// hhsearch.cpp:

#include "hhsearch.h"
#include "hhsuite_config.h"

void HHsearch::prepareDatabases(Parameters& par,
                                std::vector<HHblitsDatabase*>& databases) {
    for (size_t i = 0; i < par.db_bases.size(); i++) {
        HHblitsDatabase* db = new HHblitsDatabase(par.db_bases[i].c_str(), true);
        databases.push_back(db);
    }

    par.dbsize = 0;
    for (size_t i = 0; i < databases.size(); i++) {
        par.dbsize += databases[i]->query_database->db_index->n_entries;
    }
}

void HHsearch::ProcessAllArguments(Parameters& par) {
	const int argc = par.argc;
	const char** argv = par.argv;

    par.prefilter = false;
	par.num_rounds = 1;

	ProcessArguments(par);

	if (par.db_bases.size() == 0) {
		help(par);
		HH_LOG(ERROR) << "Database is missing (see -d)!" << std::endl;
		exit(4);
	}

	// Check option compatibilities
	if (par.nseqdis > MAXSEQDIS - 3 - par.showcons)
		par.nseqdis = MAXSEQDIS - 3 - par.showcons; //3 reserved for secondary structure
	if (par.aliwidth < 20)
		par.aliwidth = 20;
	if (par.pc_hhm_context_engine.pca < 0.001)
		par.pc_hhm_context_engine.pca = 0.001; // to avoid log(0)
	if (par.b > par.B)
		par.B = par.b;
	if (par.z > par.Z)
		par.Z = par.z;
	if (par.maxmem < 1.0) {
	  HH_LOG(WARNING) << "Setting -maxmem to its minimum allowed value of 1.0" << std::endl;
		par.maxmem = 1.0;
	}
	if (par.mact >= 1.0)
		par.mact = 0.999;
	else if (par.mact < 0)
		par.mact = 0.0;
	if (par.altali < 1)
		par.altali = 1;
}

void HHsearch::help(Parameters& par, char all) {
  printf("HHsearch %i.%i.%i\n", HHSUITE_VERSION_MAJOR, HHSUITE_VERSION_MINOR, HHSUITE_VERSION_PATCH);
  printf("Search a database of HMMs with a query alignment or query HMM\n");
  printf("%s", COPYRIGHT);
  printf("%s", REFERENCE);
  printf("\n");
  printf("Usage: hhsearch -i query -d database [options]                       \n");
  printf(" -i <file>      input/query multiple sequence alignment (a2m, a3m, FASTA) or HMM\n");

	if (all) {
		printf("\n");
		printf("<file> may be 'stdin' or 'stdout' throughout.\n");
	}

  printf("Options:                                                                        \n");
  printf(" -d <name>      database name (e.g. uniprot20_29Feb2012)                        \n");
  printf("                Multiple databases may be specified with '-d <db1> -d <db2> ...'\n");
  printf(" -e     [0,1]   E-value cutoff for inclusion in result alignment (def=%G)       \n", par.e);
  printf("\n");

  printf("Input alignment format:                                                       \n");
  printf(" -M a2m         use A2M/A3M (default): upper case = Match; lower case = Insert;\n");
  printf("               '-' = Delete; '.' = gaps aligned to inserts (may be omitted)   \n");
  printf(" -M first       use FASTA: columns with residue in 1st sequence are match states\n");
  printf(" -M [0,100]     use FASTA: columns with fewer than X%% gaps are match states   \n");
  printf(" -tags/-notags  do NOT / do neutralize His-, C-myc-, FLAG-tags, and trypsin \n");
  printf("                recognition sequence to background distribution (def=-notags)  \n");
  printf("\n");

  printf("Output options: \n");
  printf(" -o <file>      write results in standard format to file (default=<infile.hhr>)\n");
  printf(" -oa3m <file>   write result MSA with significant matches in a3m format\n");
  printf(" -blasttab <name> write result in tabular BLAST format (compatible to -m 8 or -outfmt 6 output)\n");
  printf("                  1     2      3           4      5         6        7      8    9      10   11   12\n");
  printf("                  query target #match/tLen alnLen #mismatch #gapOpen qstart qend tstart tend eval score\n");
  if (all) {
    printf(" -opsi <file>   write result MSA of significant matches in PSI-BLAST format\n");
    printf(" -ohhm <file>   write HHM file for result MSA of significant matches\n");
  }

