/dports/biology/infernal/infernal-1.1.3/src/ |
H A D | cm_p7_modelconfig_trunc.c | 142 …gm->xsc[p7P_C][p7P_LOOP] = gm->xsc[p7P_J][p7P_LOOP] = log(ploop); /* J should be irrelevant, b/c w… in p7_ReconfigLength5PrimeTrunc() 143 gm->xsc[p7P_C][p7P_MOVE] = gm->xsc[p7P_J][p7P_MOVE] = log(pmove); in p7_ReconfigLength5PrimeTrunc() 167 …gm->xsc[p7P_N][p7P_LOOP] = gm->xsc[p7P_J][p7P_LOOP] = log(ploop); /* J should be irrelevant, b/c w… in p7_ReconfigLength3PrimeTrunc() 168 gm->xsc[p7P_N][p7P_MOVE] = gm->xsc[p7P_J][p7P_MOVE] = log(pmove); in p7_ReconfigLength3PrimeTrunc()
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/dports/biology/infernal/infernal-1.1.3/hmmer/src/ |
H A D | generic_fwdback_banded.c | 56 xJ = xJ + (ia - last_ib - 1) * gm->xsc[p7P_J][p7P_LOOP]; in p7_GForwardBanded() 57 xB = p7_FLogsum( xN + gm->xsc[p7P_N][p7P_MOVE], xJ + gm->xsc[p7P_J][p7P_MOVE]); in p7_GForwardBanded() 108 *xpc++ = xJ = p7_FLogsum( xJ + gm->xsc[p7P_J][p7P_LOOP], xE + gm->xsc[p7P_E][p7P_MOVE]); in p7_GForwardBanded() 109 *xpc++ = xB = p7_FLogsum( xJ + gm->xsc[p7P_J][p7P_MOVE], xN + gm->xsc[p7P_N][p7P_MOVE]); in p7_GForwardBanded()
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H A D | generic_optacc.c | 127 t1 = ( (gm->xsc[p7P_J][p7P_LOOP] == -eslINFINITY) ? FLT_MIN : 1.0); in p7_GOptimalAccuracy() 141 t2 = ( (gm->xsc[p7P_J][p7P_MOVE] == -eslINFINITY) ? FLT_MIN : 1.0); in p7_GOptimalAccuracy() 317 float t1 = ( (gm->xsc[p7P_J][p7P_LOOP] == -eslINFINITY) ? FLT_MIN : 1.0); in select_j() 355 float t2 = ( (gm->xsc[p7P_J][p7P_MOVE] == -eslINFINITY) ? FLT_MIN : 1.0); in select_b()
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H A D | generic_viterbi.c | 136 sc = XMX(i-1,p7G_J) + gm->xsc[p7P_J][p7P_LOOP]; /* J->J */ in p7_GViterbi() 148 XMX(i,p7G_B) = ESL_MAX(sc, XMX(i,p7G_J) + gm->xsc[p7P_J][p7P_MOVE]); /* J->B is J's move */ in p7_GViterbi() 292 sc = XMX(i-1,p7G_J) + gm->xsc[p7P_J][p7P_LOOP]; /* J->J */ in p7_GViterbi_longtarget() 304 XMX(i,p7G_B) = ESL_MAX(sc, XMX(i,p7G_J) + gm->xsc[p7P_J][p7P_MOVE]); /* J->B is J's move */ in p7_GViterbi_longtarget()
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H A D | generic_vtrace.c | 138 …else if (esl_FCompare(XMX(i,p7G_B), XMX(i, p7G_J) + gm->xsc[p7P_J][p7P_MOVE], tol) == eslOK) scur … in p7_GTrace() 145 …if (esl_FCompare(XMX(i,p7G_J), XMX(i-1,p7G_J) + gm->xsc[p7P_J][p7P_LOOP], tol) == eslOK) scur… in p7_GTrace()
