Wrapper for Clustal Omega.

[jabaws.git] / binaries / src / clustalo / src / squid / a2m.c

diff --git a/binaries/src/clustalo/src/squid/a2m.c b/binaries/src/clustalo/src/squid/a2m.c
new file mode 100644 (file)
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--- /dev/null
+++ b/binaries/src/clustalo/src/squid/a2m.c
@@ -0,0 +1,134 @@
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ * 
+ *     This source code is freely distributed under the terms of the
+ *     GNU General Public License. See the files COPYRIGHT and LICENSE
+ *     for details.
+ *****************************************************************/
+
+/* a2m.c
+ * 
+ * reading/writing A2M (aligned FASTA) files.
+ * 
+ * RCS $Id: a2m.c 242 2011-05-27 14:04:21Z andreas $ (Original squid RCS Id: a2m.c,v 1.1 1999/07/15 22:26:40 eddy Exp)
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "squid.h"
+#include "msa.h"
+
+/* Function: ReadA2M()
+ * Date:     SRE, Sun Jun  6 17:11:29 1999 [bus from Madison 1999 worm mtg]
+ *
+ * Purpose:  Parse an alignment read from an open A2M format
+ *           alignment file. A2M is a single alignment format.
+ *           Return the alignment, or NULL if we've already
+ *           read the alignment.
+ *
+ * Args:     afp - open alignment file
+ *
+ * Returns:  MSA *  - an alignment object. 
+ *                    Caller responsible for an MSAFree()
+ */
+MSA *
+ReadA2M(MSAFILE *afp)
+{
+  MSA  *msa;
+  char *buf;
+  char *name;
+  char *desc;
+  char *seq;
+  int   idx;
+  int   len1, len2;
+  
+  if (feof(afp->f)) return NULL;
+
+  name = NULL;
+  msa  = MSAAlloc(10, 0);
+  idx  = 0;
+  while ((buf = MSAFileGetLine(afp)) != NULL) 
+    {
+      if (*buf == '>') 
+       {
+         buf++;                /* skip the '>' */
+         if ((name = sre_strtok(&buf, WHITESPACE, &len1)) == NULL)
+           Die("Blank name in A2M file %s (line %d)\n", afp->fname, afp->linenumber);
+         desc = sre_strtok(&buf, "\n", &len2);
+       
+         idx = GKIStoreKey(msa->index, name);
+         if (idx >= msa->nseqalloc) MSAExpand(msa);
+
+         msa->sqname[idx] = sre_strdup(name, len1);
+         if (desc != NULL) MSASetSeqDescription(msa, idx, desc);
+         msa->nseq++;
+       } 
+      else if (name != NULL) 
+       {
+         if ((seq = sre_strtok(&buf, WHITESPACE, &len1)) == NULL) continue; 
+         msa->sqlen[idx] = sre_strcat(&(msa->aseq[idx]), msa->sqlen[idx], seq, len1);
+       }
+    } 
+  if (name == NULL) { MSAFree(msa); return NULL; }
+
+  MSAVerifyParse(msa);
+  return msa;
+}
+
+
+/* Function: WriteA2M()
+ * Date:     SRE, Sun Jun  6 17:40:35 1999 [bus from Madison, 1999 worm mtg]
+ *
+ * Purpose:  Write an "aligned FASTA" (aka a2m, to UCSC) formatted
+ *           alignment.
+ *
+ * Args:     fp    - open FILE to write to.
+ *           msa   - alignment to write
+ * 
+ * Returns:  void
+ */
+void
+#ifdef CLUSTALO
+WriteA2M(FILE *fp, MSA *msa, int vienna)
+#else
+WriteA2M(FILE *fp, MSA *msa)
+#endif
+{
+  int  idx;                    /* sequence index */
+  int  pos;                    /* position in sequence */
+  char buf[64];                        /* buffer for individual lines */
+  int  cpl = 60;               /* char per line; must be < 64 unless buf is bigger */
+
+  buf[cpl] = '\0';
+  for (idx = 0; idx < msa->nseq; idx++)
+    {
+#ifdef CLUSTALO
+               /* most fasta sequences don't have a description, which
+         * leads to a trailing white space in the original code 
+                */
+               fprintf(fp, ">%s",  msa->sqname[idx]);
+
+        if (msa->sqdesc != NULL && msa->sqdesc[idx] != NULL && !vienna) {
+            fprintf(fp, " %s", msa->sqdesc[idx]);
+        }
+        fprintf(fp, "\n");
+#else
+        fprintf(fp, ">%s %s\n", 
+                msa->sqname[idx],
+                (msa->sqdesc != NULL && msa->sqdesc[idx] != NULL) ? msa->sqdesc[idx] : "");
+#endif
+        for (pos = 0; pos < msa->alen; pos+=cpl)
+        {
+            strncpy(buf, &(msa->aseq[idx][pos]), cpl);
+                       if (vienna)
+                           fprintf(fp, "%s", buf);
+                       else
+                               fprintf(fp, "%s\n", buf);
+        }
+               if (vienna)
+                   fprintf(fp, "\n");
+
+    }
+}