  printf(" -add_cons      generate consensus sequence as master sequence of query MSA (default=don't)\n");
	printf(" -hide_cons     don't show consensus sequence in alignments (default=show)     \n");
	printf(" -hide_pred     don't show predicted 2ndary structure in alignments (default=show)\n");
	printf(" -hide_dssp     don't show DSSP 2ndary structure in alignments (default=show)  \n");
	printf(" -show_ssconf   show confidences for predicted 2ndary structure in alignments\n");
  if (all) {
    printf(" -Ofas <file>   write pairwise alignments in FASTA xor A2M (-Oa2m) xor A3M (-Oa3m) format   \n");
    printf(" -seq <int>     max. number of query/template sequences displayed (default=%i)  \n", par.nseqdis);
    printf(" -aliw <int>    number of columns per line in alignment list (default=%i)       \n", par.aliwidth);
    printf(" -p [0,100]     minimum probability in summary and alignment list (default=%G)  \n", par.p);
    printf(" -E [0,inf[     maximum E-value in summary and alignment list (default=%G)      \n", par.E);
    printf(" -Z <int>       maximum number of lines in summary hit list (default=%i)        \n", par.Z);
    printf(" -z <int>       minimum number of lines in summary hit list (default=%i)        \n", par.z);
    printf(" -B <int>       maximum number of alignments in alignment list (default=%i)     \n", par.B);
    printf(" -b <int>       minimum number of alignments in alignment list (default=%i)     \n", par.b);
    printf("\n");
  }

  printf("Filter options applied to query MSA, database MSAs, and result MSA              \n");
  printf(" -all           show all sequences in result MSA; do not filter result MSA      \n");
  printf(" -id   [0,100]  maximum pairwise sequence identity (def=%i)\n", par.max_seqid);
  printf(" -diff [0,inf[  filter MSAs by selecting most diverse set of sequences, keeping \n");
  printf("                at least this many seqs in each MSA block of length 50 \n");
  printf("                Zero and non-numerical values turn off the filtering. (def=%i) \n", par.Ndiff);
  printf(" -cov  [0,100]  minimum coverage with master sequence (%%) (def=%i)             \n", par.coverage);
  printf(" -qid  [0,100]  minimum sequence identity with master sequence (%%) (def=%i)    \n", par.qid);
  printf(" -qsc  [0,100]  minimum score per column with master sequence (default=%.1f)    \n", par.qsc);
  printf(" -neff [1,inf]  target diversity of multiple sequence alignment (default=off)   \n");
  printf(" -mark          do not filter out sequences marked by \">@\"in their name line  \n");
  printf("\n");

  printf("HMM-HMM alignment options:                                                       \n");
  printf(" -norealign          do NOT realign displayed hits with MAC algorithm (def=realign)   \n");
  printf(" -ovlp <int>         banded alignment: forbid <ovlp> largest diagonals |i-j| of DP matrix (def=%i)\n", par.min_overlap);
  printf(" -mact [0,1[         posterior prob threshold for MAC realignment controlling greedi- \n");
  printf("                     ness at alignment ends: 0:global >0.1:local (default=%.2f)       \n", par.mact);
  printf(" -glob/-loc          use global/local alignment mode for searching/ranking (def=local)\n");
  if (all) {
    printf(" -realign            realign displayed hits with max. accuracy (MAC) algorithm \n");
    printf(" -excl <range>       exclude query positions from the alignment, e.g. '1-33,97-168' \n");
    printf(" -realign_max <int>  realign max. <int> hits (default=%i)                        \n", par.realign_max);
    printf(" -alt <int>          show up to this many alternative alignments with raw score > smin(def=%i)  \n", par.altali);
    printf(" -smin <float>       minimum raw score for alternative alignments (def=%.1f)  \n", par.smin);
    printf(" -shift [-1,1]       profile-profile score offset (def=%-.2f)                         \n", par.shift);
    printf(" -corr [0,1]         weight of term for pair correlations (def=%.2f)                \n", par.corr);
    printf(" -sc   <int>         amino acid score         (tja: template HMM at column j) (def=%i)\n", par.columnscore);
    printf("        0       = log2 Sum(tja*qia/pa)   (pa: aa background frequencies)    \n");
    printf("        1       = log2 Sum(tja*qia/pqa)  (pqa = 1/2*(pa+ta) )               \n");
    printf("        2       = log2 Sum(tja*qia/ta)   (ta: av. aa freqs in template)     \n");
    printf("        3       = log2 Sum(tja*qia/qa)   (qa: av. aa freqs in query)        \n");
    printf("        5       local amino acid composition correction                     \n");
    printf(" -ssm {0,..,4}    0:   no ss scoring                                             \n");
    printf("                1,2: ss scoring after or during alignment  [default=%1i]         \n", par.ssm);
    printf("                3,4: ss scoring after or during alignment, predicted vs. predicted\n");
    printf(" -ssw [0,1]          weight of ss score  (def=%-.2f)                                  \n", par.ssw);
    printf(" -ssa [0,1]          SS substitution matrix = (1-ssa)*I + ssa*full-SS-substition-matrix [def=%-.2f)\n", par.ssa);
    printf(" -wg                 use global sequence weighting for realignment!                   \n");
    printf("\n");

