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+/* -*- 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()   ***/