Home
last modified time | relevance | path

Searched refs:p7P_J (Results 1 – 25 of 35) sorted by relevance

12

/dports/biology/infernal/infernal-1.1.3/src/
H A Dcm_p7_modelconfig_trunc.c142 …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()
/dports/biology/infernal/infernal-1.1.3/hmmer/src/
H A Dgeneric_fwdback_banded.c56 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()
H A Dgeneric_optacc.c127 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()
H A Dgeneric_viterbi.c136 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()
H A Dgeneric_vtrace.c138 …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()
H A Dgeneric_fwdback_rescaled.c240 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()
H A Dgeneric_fwdback.c120 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()
H A Dgeneric_decoding.c115 …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()
H A Dgeneric_fwdback_chk.c91 …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()
H A Dgeneric_stotrace.c153 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()
H A Dp7_profile.c462 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()
H A Ditest_brute.c393 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()
/dports/biology/hmmer/hmmer-3.3/src/
H A Dgeneric_fwdback_banded.c56 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()
H A Dgeneric_optacc.c127 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()
H A Dgeneric_viterbi.c136 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()
H A Dgeneric_vtrace.c138 …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()
H A Dgeneric_fwdback_rescaled.c240 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()
H A Dgeneric_fwdback.c120 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()
H A Dgeneric_decoding.c115 …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()
H A Dgeneric_fwdback_chk.c91 …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()
H A Dgeneric_stotrace.c153 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()
H A Dp7_profile.c462 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()
H A Ditest_brute.c393 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()
/dports/biology/infernal/infernal-1.1.3/hmmer/src/impl_sse/
H A Dp7_oprofile.c903 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()
/dports/biology/infernal/infernal-1.1.3/hmmer/src/impl_vmx/
H A Dp7_oprofile.c824 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()

12