    printf("Gap cost options:                                                                \n");
    printf(" -gapb [0,inf[  Transition pseudocount admixture (def=%-.2f)                     \n", par.gapb);
    printf(" -gapd [0,inf[  Transition pseudocount admixture for open gap (default=%-.2f)    \n", par.gapd);
    printf(" -gape [0,1.5]  Transition pseudocount admixture for extend gap (def=%-.2f)      \n", par.gape);
    printf(" -gapf ]0,inf]  factor to increase/reduce gap open penalty for deletes (def=%-.2f) \n", par.gapf);
    printf(" -gapg ]0,inf]  factor to increase/reduce gap open penalty for inserts (def=%-.2f) \n", par.gapg);
    printf(" -gaph ]0,inf]  factor to increase/reduce gap extend penalty for deletes(def=%-.2f)\n", par.gaph);
    printf(" -gapi ]0,inf]  factor to increase/reduce gap extend penalty for inserts(def=%-.2f)\n", par.gapi);
    printf(" -egq  [0,inf[  penalty (bits) for end gaps aligned to query residues (def=%-.2f) \n",  par.egq);
    printf(" -egt  [0,inf[  penalty (bits) for end gaps aligned to template residues (def=%-.2f)\n", par.egt);
    printf("\n");

    printf("Pseudocount (pc) options:                                                        \n");
    printf(" Context specific hhm pseudocounts:\n");
    printf("  -pc_hhm_contxt_mode {0,..,3}   position dependence of pc admixture 'tau' (pc mode, default=%-i) \n", par.pc_hhm_context_engine.admix);
    printf("               0: no pseudo counts:    tau = 0                                  \n");
    printf("               1: constant             tau = a                                  \n");
    printf("               2: diversity-dependent: tau = a/(1+((Neff[i]-1)/b)^c)            \n");
    printf("               3: CSBlast admixture:   tau = a(1+b)/(Neff[i]+b)                 \n");
    printf("               (Neff[i]: number of effective seqs in local MSA around column i) \n");
    printf("  -pc_hhm_contxt_a  [0,1]        overall pseudocount admixture (def=%-.1f)                        \n", par.pc_hhm_context_engine.pca);
    printf("  -pc_hhm_contxt_b  [1,inf[      Neff threshold value for mode 2 (def=%-.1f)                      \n", par.pc_hhm_context_engine.pcb);
    printf("  -pc_hhm_contxt_c  [0,3]        extinction exponent c for mode 2 (def=%-.1f)                     \n", par.pc_hhm_context_engine.pcc);
    printf("\n");

    printf(" Context independent hhm pseudocounts (used for templates; used for query if contxt file is not available):\n");
    printf("  -pc_hhm_nocontxt_mode {0,..,3}   position dependence of pc admixture 'tau' (pc mode, default=%-i) \n", par.pc_hhm_nocontext_mode);
    printf("               0: no pseudo counts:    tau = 0                                  \n");
    printf("               1: constant             tau = a                                  \n");
    printf("               2: diversity-dependent: tau = a/(1+((Neff[i]-1)/b)^c)            \n");
    printf("               (Neff[i]: number of effective seqs in local MSA around column i) \n");
    printf("  -pc_hhm_nocontxt_a  [0,1]        overall pseudocount admixture (def=%-.1f)                        \n", par.pc_hhm_nocontext_a);
    printf("  -pc_hhm_nocontxt_b  [1,inf[      Neff threshold value for mode 2 (def=%-.1f)                      \n", par.pc_hhm_nocontext_b);
    printf("  -pc_hhm_nocontxt_c  [0,3]        extinction exponent c for mode 2 (def=%-.1f)                     \n", par.pc_hhm_nocontext_c);
    printf("\n");