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H A D | generic_fwdback_rescaled.c | 240 XMX(i,p7G_J) = XMX(i-1,p7G_J) * gm->xsc[p7P_J][p7P_LOOP] in p7_GForwardOdds() 250 + XMX(i, p7G_J) * gm->xsc[p7P_J][p7P_MOVE]; in p7_GForwardOdds() 333 gm->xsc[p7P_N][p7P_LOOP] = gm->xsc[p7P_C][p7P_LOOP] = gm->xsc[p7P_J][p7P_LOOP] = ploop; in p7_profile_ReconfigLengthInOdds() 334 gm->xsc[p7P_N][p7P_MOVE] = gm->xsc[p7P_C][p7P_MOVE] = gm->xsc[p7P_J][p7P_MOVE] = pmove; in p7_profile_ReconfigLengthInOdds()
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H A D | generic_fwdback.c | 120 XMX(i,p7G_J) = p7_FLogsum(XMX(i-1,p7G_J) + gm->xsc[p7P_J][p7P_LOOP], in p7_GForward() 130 XMX(i, p7G_J) + gm->xsc[p7P_J][p7P_MOVE]); in p7_GForward() 203 XMX(i,p7G_J) = p7_FLogsum( XMX(i+1,p7G_J) + gm->xsc[p7P_J][p7P_LOOP], in p7_GBackward() 204 XMX(i, p7G_B) + gm->xsc[p7P_J][p7P_MOVE]); in p7_GBackward()
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H A D | generic_decoding.c | 115 …mx[p7G_NXCELLS*(i-1) + p7G_J] + bck->xmx[p7G_NXCELLS*i + p7G_J] + gm->xsc[p7P_J][p7P_LOOP] - overa… in p7_GDecoding() 221 …mx[p7G_NXCELLS*(i-1) + p7G_J] + bck->xmx[p7G_NXCELLS*i + p7G_J] + gm->xsc[p7P_J][p7P_LOOP] - overa… in p7_GDomainDecoding()
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H A D | generic_fwdback_chk.c | 91 …dpc[p7GC_JJ] = dpp[p7GC_J] + gm->xsc[p7P_J][p7P_LOOP]; … in forward_row() 93 …dpc[p7GC_B] = p7_FLogsum( dpc[p7GC_N] + gm->xsc[p7P_N][p7P_MOVE], dpc[p7GC_J] + gm->xsc[p7P_J][p… in forward_row() 202 …c,p7GC_JJ) = p7_FLogsum( XMR(dpp,p7GC_J) + gm->xsc[p7P_J][p7P_LOOP], XMR(dpc,p7GC_B) + gm->xsc[p7… in backward_row()
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H A D | generic_stotrace.c | 153 sc[1] = XMX(i, p7G_J) + gm->xsc[p7P_J][p7P_MOVE]; in p7_GStochasticTrace() 162 sc[0] = XMX(i-1,p7G_J) + gm->xsc[p7P_J][p7P_LOOP]; in p7_GStochasticTrace()
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H A D | p7_profile.c | 462 case p7T_B: tsc = gm->xsc[p7P_J][p7P_MOVE]; break; in p7_profile_GetT() 463 case p7T_J: tsc = gm->xsc[p7P_J][p7P_LOOP]; break; in p7_profile_GetT()
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H A D | itest_brute.c | 393 gm->xsc[p7P_J][p7P_MOVE] = log(prm->r); in create_brute_profile() 394 gm->xsc[p7P_J][p7P_LOOP] = log(zerofy(1. - prm->r)); in create_brute_profile()
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/dports/biology/hmmer/hmmer-3.3/src/ |
H A D | generic_fwdback_banded.c | 56 xJ = xJ + (ia - last_ib - 1) * gm->xsc[p7P_J][p7P_LOOP]; in p7_GForwardBanded() 57 xB = p7_FLogsum( xN + gm->xsc[p7P_N][p7P_MOVE], xJ + gm->xsc[p7P_J][p7P_MOVE]); in p7_GForwardBanded() 108 *xpc++ = xJ = p7_FLogsum( xJ + gm->xsc[p7P_J][p7P_LOOP], xE + gm->xsc[p7P_E][p7P_MOVE]); in p7_GForwardBanded() 109 *xpc++ = xB = p7_FLogsum( xJ + gm->xsc[p7P_J][p7P_MOVE], xN + gm->xsc[p7P_N][p7P_MOVE]); in p7_GForwardBanded()
