diff --git a/CMakeLists.txt b/CMakeLists.txt index 26e0f3fd5..5e8c74429 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -215,14 +215,12 @@ include_directories(lib/simde) include_directories(lib) include_directories(lib/simd) include_directories(lib/alp) -include_directories(lib/cacode) include_directories(lib/ksw2) include_directories(lib/xxhash) if (NOT DISABLE_IPS4O) include_directories(lib/ips4o) endif () -add_subdirectory(lib/cacode) add_subdirectory(lib/alp) add_subdirectory(lib/ksw2) add_subdirectory(data) diff --git a/lib/cacode/CMakeLists.txt b/lib/cacode/CMakeLists.txt deleted file mode 100644 index 0d126b5dd..000000000 --- a/lib/cacode/CMakeLists.txt +++ /dev/null @@ -1,9 +0,0 @@ -add_library(cacode OBJECT - lambda_calculator.cpp - lambda_calculator.h - lubksb.cpp - ludcmp.cpp - nrutil.cpp - nrutil.h - ) -set_target_properties(cacode PROPERTIES COMPILE_FLAGS "${MMSEQS_CXX_FLAGS} -w" LINK_FLAGS "${MMSEQS_CXX_FLAGS} -w") diff --git a/lib/cacode/LICENSE.LAST b/lib/cacode/LICENSE.LAST deleted file mode 100644 index 94a9ed024..000000000 --- a/lib/cacode/LICENSE.LAST +++ /dev/null @@ -1,674 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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If not, see . - -Also add information on how to contact you by electronic and paper mail. - - If the program does terminal interaction, make it output a short -notice like this when it starts in an interactive mode: - - Copyright (C) - This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. - This is free software, and you are welcome to redistribute it - under certain conditions; type `show c' for details. - -The hypothetical commands `show w' and `show c' should show the appropriate -parts of the General Public License. Of course, your program's commands -might be different; for a GUI interface, you would use an "about box". - - You should also get your employer (if you work as a programmer) or school, -if any, to sign a "copyright disclaimer" for the program, if necessary. -For more information on this, and how to apply and follow the GNU GPL, see -. - - The GNU General Public License does not permit incorporating your program -into proprietary programs. If your program is a subroutine library, you -may consider it more useful to permit linking proprietary applications with -the library. If this is what you want to do, use the GNU Lesser General -Public License instead of this License. But first, please read -. diff --git a/lib/cacode/LICENSE.NCBI b/lib/cacode/LICENSE.NCBI deleted file mode 100644 index f2b2df75b..000000000 --- a/lib/cacode/LICENSE.NCBI +++ /dev/null @@ -1,26 +0,0 @@ -https://github.com/superwills/NibbleAndAHalf -base64.h -- Fast base64 encoding and decoding. -version 1.0.0, April 17, 2013 143a - -Copyright (C) 2013 William Sherif - -This software is provided 'as-is', without any express or implied -warranty. In no event will the authors be held liable for any damages -arising from the use of this software. - -Permission is granted to anyone to use this software for any purpose, -including commercial applications, and to alter it and redistribute it -freely, subject to the following restrictions: - -1. The origin of this software must not be misrepresented; you must not - claim that you wrote the original software. If you use this software - in a product, an acknowledgment in the product documentation would be - appreciated but is not required. -2. Altered source versions must be plainly marked as such, and must not be - misrepresented as being the original software. -3. This notice may not be removed or altered from any source distribution. - -William Sherif -will.sherif@gmail.com - -YWxsIHlvdXIgYmFzZSBhcmUgYmVsb25nIHRvIHVz diff --git a/lib/cacode/README b/lib/cacode/README deleted file mode 100644 index 45d7b8470..000000000 --- a/lib/cacode/README +++ /dev/null @@ -1,2 +0,0 @@ -CA_code was extracted from LAST (http://last.cbrc.jp) which is licensed under GPLv3-or-later (see LICENSE.LAST). -CA_code itself is public domain developed by members of the NCBI (see LICENSE.NCBI). diff --git a/lib/cacode/lambda_calculator.cpp b/lib/cacode/lambda_calculator.cpp deleted file mode 100644 index 560d6d6f9..000000000 --- a/lib/cacode/lambda_calculator.cpp +++ /dev/null @@ -1,478 +0,0 @@ -// Copyright 2008 Michiaki Hamada -// Adapted from public domain code by Yi-Kuo Yu, NCBI - -/** - * See lambda_calculator.h - */ -#include -#include -#include -#include "nrutil.h" - -int Alphsize; - -#include "nrutil.cpp" -#include "ludcmp.cpp" -#include "lubksb.cpp" -#include "lambda_calculator.h" - -#define Epsilon 1.0e-36 -#define E_bound 1.0e-12 -#define Infty 1000000.0 -#define min(A, B) ((A) > (B) ? (B) : (A) ) -#define max(A, B) ((A) > (B) ? (A) : (B) ) -#define bool int -#define true 1 -#define false 0 -double Lambda_UB; //lambda upper bound -double r_max_m, c_max_m; //min of each row's (column's) max - -void makematrix(const double **mat_b, double **a, double lambda); - -typedef struct Lambda { - double min; - double max; - int flag; // 1 means there is a range, -1 means no solution possible. -} Lambda; -typedef struct Sum { - double value; - int flag; // 1 means no negative bg_freq, -1 means there is negative bg_freq -} Sum; - -Lambda Find_JP(const double **mat_b, double la_min, double la_max, double **JP, double *p_in, double *q_in); - -Sum Check_root(const double **mat_b, double **a, double lambda, double *p, double *q); - -double Check_det(const double **mat_b, double **a, double lambda); - -Sum Nail_lambda(const double **mat_b, int flag_sign, double lambda_min, double lambda_max, double *p, double *q, - double *la_add); - -double Nail_det(const double **mat_b, int flag_sign, double lambda_min, double lambda_max); - -bool Check_range(const double **mat_b); - -double *Locate_det_zero(const double **mat_b, int *); //pointer to root list are returned with how many of them by int - - -double calculate_lambda(const double **mat_b, int alpha_size, - double *p, double *q) { - double **JP/*, *q, *p*/; - int k; - double *root_location; - int N_root; - Lambda Lambda_local; - - Alphsize = alpha_size; - - if (!Check_range(mat_b)) return -1.0; - - root_location = Locate_det_zero(mat_b, &N_root); - if (root_location == NULL && N_root > 0) return -1.0; - - //q=dvector(1,Alphsize); - //p=dvector(1,Alphsize); - JP = dmatrix(1, Alphsize, 