    printf(" Context-specific pseudo-counts:                                                  \n");
    printf("  -nocontxt      use substitution-matrix instead of context-specific pseudocounts \n");
    printf("  -contxt <file> context file for computing context-specific pseudocounts (default=%s)\n", par.clusterfile.c_str());
    printf("  -csw  [0,inf]  weight of central position in cs pseudocount mode (def=%.1f)\n", par.csw);
    printf("  -csb  [0,1]    weight decay parameter for positions in cs pc mode (def=%.1f)\n", par.csb);
    printf("\n");
  }

	printf("Other options:                                                                   \n");
  printf(" -v <int>       verbose mode: 0:no screen output  1:only warnings  2: verbose (def=%i)\n", par.v);
  printf(" -cpu <int>     number of CPUs to use (for shared memory SMPs) (default=%i)      \n", par.threads);
  if (all) {
    printf(" -scores <file> write scores for all pairwise comparisons to file               \n");
    printf(" -atab   <file> write all alignments in tabular layout to file                   \n");
	printf(" -maxseq <int>  max number of input rows (def=%5i)\n", par.maxseq);
    printf(" -maxres <int>  max number of HMM columns (def=%5i)\n", par.maxres);
    printf(" -maxmem [1,inf[ limit memory for realignment (in GB) (def=%.1f)          \n", par.maxmem);
  }
  printf("\n");

  if (!all) {
    printf("An extended list of options can be obtained by calling 'hhblits -h all'\n");
    printf("\n");
  }

	printf("Example: hhsearch -i a.1.1.1.a3m -d scop70_1.71\n");
  printf("\n");
  printf("Download databases from <http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/>.\n");
}

/////////////////////////////////////////////////////////////////////////////////////
//// Processing input options from command line
/////////////////////////////////////////////////////////////////////////////////////
void HHsearch::ProcessArguments(Parameters& par) {
	const int argc = par.argc;
	const char** argv = par.argv;

