--- /dev/null
+changed
+void PairCoilData (FILE *fgin, FILE **fpin, int *number_tables,
+ int ProlineFree, int table_to_remove_from,
+ char *input_filename, int mode,
+ double prior_freq_single[MAX_TABLE_NUMBER],
+ double prior_freq_pair[MAX_TABLE_NUMBER], int which_priors,
+ int which_priorp, int good_turing,
+ int structural_pos[POSNUM+1])
+to
+void PairCoilData (FILE *fgin, FILE **fpin, int *number_tables,
+ int ProlineFree, int table_to_remove_from,
+ char *input_filename, int mode)
+
+changed
+ if (!(mode & WEIGHTED_PROBS)) {
+
+ set_unimportant_pos_to_genbnk(many_pprobs[i], many_pprobp[i],
+ gprobs, gprobp, structural_pos);
+ estimate_database_probs(i, pfreqs[i], ptotals[i], many_pprobs,
+ pfreqp[i], ptotalp[i], many_pprobp,
+ ProlineFree, which_priors, which_priorp,
+ prior_freq_single[i],
+ prior_freq_pair[i], good_turing,
+ structural_pos);
+to
+ if (!(mode & WEIGHTED_PROBS)) {
+ estimate_database_probs(i, pfreqs[i], ptotals[i], many_pprobs,
+ pfreqp[i], ptotalp[i], many_pprobp,
+ ProlineFree);
+
+
+changed
+void recalc_prob(Sequence sequence, int input_table, int mode,
+ int which_priors, int which_priorp,
+ double prior_freq_single[MAX_TABLE_NUMBER],
+ double prior_freq_pair[MAX_TABLE_NUMBER],
+ int good_turing, int structural_pos[POSNUM+1])
+to
+void recalc_prob(Sequence sequence, int input_table, int mode)
+
+and
+ estimate_database_probs(input_table, pfreqs[input_table],
+ ptotals[input_table], many_pprobs,
+ pfreqp[input_table], ptotalp[input_table],
+ many_pprobp, ProlineFreeWindow, which_priors,
+ which_priorp, prior_freq_single[input_table],
+ prior_freq_pair[input_table], good_turing,
+ structural_pos);
+to
+ estimate_database_probs2(input_table, pfreqs[input_table],
+ ptotals[input_table], many_pprobs,
+ pfreqp[input_table], ptotalp[input_table],
+ many_pprobp, ProlineFreeWindow);
+
+
+
+
+
+in PairCoilData
+changed
+ for (i=0; i<*number_tables; i++)
+
+
+change
+
+void average_score_over_coils3(Sequence seq,
+ double StructureResLike[MAXSEQLEN][POSNUM+1],
+ double StructureCoilLike[MAXSEQLEN][POSNUM+1],
+ double CoilLike[MAXSEQLEN][POSNUM+1],
+ int weighted_avg, int offset_to_use,
+ char offsets[MAXSEQLEN],
+ int start_at_reg_shift, double bound,
+ int avg_max)
+to
+void average_score_over_coils3(Sequence seq,
+ double StructureResLike[MAXSEQLEN][POSNUM+1],
+ double StructureCoilLike[MAXSEQLEN][POSNUM+1],
+ double CoilLike[MAXSEQLEN][POSNUM+1],
+ int offset_to_use,
+ char offsets[MAXSEQLEN],
+ int start_at_reg_shift, double bound,
+ int avg_max)
+
+
+replaced
+
+void MultiCoilDimensionScore (int mode, Sequence sequence, char lib[MAXFUNCTNUM], double *maxscore, int table, char offsets[MAXSEQLEN], double scores[MAXSEQLEN][POSNUM+1], int offset_to_use, int pairs)
+by
+void MultiCoilDimensionScore (int mode, Sequence sequence, char lib[MAXFUNCTNUM], double *maxscore, int table, char offsets[MAXSEQLEN], double scores[MAXSEQLEN][POSNUM+1], int offset_to_use)
+
+
+
+in PairCoilData:
+ changed
+ else if (i > 1) { /* If there are 2 other tables average them. */
+ average_many_pprob(i);
+ combine_many_weight(i);
+ }
+ else {
+ fprintf(stderr, "\nCould not make combination table number %d.",i);
+ fprintf(stderr, "\nAll later tables will be unavailable.\n");
+ *number_tables=i;
+ }
+
+to
+ else {
+ fprintf(stderr, "\nCould not make input table number %d.",i);
+ exit(-1);
+ }
+
+
+and
+ if (*number_tables != i) { /* Just check for above where couldn't */
+ #ifdef AVG_WEIRD_PROBS /* make table. */
+ calc_weird_pprob_avg(many_pprobp[i], many_pprobs[i]);
+ #else
+ calc_weird_pprob_sum(many_pprobp[i], many_pprobs[i]);
+ #endif
+ }
+to
+#ifdef AVG_WEIRD_PROBS /* make table. */
+ calc_weird_pprob_avg(many_pprobp[i], many_pprobs[i]);
+#else
+ calc_weird_pprob_sum(many_pprobp[i], many_pprobs[i]);
+#endif
+
+
+
+/*******************************ROUND 2 *****************************/
+CUT
+
+/* #define PAIR_PIR_TXT "/local/bab/pir_pair.txt" */
