/dports/biology/infernal/infernal-1.1.3/hmmer/src/ |
H A D | generic_fwdback_rescaled.c | 218 + DMX(i,k-1) * TSC(p7P_DD,k-1); in p7_GForwardOdds() 234 + DMX(i,M-1) * TSC(p7P_DD,M-1); in p7_GForwardOdds() 364 p7P_TSC(gm, 1, p7P_DD) = 0.0f; in p7_profile_ConfigInOdds() 429 tp[p7P_DD] = hmm->t[k][p7H_DD]; in p7_profile_ConfigInOdds() 494 p7P_TSC(gm, 1, p7P_DD) = 0.0f; in p7_profile_ConfigInOdds_DDScaled() 529 tp[p7P_DD] = 1.0; in p7_profile_ConfigInOdds_DDScaled()
|
H A D | generic_viterbi.c | 111 DMX(i,k-1) + TSC(p7P_DD,k-1)); in p7_GViterbi() 126 DMX(i,M-1) + TSC(p7P_DD,M-1)); in p7_GViterbi() 255 DMX(i,k-1) + TSC(p7P_DD,k-1)); in p7_GViterbi_longtarget() 270 DMX(i,M-1) + TSC(p7P_DD,M-1)); in p7_GViterbi_longtarget()
|
H A D | generic_fwdback.c | 95 DMX(i,k-1) + TSC(p7P_DD,k-1)); in p7_GForward() 112 DMX(i,M-1) + TSC(p7P_DD,M-1)); in p7_GForward() 190 DMX(L, k+1) + TSC(p7P_DD,k)); in p7_GBackward() 228 p7_FLogsum( DMX(i, k+1) + TSC(p7P_DD,k), in p7_GBackward()
|
H A D | generic_optacc.c | 109 TSCDELTA(p7P_DD, k-1) * DMX(i,k-1)); in p7_GOptimalAccuracy() 119 TSCDELTA(p7P_DD, M-1) * DMX(i,M-1)); in p7_GOptimalAccuracy() 279 path[1] = TSCDELTA(p7P_DD, k-1) * DMX(i, k-1); in select_d()
|
H A D | p7_profile.c | 87 p7P_TSC(gm, 1, p7P_DD) = -eslINFINITY; in p7_profile_Create() 435 case p7T_D: tsc = p7P_TSC(gm, k1, p7P_DD); break; in p7_profile_GetT()
|
H A D | generic_fwdback_chk.c | 75 dc + *(tsc+p7P_DD)); /* D(i,k) * t_D(k)->D(k+1) */ in forward_row() 213 DMR(dpc,k) = p7_FLogsum( p7_FLogsum( DMR(dpc, k+1) + TSC(p7P_DD,k), in backward_row() 272 DMR(bck, k+1) + TSC(p7P_DD, k)); in p7_GBackwardCheckpointed()
|
H A D | generic_fwdback_banded.c | 94 dc = p7_FLogsum( sc + TSC(p7P_MD, k), dc + TSC(p7P_DD, k)); in p7_GForwardBanded()
|
H A D | generic_vtrace.c | 115 else if (esl_FCompare(DMX(i,k), DMX(i, k-1) + TSC(p7P_DD, k-1), tol) == eslOK) scur = p7T_D; in p7_GTrace()
|
H A D | generic_stotrace.c | 125 sc[1] = DMX(i, k-1) + TSC(p7P_DD, k-1); in p7_GStochasticTrace()
|
H A D | modelconfig.c | 134 tp[p7P_DD] = log(hmm->t[k][p7H_DD]); in p7_ProfileConfig()
|
H A D | hmmer.h | 227 p7P_DD = 5, enumerator
|
/dports/biology/hmmer/hmmer-3.3/src/ |
H A D | generic_fwdback_rescaled.c | 218 + DMX(i,k-1) * TSC(p7P_DD,k-1); in p7_GForwardOdds() 234 + DMX(i,M-1) * TSC(p7P_DD,M-1); in p7_GForwardOdds() 364 p7P_TSC(gm, 1, p7P_DD) = 0.0f; in p7_profile_ConfigInOdds() 429 tp[p7P_DD] = hmm->t[k][p7H_DD]; in p7_profile_ConfigInOdds() 494 p7P_TSC(gm, 1, p7P_DD) = 0.0f; in p7_profile_ConfigInOdds_DDScaled() 529 tp[p7P_DD] = 1.0; in p7_profile_ConfigInOdds_DDScaled()
|
H A D | generic_viterbi.c | 111 DMX(i,k-1) + TSC(p7P_DD,k-1)); in p7_GViterbi() 126 DMX(i,M-1) + TSC(p7P_DD,M-1)); in p7_GViterbi() 255 DMX(i,k-1) + TSC(p7P_DD,k-1)); in p7_GViterbi_longtarget() 270 DMX(i,M-1) + TSC(p7P_DD,M-1)); in p7_GViterbi_longtarget()
|