	//Processing command line input
	for (int i = 1; i < argc; i++) {
		HH_LOG(DEBUG1) << i << "  " << argv[i] << std::endl;
		if (!strcmp(argv[i], "-i")) {
			if (++i >= argc || argv[i][0] == '-') {
				help(par);
				HH_LOG(ERROR) << "No query file following -i" << std::endl;
				exit(4);
			} else
				strcpy(par.infile, argv[i]);
		} else if (!strcmp(argv[i], "-d")) {
			if (++i >= argc || argv[i][0] == '-') {
				help(par);
				HH_LOG(ERROR) << "No database file following -d" << std::endl;
				exit(4);
			} else {
				std::string db(argv[i]);
				if (HHDatabase::checkDatabaseConflicts(argv[i])) {
					HH_LOG(ERROR) << "Ambiguous database basename. Choose either a A3M or CA3M database." << std::endl;
					exit(4);
				}
				par.db_bases.push_back(db);
			}
		} else if (!strcmp(argv[i], "-o")) {
			par.append = 0;
			if (++i >= argc || argv[i][0] == '-') {
				help(par);
				HH_LOG(ERROR) << "No output file following -o" << std::endl;
				exit(4);
			} else
				strcpy(par.outfile, argv[i]);
		} else if (!strcmp(argv[i], "-Ofas")) {
			par.append = 0;
			par.outformat = 1;
			if (++i >= argc || argv[i][0] == '-') {
				help(par);
				HH_LOG(ERROR) << "No output file following -o" << std::endl;
				exit(4);
			} else
				strcpy(par.pairwisealisfile, argv[i]);
		} else if (!strcmp(argv[i], "-Oa2m")) {
			par.append = 0;
			par.outformat = 2;
			if (++i >= argc || argv[i][0] == '-') {
				help(par);
				HH_LOG(ERROR) << "No output file following -o" << std::endl;
				exit(4);
			} else
				strcpy(par.pairwisealisfile, argv[i]);
		} else if (!strcmp(argv[i], "-Oa3m")) {
			par.append = 0;
			par.outformat = 3;
			if (++i >= argc || argv[i][0] == '-') {
				help(par);
				HH_LOG(ERROR) << "No output file following -o" << std::endl;
				exit(4);
			} else
				strcpy(par.pairwisealisfile, argv[i]);
		} else if (!strcmp(argv[i], "-oa3m")) {
			if (++i >= argc || argv[i][0] == '-') {
				help(par);
				HH_LOG(ERROR) << "No output file following -Oa3m" << std::endl;
				exit(4);
			} else
				strcpy(par.alnfile, argv[i]);
		} else if (!strcmp(argv[i], "-ohhm")) {
			if (++i >= argc || argv[i][0] == '-') {
				help(par);
				HH_LOG(ERROR) << "No output file following -ohhm" << std::endl;
				exit(4);
			} else
				strcpy(par.hhmfile, argv[i]);
		} else if (!strcmp(argv[i], "-opsi")) {
			if (++i >= argc || argv[i][0] == '-') {
				help(par);
				HH_LOG(ERROR) << "No output file following -Opsi" << std::endl;
				exit(4);
			} else
				strcpy(par.psifile, argv[i]);
		} else if (!strcmp(argv[i], "-scores")) {
			if (++i >= argc || argv[i][0] == '-') {
				help(par);
				HH_LOG(ERROR) << "No file following -scores" << std::endl;
				exit(4);
			} else {
				strcpy(par.scorefile, argv[i]);
			}
		}
        else if (!strcmp(argv[i], "-blasttab")) {
            if (++i >= argc || argv[i][0] == '-') {
                help(par);
                HH_LOG(ERROR) << "No file following -blasttab" << std::endl;
                exit(4);
            } else {
                strcpy(par.m8file, argv[i]);
            }
        }
        else if (!strcmp(argv[i], "-atab")) {
			if (++i >= argc || argv[i][0] == '-') {
				help(par);
				HH_LOG(ERROR) << "No query file following -atab" << std::endl;
				exit(4);
			} else
				strmcpy(par.alitabfile, argv[i], NAMELEN - 1);
		} else if (!strcmp(argv[i], "-h") || !strcmp(argv[i], "-help")) {