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H A D | generic_optacc.c | 127 t1 = ( (gm->xsc[p7P_J][p7P_LOOP] == -eslINFINITY) ? FLT_MIN : 1.0); in p7_GOptimalAccuracy() 141 t2 = ( (gm->xsc[p7P_J][p7P_MOVE] == -eslINFINITY) ? FLT_MIN : 1.0); in p7_GOptimalAccuracy() 317 float t1 = ( (gm->xsc[p7P_J][p7P_LOOP] == -eslINFINITY) ? FLT_MIN : 1.0); in select_j() 355 float t2 = ( (gm->xsc[p7P_J][p7P_MOVE] == -eslINFINITY) ? FLT_MIN : 1.0); in select_b()
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H A D | generic_viterbi.c | 136 sc = XMX(i-1,p7G_J) + gm->xsc[p7P_J][p7P_LOOP]; /* J->J */ in p7_GViterbi() 148 XMX(i,p7G_B) = ESL_MAX(sc, XMX(i,p7G_J) + gm->xsc[p7P_J][p7P_MOVE]); /* J->B is J's move */ in p7_GViterbi() 292 sc = XMX(i-1,p7G_J) + gm->xsc[p7P_J][p7P_LOOP]; /* J->J */ in p7_GViterbi_longtarget() 304 XMX(i,p7G_B) = ESL_MAX(sc, XMX(i,p7G_J) + gm->xsc[p7P_J][p7P_MOVE]); /* J->B is J's move */ in p7_GViterbi_longtarget()
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H A D | generic_vtrace.c | 138 …else if (esl_FCompare(XMX(i,p7G_B), XMX(i, p7G_J) + gm->xsc[p7P_J][p7P_MOVE], tol) == eslOK) scur … in p7_GTrace() 145 …if (esl_FCompare(XMX(i,p7G_J), XMX(i-1,p7G_J) + gm->xsc[p7P_J][p7P_LOOP], tol) == eslOK) scur… in p7_GTrace()
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H A D | generic_fwdback_rescaled.c | 240 XMX(i,p7G_J) = XMX(i-1,p7G_J) * gm->xsc[p7P_J][p7P_LOOP] in p7_GForwardOdds() 250 + XMX(i, p7G_J) * gm->xsc[p7P_J][p7P_MOVE]; in p7_GForwardOdds() 333 gm->xsc[p7P_N][p7P_LOOP] = gm->xsc[p7P_C][p7P_LOOP] = gm->xsc[p7P_J][p7P_LOOP] = ploop; in p7_profile_ReconfigLengthInOdds() 334 gm->xsc[p7P_N][p7P_MOVE] = gm->xsc[p7P_C][p7P_MOVE] = gm->xsc[p7P_J][p7P_MOVE] = pmove; in p7_profile_ReconfigLengthInOdds()
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H A D | generic_fwdback.c | 120 XMX(i,p7G_J) = p7_FLogsum(XMX(i-1,p7G_J) + gm->xsc[p7P_J][p7P_LOOP], in p7_GForward() 130 XMX(i, p7G_J) + gm->xsc[p7P_J][p7P_MOVE]); in p7_GForward() 203 XMX(i,p7G_J) = p7_FLogsum( XMX(i+1,p7G_J) + gm->xsc[p7P_J][p7P_LOOP], in p7_GBackward() 204 XMX(i, p7G_B) + gm->xsc[p7P_J][p7P_MOVE]); in p7_GBackward()
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H A D | generic_decoding.c | 115 …mx[p7G_NXCELLS*(i-1) + p7G_J] + bck->xmx[p7G_NXCELLS*i + p7G_J] + gm->xsc[p7P_J][p7P_LOOP] - overa… in p7_GDecoding() 221 …mx[p7G_NXCELLS*(i-1) + p7G_J] + bck->xmx[p7G_NXCELLS*i + p7G_J] + gm->xsc[p7P_J][p7P_LOOP] - overa… in p7_GDomainDecoding()
