Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / clustalo / src / clustalo-api-test.c

diff --git a/website/archive/binaries/mac/src/clustalo/src/clustalo-api-test.c b/website/archive/binaries/mac/src/clustalo/src/clustalo-api-test.c
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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 213 2011-03-11 16:10:15Z andreas $
+ */
+
+
+#include <stdio.h>
+
+/* 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;
+
+    /* use LOGLEVEL_QUIET to make Clustal shut up */
+    iVerbosityLevel = LOGLEVEL_INFO;
+
+    SetDefaultAlnOpts(&rAlnOpts);
+
+    InitClustalOmega(iThreads);
+
+    /* Get sequence input file name from command line
+     */
+    if (argc!=2) {
+        Fatal("Need sequence file as argument");
+    }
+    pcSeqInfile = argv[1];
+
+    /* Read sequence file
+     */
+    NewMSeq(&prMSeq);
+    if (ReadSequences(prMSeq, pcSeqInfile,
+                      SEQTYPE_UNKNOWN,
+                      INT_MAX, INT_MAX)) {
+        Fatal("Reading sequence file '%s' failed", pcSeqInfile);
+    }
+
+    /* Dump some info about the sequences
+     */
+    for (iAux=0; iAux<prMSeq->nseqs; iAux++) {
+        Info(LOGLEVEL_INFO, 
+             "Sequence no %d has the following name: %s",
+             iAux, prMSeq->sqinfo[iAux].name);
+        Info(LOGLEVEL_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)) {
+        Fatal("A fatal error happended during the alignment process");
+    }
+
+
+    /* Output of final alignment to stdout (NULL) as aligned fasta/a2m
+     */
+    if (WriteAlignment(prMSeq, NULL, MSAFILE_A2M)) {
+        Fatal("Could not save alignment");
+    } 
+
+    FreeMSeq(&prMSeq);
+
+    Info(LOGLEVEL_INFO, "Successfull program exit");
+
+    return EXIT_SUCCESS;
+}
+/***   end of main()   ***/