			help(par, 1);
			exit(0);
		} else if (!strcmp(argv[i], "-v")) {
			if (++i >= argc) {
				help(par);
				exit(4);
			}
			int v = atoi(argv[i]);
			par.v = Log::from_int(v);
			Log::reporting_level() = par.v;
		} else if (!strcmp(argv[i], "-p") && (i < argc - 1))
			par.p = atof(argv[++i]);
		else if (!strcmp(argv[i], "-e") && (i < argc - 1))
			par.e = atof(argv[++i]);
		else if (!strcmp(argv[i], "-E") && (i < argc - 1))
			par.E = atof(argv[++i]);
		else if (!strcmp(argv[i], "-b") && (i < argc - 1))
			par.b = atoi(argv[++i]);
		else if (!strcmp(argv[i], "-B") && (i < argc - 1))
			par.B = atoi(argv[++i]);
		else if (!strcmp(argv[i], "-z") && (i < argc - 1))
			par.z = atoi(argv[++i]);
		else if (!strcmp(argv[i], "-Z") && (i < argc - 1))
			par.Z = atoi(argv[++i]);
		else if (!strncmp(argv[i], "-hide_cons", 7))
			par.showcons = 0;
		else if (!strncmp(argv[i], "-hide_pred", 7))
			par.showpred = 0;
		else if (!strncmp(argv[i], "-hide_dssp", 7))
			par.showdssp = 0;
		else if (!strncmp(argv[i], "-show_ssconf", 7))
			par.showconf = 1;
		else if (!strncmp(argv[i], "-add_cons", 5))
			par.cons = 1;
    else if (!strcmp(argv[i], "-realign_max") && (i < argc - 1))
      par.realign_max = atoi(argv[++i]);
    else if (!strcmp(argv[i], "-realign_max") && (i < argc - 1))
      par.realign_max = atoi(argv[++i]);
		else if (!strncmp(argv[i], "-mark", 5))
			par.mark = 1;
		else if (!strcmp(argv[i], "-seq") && (i < argc - 1))
			par.nseqdis = atoi(argv[++i]);
		else if (!strcmp(argv[i], "-aliw") && (i < argc - 1))
			par.aliwidth = atoi(argv[++i]);
		else if (!strcmp(argv[i], "-id") && (i < argc - 1))
			par.max_seqid = atoi(argv[++i]);
		else if (!strcmp(argv[i], "-qid") && (i < argc - 1))
			par.qid = atoi(argv[++i]);
		else if (!strcmp(argv[i], "-qsc") && (i < argc - 1))
			par.qsc = atof(argv[++i]);
		else if (!strcmp(argv[i], "-cov") && (i < argc - 1))
			par.coverage = atoi(argv[++i]);
		else if (!strcmp(argv[i], "-diff") && (i < argc - 1))
			par.Ndiff = atoi(argv[++i]);
    else if (!strcmp(argv[i], "-all") || !strcmp(argv[i], "-nodiff")) {
      par.allseqs = true;
    }
		else if (!strcmp(argv[i], "-neff") && (i < argc - 1))
			par.Neff = atof(argv[++i]);
		//no help required
		else if (!strcmp(argv[i], "-Gonnet"))
			par.matrix = 0;
		//no help required
		else if (!strncmp(argv[i], "-Blosum", 7)) {
			if (!strcmp(argv[i] + 7, "30"))
				par.matrix = 30;
			else if (!strcmp(argv[i] + 7, "40"))
				par.matrix = 40;
			else if (!strcmp(argv[i] + 7, "50"))
				par.matrix = 50;
			else if (!strcmp(argv[i] + 7, "65"))
				par.matrix = 65;
			else if (!strcmp(argv[i] + 7, "80"))
				par.matrix = 80;
			else
			  HH_LOG(WARNING) << "Ignoring unknown option " << argv[i] << std::endl;
		} else if (!strcmp(argv[i], "-wg")) {
			par.wg = 1;
		}
		else if (!strcmp(argv[i], "-pc_hhm_contxt_mode") && (i < argc - 1))
			par.pc_hhm_context_engine.admix = (Pseudocounts::Admix) atoi(
					argv[++i]);
		else if (!strcmp(argv[i], "-pc_hhm_contxt_a") && (i < argc - 1))
			par.pc_hhm_context_engine.pca = atof(argv[++i]);
		else if (!strcmp(argv[i], "-pc_hhm_contxt_b") && (i < argc - 1))
			par.pc_hhm_context_engine.pcb = atof(argv[++i]);
		else if (!strcmp(argv[i], "-pc_hhm_contxt_c") && (i < argc - 1))
			par.pc_hhm_context_engine.pcc = atof(argv[++i]);