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H A D | generic_fwdback_chk.c | 91 …dpc[p7GC_JJ] = dpp[p7GC_J] + gm->xsc[p7P_J][p7P_LOOP]; … in forward_row() 93 …dpc[p7GC_B] = p7_FLogsum( dpc[p7GC_N] + gm->xsc[p7P_N][p7P_MOVE], dpc[p7GC_J] + gm->xsc[p7P_J][p… in forward_row() 202 …c,p7GC_JJ) = p7_FLogsum( XMR(dpp,p7GC_J) + gm->xsc[p7P_J][p7P_LOOP], XMR(dpc,p7GC_B) + gm->xsc[p7… in backward_row()
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H A D | generic_stotrace.c | 153 sc[1] = XMX(i, p7G_J) + gm->xsc[p7P_J][p7P_MOVE]; in p7_GStochasticTrace() 162 sc[0] = XMX(i-1,p7G_J) + gm->xsc[p7P_J][p7P_LOOP]; in p7_GStochasticTrace()
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H A D | p7_profile.c | 462 case p7T_B: tsc = gm->xsc[p7P_J][p7P_MOVE]; break; in p7_profile_GetT() 463 case p7T_J: tsc = gm->xsc[p7P_J][p7P_LOOP]; break; in p7_profile_GetT()
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H A D | itest_brute.c | 393 gm->xsc[p7P_J][p7P_MOVE] = log(prm->r); in create_brute_profile() 394 gm->xsc[p7P_J][p7P_LOOP] = log(zerofy(1. - prm->r)); in create_brute_profile()
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/dports/biology/infernal/infernal-1.1.3/hmmer/src/impl_sse/ |
H A D | p7_oprofile.c | 903 om->xw[p7O_J][p7O_MOVE] = wordify(om, gm->xsc[p7P_J][p7P_MOVE]); in vf_conversion() 990 om->xf[p7O_J][p7O_LOOP] = expf(gm->xsc[p7P_J][p7P_LOOP]); in fb_conversion() 991 om->xf[p7O_J][p7O_MOVE] = expf(gm->xsc[p7P_J][p7P_MOVE]); in fb_conversion() 1921 gm->xsc[p7P_N][p7P_LOOP] = gm->xsc[p7P_J][p7P_LOOP] = gm->xsc[p7P_C][p7P_LOOP] = 0; in p7_profile_SameAsMF() 1986 gm->xsc[p7P_N][p7P_LOOP] = gm->xsc[p7P_J][p7P_LOOP] = gm->xsc[p7P_C][p7P_LOOP] = 0.0; in p7_profile_SameAsVF()
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/dports/biology/infernal/infernal-1.1.3/hmmer/src/impl_vmx/ |
H A D | p7_oprofile.c | 824 om->xw[p7O_J][p7O_MOVE] = wordify(om, gm->xsc[p7P_J][p7P_MOVE]); in vf_conversion() 912 om->xf[p7O_J][p7O_LOOP] = expf(gm->xsc[p7P_J][p7P_LOOP]); in fb_conversion() 913 om->xf[p7O_J][p7O_MOVE] = expf(gm->xsc[p7P_J][p7P_MOVE]); in fb_conversion() 1849 gm->xsc[p7P_N][p7P_LOOP] = gm->xsc[p7P_J][p7P_LOOP] = gm->xsc[p7P_C][p7P_LOOP] = 0; in p7_profile_SameAsMF() 1914 gm->xsc[p7P_N][p7P_LOOP] = gm->xsc[p7P_J][p7P_LOOP] = gm->xsc[p7P_C][p7P_LOOP] = 0.0; in p7_profile_SameAsVF()
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