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Searched refs:p7P_TSC (Results 1 – 17 of 17) sorted by relevance

/dports/biology/infernal/infernal-1.1.3/hmmer/src/
H A Dp7_profile.c86 p7P_TSC(gm, 1, p7P_DM) = -eslINFINITY; /* delete state D_1 is wing-retracted */ in p7_profile_Create()
87 p7P_TSC(gm, 1, p7P_DD) = -eslINFINITY; in p7_profile_Create()
414 …case p7T_M: tsc = p7P_TSC(gm, k2-1, p7P_BM); break; /* remember, B->Mk is stored in [k-1][p7P_BM] … in p7_profile_GetT()
421 case p7T_M: tsc = p7P_TSC(gm, k1, p7P_MM); break; in p7_profile_GetT()
422 case p7T_I: tsc = p7P_TSC(gm, k1, p7P_MI); break; in p7_profile_GetT()
423 case p7T_D: tsc = p7P_TSC(gm, k1, p7P_MD); break; in p7_profile_GetT()
434 case p7T_M: tsc = p7P_TSC(gm, k1, p7P_DM); break; in p7_profile_GetT()
435 case p7T_D: tsc = p7P_TSC(gm, k1, p7P_DD); break; in p7_profile_GetT()
446 case p7T_M: tsc = p7P_TSC(gm, k1, p7P_IM); break; in p7_profile_GetT()
447 case p7T_I: tsc = p7P_TSC(gm, k1, p7P_II); break; in p7_profile_GetT()
[all …]
H A Dgeneric_fwdback_rescaled.c363 p7P_TSC(gm, 1, p7P_DM) = 0.0f; /* delete state D_1 is wing-retracted */ in p7_profile_ConfigInOdds()
364 p7P_TSC(gm, 1, p7P_DD) = 0.0f; in p7_profile_ConfigInOdds()
391 p7P_TSC(gm, k-1, p7P_BM) = occ[k] / Z; /* note off-by-one: entry at Mk stored as [k-1][BM] */ in p7_profile_ConfigInOdds()
397 p7P_TSC(gm, 0, p7P_BM) = 1.0 - Z; in p7_profile_ConfigInOdds()
400 p7P_TSC(gm, k, p7P_BM) = Z * hmm->t[k][p7H_DM]; in p7_profile_ConfigInOdds()
403 if (p7P_TSC(gm, hmm->M-1, p7P_BM) == 0.0f) did_underflow = TRUE; in p7_profile_ConfigInOdds()
493 p7P_TSC(gm, 1, p7P_DM) = 0.0f; /* delete state D_1 is wing-retracted */ in p7_profile_ConfigInOdds_DDScaled()
494 p7P_TSC(gm, 1, p7P_DD) = 0.0f; in p7_profile_ConfigInOdds_DDScaled()
508 p7P_TSC(gm, 0, p7P_BM) = 1.0 - hmm->t[0][p7H_MD]; in p7_profile_ConfigInOdds_DDScaled()
510 p7P_TSC(gm, k, p7P_BM) = hmm->t[0][p7H_MD] * hmm->t[k][p7H_DM] / hmm->t[k][p7H_DD]; in p7_profile_ConfigInOdds_DDScaled()
H A Dmodelconfig.c97 p7P_TSC(gm, k-1, p7P_BM) = log(occ[k] / Z); /* note off-by-one: entry at Mk stored as [k-1][BM] */ in p7_ProfileConfig()
104 p7P_TSC(gm, 0, p7P_BM) = log(1.0 - hmm->t[0][p7H_MD]); in p7_ProfileConfig()
107 p7P_TSC(gm, k, p7P_BM) = Z + log(hmm->t[k][p7H_DM]); in p7_ProfileConfig()
H A Dgeneric_msv.c384 for (k = 1; k < g2->M; k++) p7P_TSC(g2, k, p7P_MM) = 0.0f; in utest_msv()
385 …for (k = 0; k < g2->M; k++) p7P_TSC(g2, k, p7P_BM) = log(2.0f / ((float) g2->M * (float) (g2->M+1… in utest_msv()
H A Demit.c419 …pstart[k] = exp(p7P_TSC(gm, k-1, p7P_BM)) * (gm->M - k + 1); /* multiply p_ij by the number of exi… in sample_endpoints()
H A Dhmmer.h243 #define p7P_TSC(gm, k, s) ((gm)->tsc[(k) * p7P_NTRANS + (s)]) macro
/dports/biology/hmmer/hmmer-3.3/src/
H A Dp7_profile.c86 p7P_TSC(gm, 1, p7P_DM) = -eslINFINITY; /* delete state D_1 is wing-retracted */ in p7_profile_Create()