		else if (!strcmp(argv[i], "-pc_hhm_nocontxt_mode") && (i < argc - 1))
      par.pc_hhm_nocontext_mode = atoi(argv[++i]);
    else if (!strcmp(argv[i], "-pc_hhm_nocontxt_a") && (i < argc - 1))
      par.pc_hhm_nocontext_a = atof(argv[++i]);
    else if (!strcmp(argv[i], "-pc_hhm_nocontxt_b") && (i < argc - 1))
      par.pc_hhm_nocontext_b = atof(argv[++i]);
    else if (!strcmp(argv[i], "-pc_hhm_nocontxt_c") && (i < argc - 1))
      par.pc_hhm_nocontext_c = atof(argv[++i]);

    else if (!strcmp(argv[i], "-gapb") && (i < argc - 1)) {
			par.gapb = atof(argv[++i]);
			if (par.gapb <= 0.01)
				par.gapb = 0.01;
		} else if (!strcmp(argv[i], "-gapd") && (i < argc - 1))
			par.gapd = atof(argv[++i]);
		else if (!strcmp(argv[i], "-gape") && (i < argc - 1))
			par.gape = atof(argv[++i]);
		else if (!strcmp(argv[i], "-gapf") && (i < argc - 1))
			par.gapf = atof(argv[++i]);
		else if (!strcmp(argv[i], "-gapg") && (i < argc - 1))
			par.gapg = atof(argv[++i]);
		else if (!strcmp(argv[i], "-gaph") && (i < argc - 1))
			par.gaph = atof(argv[++i]);
		else if (!strcmp(argv[i], "-gapi") && (i < argc - 1))
			par.gapi = atof(argv[++i]);
		else if (!strcmp(argv[i], "-egq") && (i < argc - 1))
			par.egq = atof(argv[++i]);
		else if (!strcmp(argv[i], "-egt") && (i < argc - 1))
			par.egt = atof(argv[++i]);
		else if (!strcmp(argv[i], "-ssm") && (i < argc - 1))
			par.ssm = atoi(argv[++i]);
		else if (!strcmp(argv[i], "-ssw") && (i < argc - 1))
			par.ssw = atof(argv[++i]);
		else if (!strcmp(argv[i], "-ssa") && (i < argc - 1))
			par.ssa = atof(argv[++i]);
		else if (!strcmp(argv[i], "-realign"))
			par.realign = 1;
		else if (!strcmp(argv[i], "-norealign"))
			par.realign = 0;
		else if (!strncmp(argv[i], "-glob", 5)) {
			par.loc = 0;
			if (par.mact > 0.35 && par.mact < 0.3502) {
				par.mact = 0;
			}
		} else if (!strncmp(argv[i], "-loc", 4))
			par.loc = 1;
		else if (!strncmp(argv[i], "-alt", 4) && (i < argc - 1))
			par.altali = atoi(argv[++i]);
    else if (!strncmp(argv[i], "-smin", 4) && (i < argc - 1))
      par.smin = atof(argv[++i]);
		else if (!strcmp(argv[i], "-M") && (i < argc - 1)) {
			if (!strcmp(argv[++i], "a2m") || !strcmp(argv[i], "a3m"))
				par.M = 1;
			else if (!strcmp(argv[i], "first"))
				par.M = 3;
			else if (argv[i][0] >= '0' && argv[i][0] <= '9') {
				par.Mgaps = atoi(argv[i]);
				par.M = 2;
			} else
			  HH_LOG(WARNING) << "Ignoring unknown argument: -M " 	<< argv[i] << std::endl;
		}
		else if (!strcmp(argv[i], "-shift") && (i < argc - 1))
			par.shift = atof(argv[++i]);
		else if ((!strcmp(argv[i], "-mact"))
				&& (i < argc - 1))
			par.mact = atof(argv[++i]);
		else if (!strcmp(argv[i], "-sc") && (i < argc - 1))
			par.columnscore = atoi(argv[++i]);
		//no help required
		else if (!strcmp(argv[i], "-scwin") && (i < argc - 1)) {
			par.columnscore = 5;
			par.half_window_size_local_aa_bg_freqs = imax(1, atoi(argv[++i]));
		}
		else if (!strcmp(argv[i], "-maxseq") && (i < argc - 1))
			par.maxseq = atoi(argv[++i]);
		else if (!strcmp(argv[i], "-maxres") && (i < argc - 1)) {
			par.maxres = atoi(argv[++i]);
			par.maxcol = 2 * par.maxres;
		} else if (!strncmp(argv[i], "-cpu", 4) && (i < argc - 1))
			par.threads = atoi(argv[++i]);
		else if (!strcmp(argv[i], "-maxmem") && (i < argc - 1)) {
			par.maxmem = atof(argv[++i]);
		} else if (!strcmp(argv[i], "-corr") && (i < argc - 1))
			par.corr = atof(argv[++i]);
		else if (!strcmp(argv[i], "-ovlp") && (i < argc - 1))
			par.min_overlap = atoi(argv[++i]);
		//no help required
		else if (!strcmp(argv[i], "-dbstrlen") && (i < argc - 1))
			par.maxdbstrlen = atoi(argv[++i]);
		else if (!strcmp(argv[i], "-tags"))
			par.notags = 0;
		else if (!strcmp(argv[i], "-notags"))
			par.notags = 1;
		else if (!strcmp(argv[i], "-nocontxt"))
			par.nocontxt = 1;
		else if (!strcmp(argv[i], "-csb") && (i < argc - 1))
			par.csb = atof(argv[++i]);
		else if (!strcmp(argv[i], "-csw") && (i < argc - 1))
			par.csw = atof(argv[++i]);
		else if (!strcmp(argv[i], "-contxt") || !strcmp(argv[i], "-cs")) {
			if (++i >= argc || argv[i][0] == '-') {
				help(par);
				HH_LOG(ERROR) << "No query file following -contxt" << std::endl;
				exit(4);
			} else
				par.clusterfile = argv[i];
		}
    else if (!strcmp(argv[i],"-excl")) {
      if (++i>=argc) {
        help(par);
        HH_LOG(ERROR) << "No expression following -excl" << std::endl;
        exit(4);
      }
      par.exclstr = new char[strlen(argv[i])+1];
      strcpy(par.exclstr,argv[i]);
    }
    else {
			HH_LOG(WARNING) << "Ignoring unknown option " << argv[i] << std::endl;
		}
		HH_LOG(DEBUG1) << i << "  " << argv[i] << std::endl;
	} // end of for-loop for command line input
}
