X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Farchive%2Fbinaries%2Fmac%2Fsrc%2Fclustalo%2Fsrc%2Fsquid%2Fphylip.c;fp=website%2Farchive%2Fbinaries%2Fmac%2Fsrc%2Fclustalo%2Fsrc%2Fsquid%2Fphylip.c;h=0000000000000000000000000000000000000000;hb=fb21789ba11ae9b9f6abed1b01d4542e54abfe34;hp=9b01e924d6246df36f43166a258bc6c0a982a0df;hpb=7d68cf3489c816b2ed7afb1925a6de2168eccf4a;p=jabaws.git

diff --git a/website/archive/binaries/mac/src/clustalo/src/squid/phylip.c b/website/archive/binaries/mac/src/clustalo/src/squid/phylip.c
deleted file mode 100644
index 9b01e92..0000000
--- a/website/archive/binaries/mac/src/clustalo/src/squid/phylip.c
+++ /dev/null
@@ -1,173 +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.
- *****************************************************************/
-
-/* phylip.c
- * SRE, Mon Jun 14 14:08:33 1999 [St. Louis]
- * 
- * Import/export of PHYLIP interleaved multiple sequence alignment
- * format files.
- * 
- * RCS $Id: phylip.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: phylip.c,v 1.1 1999/07/15 22:29:20 eddy Exp)
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <ctype.h>
-#include "squid.h"
-#include "msa.h"
-
-#ifdef TESTDRIVE_PHYLIP
-/*****************************************************************
- * phylip.c test driver:
- * 
- */
-int 
-main(int argc, char **argv)
-{
-  MSAFILE *afp;
-  MSA     *msa;
-  char    *file;
-  
-  file = argv[1];
-
-  if ((afp = MSAFileOpen(file, MSAFILE_UNKNOWN, NULL)) == NULL)
-    Die("Couldn't open %s\n", file);
-
-  printf("format %d\n", afp->format);
-
-  while ((msa = ReadPhylip(afp)) != NULL)
-    {
-      WritePhylip(stdout, msa);
-      MSAFree(msa); 
-    }
-  
-  MSAFileClose(afp);
-  exit(0);
-}
-/******************************************************************/
-#endif /* testdrive_phylip */
-
-
-
-/* Function: ReadPhylip()
- * Date:     SRE, Fri Jun 18 12:59:37 1999 [Sanger Centre]
- *
- * Purpose:  Parse an alignment from an open Phylip format
- *           alignment file. Phylip is a single-alignment format.
- *           Return the alignment, or NULL if we have no data.
- *
- * Args:     afp - open alignment file
- *
- * Returns:  MSA * - an alignment object
- *                   Caller responsible for an MSAFree()
- *           NULL if no more alignments        
- */
-MSA *
-ReadPhylip(MSAFILE *afp)
-{
-  MSA  *msa;
-  char *s, *s1, *s2;
-  char  name[11];		/* seq name max len = 10 char */
-  int   nseq, alen;
-  int   idx;			/* index of current sequence */
-  int   slen;
-  int   nblock;
-  
-  if (feof(afp->f)) return NULL;
-
-  /* Skip until we see a nonblank line; it's the header,
-   * containing nseq/alen
-   */
-  nseq = 0; alen = 0;
-  while ((s = MSAFileGetLine(afp)) != NULL)
-    {
-      if ((s1 = sre_strtok(&s, WHITESPACE, NULL)) == NULL) continue;
-      if ((s2 = sre_strtok(&s, WHITESPACE, NULL)) == NULL)
-	Die("Failed to parse nseq/alen from first line of PHYLIP file %s\n", afp->fname);
-      if (! IsInt(s1) || ! IsInt(s2))
-	Die("nseq and/or alen not an integer in first line of PHYLIP file %s\n", afp->fname);
-      nseq = atoi(s1);
-      alen = atoi(s2);
-      break;
-    }
-
-  msa = MSAAlloc(nseq, 0);
-  idx    = 0;
-  nblock = 0;
-  while ((s = MSAFileGetLine(afp)) != NULL) 
-    {
-      /* ignore blank lines. nonblank lines start w/ nonblank char */
-      if (isspace(*s)) continue;
-				/* First block has seq names */
-      if (nblock == 0) {
-	strncpy(name, s, 10);
-	name[10] = '\0';
-	GKIStoreKey(msa->index, name);
-	msa->sqname[idx] = sre_strdup(name, -1);
-	s += 10;		
-      }
-				/* be careful of trailing whitespace on lines */
-      if ((s1 = sre_strtok(&s, WHITESPACE, &slen)) == NULL)
-	Die("Failed to parse sequence at line %d of PHYLIP file %s\n", 
-	    afp->linenumber, afp->fname);
-      msa->sqlen[idx] = sre_strcat(&(msa->aseq[idx]), msa->sqlen[idx], s1, slen);
-
-      idx++;
-      if (idx == nseq) { idx = 0; nblock++; }
-    }
-  msa->nseq = nseq;
-  MSAVerifyParse(msa);		/* verifies; sets alen, wgt; frees sqlen[] */
-  return msa;
-}
-
-
-
-/* Function: WritePhylip()
- * Date:     SRE, Fri Jun 18 12:07:41 1999 [Sanger Centre]
- *
- * Purpose:  Write an alignment in Phylip format to an open file.
- *
- * Args:     fp    - file that's open for writing.
- *           msa   - alignment to write. 
- *
- * Returns:  (void)
- */
-void
-WritePhylip(FILE *fp, MSA *msa)
-{
-  int    idx;			/* counter for sequences         */
-  int    cpl = 50;		/* 50 seq char per line          */
-  char   buf[51];		/* buffer for writing seq        */
-  int    pos;
-
-  /* First line has nseq, alen
-   */
-  fprintf(fp, " %d  %d\n", msa->nseq, msa->alen);
-
-  /* Alignment section.
-   * PHYLIP is a multiblock format, blocks (optionally) separated
-   * by blanks; names only attached to first block. Names are
-   * restricted to ten char; we achieve this by simple truncation (!).
-   * (Do we need to convert gap characters from our ./- convention?)
-   */
-  for (pos = 0; pos < msa->alen; pos += cpl)
-    {
-      if (pos > 0) fprintf(fp, "\n");
-
-      for (idx = 0; idx < msa->nseq; idx++)
-	{
-	  strncpy(buf, msa->aseq[idx] + pos, cpl);
-	  buf[cpl] = '\0';	      
-	  if (pos > 0) fprintf(fp, "%s\n", buf);
-	  else         fprintf(fp, "%-10.10s%s\n", msa->sqname[idx], buf);
-	}
-    }
-  return;
-}