));
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc addss(answer_macrostate_pfunc e,Subsequence rregion) {
answer_macrostate_pfunc res = e;
res.pf = mult_tup(scale(rregion.j - rregion.i) * mk_pf(ss_energy(rregion)), e.pf);
return res;
}
answer_macrostate_pfunc ssadd(Subsequence lregion,answer_macrostate_pfunc e) {
answer_macrostate_pfunc res = e;
Subsequence test;
test.seq = lregion.seq;
test.i = lregion.i;
test.j = lregion.j+1;
res.pf = mk_tuple(e.firststem, scale(lregion.j - lregion.i) * e.pf.q1 * mk_pf(ul_energy() + ss_energy(lregion)));
return res;
}
answer_macrostate_pfunc trafo(answer_macrostate_pfunc e) {
answer_macrostate_pfunc res = e;
res.pf.q1 = sum_elems(e.pf);
res.pf.q2 = 0.0;
res.pf.q3 = 0.0;
res.pf.q4 = 0.0;
return res;
}
answer_macrostate_pfunc incl(answer_macrostate_pfunc e) {
answer_macrostate_pfunc res = e;
res.pf = mk_tuple(e.firststem, e.pf.q1 * mk_pf(ul_energy()));
return res;
}
answer_macrostate_pfunc combine(answer_macrostate_pfunc le,answer_macrostate_pfunc re) {
answer_macrostate_pfunc res = le;
res.firststem = le.firststem;
res.pf.q1 = (le.pf.q1 + le.pf.q2) * (re.pf.q1 + re.pf.q3);
res.pf.q2 = (le.pf.q1 + le.pf.q2) * (re.pf.q2 + re.pf.q4);
res.pf.q3 = (le.pf.q3 + le.pf.q4) * (re.pf.q3 + re.pf.q1);
res.pf.q4 = (le.pf.q4 + le.pf.q3) * (re.pf.q4 + re.pf.q2);
return res;
}
answer_macrostate_pfunc acomb(answer_macrostate_pfunc le,Subsequence b,answer_macrostate_pfunc re) {
answer_macrostate_pfunc res = le;
res.firststem = le.firststem;
base_t baseLeftStem = base_t(le.firststem[b.i-1]);
base_t baseRightStem = base_t(re.firststem[b.i+1]);
base_t baseAmbigious = base_t(b[b.i]);
double wcDr = dr_dangle_dg( wc_comp(baseLeftStem), baseLeftStem, baseAmbigious);
double wobDr = dr_dangle_dg( wob_comp(baseLeftStem), baseLeftStem, baseAmbigious);
double wcDl = dl_dangle_dg(baseAmbigious, baseRightStem, wc_comp(baseRightStem));
double wobDl = dl_dangle_dg(baseAmbigious, baseRightStem, wob_comp(baseRightStem));
res.pf.q1 = le.pf.q1 * (re.pf.q1 * mk_pf(min( wcDr, wcDl)) + re.pf.q3 * mk_pf(min( wcDr,wobDl))) +
le.pf.q2 * (re.pf.q1 * mk_pf(min(wobDr, wcDl)) + re.pf.q3 * mk_pf(min(wobDr,wobDl)));
res.pf.q2 = le.pf.q2 * (re.pf.q2 * mk_pf(min(wobDr, wcDl)) + re.pf.q4 * mk_pf(min(wobDr,wobDl))) +
le.pf.q1 * (re.pf.q2 * mk_pf(min( wcDr, wcDl)) + re.pf.q4 * mk_pf(min( wcDr,wobDl)));
res.pf.q3 = le.pf.q3 * (re.pf.q3 * mk_pf(min( wcDr,wobDl)) + re.pf.q1 * mk_pf(min( wcDr, wcDl))) +
le.pf.q4 * (re.pf.q3 * mk_pf(min(wobDr,wobDl)) + re.pf.q1 * mk_pf(min(wobDr, wcDl)));
res.pf.q4 = le.pf.q4 * (re.pf.q4 * mk_pf(min(wobDr,wobDl)) + re.pf.q2 * mk_pf(min(wobDr, wcDl))) +
le.pf.q3 * (re.pf.q4 * mk_pf(min( wcDr,wobDl)) + re.pf.q2 * mk_pf(min( wcDr, wcDl)));
res.pf.q1 = res.pf.q1 * scale(1);
res.pf.q2 = res.pf.q2 * scale(1);
res.pf.q3 = res.pf.q3 * scale(1);
res.pf.q4 = res.pf.q4 * scale(1);
return res;
}
choice [answer_macrostate_pfunc] h([answer_macrostate_pfunc] i) {
return list(sum(i));
//~ return i;
}
}
algebra alg_pfunc_macrostate_filter_me extends alg_pfunc_macrostate {
choice [answer_macrostate_pfunc] h([answer_macrostate_pfunc] l)
{
return l;
}
}
algebra alg_pfunc_macrostate_id extends alg_pfunc_macrostate {
choice [answer_macrostate_pfunc] h([answer_macrostate_pfunc] l)
{
return l;
}
}
