void show_help(FILE * ofp)
{
fprintf(ofp,"%s (%s)\n",program_name,VERSION_NUMBER);
fprintf(ofp,"%s <protein-input> <dna-input>\n",program_name);
/* program specific help */
fprintf(ofp,"Protein input type\n");
fprintf(ofp," -protein [default] single protein\n");
fprintf(ofp," -prodb protein fasta format db\n");
fprintf(ofp," -pfam pfam hmm library \n");
fprintf(ofp," -pfam2 pfam style model directory (2.1) \n");
fprintf(ofp," -hmmer single hmmer 1.x HMM\n");
fprintf(ofp,"DNA input type\n");
fprintf(ofp," -dnadb [default] dna fasta database\n");
fprintf(ofp," -dnas a single dna fasta sequence\n");
fprintf(ofp,"DNA sequence options\n");
fprintf(ofp," -tfor search forward strands only\n");
fprintf(ofp,"Protein comparison options\n");
fprintf(ofp," -gap [%3d] gap penalty\n",gap);
fprintf(ofp," -ext [%3d] extension penalty\n",ext);
fprintf(ofp," -matrix [%s] Comparison matrix\n",matrix_file);
fprintf(ofp,"HMM options\n");
fprintf(ofp," -hname For single hmms, use this as the name, not filename\n");
fprintf(ofp,"Model options\n");
fprintf(ofp," -init [%s] [default/global/local/wing] start-end policy\n",startend_string);
fprintf(ofp," -codon [%s] Codon file\n",codon_file);
fprintf(ofp," -subs [%2.2g] Substitution error rate\n",subs_error);
fprintf(ofp," -indel [%2.2g] Insertion/deletion error rate\n",indel_error);
fprintf(ofp," -null [syn/flat] Random Model as synchronous or flat [default syn]\n");
fprintf(ofp," -alln [%s] Probability of matching a NNN codon\n",allN_string);
fprintf(ofp," -flati Flat insert probabilities\n");
fprintf(ofp,"Algorithm options\n");
fprintf(ofp," -alg [333/312] Algorithm used for searching [default %s]\n",string_from_alg_estwrap(alg));
fprintf(ofp," -aalg [312/333/333L] Algorithm used for alignment [default %s]\n",string_from_alg_estwrap(aln_alg));
fprintf(ofp," -cut [%.2f] Bits cutoff for reporting in search algorithm\n",search_cutoff);
fprintf(ofp," -ecut [n/a] Evalue cutoff for single protein vs DNA searches.\n");
fprintf(ofp," -aln [%d] Max number of alignments (even if above cut)\n",aln_number);
fprintf(ofp," -nohis Don't show histogram on single protein/hmm vs DNA search\n");
fprintf(ofp," -report [0] Issue a report every x comparisons (default 0 comparisons)\n");
fprintf(ofp,"Output options for each alignment [default -pretty -para]\n");
fprintf(ofp," -pretty show pretty ascii output\n");
fprintf(ofp," -para show parameters\n");
fprintf(ofp," -pep show protein translation, splicing frameshifts\n");
fprintf(ofp," -mul protein mul format alignments [only for one HMM vs DNA db]\n");
fprintf(ofp," -sum show summary output\n");
fprintf(ofp," -alb show logical AlnBlock alignment\n");
fprintf(ofp," -pal show raw matrix alignment\n");
fprintf(ofp," -block [%s] Length of main block in pretty output\n",main_block_str);
fprintf(ofp," -divide [%s] divide string for multiple outputs\n",divide_str);
show_help_DBSearchImpl(ofp);
show_help_DPRunImpl(ofp);
show_standard_options(ofp);
fprintf(ofp,"\nSee WWW help at http://www.sanger.ac.uk/Software/Wise2/\n");
exit(63);
}
void show_help(FILE * ofp)
{
fprintf(ofp,"%s fivestar-directory protein-file-fasta\n",program_name);
fprintf(ofp," -ga gathering cutoff (bits)");
show_help_DBSearchImpl(ofp);
show_standard_options(ofp);
}
