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Searched refs:LENCOL (Results 1 – 7 of 7) sorted by relevance

/dports/biology/clustalw/clustalw-2.1/src/multipleAlign/
H A DProfileBase.cpp39 profile.resize(prfLength + 2, vector<int>(LENCOL + 2)); in ProfileBase()
221 profile[j+1][LENCOL] = lenCoef; in calcGapCoeff()
226 profile[j + 1][LENCOL] = lenCoef; in calcGapCoeff()
240 profile[j + 1][LENCOL] = static_cast<int>(0.5 * lenCoef); in calcGapCoeff()
251 profile[j + 1][LENCOL] *= val; in calcGapCoeff()
261 if (profile[j + 1][LENCOL] <= 0) in calcGapCoeff()
263 profile[j + 1][LENCOL] = 1; in calcGapCoeff()
271 profile[0][LENCOL] = lenCoef; in calcGapCoeff()
276 profile[0][LENCOL] = 0; in calcGapCoeff()
278 profile[prfLength][LENCOL] = 0; in calcGapCoeff()
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H A DMyersMillerProfileAlign.cpp358 cout << (*profile1)[i + 1][GAPCOL] << " " << (*profile1)[i + 1][LENCOL] in profileAlign()
399 cout << (*profile2)[i + 1][GAPCOL] << " " << (*profile2)[i + 1][LENCOL] in profileAlign()
1152 h = (*profile2)[j][LENCOL]; in extPenalty1()
1182 h += (*profile2)[ix + j][LENCOL]; in gapPenalty1()
1225 h = (*profile1)[i][LENCOL]; in extPenalty2()
1255 h += (*profile1)[ix + i][LENCOL]; in gapPenalty2()
H A DProfileStandard.cpp49 profile.resize(prfLength + 2, vector<int>(LENCOL + 2)); in calcStandardProfile()
H A DLowScoreSegProfile.cpp19 profile.resize(prfLength + 2, vector<int>(LENCOL + 2)); in LowScoreSegProfile()
/dports/biology/clustalw/clustalw-2.1/src/general/
H A Dclustalw.h242 const int LENCOL = 33; /* position of gap extension penalty in profile */ variable
/dports/math/R-cran-lpSolve/lpSolve/src/
H A Dlusol1.h39 int I, J, K, KP1, L, LAST, LENCOL, IMAX, JMAX, JLAST, JNEW; local
50 LENCOL = M+1;
57 LENCOL--;
65 L = idamaxlpsolve(LENCOL,DA+DAPOS(K,J)-LUSOL_ARRAYOFFSET,1)+K-1;
232 int I, J, K, KP1, L, LAST, LENCOL; local
249 LENCOL = (M-K)+1;
251 L = (idamaxlpsolve(LENCOL,DA+DAPOS(K,K)-LUSOL_ARRAYOFFSET,1)+K)-1;
/dports/math/lp_solve/lp_solve_5.5/bfp/bfp_LUSOL/LUSOL/
H A Dlusol1.c39 int I, J, K, KP1, L, LAST, LENCOL, IMAX, JMAX, JLAST, JNEW; local
50 LENCOL = M+1;
57 LENCOL--;
65 L = idamax(LENCOL,DA+DAPOS(K,J)-LUSOL_ARRAYOFFSET,1)+K-1;
232 int I, J, K, KP1, L, LAST, LENCOL; local
249 LENCOL = (M-K)+1;
251 L = (idamax(LENCOL,DA+DAPOS(K,K)-LUSOL_ARRAYOFFSET,1)+K)-1;