--- /dev/null
+changed
+void get_gauss_param_all_classes2(char sc_filenames[MAX_CLASS_NUMBER][MAXLINE],
+ int number_score_dim, double means[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
+ double covars[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
+ int number_of_classifications, char gauss_param[MAXLINE])
+to
+void get_gauss_param_all_classes2(char sc_filenames[MAX_CLASS_NUMBER][MAXLINE],
+ int number_score_dim, double means[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
+ double covars[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
+ char gauss_param[MAXLINE])
+
+by changing
+
+ for (class=0; class<number_of_classifications; class++) {
+
+to
+ for (class=0; class<NUMBER_CLASSES; class++) {
+
+
+
+
+changed
+void compute_submatrices2(
+ double means[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
+ double means_submatrix[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
+ double covars[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
+ int number_classes,
+ double inv[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
+ double det[MAX_CLASS_NUMBER],
+ char multi_lib[MAX_TABLE_NUMBER][MAXFUNCTNUM],
+ int old_num_dim_table0, int old_num_dim_table1,
+ int new_num_dim_table0, int new_num_dim_table1, int multi_trimer_pairs
+ )
+to
+void compute_submatrices2(
+ double means[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
+ double means_submatrix[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
+ double covars[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
+ double inv[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
+ double det[MAX_CLASS_NUMBER],
+ char multi_lib[MAX_TABLE_NUMBER][MAXFUNCTNUM],
+ int old_num_dim_table0, int old_num_dim_table1,
+ int new_num_dim_table0, int new_num_dim_table1
+ )
+changed
+ for (class=0; class<number_classes; class++)
+to
+ for (class=0; class<NUMBER_CLASSES; class++)
+
+everywhere changed
+ means_submatrix[class][dim1] = means[class]
+ [old_dimension(old_num_dim_table0, old_num_dim_table1,
+ new_num_dim_table0, new_num_dim_table1,
+ multi_lib, multi_trimer_pairs,dim1)];
+to
+ means_submatrix[class][dim1] = means[class]
+ [old_dimension(old_num_dim_table0, old_num_dim_table1,
+ new_num_dim_table0, new_num_dim_table1,
+ multi_lib, dim1)];
+
+
+
+changed
+int old_dimension(int old_num_dim_table0, int old_num_dim_table1,
+ int new_num_dim_table0, int new_num_dim_table1,
+ char multi_lib[MAX_TABLE_NUMBER][MAXFUNCTNUM],
+ int multi_trimer_pairs,
+ int new_dim_number)
+to
+int old_dimension(int old_num_dim_table0, int old_num_dim_table1,
+ int new_num_dim_table0, int new_num_dim_table1,
+ char multi_lib[MAX_TABLE_NUMBER][MAXFUNCTNUM],
+ int new_dim_number)
+
+changed
+
+type_class_score_convert(Sequence sequence,
+ double all_like[MAX_NUM_SCORE_DIM][MAXSEQLEN][POSNUM+1],
+ double bound, int new_only_coiled_classes,
+ int number_tables, int number_classes)
+to
+type_class_score_convert(Sequence sequence,
+ double all_like[MAX_NUM_SCORE_DIM][MAXSEQLEN][POSNUM+1],
+ double bound, int new_only_coiled_classes)
+
+
+ Replaced:
+
+int compute_dimension(int tablenum, int number_tables, int libnumber,
+ int number_score_dim,
+ int number_multi_lib[MAX_TABLE_NUMBER],
+ int multi_trimer_pairs)
+{
+ int prev_table;
+ int dimension=0;
+
+ if (!number_score_dim) /* old version of numbering. */
+ return (libnumber*number_tables + tablenum);
+ else { /* new version, works when use single freq score instead of paircoil*/