+
+
+double many_weights[MAX_TABLE_NUMBER][AANUM][POSNUM],
+ many_weightp[MAX_TABLE_NUMBER][AANUM][AANUM][POSNUM][POSNUM];
+
+double dist_weight[POSNUM];
+double prior_probs[NUM_RES_TYPE][POSNUM],
+ prior_probp[NUM_RES_TYPE][NUM_RES_TYPE][POSNUM][POSNUM];
+double (*weights)[POSNUM];
+double (*weightp)[AANUM][POSNUM][POSNUM];
+
+typedef double real;
+
+
+in switch_tables()
+ cut weights= many_weights[table];
+ weightp= many_weightp[table];
+
+
+Cut
+/* NOTE THAT THE many_pprob variables are globally defined in interface.h. */
+/** This gives the current_table probabilities the average of tables 1 and 2 */
+void average_many_pprob(int current_table)
+{
+ int reg1, reg2, res1, res2;
+
+ for (res1=0; res1<AANUM; res1++)
+ for (reg1=0; reg1<POSNUM; reg1++) {
+ many_pprobs[current_table][res1][reg1] =
+ (many_pprobs[0][res1][reg1] + many_pprobs[1][res1][reg1])/2;
+
+ for (res2=0; res2<AANUM; res2++)
+ for (reg2=0; reg2<POSNUM; reg2++)
+ many_pprobp[current_table][res1][res2][reg1][reg2] =
+ (many_pprobp[0][res1][res2][reg1][reg2] +
+ many_pprobp[1][res1][res2][reg1][reg2]) /2;
+ }
+}
+
+
+in recalc_prob()
+ cut
+ else { /* Do weighted paircoil. */
+ calcweight(pfreqs[input_table], pfreqp[input_table],gprobs, gprobp,
+ many_weights[input_table], many_weightp[input_table],
+ ptotals[input_table], ptotalp[input_table],NULL);
+
+ calc_weighted_pprobs(pfreqs[input_table], ptotals[input_table],
+ many_pprobs[input_table],
+ ProlineFreeWindow, many_weights[input_table],
+ gprobs, NULL);
+ calc_weighted_pprobp(pfreqp[input_table], ptotalp[input_table],
+ many_pprobs[input_table],
+ many_pprobp[input_table], ProlineFreeWindow,
+ many_weightp[input_table],
+ gprobp, NULL);
+ }
+
+and
+ average_many_pprob(2);
+ combine_many_weight(2); /*** Recompute the combination table probs. **/
+
+
+From PairCoilData, cut:
+ FILE *weight_file=NULL;
+ extern char weightfile_outname[MAXLINE];
+
+ if ((strcmp(weightfile_outname, "/dev/null")) || (mode & WEIGHTED_PROBS))
+ weight_file = sopen(weightfile_outname,"w");
+ if (weight_file) fprintf(weight_file,"\nTable number %d\n",i);
+
+and changed:
+
+ if (!(mode & WEIGHTED_PROBS)) {
+ estimate_database_probs(i, pfreqs[i], ptotals[i], many_pprobs,
+ pfreqp[i], ptotalp[i], many_pprobp,
+ ProlineFree);
+/******************
+ calcpprobs(pfreqs[i], ptotals[i], many_pprobs[i], ProlineFree);
+ calcpprobp(pfreqp[i], ptotalp[i], many_pprobs[i], many_pprobp[i],
+ ProlineFree);
+********************/
+
+ if (weight_file) printfreq_prob(pfreqs[i],pfreqp[i],
+ weight_file,many_pprobs[i], many_pprobp[i]);
+ }
+ else { /* Do weighted paircoil. */
+ double bonnies_pprobs[NUM_RES_TYPE][POSNUM];
+ double bonnies_pprobp[NUM_RES_TYPE][NUM_RES_TYPE][POSNUM][POSNUM];
+
+ calcweight(pfreqs[i], pfreqp[i],gprobs, gprobp,
+ many_weights[i], many_weightp[i],
+ ptotals[i], ptotalp[i],weight_file);
+
+ calcpprobs(pfreqs[i], ptotals[i], bonnies_pprobs, ProlineFree);
+ calcpprobp(pfreqp[i], ptotalp[i], bonnies_pprobs, bonnies_pprobp,
+ ProlineFree);
+
+ calc_weighted_pprobs(pfreqs[i], ptotals[i], many_pprobs[i],
+ ProlineFree, many_weights[i], gprobs, NULL);
+ calc_weighted_pprobp(pfreqp[i], ptotalp[i], many_pprobs[i],
+ many_pprobp[i], ProlineFree, many_weightp[i],
+ gprobp, NULL);
+
+ printweight(pfreqs[i],pfreqp[i],gprobs,gprobp,many_weights[i], many_weightp[i], ptotals[i],ptotalp[i],weight_file, many_pprobs[i], many_pprobp[i],bonnies_pprobs,bonnies_pprobp);
+ }
+
+
+
+to
+
+
+ estimate_database_probs(i, pfreqs[i], ptotals[i], many_pprobs,
+ pfreqp[i], ptotalp[i], many_pprobp,
+
+
+cut
+
+ if (mode & WEIGHTED_PROBS) fclose(weight_file);
+ calc_distance_weights(dist,weight);
+
+
+Moved functions:
+ PairCoilDiffer and average_scores_over_coil2 into file
+PairCoilDiffer_cuts.c
+and PairCoilDifferDimension() and zero_out_non_coils() and
+ zero_out_bad_windows( into PairCoilDiffer.c
+
+
+
+
git://source.jalview.org / jpred.git / blobdiff