/* -*- mode: c; tab-width: 4; c-basic-offset: 4;  indent-tabs-mode: nil -*- */
 
 /*********************************************************************
  * Clustal Omega - Multiple sequence alignment
  *
  * Copyright (C) 2010 University College Dublin
  *
  * Clustal-Omega is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License as
  * published by the Free Software Foundation; either version 2 of the
  * License, or (at your option) any later version.
  *
  * This file is part of Clustal-Omega.
  *
  ********************************************************************/
 
 /*
  *  RCS $Id: clustalo-api-test.c 280 2013-05-16 16:04:12Z fabian $
  */
 
 
 #include <stdio.h>
 
 /* see clustal-omega.c for documentation */
 
 /* Include clustal-omega's header. That's all you need 
  *
  * If you developing in C++, use the following instead:
  * extern "C" {
  * #include "clustal-omega.h"
  * }
  */
 #include "clustal-omega.h"
 
 
 int
 main(int argc, char **argv)
 {
     /* the multiple sequence structure */
     mseq_t *prMSeq = NULL;
     /* for openmp: number of threads to use */
     int iThreads = 1;
     /* alignment options to use */
     opts_t rAlnOpts;
     /* an input file */
     char *pcSeqInfile;
     int iAux;
 
     int msa_c = 0;
     char **msa_v = NULL;
 
 
     /* Must happen first: setup logger */
     LogDefaultSetup(&rLog);
 
     SetDefaultAlnOpts(&rAlnOpts);
 
     InitClustalOmega(iThreads);
 
     /* Get sequence input file name from command line
      */
     if (argc!=2) {
         Log(&rLog, LOG_FATAL, "Need sequence file as argument");
     }
     pcSeqInfile = argv[1];
 
     /* Read sequence file
      */
     NewMSeq(&prMSeq);
     if (ReadSequences(prMSeq, pcSeqInfile,
                       SEQTYPE_UNKNOWN,
                       INT_MAX, INT_MAX)) {
         Log(&rLog, LOG_FATAL, "Reading sequence file '%s' failed", pcSeqInfile);
     }
 
     /* Dump some info about the sequences
      */
     for (iAux=0; iAux<prMSeq->nseqs; iAux++) {
         Log(&rLog, LOG_INFO, 
              "Sequence no %d has the following name: %s",
              iAux, prMSeq->sqinfo[iAux].name);
         Log(&rLog, LOG_INFO, 
              "Sequence no %d has the following residues: %s",
              iAux, prMSeq->seq[iAux]);
         /* more info can be found in prMSeq->sqinfo[iAux] */
     }
 
 
     /* Align the sequences without a profile (NULL)
      */
     if (Align(prMSeq, NULL, &rAlnOpts)) {
         Log(&rLog, LOG_FATAL, "A fatal error happended during the alignment process");
     }
 
 
     /* Output of final alignment to stdout (NULL) as aligned fasta/a2m
      */
 #define LINE_WRAP 60
     ClustalOmegaOutput msaOutput;
     if (WriteAlignment(prMSeq, NULL, MSAFILE_A2M, LINE_WRAP, &msa_c, &msa_v)) {
         Log(&rLog, LOG_FATAL, "Could not save alignment");
     } 
 
     FreeMSeq(&prMSeq);
 
     Log(&rLog, LOG_INFO, "Successfull program exit");
 
     return EXIT_SUCCESS;
 }
 /***   end of main()   ***/