1, Alphsize); - - if (N_root == 0) { - Lambda_local = Find_JP(mat_b, 0, Lambda_UB, JP, p, q); - if (1 == Lambda_local.flag) { // sensible solution found - // Remember to find the right place to free the vectors - //free_dvector(p, 1,Alphsize); - //free_dvector(q, 1,Alphsize); - free(root_location); - free_dmatrix(JP, 1, Alphsize, 1, Alphsize); - return (Lambda_local.min + Lambda_local.max) / 2.0; - } else if (-1 == Lambda_local.flag) { - //printf("matrix pass first screening but no sensible solution found. :-( \n"); - } - } else if (N_root > 0) { - //printf("N_root = %d for this matirx \n", N_root); - //for (i=0;i 0) { - if (mat_b[i][j] > r_max) r_max = mat_b[i][j]; - pos_flag_r = 1; - } else if (mat_b[i][j] < 0) neg_flag_r = 1; - if (mat_b[j][i] > 0) { - if (mat_b[j][i] > c_max) c_max = mat_b[j][i]; - pos_flag_c = 1; - } else if (mat_b[j][i] < 0) neg_flag_c = 1; - } - if ((pos_flag_r == -1) || (neg_flag_r == -1) || (pos_flag_c == -1) || (neg_flag_c == -1)) { - if ((pos_flag_r == -1) && (neg_flag_r == -1)) { - printf("only zero score at row %d\n", i); - L_r++; - } else if ((pos_flag_c == -1) && (neg_flag_c == -1)) { - printf("only zero score at column %d\n", i); - L_c++; - } else { - //printf("all positive or all negative at row or column %d\n", i); - //printf("therefore invalid matrix. exit now. \n"); - return false; - //exit(1); - } - } - if ((r_max < r_max_m) && (r_max > 0)) r_max_m = r_max; - if ((c_max < c_max_m) && (c_max > 0)) c_max_m = c_max; - } - - - // Find the upper bound for lambda - if (r_max_m > c_max_m) { - Lambda_UB = 1.1 * log(1.0 * Alphsize - L_r) / r_max_m; - } else { - Lambda_UB = 1.1 * log(1.0 * Alphsize - L_c) / c_max_m; - } - //printf("the upper bound for lambda is %lf\n", Lambda_UB); - return true; -} - - -double Check_det(const double **mat_b, double **a, double lambda) { - double d; - int i, /*j,*/ *indx; - - indx = ivector(1, Alphsize); - makematrix(mat_b, a, lambda); - ludcmp(a, Alphsize, indx, &d); - for (i = 1; i <= Alphsize; i++) d *= a[i][i]; - free_ivector(indx, 1, Alphsize); - return d; //returning the determinant -} - - -Sum Check_root(const double **mat_b, double **a, double lambda, double *p, double *q) { - double **y, /* *col,*/ d; - //double sum = 0.0; - int i, j;//, *indx; - Sum Sum_here; - - y = dmatrix(1, Alphsize, 1, Alphsize); - //indx = ivector(1,Alphsize); - int indx[Alphsize + 1]; - //col = dvector(1,Alphsize); - double col[Alphsize + 1]; - - makematrix(mat_b, a, lambda); - ludcmp(a, Alphsize, indx, &d); - Sum_here.value = 0.0; - for (i = 1; i <= Alphsize; i++) q[i] = 0.0; - for (j = 1; j <= Alphsize; j++) { - for (i = 1; i <= Alphsize; i++){ - col[i] = 0.0; - } - col[j] = 1.0; - lubksb(a, Alphsize, indx, col); - p[j] = 0.0; - for (i = 1; i <= Alphsize; i++) { - y[i][j] = col[i]; - Sum_here.value += y[i][j]; - p[j] += y[i][j]; - q[i] += y[i][j]; - } - } - - Sum_here.flag = 1; - for (i = 1; i < Alphsize; i++) { - if ((p[i] < 0) || (q[i] < 0)) { - Sum_here.flag = -1; - //printf("problematic freq. p[%d] = %.4f q[%d]=%.4f\n",i,p[i],i,q[i]); - } - } - free_dmatrix(y, 1, Alphsize, 1, Alphsize); - return Sum_here; -} - - -double *Locate_det_zero(const double **mat_b, int *N_root_add) { - double **a/*, *q, *p */; // a is the exponentiated matrix of socres, p and q are bg_freqs - int i/*,j,k*/; - int N; // number of points for first round - int flag_sign; - double lambda/*, l_tmp, sum, sum_min, sum_max */; - double lambda_root, dlambda /*, dsum=0.5 */; - //double *l_here, *s_here; - double root[5000]; - double *root_temp; - //double error=0.000000000001; - int zero_monitor = 0; // record number of zeros found in the range - //int flag; - - a = dmatrix(1, Alphsize, 1, Alphsize); - //Sum_local = (Sum *)malloc(sizeof(Sum)); - //Lambda_local = (Lambda *)malloc(sizeof(Lambda)); - - N = 2 + max(400, ((int) (Lambda_UB - 0) / 0.005)); - //printf("N = %d in Locate_det_zero\n", N); - dlambda = (Lambda_UB) / (N * 1.0); - //l_here = (double *)malloc((N+1)*sizeof(double)); - //s_here = (double *)malloc((N+1)*sizeof(double)); - double l_here[N + 1]; - double s_here[N + 1]; - - for (i = 0; i < N; i++) { - lambda = (i + 1) * dlambda; - s_here[i] = Check_det(mat_b, a, lambda); - l_here[i] = lambda; - } - - if (s_here[0] < 0.0) flag_sign = -1; - if (s_here[0] > 0.0) flag_sign = 1; - if (fabs(s_here[0]) / exp(l_here[0] * (r_max_m + c_max_m) / 2.0) <= Epsilon) { - root[zero_monitor++] = l_here[0]; - flag_sign = 0; - } - - for (i = 1; i < N; i++) { - if ((flag_sign != 0) && (fabs(s_here[i]) > Epsilon)) { - if (s_here[i - 1] * s_here[i] < 0) { - //printf("occurring at regular places\n"); - lambda_root = Nail_det(mat_b, flag_sign, l_here[i - 1], l_here[i]); - root[zero_monitor++] = lambda_root; - flag_sign = -flag_sign; // the flag switch sign after one sol found - //printf("a (regular) root of det found at %12.10f, i= %d\n", lambda_root,i); - } - } else { - if (s_here[i] < 0.0) flag_sign = -1; - if (s_here[i] > 0.0) flag_sign = 1; - if (fabs(s_here[i]) / exp(l_here[i] * (r_max_m + c_max_m) / 2.0) <= Epsilon) { - root[zero_monitor++] = l_here[i]; - } - } - } - //printf("total number of solution found in range is %d\n", i_monitor); - root_temp = (double *) malloc(zero_monitor * sizeof(double)); - *N_root_add = zero_monitor; - if (zero_monitor > 0) { - if (zero_monitor >= N / 4) { - //printf("It is likely that uniform zero determinant is occurring.\n"); - //printf("number of small det points = %d out of %d, exit now....\n",zero_monitor, N); - free(root_temp); - return NULL; - //exit(1); - } - for (i = 0; i < zero_monitor; i++) { - root_temp[i] = root[i]; - //printf("root_location[%d] = %lf\n",i,root_temp[i]); - } - } - free_dmatrix(a, 1, Alphsize, 1, Alphsize); - return root_temp; - -} - - -Lambda Find_JP(const double **mat_b, double la_min, double la_max, double **JP, double *p_in, double *q_in) { - double **a, *q, *p; // a is the exponentiated matrix of socres, p and q are bg_freqs - int i, j/*,k*/; - int N; // number of points for first round - double lambda/*, l_tmp, sum, sum_min, sum_max*/; - double lambda_max, lambda_min, lambda_final, dlambda/*, dsum=0.5*/; - //double *l_here, *s_here; - //double error=0.000000000000001; - //int validity_flag; // 1 means valid, -1 means not valid. - int flag_sign; // 1 means small lambda sum > 1, -1 means otherwise - int flag_done = -1; // 1 means find sensible solution, -1 means