--- /dev/null
+ else if(!strncmp(buf,"differ_lib",10)) {/* Read in a variable number */
+ char *end; /* of distances to be used in */
+ int val; /* PairCoilDiffer scores. */
+ int do_each_dist_separately =0;
+
+ if (!strncmp(buf,"differ_lib dim",14))
+ do_each_dist_separately = 1;
+
+ if (!strncmp(buf,"differ_lib = all",16))
+ {
+ /* For scscore.c will go through each dist on own*/
+ for (i=0; i<7; i++)
+ differ_lib[i] = i;
+ *differ_functnum = 1;
+ *number_differ_lib = 7;
+ printf("differ_lib = all dimensions");
+ }
+
+ else {
+ if (do_each_dist_separately)
+ printf("differ_lib dimensions= ");
+ else printf("differ_lib = ");
+
+ tmp = strchr(buf, '=');
+ tmp++;
+ /* strip leading whitespace */
+ while(!isdigit(*tmp)&&*tmp) tmp++;
+ while(end = strchrs(tmp, " \t\n\r")) {
+ *end = 0;
+ end++;
+ /* strip leading whitespace */
+ while(*tmp&&!isdigit(*tmp)) tmp++;
+ if(*tmp) {
+ val = atoi(tmp);
+ differ_lib[(*differ_functnum)++] = val;
+ printf("%d ", val);
+ }
+ tmp = end;
+ }
+ printf("\n");
+
+ if (do_each_dist_separately) {
+ *number_differ_lib = *differ_functnum;
+ *differ_functnum=1;
+ /* Each distance is a library to itself. */
+ }
+ }
+ }
+
+
+
+ else if (!strncmp(buf, "New coil at reg shift",21))
+ *start_coil_at_reg_shift = 1;
+
+
+ else if(!strncmp(buf,"differ class scores dimer",25)) {
+
+ sscanf(buf,"differ class scores dimer = %s",
+ differ_class_sc_filenames[0]);
+ printf("differ class scores dimers = %s\n",
+ differ_class_sc_filenames[0]);
+
+ }
+
+ else if(!strncmp(buf,"differ gauss_param",18)) {
+ sscanf(buf,"differ gauss_param = %s",differ_gaussian_parameters);
+ printf("differ gauss_param = %s\n",differ_gaussian_parameters);
+ }
+
+
+ else if(!strncmp(buf,"prior freq single",17)) {
+ int the_table;
+ if (!strncmp(buf,"prior freq single =",19)) {
+ sscanf(buf,"prior freq single = %lf", &prior_freq_single[0]);
+ for (the_table =0; the_table < MAX_TABLE_NUMBER; the_table++) {
+ prior_freq_single[the_table] = prior_freq_single[0];
+ printf("prior_freq_single %d = %lf\n", the_table,
+ prior_freq_single[the_table]);
+ }
+ } /* All tables get same scale0. **/
+ else {
+ sscanf(buf,"prior freq single %d", &the_table);
+ sscanf(buf,"prior freq single %d = %lf", &the_table,
+ &prior_freq_single[the_table-1]);
+ printf("prior_freq_single %d = %lf\n",
+ the_table,prior_freq_single[the_table-1]);
+ }
+ }
+ else if(!strncmp(buf,"prior freq pair",15)) {
+ int the_table;
+ if (!strncmp(buf,"prior freq pair =",17)) {
+ sscanf(buf,"prior freq pair = %lf", &prior_freq_pair[0]);
+ for (the_table =0; the_table < MAX_TABLE_NUMBER; the_table++) {
+ prior_freq_pair[the_table] = prior_freq_pair[0];
+ printf("prior_freq_pair %d = %lf\n", the_table,
+ prior_freq_pair[the_table]);
+ }
+ } /* All tables get same scale0. **/
+ else {
+ sscanf(buf,"prior freq pair %d", &the_table);
+ sscanf(buf,"prior freq pair %d = %lf", &the_table,
+ &prior_freq_pair[the_table-1]);
+ printf("prior_freq_pair %d = %lf\n",
+ the_table,prior_freq_pair[the_table-1]);
+ }
+ }
+
+
+/***********************************************************/
+ else if(!strncmp(buf,"structurally important pos",26)) {
+ char *end;
+ int val;
+
+ i =0;
+ printf("structurally important pos = ");
+ tmp = strchr(buf, '=');
+ tmp++;
+ /* strip leading whitespace */
+ while(!islower(*tmp)&&*tmp) tmp++;
+ while(end = strchrs(tmp, " \t\n\r")) {
+ *end = 0;
+ end++;
+ /* strip leading whitespace */
+ while(*tmp&&!islower(*tmp)) tmp++;
