Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/clustalo/src/squid/a2m.c b/website/archive/binaries/mac/src/clustalo/src/squid/a2m.c
deleted file mode 100644 (file)
index 35d4a37..0000000
--- a/website/archive/binaries/mac/src/clustalo/src/squid/a2m.c
+++ /dev/null
@@ -1,134 +0,0 @@
-/*****************************************************************
- * 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");
-
-    }
-}