H A D | generic_fwdback.c | 95 DMX(i,k-1) + TSC(p7P_DD,k-1)); in p7_GForward() 112 DMX(i,M-1) + TSC(p7P_DD,M-1)); in p7_GForward() 190 DMX(L, k+1) + TSC(p7P_DD,k)); in p7_GBackward() 228 p7_FLogsum( DMX(i, k+1) + TSC(p7P_DD,k), in p7_GBackward()
|
H A D | generic_optacc.c | 109 TSCDELTA(p7P_DD, k-1) * DMX(i,k-1)); in p7_GOptimalAccuracy() 119 TSCDELTA(p7P_DD, M-1) * DMX(i,M-1)); in p7_GOptimalAccuracy() 279 path[1] = TSCDELTA(p7P_DD, k-1) * DMX(i, k-1); in select_d()
|
H A D | p7_profile.c | 87 p7P_TSC(gm, 1, p7P_DD) = -eslINFINITY; in p7_profile_Create() 435 case p7T_D: tsc = p7P_TSC(gm, k1, p7P_DD); break; in p7_profile_GetT()
|
H A D | generic_fwdback_chk.c | 75 dc + *(tsc+p7P_DD)); /* D(i,k) * t_D(k)->D(k+1) */ in forward_row() 213 DMR(dpc,k) = p7_FLogsum( p7_FLogsum( DMR(dpc, k+1) + TSC(p7P_DD,k), in backward_row() 272 DMR(bck, k+1) + TSC(p7P_DD, k)); in p7_GBackwardCheckpointed()
|
H A D | generic_fwdback_banded.c | 94 dc = p7_FLogsum( sc + TSC(p7P_MD, k), dc + TSC(p7P_DD, k)); in p7_GForwardBanded()
|
H A D | generic_vtrace.c | 115 else if (esl_FCompare(DMX(i,k), DMX(i, k-1) + TSC(p7P_DD, k-1), tol) == eslOK) scur = p7T_D; in p7_GTrace()
|
H A D | generic_stotrace.c | 125 sc[1] = DMX(i, k-1) + TSC(p7P_DD, k-1); in p7_GStochasticTrace()
|
H A D | modelconfig.c | 134 tp[p7P_DD] = log(hmm->t[k][p7H_DD]); in p7_ProfileConfig()
|
/dports/biology/infernal/infernal-1.1.3/hmmer/src/impl_sse/ |
H A D | p7_oprofile.c | 886 …for (z = 0; z < 8; z++) tmp.i[z] = ((k+ z*nq < M) ? wordify(om, p7P_TSC(gm, k+ z*nq, p7P_DD)) : -3… in vf_conversion() 914 ddtmp = (int) wordify(om, p7P_TSC(gm, k, p7P_DD)); in vf_conversion() 977 for (z = 0; z < 4; z++) tmp.x[z] = (k+z*nq < M) ? p7P_TSC(gm, k+z*nq, p7P_DD) : -eslINFINITY; in fb_conversion()
|
/dports/biology/infernal/infernal-1.1.3/hmmer/src/impl_vmx/ |
H A D | p7_oprofile.c | 807 …for (z = 0; z < 8; z++) tmp.i[z] = ((k+ z*nq < M) ? wordify(om, p7P_TSC(gm, k+ z*nq, p7P_DD)) : -3… in vf_conversion() 835 ddtmp = (int) wordify(om, p7P_TSC(gm, k, p7P_DD)); in vf_conversion() 899 for (z = 0; z < 4; z++) tmp.x[z] = (k+z*nq < M) ? p7P_TSC(gm, k+z*nq, p7P_DD) : -eslINFINITY; in fb_conversion()
|
/dports/biology/hmmer/hmmer-3.3/src/impl_sse/ |
H A D | p7_oprofile.c | 886 …for (z = 0; z < 8; z++) tmp.i[z] = ((k+ z*nq < M) ? wordify(om, p7P_TSC(gm, k+ z*nq, p7P_DD)) : -3… in vf_conversion() 914 ddtmp = (int) wordify(om, p7P_TSC(gm, k, p7P_DD)); in vf_conversion() 977 for (z = 0; z < 4; z++) tmp.x[z] = (k+z*nq < M) ? p7P_TSC(gm, k+z*nq, p7P_DD) : -eslINFINITY; in fb_conversion()
|
/dports/biology/hmmer/hmmer-3.3/src/impl_vmx/ |
H A D | p7_oprofile.c | 807 …for (z = 0; z < 8; z++) tmp.i[z] = ((k+ z*nq < M) ? wordify(om, p7P_TSC(gm, k+ z*nq, p7P_DD)) : -3… in vf_conversion() 835 ddtmp = (int) wordify(om, p7P_TSC(gm, k, p7P_DD)); in vf_conversion() 899 for (z = 0; z < 4; z++) tmp.x[z] = (k+z*nq < M) ? p7P_TSC(gm, k+z*nq, p7P_DD) : -eslINFINITY; in fb_conversion()
|