87 p7P_TSC(gm, 1, p7P_DD) = -eslINFINITY; in p7_profile_Create()
414 …case p7T_M: tsc = p7P_TSC(gm, k2-1, p7P_BM); break; /* remember, B->Mk is stored in [k-1][p7P_BM] … in p7_profile_GetT()
421 case p7T_M: tsc = p7P_TSC(gm, k1, p7P_MM); break; in p7_profile_GetT()
422 case p7T_I: tsc = p7P_TSC(gm, k1, p7P_MI); break; in p7_profile_GetT()
423 case p7T_D: tsc = p7P_TSC(gm, k1, p7P_MD); break; in p7_profile_GetT()
434 case p7T_M: tsc = p7P_TSC(gm, k1, p7P_DM); break; in p7_profile_GetT()
435 case p7T_D: tsc = p7P_TSC(gm, k1, p7P_DD); break; in p7_profile_GetT()
446 case p7T_M: tsc = p7P_TSC(gm, k1, p7P_IM); break; in p7_profile_GetT()
447 case p7T_I: tsc = p7P_TSC(gm, k1, p7P_II); break; in p7_profile_GetT()
[all …]
H A Dgeneric_fwdback_rescaled.c363 p7P_TSC(gm, 1, p7P_DM) = 0.0f; /* delete state D_1 is wing-retracted */ in p7_profile_ConfigInOdds()
364 p7P_TSC(gm, 1, p7P_DD) = 0.0f; in p7_profile_ConfigInOdds()
391 p7P_TSC(gm, k-1, p7P_BM) = occ[k] / Z; /* note off-by-one: entry at Mk stored as [k-1][BM] */ in p7_profile_ConfigInOdds()
397 p7P_TSC(gm, 0, p7P_BM) = 1.0 - Z; in p7_profile_ConfigInOdds()
400 p7P_TSC(gm, k, p7P_BM) = Z * hmm->t[k][p7H_DM]; in p7_profile_ConfigInOdds()
403 if (p7P_TSC(gm, hmm->M-1, p7P_BM) == 0.0f) did_underflow = TRUE; in p7_profile_ConfigInOdds()
493 p7P_TSC(gm, 1, p7P_DM) = 0.0f; /* delete state D_1 is wing-retracted */ in p7_profile_ConfigInOdds_DDScaled()
494 p7P_TSC(gm, 1, p7P_DD) = 0.0f; in p7_profile_ConfigInOdds_DDScaled()
508 p7P_TSC(gm, 0, p7P_BM) = 1.0 - hmm->t[0][p7H_MD]; in p7_profile_ConfigInOdds_DDScaled()
510 p7P_TSC(gm, k, p7P_BM) = hmm->t[0][p7H_MD] * hmm->t[k][p7H_DM] / hmm->t[k][p7H_DD]; in p7_profile_ConfigInOdds_DDScaled()
H A Dmodelconfig.c97 p7P_TSC(gm, k-1, p7P_BM) = log(occ[k] / Z); /* note off-by-one: entry at Mk stored as [k-1][BM] */ in p7_ProfileConfig()
104 p7P_TSC(gm, 0, p7P_BM) = log(1.0 - hmm->t[0][p7H_MD]); in p7_ProfileConfig()
107 p7P_TSC(gm, k, p7P_BM) = Z + log(hmm->t[k][p7H_DM]); in p7_ProfileConfig()
H A Dgeneric_msv.c384 for (k = 1; k < g2->M; k++) p7P_TSC(g2, k, p7P_MM) = 0.0f; in utest_msv()
385 …for (k = 0; k < g2->M; k++) p7P_TSC(g2, k, p7P_BM) = log(2.0f / ((float) g2->M * (float) (g2->M+1… in utest_msv()
H A Demit.c419 …pstart[k] = exp(p7P_TSC(gm, k-1, p7P_BM)) * (gm->M - k + 1); /* multiply p_ij by the number of exi… in sample_endpoints()
H A Dhmmer.h243 #define p7P_TSC(gm, k, s) ((gm)->tsc[(k) * p7P_NTRANS + (s)]) macro
/dports/biology/infernal/infernal-1.1.3/src/
H A Dcm_p7_modelconfig_trunc.c41 … p7P_TSC(gm, k-1, p7P_BM) = log(1. / gm->M); /* note off-by-one: entry at Mk stored as [k-1][BM] */ in p7_ProfileConfig5PrimeTrunc()
78 p7P_TSC(gm, 0, p7P_BM) = log(1.0 - hmm->t[0][p7H_MD]); in p7_ProfileConfig3PrimeTrunc()
81 p7P_TSC(gm, k, p7P_BM) = Z + log(hmm->t[k][p7H_DM]); in p7_ProfileConfig3PrimeTrunc()