+ for (prev_table =0; prev_table<tablenum; prev_table++)
+ dimension+= compute_num_multilib(prev_table, number_multi_lib,
+ multi_trimer_pairs);
+
+ return (dimension + libnumber);
+ }
+}
+
+by
+
+
+int compute_dimension2(int tablenum, int libnumber,
+ int num_dist[MAX_TABLE_NUMBER],
+ int combine_dist[MAX_TABLE_NUMBER])
+{
+ int prev_table;
+ int dimension=0;
+
+ for (prev_table =0; prev_table<tablenum; prev_table++)
+ dimension+= num_table_dimensions(num_dist[prev_table],
+ combine_dist[prev_table]);
+
+ return (dimension + libnumber);
+}
+
+
+
+added
+
+int num_table_dimensions(int num_dist_table,
+ int combine_dist_table)
+{
+
+ return ((1-combine_dist_table)*num_dist_table +
+ combine_dist_table);
+}
+
+
+
+
+/**********************************************************/
+
+
+Changed
+
+
+
+void convert_raw_scores_to_gauss_prob_like2(
+ double all_raw_scores[MAX_NUM_SCORE_DIM][MAXSEQLEN][POSNUM+1],int seq_len,
+ int number_tables, double class_means[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
+ double inverse_covars[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
+ double determinants[MAX_CLASS_NUMBER],
+ int number_classes, double init_class_prob[MAX_CLASS_NUMBER],
+ int number_score_dim, int consider_only_positive_classes, double bound,
+ int Offset_to_Use, int last_class_gets_sum_prev)
+
+to
+
+void convert_raw_scores_to_gauss_prob_like2(
+ double all_raw_scores[MAX_NUM_SCORE_DIM][MAXSEQLEN][POSNUM+1],int seq_len,
+ int number_tables, double class_means[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
+ double inverse_covars[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
+ double determinants[MAX_CLASS_NUMBER],
+ int number_classes, double init_class_prob[MAX_CLASS_NUMBER],
+ int number_score_dim, int consider_only_positive_classes, double bound,
+ int Offset_to_Use)
+
+In that function:
+
+Cut
+ if (all_one || !last_class_gets_sum_prev)
+ last_class_for_scores = number_classes;
+ else last_class_for_scores = number_classes-1; /* Last class will be sum */
+ /* of prob for prev. class*/
+
+
+Cut
+ int last_class_for_scores, number_tables_to_write;
+
+cut
+ if (number_classes > number_tables) number_tables_to_write = number_classes;
+ else number_tables_to_write = number_tables;
+
+Changed
+ if (Offset_to_Use == -1) /* Want reg 7 to have max of other reg */
+ for (tablenum =0; tablenum<last_class_for_scores; tablenum++)
+
+to
+ if (Offset_to_Use == -1) /* Want reg 7 to have max of other reg */
+ for (tablenum =0; tablenum<number_classes; tablenum++)
+
+
+Changed
+ else /** Compute reg 7 as max of previous registers for offset -1 **/
+ for (tablenum=0; tablenum < last_class_for_scores; tablenum++)
+ like_in_class[tablenum] = max_class_like[tablenum];
+
+to
+
+
+ else /** Compute reg 7 as max of previous registers for offset -1 **/
+ for (tablenum=0; tablenum < number_classes; tablenum++)
+ like_in_class[tablenum] = max_class_like[tablenum];
+
+
+
+Changed
+
+ /** Temporary hack to set the class we are interested to the table. **/
+ /** So make class 1 =cctb, class 2 = trimer-, class 3 = pdb- in .paircoil*/
+ /** Lets ASSUME that class= number_classes-1 is always pdb- */
+ /** so for table>=number_classes-1 output sum of other classes prob. **/
+ /** (which is the positive prob (prob of being coiled)). **/
+ for (tablenum=0; tablenum < number_tables_to_write; tablenum++) {
+ if (tablenum < last_class_for_scores) {
+ all_raw_scores[tablenum][i][reg] = like_in_class[tablenum];
+ }
+ else {
+ all_raw_scores[tablenum][i][reg]=
