/* Menus and command line interface for Clustal W */ /* DES was here MARCH. 1994 */ /* DES was here SEPT. 1994 */ #include #include #include #include #include #include #include #include "clustalw.h" static jmp_buf jmpbuf; #ifndef VMS #ifndef AIX #define BADSIG (void (*)())-1 #endif #endif static void jumper(int); static void jumper(int i) { (void)i; longjmp(jmpbuf,1); } /* * Prototypes */ static void pair_menu(void); static void multi_menu(void); static void gap_penalties_menu(void); static void multiple_align_menu(void); /* multiple alignments menu */ static void profile_align_menu(void); /* profile " " */ static void phylogenetic_tree_menu(void); /* NJ trees/distances menu */ static void format_options_menu(void); /* format of alignment output */ static void tree_format_options_menu(void); /* format of tree output */ static void ss_options_menu(void); static sint secstroutput_options(void); static sint read_matrix(const char *title,MatMenu menu, char *matnam, sint matn, short *mat, short *xref); /* * Global variables */ extern float gap_open, gap_extend; extern float dna_gap_open, dna_gap_extend; extern float prot_gap_open, prot_gap_extend; extern float pw_go_penalty, pw_ge_penalty; extern float dna_pw_go_penalty, dna_pw_ge_penalty; extern float prot_pw_go_penalty, prot_pw_ge_penalty; extern float transition_weight; extern char revision_level[]; extern sint wind_gap,ktup,window,signif; extern sint dna_wind_gap, dna_ktup, dna_window, dna_signif; extern sint prot_wind_gap,prot_ktup,prot_window,prot_signif; extern sint nseqs; extern sint divergence_cutoff; extern sint debug; extern Boolean neg_matrix; extern Boolean quick_pairalign; extern Boolean reset_alignments_new; /* DES */ extern Boolean reset_alignments_all; /* DES */ extern sint gap_dist; extern Boolean no_var_penalties, no_hyd_penalties, no_pref_penalties; extern sint output_order; extern sint profile_no; extern short usermat[], pw_usermat[]; extern short aa_xref[], pw_aa_xref[]; extern short userdnamat[], pw_userdnamat[]; extern short dna_xref[], pw_dna_xref[]; extern Boolean lowercase; /* Flag for GDE output - set on comm. line*/ extern Boolean cl_seq_numbers; extern Boolean seqRange; /* to append sequence range with seq names, Ranu */ extern Boolean output_clustal, output_nbrf, output_phylip, output_gcg, output_gde, output_nexus; extern Boolean output_fasta; /* Ramu */ extern Boolean output_tree_clustal, output_tree_phylip, output_tree_distances,output_tree_nexus; extern sint bootstrap_format; extern Boolean tossgaps, kimura; extern Boolean percent; extern Boolean usemenu; extern Boolean showaln, save_parameters; extern Boolean dnaflag; extern Boolean use_ambiguities; extern char hyd_residues[]; extern char mtrxname[], pw_mtrxname[]; extern char dnamtrxname[], pw_dnamtrxname[]; extern char seqname[]; extern sint output_struct_penalties; extern Boolean use_ss1, use_ss2; extern Boolean empty; extern Boolean profile1_empty, profile2_empty; /* whether or not profiles */ extern char profile1_name[FILENAMELEN+1]; extern char profile2_name[FILENAMELEN+1]; extern Boolean use_endgaps; extern sint matnum,pw_matnum; extern sint dnamatnum,pw_dnamatnum; extern sint helix_penalty; extern sint strand_penalty; extern sint loop_penalty; extern sint helix_end_minus; extern sint helix_end_plus; extern sint strand_end_minus; extern sint strand_end_plus; extern sint helix_end_penalty; extern sint strand_end_penalty; extern MatMenu matrix_menu; extern