sensible not found - int i_monitor = 0; // record number of solution found in the range, including nonsense ones - int j_monitor; - - Lambda Lambda_local; - //Sum *Sum_local; - Sum Sum_local; - - lambda_min = la_min; - lambda_max = la_max; - q = q_in; - p = p_in; - a = dmatrix(1, Alphsize, 1, Alphsize); - //Sum_local = (Sum *)malloc(sizeof(Sum)); - //Lambda_local = (Lambda *)malloc(sizeof(Lambda)); - - N = 2 + max(400, ((int) (lambda_max - lambda_min) / 0.005)); - //printf("N = %d in Find_JP\n", N); - dlambda = (lambda_max - lambda_min) / (N * 1.0); - //l_here = (double *)malloc((N+1)*sizeof(double)); - //s_here = (double *)malloc((N+1)*sizeof(double)); - double l_here[N + 1]; - double s_here[N + 1]; - //printf("lambda_min enter = %12.10e, lambda_max = %12.10f\n", lambda_min, lambda_max); - for (i = 0; i < N - 1; i++) { - lambda = lambda_min + (i + 1) * dlambda; - makematrix(mat_b, a, lambda); - Sum_local = Check_root(mat_b, a, lambda, p, q); - l_here[i] = lambda; - s_here[i] = Sum_local.value - 1.0; - //printf("scan %d th time in Find_JP\n",i ); - } - //printf("finish first time scanining in Find_JP\n"); - if (s_here[0] < 0.0) flag_sign = -1; - else if (s_here[0] > 0.0) flag_sign = 1; - else if (s_here[0] == 0.0) { //needs refined definition on flag_sign - printf("enter the exact hit, rarely occurs other than when lambda = 0 \n"); - j_monitor = 1; - flag_sign = 0; - while ((flag_sign == 0) && (j_monitor < N)) { - Sum_local = Check_root(mat_b, a, l_here[0] + j_monitor * dlambda / N, p, q); - if (Sum_local.value > 1.0) { - flag_sign = 1; - } else if (Sum_local.value < 1.0) { - flag_sign = -1; - } - j_monitor++; - } - } - - for (i = 1; i < N; i++) { // should be N-1 ??? - if (flag_sign == 0) { - printf("flag_sign = 0 \n"); - exit(1); - } - if (s_here[i - 1] * s_here[i] < 0) { - lambda_min = l_here[i - 1]; - lambda_max = l_here[i]; - Sum_local = Nail_lambda(mat_b, flag_sign, lambda_min, lambda_max, p, q, &lambda_final); - if (Sum_local.flag == 1) { - i = N; - flag_done = 1; - Lambda_local.flag = 1; - Lambda_local.min = lambda_final, Lambda_local.max = lambda_final; - } - flag_sign = -flag_sign; // the flag switch sign after one sol found - i_monitor++; - } - } - - if (flag_done == 1) { - // Write correct JP to the matrix - makematrix(mat_b, a, lambda_final); - for (i = 1; i <= Alphsize; i++) { - for (j = 1; j <= Alphsize; j++) { - JP[i][j] = a[i][j] * p[i] * q[j]; - } - } - free_dmatrix(a, 1, Alphsize, 1, Alphsize); - return Lambda_local; - } else if (flag_done == -1) { - //printf("no sensible solution in the plausible x range: (%lf,%lf)\n", la_min, la_max); - Lambda_local.flag = -1; - Lambda_local.min = 0; - Lambda_local.max = Infty; - return Lambda_local; - } - // never come here - return Lambda_local; -} - - -Sum Nail_lambda(const double **mat_b, int flag_sign, double lambda_min, double lambda_max, double *p, double *q, - double *lam_add) { - double **a; - double lambda; - - //Sum *Sum_local; - Sum Sum_local; - a = dmatrix(1, Alphsize, 1, Alphsize); - //Sum_local = (Sum *)malloc(sizeof(Sum)); - - lambda = (lambda_min + lambda_max) / 2.0; - Sum_local = Check_root(mat_b, a, lambda, p, q); - while (fabs(Sum_local.value - 