algebra alg_HairpinCenter implements sig_foldrna(alphabet = char, answer = string) {
string sadd(Subsequence lb,string e) {
return e;
}
string cadd(string le,string re) {
string res;
append(res, le);
append(res, re);
return res;
}
string cadd_Pr(string le,string re) {
string res;
append(res, le);
append(res, re);
return res;
}
string cadd_Pr_Pr(string le,string re) {
string res;
append(res, le);
append(res, re);
return res;
}
string cadd_Pr_Pr_Pr(string le,string re) {
string res;
append(res, le);
append(res, re);
return res;
}
string ambd(string le,Subsequence b,string re) {
string res;
append(res, le);
append(res, re);
return res;
}
string ambd_Pr(string le,Subsequence b,string re) {
string res;
append(res, le);
append(res, re);
return res;
}
string nil(Subsequence loc) {
string r;
return r;
}
string edl(Subsequence lb,string e, Subsequence loc) {
return e;
}
string edr(Subsequence loc, string e,Subsequence rb) {
return e;
}
string edlr(Subsequence lb,string e,Subsequence rb) {
return e;
}
string drem(Subsequence lloc, string e, Subsequence rloc) {
return e;
}
string sr(Subsequence lb,string e,Subsequence rb) {
return e;
}
string hl(Subsequence lb,Subsequence region,Subsequence rb) {
string res;
return res;
}
string hlTag(Subsequence lb,Subsequence region,Subsequence rb) {
string res;
int pos;
pos = (lb.i+rb.j+1)/2;
if ( pos*2 > lb.i+rb.j+1 ) pos = pos - 1;
append(res, pos);
if ( pos*2 != lb.i+rb.j+1 ) append(res, ".5", 2);
return res;
}
string bl(Subsequence lb,Subsequence lregion,string e,Subsequence rb) {
return e;
}
string br(Subsequence lb,string e,Subsequence rregion,Subsequence rb) {
return e;
}
string il(Subsequence lb,Subsequence lregion,string e,Subsequence rregion,Subsequence rb) {
return e;
}
string ml(Subsequence lb,string e,Subsequence rb) {
return e;
}
string mldr(Subsequence lb,string e,Subsequence dr,Subsequence rb) {
return e;
}
string mladr(Subsequence lb,string e,Subsequence dr,Subsequence rb) {
return e;
}
string mldlr(Subsequence lb,Subsequence dl,string e,Subsequence dr,Subsequence rb) {
return e;
}
string mladlr(Subsequence lb,Subsequence dl,string e,Subsequence dr,Subsequence rb) {
return e;
}
string mldladr(Subsequence lb,Subsequence dl,string e,Subsequence dr,Subsequence rb) {
return e;
}
string mladldr(Subsequence lb,Subsequence dl,string e,Subsequence dr,Subsequence rb) {
return e;
}
string mldl(Subsequence lb,Subsequence dl,string e,Subsequence rb) {
return e;
}
string mladl(Subsequence lb,Subsequence dl,string e,Subsequence rb) {
return e;
}
string addss(string e,Subsequence rb) {
return e;
}
string ssadd(Subsequence lb,string e) {
return e;
}
string trafo(string e) {
return e;
}
string incl(string e) {
return e;
}
string combine(string le,string re) {
string res;
append(res, le);
append(res, re);
return res;
}
string acomb(string le,Subsequence b,string re) {
string res;
append(res, le);
append(res, re);
return res;
}
choice [string] h([string] i) {
//~ return list(minimum(i));
return unique(i);
}
}
algebra alg_count auto count ;
algebra alg_enum auto enum ;
include "Grammars/gra_macrostate_centers.gap"
instance count = gra_macrostate_centers (alg_count);
instance enum = gra_macrostate_centers (alg_enum);
instance centerpfx = gra_macrostate_centers(alg_HairpinCenter * alg_pfunc_macrostate);