+ calc_total_coil_likelihood(like_in_class, number_classes,reg,
+ Offset_to_Use,
+ &max_class_like[tablenum],
+ init_class_prob);
+ }
+
+to
+
+ for (tablenum=0; tablenum < number_classes; tablenum++) {
+ all_raw_scores[tablenum][i][reg] = like_in_class[tablenum];
+ }
+
+
+
+/********************************************************************/
+
+
+Cut
+
+
+
+int compute_num_multilib(int tablenum, int number_multi_lib[MAX_TABLE_NUMBER],
+ int multi_trimer_pairs)
+{
+ int use_pairs;
+
+ if (tablenum <0) return 0;
+ else if (tablenum ==0) use_pairs =1; /* Use pairs for cctb */
+ else if (tablenum ==1) use_pairs = multi_trimer_pairs;
+
+ if (!use_pairs) return 1;
+ else return number_multi_lib[tablenum];
+}
+
+
+
+changed
+
+void get_gauss_param_all_classes2(char sc_filenames[MAX_CLASS_NUMBER][MAXLINE],
+ int number_score_dim, double means[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
+ double covars[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
+ char gauss_param[MAXLINE])
+to
+
+void get_gauss_param_all_classes2(char sc_filenames[MAX_CLASS_NUMBER][MAXLINE],
+ int number_score_dim,
+ double means[MAX_CLASS_NUMBER][NUM_DIM_IN_ORIG_MATRIX],
+ double covars[MAX_CLASS_NUMBER]
+ [NUM_DIM_IN_ORIG_MATRIX][NUM_DIM_IN_ORIG_MATRIX],
+ char gauss_param[MAXLINE])
+
+
+
+Changed
+
+void compute_submatrices2(
+ double means[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
+ double means_submatrix[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
+ double covars[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
+ double inv[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
+ double det[MAX_CLASS_NUMBER],
+ char multi_lib[MAX_TABLE_NUMBER][MAXFUNCTNUM],
+ int old_num_dim_table0, int old_num_dim_table1,
+ int new_num_dim_table0, int new_num_dim_table1
+ )
+
+to
+void compute_submatrices2(
+ double means[MAX_CLASS_NUMBER][NUM_DIM_IN_ORIG_MATRIX],
+ double means_submatrix[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
+ double covars[MAX_CLASS_NUMBER]
+ [NUM_DIM_IN_ORIG_MATRIX][NUM_DIM_IN_ORIG_MATRIX],
+ double inv[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
+ double det[MAX_CLASS_NUMBER],
+ char multi_lib[MAX_TABLE_NUMBER][MAXFUNCTNUM],
+ int old_num_dim_table0, int old_num_dim_table1,
+ int new_num_dim_table0, int new_num_dim_table1
+ )
+
+Changed
+
+void multivariate_gauss_from_scfile2(char *sc_filename, int number_score_dim,
+ double mean[MAX_NUM_SCORE_DIM],
+ double covar[MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM])
+
+to
+void multivariate_gauss_from_scfile2(char *sc_filename, int number_score_dim,
+ double mean[NUM_DIM_IN_ORIG_MATRIX],
+ double covar[NUM_DIM_IN_ORIG_MATRIX][NUM_DIM_IN_ORIG_MATRIX])
+and in that function changed
+
+ long n_below_mean[MAX_NUM_SCORE_DIM];
+ long _counts[MAX_NUM_SCORE_DIM][-4*MINSCORE +1];
+ long *counts[MAX_NUM_SCORE_DIM];
+ int table,table2;
+ int all_places_good, place[MAX_NUM_SCORE_DIM];
+ int number_high=0, number_low=0;
+ int maxplaces[MAX_NUM_SCORE_DIM], minplaces[MAX_NUM_SCORE_DIM];
+
+ double score[MAX_NUM_SCORE_DIM];
+
+to
+ long n_below_mean[NUM_DIM_IN_ORIG_MATRIX];
+ long _counts[NUM_DIM_IN_ORIG_MATRIX][-4*MINSCORE +1];
+ long *counts[NUM_DIM_IN_ORIG_MATRIX];
+ int table,table2;
+ int all_places_good, place[NUM_DIM_IN_ORIG_MATRIX];
+ int number_high=0, number_low=0;
+ int maxplaces[NUM_DIM_IN_ORIG_MATRIX], minplaces[NUM_DIM_IN_ORIG_MATRIX];
+
+ double score[NUM_DIM_IN_ORIG_MATRIX];
git://source.jalview.org / jpred.git / blobdiff