MatMenu pw_matrix_menu; extern MatMenu dnamatrix_menu; static char phylip_name[FILENAMELEN]=""; static char clustal_name[FILENAMELEN]=""; static char dist_name[FILENAMELEN]=""; static char nexus_name[FILENAMELEN]=""; static char pim_name[FILENAMELEN]=""; static char p1_tree_name[FILENAMELEN]=""; static char p2_tree_name[FILENAMELEN]=""; static const char *secstroutput_txt[] = { "Secondary Structure", "Gap Penalty Mask", "Structure and Penalty Mask", "None" }; static char *lin1, *lin2, *lin3; void init_amenu(void) { lin1 = (char *)ckalloc( (MAXLINE+1) * sizeof (char) ); lin2 = (char *)ckalloc( (MAXLINE+1) * sizeof (char) ); lin3 = (char *)ckalloc( (MAXLINE+1) * sizeof (char) ); } void main_menu(void) { int catchint; catchint = signal(SIGINT, SIG_IGN) != SIG_IGN; if (catchint) { if (setjmp(jmpbuf) != 0) fprintf(stdout,"\n.. Interrupt\n"); #ifdef UNIX if (signal(SIGINT,jumper) == BADSIG) fprintf(stdout,"Error: signal\n"); #else if (signal(SIGINT,SIG_DFL) == BADSIG) fprintf(stdout,"Error: signal\n"); #endif } while(TRUE) { fprintf(stdout,"\n\n\n"); fprintf(stdout," **************************************************************\n"); fprintf(stdout," ******** CLUSTAL %s Multiple Sequence Alignments ********\n",revision_level); fprintf(stdout," **************************************************************\n"); fprintf(stdout,"\n\n"); fprintf(stdout," 1. Sequence Input From Disc\n"); fprintf(stdout," 2. Multiple Alignments\n"); fprintf(stdout," 3. Profile / Structure Alignments\n"); fprintf(stdout," 4. Phylogenetic trees\n"); fprintf(stdout,"\n"); fprintf(stdout," S. Execute a system command\n"); fprintf(stdout," H. HELP\n"); fprintf(stdout," X. EXIT (leave program)\n\n\n"); getstr("Your choice",lin1, MAXLINE+1); switch(toupper(*lin1)) { case '1': seq_input(FALSE); phylip_name[0]=EOS; clustal_name[0]=EOS; dist_name[0]=EOS; nexus_name[0]=EOS; pim_name[0]=EOS; break; case '2': multiple_align_menu(); break; case '3': profile_align_menu(); break; case '4': phylogenetic_tree_menu(); break; case 'S': do_system(); break; case '?': case 'H': get_help('1'); break; case 'Q': case 'X': exit(0); break; default: fprintf(stdout,"\n\nUnrecognised Command\n\n"); break; } } } static void multiple_align_menu(void) { int catchint; catchint = signal(SIGINT, SIG_IGN) != SIG_IGN; if (catchint) { if (setjmp(jmpbuf) != 0) fprintf(stdout,"\n.. Interrupt\n"); #ifdef UNIX if (signal(SIGINT,jumper) == BADSIG) fprintf(stdout,"Error: signal\n"); #else if (signal(SIGINT,SIG_DFL) == BADSIG) fprintf(stdout,"Error: signal\n"); #endif } while(TRUE) { fprintf(stdout,"\n\n\n"); fprintf(stdout,"****** MULTIPLE ALIGNMENT MENU ******\n"); fprintf(stdout,"\n\n"); fprintf(stdout," 1. Do complete multiple alignment now (%s)\n", (!quick_pairalign) ? "Slow/Accurate" : "Fast/Approximate"); fprintf(stdout," 2. Produce guide tree file only\n"); fprintf(stdout," 3. Do alignment using old guide tree file\n\n"); fprintf(stdout," 4. Toggle Slow/Fast pairwise alignments = %s\n\n", (!quick_pairalign) ? "SLOW" : "FAST"); fprintf(stdout," 5. Pairwise alignment parameters\n"); fprintf(stdout," 6. Multiple alignment parameters\n\n"); fprintf(stdout," 7. Reset gaps before alignment?"); if(reset_alignments_new) fprintf(stdout," = ON\n"); else fprintf(stdout," = OFF\n"); fprintf(stdout," 8. Toggle screen display = %s\n", (!showaln) ? "OFF" : "ON"); fprintf(stdout," 9. Output format options\n"); fprintf(stdout,"\n"); fprintf(stdout," S. Execute