1.0) > E_bound) { - if (flag_sign * (Sum_local.value - 1.0) < 0) lambda_max = lambda; - else if (flag_sign * (Sum_local.value - 1.0) > 0) lambda_min = lambda; - - // Added by MCF to avoid infinite loop: - if (lambda == (lambda_min + lambda_max) / 2.0) { - Sum_local.flag = -1; - break; - } - - lambda = (lambda_min + lambda_max) / 2.0; - Sum_local = Check_root(mat_b, a, lambda, p, q); - } - free_dmatrix(a, 1, Alphsize, 1, Alphsize); - *lam_add = lambda; - return Sum_local; -} - - -double Nail_det(const double **mat_b, int flag_sign, double lambda_min, double lambda_max) { - double **a; - double lambda; - double value; - - a = dmatrix(1, Alphsize, 1, Alphsize); - - lambda = (lambda_min + lambda_max) / 2.0; - value = Check_det(mat_b, a, lambda); - while ((fabs(value) > E_bound) && (lambda > 0)) { - if (flag_sign * (value) < 0) lambda_max = lambda; - else if (flag_sign * (value) > 0) lambda_min = lambda; - lambda = (lambda_min + lambda_max) / 2.0; - value = Check_det(mat_b, a, lambda); - } - free_dmatrix(a, 1, Alphsize, 1, Alphsize); - return lambda; -} - -void makematrix(const double **mat_b, double **a, double lambda) { - - int i, j; - - for (i = 1; i <= Alphsize; i++) - for (j = 1; j <= Alphsize; j++) { - *(*(a + i) + j) = exp(lambda * mat_b[i][j]); - } -} - - - diff --git a/lib/cacode/lambda_calculator.h b/lib/cacode/lambda_calculator.h deleted file mode 100644 index 70f2f1800..000000000 --- a/lib/cacode/lambda_calculator.h +++ /dev/null @@ -1,10 +0,0 @@ -// Copyright 2008 Michiaki Hamada - -#ifndef __H_INCLUDE_LAMBDA_CALCULATOR_HH -#define __H_INCLUDE_LAMBDA_CALCULATOR_HH - -// These pointers are 1-based! -double calculate_lambda( const double** mat_b, int alpha_size, - double* p, double* q ); - -#endif // __H_INCLUDE_LAMBDA_CALCULATOR_HH diff --git a/lib/cacode/lubksb.cpp b/lib/cacode/lubksb.cpp deleted file mode 100644 index 7725d5668..000000000 --- a/lib/cacode/lubksb.cpp +++ /dev/null @@ -1,27 +0,0 @@ -// Public domain code from Yi-Kuo Yu & Stephen Altschul, NCBI - -void lubksb(double **a, int n, int *indx, double b[]) { - int i, ii = 0, ip, j; - double sum; - - for (i = 1; i <= n; i++) { - ip = indx[i]; - sum = b[ip]; - b[ip] = b[i]; - if (ii) { - for (j = ii; j <= i - 1; j++) { - sum -= a[i][j] * b[j]; - } - } else if (sum) { - ii = i; - } - b[i] = sum; - } - for (i = n; i >= 1; i--) { - sum = b[i]; - for (j = i + 1; j <= n; j++) { - sum -= a[i][j] * b[j]; - } - b[i] = sum / a[i][i]; - } -} diff --git a/lib/cacode/ludcmp.cpp b/lib/cacode/ludcmp.cpp deleted file mode 100644 index 8d401b9e0..000000000 --- a/lib/cacode/ludcmp.cpp +++ /dev/null @@ -1,63 +0,0 @@ -// Public domain code from Yi-Kuo Yu & Stephen Altschul, NCBI - -#include - -#define TINY 1.0e-20; - -double *dvector(int, int); - -void nrerror(const char *); - -void free_dvector(double *, int, int); - -void ludcmp(double **a, int n, int *indx, double *d) { - int i, imax, j, k; - double big, dum, sum, temp; - double *vv; - - vv = dvector(1, n); - *d = 1.0; - for (i = 1; i <= n; i++) { - big = 0.0; - for (j = 1; j <= n; j++) - if ((temp = fabs(a[i][j])) > big) big = temp; - if (big == 0.0) nrerror("Singular matrix in routine LUDCMP"); - vv[i] = 1.0 / big; - } - for (j = 1; j <= n; j++) { - for (i = 1; i < j; i++) { - sum = a[i][j]; - for (k = 1; k < i; k++) sum -= a[i][k] * a[k][j]; - a[i][j] = sum; - } - big = 0.0; - for (i = j; i <= n; i++) { - sum = a[i][j]; - for (k = 1; k < j; k++) - sum -= a[i][k] * a[k][j]; - a[i][j] = sum; - if ((dum = vv[i] * fabs(sum)) >= big) { - big = dum; - imax = i; - } - } - if (j != imax) { - for (k = 1; k <= n; k++) { - dum = a[imax][k]; - a[imax][k] = a[j][k]; - a[j][k] = dum; - } - *d = -(*d); - vv[imax] = vv[j]; - } - indx[j] = imax; - if (a[j][j] == 0.0) a[j][j] = TINY; - if (j != n) { - dum = 1.0 / (a[j][j]); - for (i = j + 1; i <= n; i++) a[i][j] *= dum; - } - } - free_dvector(vv, 1, n); -} - -#undef TINY diff --git a/lib/cacode/nrutil.cpp b/lib/cacode/nrutil.cpp deleted file mode 100644 index dcb8fb217..000000000 --- a/lib/cacode/nrutil.cpp +++ /dev/null @@ -1,97 +0,0 @@ -// Public domain code from Yi-Kuo Yu & Stephen Altschul, NCBI - -//#include -#include -#include - -void nrerror(const char *error_text) { - - fprintf(stderr, "Numerical Recipes run-time error...\n"); - fprintf(stderr, "%s\n", error_text); - fprintf(stderr, "...now exiting to system...\n"); - exit(1); -} - -float *vector(int nl, int nh) { - float *v; - - v = (float *) malloc((unsigned) (nh - nl + 1) * sizeof(float)); - if (!v) nrerror("allocation failure in vector()"); - return v - nl; -} - -int *ivector(int nl, int nh) { - int *v; - - v = (int *) malloc((unsigned) (nh - nl + 1) * sizeof(int)); - if (!v) nrerror("allocation failure in ivector()"); - return v - nl; -} - -double *dvector(int nl, int nh) { - double *v; - - v = (double *) malloc((unsigned) (nh - nl + 1) * sizeof(double)); - if (!v) nrerror("allocation failure in dvector()"); - return v - nl; -} - -float **matrix(int nrl, int nrh, int ncl, int nch) { - int i; - float **m; - - m = (float **) malloc((unsigned) (nrh - nrl + 1) * sizeof(float *)); - if (!m) nrerror("allocation failure 1 in matrix()"); - m -= nrl; - - for (i = nrl; i <= nrh; i++) { - m[i] = (float *) malloc((unsigned) (nch - ncl + 1) * sizeof(float)); - if (!m[i]) nrerror("allocation failure 2 in matrix()"); - m[i] -= ncl; - } - return m; -} - -double **dmatrix(int nrl, int nrh, int ncl, int nch) { - int i; - double **m; - - m = (double **) malloc((unsigned) (nrh - nrl + 1) * sizeof(double *)); - if (!m) nrerror("allocation failure 1 in dmatrix()"); - m -= nrl; - - for (i = nrl; i <= nrh; i++) { - m[i] = (double *) malloc((unsigned) (nch - ncl + 1) * sizeof(double)); - if (!m[i]) nrerror("allocation failure 2 in dmatrix()"); - m[i] -= ncl; - } - return m; -} - -float **submatrix(float **a, int oldrl, int oldrh, int oldcl, int oldch, int newrl, int newcl) { - int i, j; - float **m; - - m = (float **) malloc((unsigned) (oldrh - oldrl + 1) * sizeof(float *)); - if (!m) nrerror("allocation failure in submatrix()"); - m -= newrl; - - for (i = oldrl, j = newrl; i <= oldrh; i++, j++) m[j] = a[i] + oldcl - newcl; - - return m; -} - -void free_ivector(int *v, int nl, int nh) { - free((char *) (v + nl)); -} - -void free_dvector(double *v, int nl, int nh) { - free((char *) (v + nl)); -} - -void free_dmatrix(double **m, int nrl, int nrh, int ncl, int