+ if(*tmp) {
+ val = (*tmp)- 'a';
+ if ((val>=7) || (val<0))
+ printf(" **ILLEGAL position %c ignored** ", 'a' + val);
+ else {
+ printf("%c ", 'a' + val);
+ structural_pos[i]= val;
+ i++;
+ }
+ }
+ tmp = end;
+ }
+ printf("\n");
+ structural_pos[i] = -1; /* Flag that at end. */
+ }
+
+ else if(!strncmp(buf,"good_turing",11)) {
+ *good_turing_fixed_disc = 1;
+ printf("Estimating prob using good_turing method.\n");
+ }
+ else if(!strncmp(buf,"modified_good_turing",20)) {
+ *good_turing_fixed_disc = 3;
+ printf("Estimating prob using modified good_turing method.\n");
+ }
+ else if(!strncmp(buf,"fixed_disc",10)) {
+ *good_turing_fixed_disc = 2;
+ printf("Estimating prob using fixed_discount method with discount determined by SCALE0.\n");
+ }
+/**********************************************************/
+ else if(!strncmp(buf,"zero freqs from dimers",22)) {
+ *priors =-1;
+ printf("zero freqs for trimers from dimers.\n");
+ }
+
+ else if(!strncmp(buf,"add priors if less than dimer expectation",41)) {
+ *priors =-2;
+ printf("Add priors only if freq is less than dimer expectation.\n");
+ }
+
+ else if(!strncmp(buf,"prior singles from",18)) {
+ /* Reads in what to use as */
+ tmp = &buf[19]; /* One past space */
+ if (!strncmp(tmp,"dimers",6 )) { /* prior prob in estimating */
+ *priors = 1;
+ printf("priors from dimers\n"); /* trimer table probs. */
+ }
+ else if (!strncmp(tmp,"genbnk",6 )) {
+ *priors = 2;
+ printf("priors from genbnk\n");
+ }
+ else if (!strncmp(tmp,"average",7 )) {
+ *priors = 3;
+ printf("priors from average of dimers and genbnk\n");
+ }
+ }
+
+ else if(!strncmp(buf,"zero freqp from dimers",22)) {
+ *priorp =-1;
+ printf("zero freqp for trimers from dimers.\n");
+ }
+ else if(!strncmp(buf,"add priorp if less than dimer expectation",41)) {
+ *priorp =-2;
+ printf("Add priorp only if freq is less than dimer expectation.\n");
+ }
+
+ else if(!strncmp(buf,"prior pairs from",16)) {
+ /* Reads in what to use as */
+ tmp = &buf[17]; /* One past space */
+ if (!strncmp(tmp,"dimers",6 )) { /* prior prob in estimating */
+ *priorp = 1;
+ printf("priorp from dimers\n"); /* trimer table probs. */
+ }
+ else if (!strncmp(tmp,"genbnk",6 )) {
+ *priorp = 2;
+ printf("priorp from genbnk\n");
+ }
+ else if (!strncmp(tmp,"average",7 )) {
+ *priorp = 3;
+ printf("priorp from average of dimers and genbnk\n");
+ }
+
+ else if (!strncmp(tmp,"product of singles",18 )) {
+ *priorp = 4;
+ printf("priorp from product of singles\n");
+ }
+ }
+/**************************************************************/
+ else if(!strncmp(buf,"differentiator window length",28)) {
+ sscanf(buf,"differentiator window length = %d",
+ differ_window_length);
+ printf("differentiator window length = %d\n",
+ *differ_window_length);
+ }
+
+
+
+
+/**************************************************************/
+/************************Round 2 of cuts **********************/
+/**************************************************************/
+
+ else if(!strncmp(buf,"coil conflicts",14)) {
+ if (!strncmp(buf,"coil conflicts dir",19)){ /* automate the name **/
+ sscanf(buf,"coil conflicts dir = %s",name);
+ strcat(name,input_name);
+ strcat(name,".coil_conflicts");
+
+ /**** Apend on the library distances. ***/
+ if (multi_functnum[0] == 1) { /* make sure do dimension scores */
+ lib_numb=0;
+ while (lib_numb < number_multi_lib[0]) {
+ sprintf(&buf[lib_numb],"%d",multi_lib[0][lib_numb]);