/dports/biology/infernal/infernal-1.1.3/hmmer/src/impl_sse/
H A Dp7_oprofile.c876 val = ((kb+ z*nq < M) ? wordify(om, p7P_TSC(gm, kb+ z*nq, tg)) : -32768); in vf_conversion()
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()
915 ddtmp += (int) wordify(om, p7P_TSC(gm, k+1, p7P_DM)); in vf_conversion()
916 ddtmp -= (int) wordify(om, p7P_TSC(gm, k+1, p7P_BM)); in vf_conversion()
969 for (z = 0; z < 4; z++) tmp.x[z] = (kb+z*nq < M) ? p7P_TSC(gm, kb+z*nq, tg) : -eslINFINITY; in fb_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()
1904 for (k = 1; k < gm->M; k++) p7P_TSC(gm, k, p7P_MM) = 0.0f; in p7_profile_SameAsMF()
1905 for (k = 0; k < gm->M; k++) p7P_TSC(gm, k, p7P_BM) = tbm; in p7_profile_SameAsMF()
/dports/biology/infernal/infernal-1.1.3/hmmer/src/impl_vmx/
H A Dp7_oprofile.c797 val = ((kb+ z*nq < M) ? wordify(om, p7P_TSC(gm, kb+ z*nq, tg)) : -32768); in vf_conversion()
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()
836 ddtmp += (int) wordify(om, p7P_TSC(gm, k+1, p7P_DM)); in vf_conversion()
837 ddtmp -= (int) wordify(om, p7P_TSC(gm, k+1, p7P_BM)); in vf_conversion()
891 for (z = 0; z < 4; z++) tmp.x[z] = (kb+z*nq < M) ? p7P_TSC(gm, kb+z*nq, tg) : -eslINFINITY; in fb_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()
1832 for (k = 1; k < gm->M; k++) p7P_TSC(gm, k, p7P_MM) = 0.0f; in p7_profile_SameAsMF()
1833 for (k = 0; k < gm->M; k++) p7P_TSC(gm, k, p7P_BM) = tbm; in p7_profile_SameAsMF()
/dports/biology/hmmer/hmmer-3.3/src/impl_sse/
H A Dp7_oprofile.c876 val = ((kb+ z*nq < M) ? wordify(om, p7P_TSC(gm, kb+ z*nq, tg)) : -32768); in vf_conversion()
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()
915 ddtmp += (int) wordify(om, p7P_TSC(gm, k+1, p7P_DM)); in vf_conversion()
916 ddtmp -= (int) wordify(om, p7P_TSC(gm, k+1, p7P_BM)); in vf_conversion()
969 for (z = 0; z < 4; z++) tmp.x[z] = (kb+z*nq < M) ? p7P_TSC(gm, kb+z*nq, tg) : -eslINFINITY; in fb_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()
1904 for (k = 1; k < gm->M; k++) p7P_TSC(gm, k, p7P_MM) = 0.0f; in p7_profile_SameAsMF()
1905 for (k = 0; k < gm->M; k++) p7P_TSC(gm, k, p7P_BM) = tbm; in p7_profile_SameAsMF()
/dports/biology/hmmer/hmmer-3.3/src/impl_vmx/
H A Dp7_oprofile.c797 val = ((kb+ z*nq < M) ? wordify(om, p7P_TSC(gm, kb+ z*nq, tg)) : -32768); in vf_conversion()
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()
836 ddtmp += (int) wordify(om, p7P_TSC(gm, k+1, p7P_DM)); in vf_conversion()
837 ddtmp -= (int) wordify(om, p7P_TSC(gm, k+1, p7P_BM)); in vf_conversion()
891 for (z = 0; z < 4; z++) tmp.x[z] = (kb+z*nq < M) ? p7P_TSC(gm, kb+z*nq, tg) : -eslINFINITY; in fb_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()
1832 for (k = 1; k < gm->M; k++) p7P_TSC(gm, k, p7P_MM) = 0.0f; in p7_profile_SameAsMF()
1833 for (k = 0; k < gm->M; k++) p7P_TSC(gm, k, p7P_BM) = tbm; in p7_profile_SameAsMF()