nch) { - int i; - - for (i = nrh; i >= nrl; i--) free((char *) (m[i] + ncl)); - free((char *) (m + nrl)); -} \ No newline at end of file diff --git a/lib/cacode/nrutil.h b/lib/cacode/nrutil.h deleted file mode 100644 index 0de5f5f9b..000000000 --- a/lib/cacode/nrutil.h +++ /dev/null @@ -1,19 +0,0 @@ -// Public domain code from Yi-Kuo Yu & Stephen Altschul, NCBI - -float *vector(); -float **matrix(); -float **convert_matrix(); -double *dvector(); -double **dmatrix(); -int *ivector(); -int **imatrix(); -float **submatrix(); -void free_vector(); -void free_dvector(); -void free_ivector(); -void free_matrix(); -void free_dmatrix(); -void free_imatrix(); -void free_submatrix(); -void free_convert_matrix(); -void nrerror(); diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 320cd3a38..ef52ede7e 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -21,7 +21,6 @@ add_subdirectory(workflow) add_library(mmseqs-framework $ $ - $ ${alignment_header_files} ${alignment_source_files} ${clustering_header_files} diff --git a/src/commons/SubstitutionMatrix.cpp b/src/commons/SubstitutionMatrix.cpp index f15bc9981..d223fb53e 100644 --- a/src/commons/SubstitutionMatrix.cpp +++ b/src/commons/SubstitutionMatrix.cpp @@ -1,8 +1,7 @@ #include "SubstitutionMatrix.h" #include "Util.h" #include "Debug.h" -#include "lambda_calculator.h" - +// #include "lambda_calculator.h" #include #include @@ -60,32 +59,34 @@ SubstitutionMatrix::SubstitutionMatrix(const char *filename, float bitFactor, fl bool SubstitutionMatrix::estimateLambdaAndBackground(const double **scoreMatrix, int alphabetSize, double *pBack, double &lambda) { + Debug(Debug::ERROR) << "Custom Substitution Matrix not supported in the release. Please use previous release\n"; + return false; // We need to pass the parameters as 1-based pointers, hence the +1s and -1s. - std::vector cells(alphabetSize * (alphabetSize + 1)); - std::vector pointers(alphabetSize + 1); - - for (int i = 0; i < alphabetSize; ++i) { - pointers[i + 1] = &cells[i * alphabetSize]; - for (int j = 0; j < alphabetSize; ++j) { - cells[i * alphabetSize + j + 1] = scoreMatrix[i][j]; - } - } - - std::vector letterProbs1(alphabetSize, 0); - std::vector letterProbs2(alphabetSize, 0); - - lambda = calculate_lambda(&pointers[0], alphabetSize, - &letterProbs1[0] - 1, - &letterProbs2[0] - 1); - - for (int i = 0; i < alphabetSize; i++) { - pBack[i] = letterProbs1[i]; - } - - if (lambda < 0) - return false; //bad - else - return true; //good + // std::vector cells(alphabetSize * (alphabetSize + 1)); + // std::vector pointers(alphabetSize + 1); + + // for (int i = 0; i < alphabetSize; ++i) { + // pointers[i + 1] = &cells[i * alphabetSize]; + // for (int j = 0; j < alphabetSize; ++j) { + // cells[i * alphabetSize + j + 1] = scoreMatrix[i][j]; + // } + // } + + // std::vector letterProbs1(alphabetSize, 0); + // std::vector letterProbs2(alphabetSize, 0); + + // lambda = calculate_lambda(&pointers[0], alphabetSize, + // &letterProbs1[0] - 1, + // &letterProbs2[0] - 1); + + // for (int i = 0; i < alphabetSize; i++) { + // pBack[i] = letterProbs1[i]; + // } + + // if (lambda < 0) + // return false; //bad + // else + // return true; //good }