+ lib_numb++; }
+ sprintf(&buf[lib_numb],"_");
+ strncat(name,buf,number_multi_lib[0]+1);
+
+
+ lib_numb=0;
+ while (lib_numb < number_multi_lib[1]) {
+ sprintf(&buf[lib_numb],"%d",multi_lib[1][lib_numb]);
+ lib_numb++; }
+ strncat(name,buf,number_multi_lib[1]);
+ }
+
+ }
+ else sscanf(buf,"coil conflicts = %s",name);
+ *flog_coil_conflicts = sopen(name,"w");
+ printf("coil conflicts = %s\n",name);
+ }
+
+changed
+ else if(!strncmp(buf,"table",5)) { /* Get location of postable file */
+ sscanf(buf,"table %d = %s",&i, name);
+ if (strcmp("combination",name)) { /* If it is combination, just */
+ fpin[*number_tables] = sopen(name,"r"); /* increment number tables*/
+ } /* Otherwise open file. */
+ printf("table %d = %s\n",*number_tables,name);
+ (*number_tables)++;
+ fpin[*number_tables]= NULL;
+ }
+
+to
+
+ else if(!strncmp(buf,"table",5)) { /* Get location of postable file */
+ sscanf(buf,"table %d = %s",&i, name);
+ fpin[i-1] = sopen(name,"r");
+ printf("table %d = %s\n",i,name);
+ (*number_tables)++;
+ fpin[i]= NULL;
+ }
+
+
+changed
+ if (!strncmp(buf,"multi_lib dim =",15)) {
+ first_table=0; last_table=*number_tables;
+ } /* All tables get same lib. **/
+ else {
+ sscanf(buf,"multi_lib dim %d", &last_table);
+ first_table = last_table-1;
+ }
+ }
+ else if (!strncmp(buf,"multi_lib =",11)) {
+ first_table=0; last_table=*number_tables;
+ } /* All tables get same lib. **/
+
+to
+
+ if (!strncmp(buf,"multi_lib dim =",15)) {
+ first_table=0; last_table=NUMBER_TABLES;
+ } /* All tables get same lib. **/
+
+ else {
+ sscanf(buf,"multi_lib dim %d", &last_table);
+ first_table = last_table-1;
+ }
+ }
+ else if (!strncmp(buf,"multi_lib =",11)) {
+ first_table=0; last_table= NUMBER_TABLES;
+ } /* All tables get same lib. **/
+
+
+
+
+cut
+ if (*weighted_avg)
+ strcat(name,"_WtdAvg");
+
+
+ else if (!strncmp(buf,"weighted_avg", 12)) {
+ sscanf(buf, "weighted_avg = %d", weighted_avg);
+ /* 0 means just avg. res score over coil. */
+ /* 1 means do weighted avg. by likelihoods */
+ if ( (*weighted_avg !=0) &&(*weighted_avg !=1)) {
+ fprintf(stderr,"\n Illegal weighted_avg method. Defaults to 0.\n");
+ *weighted_avg = 0;
+ }
+ else fprintf(stderr,"weighted_avg = %d\n", *weighted_avg);
+ }
+ }
+
+
+
+
+cut
+
+ else if(!strncmp(buf,"tab diff stats",14)) {
+ sscanf(buf,"tab diff stats = %s",table_diff_stats_filename);
+ printf("tablediff stats = %s\n",table_diff_stats_filename);
+ }
+ else if(!strncmp(buf,"weightfile outname",18)) {
+ sscanf(buf,"weightfile outname = %s",weightfile_outname);
+ printf("weightfile outname = %s\n",weightfile_outname);
+ }
+
+
+changed
+
+ else if(!strncmp(buf,"class scores combo",18)) {
+ sscanf(buf,"class scores combo %d with init prob %lf = %s",&i,
+ &init_class_prob[*number_classes],
+ class_sc_filenames[0][*number_classes]);
+ printf("combo class scores %d = %s with init prob %lf\n",
+ *number_classes,class_sc_filenames[0][*number_classes],
+ init_class_prob[*number_classes]); /* likelihood lines. */
+ (*number_classes)++;
+ class_sc_filenames[0][*number_classes][0]= ',';
+ }
+
+
+ else if(!strncmp(buf,"class scores max",16)) {
+ sscanf(buf,"class scores max %d with init prob %lf = %s",&i,
+ &init_class_prob[number_max_classes],
+ class_sc_filenames[1][number_max_classes]);
+ printf("max class scores %d = %s with init prob %lf\n",
+ number_max_classes,class_sc_filenames[1][number_max_classes],
+ init_class_prob[number_max_classes]); /* likelihood lines. */