a system command\n"); fprintf(stdout," H. HELP\n"); fprintf(stdout," or press [RETURN] to go back to main menu\n\n\n"); getstr("Your choice",lin1, MAXLINE+1); if(*lin1 == EOS) return; switch(toupper(*lin1)) { case '1': align(phylip_name); break; case '2': make_tree(phylip_name); break; case '3': get_tree(phylip_name); break; case '4': quick_pairalign ^= TRUE; break; case '5': pair_menu(); break; case '6': multi_menu(); break; case '7': reset_alignments_new ^= TRUE; if(reset_alignments_new==TRUE) reset_alignments_all=FALSE; break; case '8': showaln ^= TRUE; break; case '9': format_options_menu(); break; case 'S': do_system(); break; case '?': case 'H': get_help('2'); break; case 'Q': case 'X': return; default: fprintf(stdout,"\n\nUnrecognised Command\n\n"); break; } } } static void profile_align_menu(void) { int catchint; catchint = signal(SIGINT, SIG_IGN) != SIG_IGN; if (catchint) { if (setjmp(jmpbuf) != 0) fprintf(stdout,"\n.. Interrupt\n"); #ifdef UNIX if (signal(SIGINT,jumper) == BADSIG) fprintf(stdout,"Error: signal\n"); #else if (signal(SIGINT,SIG_DFL) == BADSIG) fprintf(stdout,"Error: signal\n"); #endif } while(TRUE) { fprintf(stdout,"\n\n\n"); fprintf(stdout,"****** PROFILE AND STRUCTURE ALIGNMENT MENU ******\n"); fprintf(stdout,"\n\n"); fprintf(stdout," 1. Input 1st. profile "); if (!profile1_empty) fprintf(stdout,"(loaded)"); fprintf(stdout,"\n"); fprintf(stdout," 2. Input 2nd. profile/sequences "); if (!profile2_empty) fprintf(stdout,"(loaded)"); fprintf(stdout,"\n\n"); fprintf(stdout," 3. Align 2nd. profile to 1st. profile\n"); fprintf(stdout," 4. Align sequences to 1st. profile (%s)\n\n", (!quick_pairalign) ? "Slow/Accurate" : "Fast/Approximate"); fprintf(stdout," 5. Toggle Slow/Fast pairwise alignments = %s\n\n", (!quick_pairalign) ? "SLOW" : "FAST"); fprintf(stdout," 6. Pairwise alignment parameters\n"); fprintf(stdout," 7. Multiple alignment parameters\n\n"); fprintf(stdout," 8. Toggle screen display = %s\n", (!showaln) ? "OFF" : "ON"); fprintf(stdout," 9. Output format options\n"); fprintf(stdout," 0. Secondary structure options\n"); fprintf(stdout,"\n"); fprintf(stdout," S. Execute a system command\n"); fprintf(stdout," H. HELP\n"); fprintf(stdout," or press [RETURN] to go back to main menu\n\n\n"); getstr("Your choice",lin1, MAXLINE+1); if(*lin1 == EOS) return; switch(toupper(*lin1)) { case '1': profile_no = 1; /* 1 => 1st profile */ profile_input(); strcpy(profile1_name, seqname); break; case '2': profile_no = 2; /* 2 => 2nd profile */ profile_input(); strcpy(profile2_name, seqname); break; case '3': profile_align(p1_tree_name,p2_tree_name); /* align the 2 alignments now */ break; case '4': new_sequence_align(phylip_name); /* align new sequences to profile 1 */ break; case '5': quick_pairalign ^= TRUE; break; case '6': pair_menu(); break; case '7': multi_menu(); break; case '8': showaln ^= TRUE; break; case '9': format_options_menu(); break; case '0': ss_options_menu(); break; case 'S': do_system(); break; case '?': case 'H': get_help('6'); break; case 'Q': case 'X': return; default: fprintf(stdout,"\n\nUnrecognised Command\n\n"); break; } } } static void ss_options_menu(void) { int catchint; catchint = signal(SIGINT, SIG_IGN) != SIG_IGN; if (catchint) { if (setjmp(jmpbuf) != 0) fprintf(stdout,"\n.. Interrupt\n"); #ifdef UNIX if (signal(SIGINT,jumper) == BADSIG) fprintf(stdout,"Error: signal\n"); #else if (signal(SIGINT,SIG_DFL) == BADSIG) fprintf(stdout,"Error: signal\n"); #endif } while(TRUE) { fprintf(stdout,"\n\n\n"); fprintf(stdout," ********* SECONDARY STRUCTURE OPTIONS *********\n"); fprintf(stdout,"\n\n"); fprintf(stdout," 1. Use profile 1 secondary structure / penalty mask "); if(use_ss1) fprintf(stdout,"= YES\n"); else fprintf(stdout,"= NO\n"); fprintf(stdout," 2. Use profile 2 secondary structure / penalty mask "); if(use_ss2) fprintf(stdout,"= YES\n"); else fprintf(stdout,"= NO\n"); fprintf(stdout,"\n"); fprintf(stdout," 3. Output in alignment "); fprintf(stdout,"= %s\n",secstroutput_txt[output_struct_penalties]); fprintf(stdout,"\n"); fprintf(stdout," 4. Helix gap penalty :%d\n",(pint)helix_penalty); fprintf(stdout," 5. Strand gap penalty :%d\n",(pint)strand_penalty); fprintf(stdout," 6. Loop gap penalty :%d\n",(pint)loop_penalty); fprintf(stdout," 7. Secondary structure terminal penalty :%d\n",(pint)helix_end_penalty); fprintf(stdout," 8. Helix terminal positions within :%d outside :%d\n", (pint)helix_end_minus,(pint)helix_end_plus); fprintf(stdout," 9. Strand terminal positions within :%d outside :%d\n", (pint)strand_end_minus,(pint)strand_end_plus); fprintf(stdout,"\n\n"); fprintf(stdout," H. HELP\n\n\n"); getstr("Enter number (or [RETURN] to exit)",lin2, MAXLINE+1); if( *lin2 == EOS) { return; } switch(toupper(*lin2)) { case '1': use_ss1 ^= TRUE; break; case '2': use_ss2 ^= TRUE; break; case '3': output_struct_penalties = secstroutput_options(); break; case '4': fprintf(stdout,"Helix Penalty Currently: %d\n",(pint)helix_penalty); helix_penalty=getint("Enter number",1,9,helix_penalty); break; case '5': fprintf(stdout,"Strand Gap Penalty Currently: %d\n",(pint)strand_penalty); strand_penalty=getint("Enter number",1,9,strand_penalty); break; case '6': fprintf(stdout,"Loop Gap Penalty Currently: %d\n",(pint)loop_penalty); loop_penalty=getint("Enter number",1,9,loop_penalty); break; case '7': fprintf(stdout,"Secondary Structure Terminal Penalty Currently: %d\n", (pint)helix_end_penalty); helix_end_penalty=getint("Enter number",1,9,helix_end_penalty); strand_end_penalty = helix_end_penalty; break; case '8': fprintf(stdout,"Helix Terminal Positions Currently: \n"); fprintf(stdout," within helix: %d outside helix: %d\n", (pint)helix_end_minus,(pint)helix_end_plus); helix_end_minus=getint("Enter number of residues within helix",0,3,helix_end_minus); helix_end_plus=getint("Enter number of residues outside helix",0,3,helix_end_plus); break; case '9': fprintf(stdout,"Strand Terminal Positions Currently: \n"); fprintf(stdout," within strand: %d outside strand: %d\n", (pint)strand_end_minus,(pint)strand_end_plus); strand_end_minus=getint("Enter number of residues within strand",0,3,strand_end_minus); strand_end_plus=getint("Enter number of residues outside strand",0,3,strand_end_plus); break; case '?': case 'H': get_help('B'); break; default: fprintf(stdout,"\n\nUnrecognised Command\n\n"); break; } } } static sint secstroutput_options(void) { while(TRUE) { fprintf(stdout,"\n\n\n"); fprintf(stdout," ********* Secondary Structure Output Menu *********\n"); fprintf(stdout,"\n\n"); fprintf(stdout," 1. %s\n",secstroutput_txt[0]); fprintf(stdout," 2. %s\n",secstroutput_txt[1]); fprintf(stdout," 3. %s\n",secstroutput_txt[2]); fprintf(stdout," 4. %s\n",secstroutput_txt[3]); fprintf(stdout," H. HELP\n\n"); fprintf(stdout, " -- Current output is %s ",secstroutput_txt[output_struct_penalties]); fprintf(stdout,"--\n"); getstr("\n\nEnter number (or [RETURN] to exit)",lin2, MAXLINE+1); if(*lin2 == EOS) return(output_struct_penalties); switch(toupper(*lin2)) { case '1': return(0); case '2': return(1); case '3': return(2); case '4': return(3); case '?': case 'H': get_help('C'); __attribute__ ((fallthrough)); // implicit fallthrough case 'Q': case 'X': return(0); default: fprintf(stdout,"\n\nUnrecognised Command\n\n"); break; } } } static void phylogenetic_tree_menu(void) { int catchint; catchint = signal(SIGINT, SIG_IGN) != SIG_IGN; if (catchint) { if (setjmp(jmpbuf) != 0) fprintf(stdout,"\n.. Interrupt\n"); #ifdef UNIX if (signal(SIGINT,jumper) == BADSIG) fprintf(stdout,"Error: signal\n"); #else if (signal(SIGINT,SIG_DFL) == BADSIG) fprintf(stdout,"Error: signal\n"); #endif } while(TRUE) { fprintf(stdout,"\n\n\n"); fprintf(stdout,"****** PHYLOGENETIC TREE MENU ******\n"); fprintf(stdout,"\n\n"); fprintf(stdout," 1. Input an alignment\n"); fprintf(stdout," 2. Exclude positions with gaps? "); if(tossgaps) fprintf(stdout,"= ON\n"); else fprintf(stdout,"= OFF\n"); fprintf(stdout," 3. Correct for multiple substitutions? "); if(kimura) fprintf(stdout,"= ON\n"); else fprintf(stdout,"= OFF\n"); fprintf(stdout," 4. Draw tree now\n"); fprintf(stdout," 5. Bootstrap tree\n"); fprintf(stdout," 6. Output format options\n"); fprintf(stdout,"\n"); fprintf(stdout," S. Execute a system command\n"); fprintf(stdout," H. HELP\n"); fprintf(stdout," or press [RETURN] to go back to main menu\n\n\n"); getstr("Your choice",lin1, MAXLINE+1); if(*lin1 == EOS) return; switch(toupper(*lin1)) { case '1': seq_input(FALSE); phylip_name[0]=EOS; clustal_name[0]=EOS; dist_name[0]=EOS; nexus_name[0]=EOS; pim_name[0]=EOS; break; case '2': tossgaps ^= TRUE; break; case '3': kimura ^= TRUE;; break; case '4': phylogenetic_tree(phylip_name,clustal_name,dist_name,nexus_name,pim_name); break; case '5': bootstrap_tree(phylip_name,clustal_name,nexus_name); break; case '6': tree_format_options_menu(); break; case 'S': do_system(); break; case '?': case 'H': get_help('7'); break; case 'Q': case 'X': return; default: fprintf(stdout,"\n\nUnrecognised Command\n\n"); break; } } } static void tree_format_options_menu(void) /* format of tree output */ { int catchint; catchint = signal(SIGINT, SIG_IGN) != SIG_IGN; if (catchint) { if (setjmp(jmpbuf) != 0) fprintf(stdout,"\n.. Interrupt\n"); #ifdef UNIX if (signal(SIGINT,jumper) == BADSIG) fprintf(stdout,"Error: signal\n"); #else if (signal(SIGINT,SIG_DFL) == BADSIG) fprintf(stdout,"Error: signal\n"); #endif } while(TRUE) { fprintf(stdout,"\n\n\n"); fprintf(stdout," ****** Format of Phylogenetic Tree Output ******\n"); fprintf(stdout,"\n\n"); fprintf(stdout," 1. Toggle CLUSTAL format tree output = %s\n", (!output_tree_clustal) ? "OFF" : "ON"); fprintf(stdout," 2. Toggle Phylip format tree output = %s\n", (!output_tree_phylip) ? "OFF" : "ON"); fprintf(stdout," 3. Toggle Phylip distance matrix output = %s\n", (!output_tree_distances)? "OFF" : "ON"); fprintf(stdout," 4. Toggle Nexus format tree output = %s\n\n", (!output_tree_nexus)? "OFF" : "ON"); fprintf(stdout," 5. Toggle Phylip bootstrap positions = %s\n\n", (bootstrap_format==BS_NODE_LABELS) ? "NODE LABELS" : "BRANCH LABELS"); fprintf(stdout,"\n"); fprintf(stdout," H. HELP\n\n\n"); getstr("Enter number (or [RETURN] to exit)",lin2, MAXLINE+1); if(*lin2 == EOS) return; switch(toupper(*lin2)) { case '1': output_tree_clustal ^= TRUE; break; case '2': output_tree_phylip ^= TRUE; break; case '3': output_tree_distances ^= TRUE; break; case '4': output_tree_nexus ^= TRUE; break; case '5': if (bootstrap_format == BS_NODE_LABELS) bootstrap_format = BS_BRANCH_LABELS; else bootstrap_format = BS_NODE_LABELS; break; case '?': case 'H': get_help('0'); break; default: fprintf(stdout,"\n\nUnrecognised Command\n\n"); break; } } } static void format_options_menu(void) /* format of alignment output */ { char path[FILENAMELEN+1]; int catchint; catchint = signal(SIGINT, SIG_IGN) != SIG_IGN; if (catchint) { if (setjmp(jmpbuf) != 0) fprintf(stdout,"\n.. Interrupt\n"); #ifdef UNIX if (signal(SIGINT,jumper) == BADSIG) fprintf(stdout,"Error: signal\n"); #else if (signal(SIGINT,SIG_DFL) == BADSIG) fprintf(stdout,"Error: signal\n"); #endif } while(TRUE) { fprintf(stdout,"\n\n\n"); fprintf(stdout," ********* Format of Alignment Output *********\n"); fprintf(stdout,"\n\n"); fprintf(stdout," F. Toggle FASTA format output = %s\n\n", (!output_fasta) ? "OFF" : "ON"); fprintf(stdout," 1. Toggle CLUSTAL format output = %s\n", (!output_clustal) ? "OFF" : "ON"); fprintf(stdout," 2. Toggle NBRF/PIR format output = %s\n", (!output_nbrf) ? "OFF" : "ON"); fprintf(stdout," 3. Toggle GCG/MSF format output = %s\n", (!output_gcg) ? "OFF" : "ON"); fprintf(stdout," 4. Toggle PHYLIP format output = %s\n", (!output_phylip) ? "OFF" : "ON"); fprintf(stdout," 5. Toggle NEXUS format output = %s\n", (!output_nexus) ? "OFF" : "ON"); fprintf(stdout," 6. Toggle GDE format output = %s\n\n", (!output_gde) ? "OFF" : "ON"); fprintf(stdout," 7. Toggle GDE output case = %s\n", (!lowercase) ? "UPPER" : "LOWER"); fprintf(stdout," 8. Toggle CLUSTALW sequence numbers = %s\n", (!cl_seq_numbers) ? "OFF" : "ON"); fprintf(stdout," 9. Toggle output order = %s\n\n", (output_order==0) ? "INPUT FILE" : "ALIGNED"); fprintf(stdout," 0. Create alignment output file(s) now?\n\n"); fprintf(stdout," T. Toggle parameter output = %s\n", (!save_parameters) ? "OFF" : "ON"); fprintf(stdout," R. Toggle sequence range numbers = %s\n", (!seqRange) ? "OFF" : "ON"); fprintf(stdout,"\n"); fprintf(stdout," H. HELP\n\n\n"); getstr("Enter number (or [RETURN] to exit)",lin2, MAXLINE+1); if(*lin2 == EOS) return; switch(toupper(*lin2)) { case '1': output_clustal ^= TRUE; break; case '2': output_nbrf ^= TRUE; break; case '3': output_gcg ^= TRUE; break; case '4': output_phylip ^= TRUE; break; case '5': output_nexus ^= TRUE; break; case '6': output_gde ^= TRUE; break; case '7': lowercase ^= TRUE; break; case '8': cl_seq_numbers ^= TRUE; break; case '9': if (output_order == INPUT) output_order = ALIGNED; else output_order = INPUT; break; case 'F': output_fasta ^= TRUE; break; case 'R': seqRange ^= TRUE; break; case '0': /* DES */ if(empty) { error("No sequences loaded"); break; } get_path(seqname,path); if(!open_alignment_output(path)) break; create_alignment_output(1,nseqs); break; case 'T': save_parameters ^= TRUE; break; case '?': case 'H': get_help('5'); break; default: fprintf(stdout,"\n\nUnrecognised Command\n\n"); break; } } } static void pair_menu(void) { int catchint; catchint = signal(SIGINT, SIG_IGN) != SIG_IGN; if (catchint) { if (setjmp(jmpbuf) != 0) fprintf(stdout,"\n.. Interrupt\n"); #ifdef UNIX if (signal(SIGINT,jumper) == BADSIG) fprintf(stdout,"Error: signal\n"); #else if (signal(SIGINT,SIG_DFL) == BADSIG) fprintf(stdout,"Error: signal\n"); #endif } if(dnaflag) { pw_go_penalty = dna_pw_go_penalty; pw_ge_penalty = dna_pw_ge_penalty; ktup = dna_ktup; window = dna_window; signif = dna_signif; wind_gap = dna_wind_gap; } else { pw_go_penalty = prot_pw_go_penalty; pw_ge_penalty = prot_pw_ge_penalty; ktup = prot_ktup; window = prot_window; signif = prot_signif; wind_gap = prot_wind_gap; } while(TRUE) { fprintf(stdout,"\n\n\n"); fprintf(stdout," ********* PAIRWISE ALIGNMENT PARAMETERS *********\n"); fprintf(stdout,"\n\n"); fprintf(stdout," Slow/Accurate alignments:\n\n"); fprintf(stdout," 1. Gap Open Penalty :%4.2f\n",pw_go_penalty); fprintf(stdout," 2. Gap Extension Penalty :%4.2f\n",pw_ge_penalty); fprintf(stdout," 3. Protein weight matrix :%s\n" , matrix_menu.opt[pw_matnum-1].title); fprintf(stdout," 4. DNA weight matrix :%s\n" , dnamatrix_menu.opt[pw_dnamatnum-1].title); fprintf(stdout,"\n"); fprintf(stdout," Fast/Approximate alignments:\n\n"); fprintf(stdout," 5. Gap penalty :%d\n",(pint)wind_gap); fprintf(stdout," 6. K-tuple (word) size :%d\n",(pint)ktup); fprintf(stdout," 7. No. of top diagonals :%d\n",(pint)signif); fprintf(stdout," 8. Window size :%d\n\n",(pint)window); fprintf(stdout," 9. Toggle Slow/Fast pairwise alignments "); if(quick_pairalign) fprintf(stdout,"= FAST\n\n"); else fprintf(stdout,"= SLOW\n\n"); fprintf(stdout," H. HELP\n\n\n"); getstr("Enter number (or [RETURN] to exit)",lin2, MAXLINE+1); if( *lin2 == EOS) { if(dnaflag) { dna_pw_go_penalty = pw_go_penalty; dna_pw_ge_penalty = pw_ge_penalty; dna_ktup = ktup; dna_window = window; dna_signif = signif; dna_wind_gap = wind_gap; } else { prot_pw_go_penalty = pw_go_penalty; prot_pw_ge_penalty = pw_ge_penalty; prot_ktup = ktup; prot_window = window; prot_signif = signif; prot_wind_gap = wind_gap; } return; } switch(toupper(*lin2)) { case '1': fprintf(stdout,"Gap Open Penalty Currently: %4.2f\n",pw_go_penalty); pw_go_penalty=(float)getreal("Enter number",(double)0.0,(double)100.0,(double)pw_go_penalty); break; case '2': fprintf(stdout,"Gap Extension Penalty Currently: %4.2f\n",pw_ge_penalty); pw_ge_penalty=(float)getreal("Enter number",(double)0.0,(double)10.0,(double)pw_ge_penalty); break; case '3': pw_matnum = read_matrix("PROTEIN",pw_matrix_menu,pw_mtrxname,pw_matnum,pw_usermat,pw_aa_xref); break; case '4': pw_dnamatnum = read_matrix("DNA",dnamatrix_menu,pw_dnamtrxname,pw_dnamatnum,pw_userdnamat,pw_dna_xref); break; case '5': fprintf(stdout,"Gap Penalty Currently: %d\n",(pint)wind_gap); wind_gap=getint("Enter number",1,500,wind_gap); break; case '6': fprintf(stdout,"K-tuple Currently: %d\n",(pint)ktup); if(dnaflag) ktup=getint("Enter number",1,4,ktup); else ktup=getint("Enter number",1,2,ktup); break; case '7': fprintf(stdout,"Top diagonals Currently: %d\n",(pint)signif); signif=getint("Enter number",1,50,signif); break; case '8': fprintf(stdout,"Window size Currently: %d\n",(pint)window); window=getint("Enter number",1,50,window); break; case '9': quick_pairalign ^= TRUE; break; case '?': case 'H': get_help('3'); break; default: fprintf(stdout,"\n\nUnrecognised Command\n\n"); break; } } } static void multi_menu(void) { int catchint; catchint = signal(SIGINT, SIG_IGN) != SIG_IGN; if (catchint) { if (setjmp(jmpbuf) != 0) fprintf(stdout,"\n.. Interrupt\n"); #ifdef UNIX if (signal(SIGINT,jumper) == BADSIG) fprintf(stdout,"Error: signal\n"); #else if (signal(SIGINT,SIG_DFL) == BADSIG) fprintf(stdout,"Error: signal\n"); #endif } if(dnaflag) { gap_open = dna_gap_open; gap_extend = dna_gap_extend; } else { gap_open = prot_gap_open; gap_extend = prot_gap_extend; } while(TRUE) { fprintf(stdout,"\n\n\n"); fprintf(stdout," ********* MULTIPLE ALIGNMENT PARAMETERS *********\n"); fprintf(stdout,"\n\n"); fprintf(stdout," 1. Gap Opening Penalty :%4.2f\n",gap_open); fprintf(stdout," 2. Gap Extension Penalty :%4.2f\n",gap_extend); fprintf(stdout," 3. Delay divergent sequences :%d %%\n\n",(pint)divergence_cutoff); fprintf(stdout," 4. DNA Transitions Weight :%1.2f\n\n",transition_weight); fprintf(stdout," 5. Protein weight matrix :%s\n" ,matrix_menu.opt[matnum-1].title); fprintf(stdout," 6. DNA weight matrix :%s\n" ,dnamatrix_menu.opt[dnamatnum-1].title); fprintf(stdout," 7. Use negative matrix :%s\n\n",(!neg_matrix) ? "OFF" : "ON"); fprintf(stdout," 8. Protein Gap Parameters\n\n"); fprintf(stdout," H. HELP\n\n\n"); getstr("Enter number (or [RETURN] to exit)",lin2, MAXLINE+1); if(*lin2 == EOS) { if(dnaflag) { dna_gap_open = gap_open; dna_gap_extend = gap_extend; } else { prot_gap_open = gap_open; prot_gap_extend = gap_extend; } return; } switch(toupper(*lin2)) { case '1': fprintf(stdout,"Gap Opening Penalty Currently: %4.2f\n",gap_open); gap_open=(float)getreal("Enter number",(double)0.0,(double)100.0,(double)gap_open); break; case '2': fprintf(stdout,"Gap Extension Penalty Currently: %4.2f\n",gap_extend); gap_extend=(float)getreal("Enter number",(double)0.0,(double)10.0,(double)gap_extend); break; case '3': fprintf(stdout,"Min Identity Currently: %d\n",(pint)divergence_cutoff); divergence_cutoff=getint("Enter number",0,100,divergence_cutoff); break; case '4': fprintf(stdout,"Transition Weight Currently: %1.2f\n", transition_weight); transition_weight=(float)getreal("Enter number",(double)0.0,(double)1.0,(double)transition_weight); break; case '5': matnum = read_matrix("PROTEIN",matrix_menu,mtrxname,matnum,usermat,aa_xref); break; case '6': dnamatnum = read_matrix("DNA",dnamatrix_menu,dnamtrxname,dnamatnum,userdnamat,dna_xref); break; case '7': neg_matrix ^= TRUE; break; case '8': gap_penalties_menu(); break; case '?': case 'H': get_help('4'); break; default: fprintf(stdout,"\n\nUnrecognised Command\n\n"); break; } } } static void gap_penalties_menu(void) { char c; sint i; int catchint; catchint = signal(SIGINT, SIG_IGN) != SIG_IGN; if (catchint) { if (setjmp(jmpbuf) != 0) fprintf(stdout,"\n.. Interrupt\n"); #ifdef UNIX if (signal(SIGINT,jumper) == BADSIG) fprintf(stdout,"Error: signal\n"); #else if (signal(SIGINT,SIG_DFL) == BADSIG) fprintf(stdout,"Error: signal\n"); #endif } while(TRUE) { fprintf(stdout,"\n\n\n"); fprintf(stdout," ********* PROTEIN GAP PARAMETERS *********\n"); fprintf(stdout,"\n\n\n"); fprintf(stdout," 1. Toggle Residue-Specific Penalties :%s\n\n",(no_pref_penalties) ? "OFF" : "ON"); fprintf(stdout," 2. Toggle Hydrophilic Penalties :%s\n",(no_hyd_penalties) ? "OFF" : "ON"); fprintf(stdout," 3. Hydrophilic Residues :%s\n\n" ,hyd_residues); fprintf(stdout," 4. Gap Separation Distance :%d\n",(pint)gap_dist); fprintf(stdout," 5. Toggle End Gap Separation :%s\n\n",(!use_endgaps) ? "OFF" : "ON"); fprintf(stdout," H. HELP\n\n\n"); getstr("Enter number (or [RETURN] to exit)",lin2, MAXLINE+1); if(*lin2 == EOS) return; switch(toupper(*lin2)) { case '1': no_pref_penalties ^= TRUE; break; case '2': no_hyd_penalties ^= TRUE; break; case '3': fprintf(stdout,"Hydrophilic Residues Currently: %s\n",hyd_residues); getstr("Enter residues (or [RETURN] to quit)",lin1, MAXLINE+1); if (*lin1 != EOS) { { int hyd_residues_len = strlen(hyd_residues); for (i=0;i0 && i