+ number_max_classes++;
+ class_sc_filenames[1][number_max_classes][0]= ',';
+ }
+
+to
+ else if(!strncmp(buf,"class scores combo",18)) {
+ sscanf(buf,"class scores combo %d with init prob %lf = %s",&i,
+ &init_class_prob[i-1],
+ class_sc_filenames[0][i-1]);
+ printf("combo class scores %d = %s with init prob %lf\n",
+ i,class_sc_filenames[0][i-1],
+ init_class_prob[*number_classes]); /* likelihood lines. */
+ class_sc_filenames[0][i][0]= ',';
+ }
+
+
+ else if(!strncmp(buf,"class scores max",16)) {
+ sscanf(buf,"class scores max %d with init prob %lf = %s",&i,
+ &init_class_prob[i-1],
+ class_sc_filenames[1][i-1]);
+ printf("max class scores %d = %s with init prob %lf\n",
+ i,class_sc_filenames[1][i-1],
+ init_class_prob[i-1]); /* likelihood lines. */
+ class_sc_filenames[1][i][0]= ',';
+
+
+
+CUT
+ else if(!strncmp(buf,"average differentiator by coil window",37)) {
+ *which_differentiator = 4;
+ printf("The differentiator score is over the entire coiled region\n");
+ }
+
+
+ else if(!strncmp(buf,"differentiator by coil window",29)) {
+ *which_differentiator = 3;
+ printf("The differentiator score is over the entire coiled region\n");
+ }
+ else if(!strncmp(buf,"differentiator by window score",30)) {
+ *which_differentiator = 1;
+ printf("The differentiator residue score is the score of the window starting at that residue\n");
+ }
+ else if(!strncmp(buf,"differentiator by max-min window score",38)) {
+ *which_differentiator = 2;
+ printf("The differentiator residue score is the scores for the max and min window containing that residue\n");
+ }
+
+
+
+
+Completely rewrote stuff to read in multi_lib to deal with variables
+num_dist and combined_dist.
+
+
+Cut
+
+ else if(!strncmp(buf,"differ class scores trimer",26)) {
+
+ sscanf(buf,"differ class scores trimer = %s",
+ differ_class_sc_filenames[1]);
+ printf("differ class scores trimers = %s\n",
+ differ_class_sc_filenames[1]);
+
+ }
+
+
+Changed
+
+ lib_numb=0;
+ while (lib_numb < number_multi_lib[0]) {
+ sprintf(&buf[lib_numb],"%d",multi_lib[0][lib_numb]);
+ lib_numb++; }
+ sprintf(&buf[lib_numb],"_");
+ strncat(name,buf,number_multi_lib[0]+1);
+
+ lib_numb=0;
+ while (lib_numb < number_multi_lib[1]) {
+ sprintf(&buf[lib_numb],"%d",multi_lib[1][lib_numb]);
+ lib_numb++; }
+ strncat(name,buf,number_multi_lib[1]);
+
+to
+
+ while (lib_numb < num_dist[0]) {
+ sprintf(&buf[lib_numb],"%d",multi_lib[0][lib_numb]);
+ lib_numb++; }
+ sprintf(&buf[lib_numb],"_");
+ strncat(name,buf,num_dist[0]+1);
+
+ lib_numb=0;
+ while (lib_numb < num_dist[1]) {
+ sprintf(&buf[lib_numb],"%d",multi_lib[1][lib_numb]);
+ lib_numb++; }
+ strncat(name,buf,num_dist[1]);
+
+
+
+Changed
+ /**** Apend on the library distances. ***/
+ if (multi_functnum[0] == 1) { /* make sure do dimension scores */
+ lib_numb=0;
+to
+ if (combine_dist[0] == 0)
+
+
+
+Cut
+ class_sc_filenames[0][number_classes][0]= ',';
+and
+ class_sc_filenames[1][number_max_classes][0]= ',';
+ }
+
+from when reading in class filenames.
+
+
+
+Modified stuff that reads in "coil scores = ...."
+so can also read it in as "seq scores = ...."
+and seq by_coil_or_seq based on if used "coil" or "seq".
+Therefore, could eliminate
+ else if (!strncmp(buf,"By coil",7))
+ *by_coil_or_seq = 0;
+ else if (!strncmp(buf,"By seq",6))
+ *by_coil_or_seq =2;
+but kept
+ else if (!strncmp(buf,"By seq pos regions",18))
+ *by_coil_or_seq =1;
+
git://source.jalview.org / jpred.git / blobdiff