blimps (3.9-1) patch001

Summary

 Makefile                       |  117 +++
 blimps/LAMA.c                  |    6 
 blimps/LAMA_search.c           |   10 
 blimps/Makefile.Linux          | 1419 ++---------------------------------------
 blimps/addseqs.c               |    6 
 blimps/biassed_blocks_finder.c |   13 
 blimps/blDR.c                  |    6 
 blimps/blalign.c               |    2 
 blimps/bldist.c                |    8 
 blimps/blexplode.c             |    2 
 blimps/blk2DR.c                |    2 
 blimps/blk2GC.c                |    2 
 blimps/blk2lis.c               |    2 
 blimps/blk2mot.c               |   10 
 blimps/blk2pssm.c              |    9 
 blimps/blk2slx.c               |    4 
 blimps/blklis.c                |    4 
 blimps/blkprob.c               |    6 
 blimps/block_vis.c             |    4 
 blimps/blocks.c                |    2 
 blimps/blocks_search.c         |   15 
 blimps/blpssm.c                |    2 
 blimps/blweight.c              |   11 
 blimps/cobbler.c               |    2 
 blimps/coduse.c                |    6 
 blimps/email.c                 |    2 
 blimps/fastaseqs.c             |    4 
 blimps/find_biassed_blocks.c   |    2 
 blimps/format_block.c          |   44 -
 blimps/htmlize-LAMA.c          |    1 
 blimps/htmlize-codehop.c       |    4 
 blimps/interpro.c              |    4 
 blimps/lisblk.c                |   10 
 blimps/mablock.c               |    9 
 blimps/makelogob.c             |    8 
 blimps/matrix_logob.c          |    8 
 blimps/narrow.c                |    4 
 blimps/oligo_melt.c            |    2 
 blimps/papssm.c                |    4 
 blimps/prints2blocks.c         |    2 
 blimps/protomat.c              |    3 
 blimps/protxblk.c              |    4 
 blimps/pssmBL.c                |    6 
 blimps/pssmdist.c              |   12 
 blimps/rank_matrix.c           |    2 
 blimps/readchk.c               |    2 
 blimps/readmast.c              |    2 
 blimps/retblock.c              |    4 
 blimps/sequences.c             |    4 
 blimps/sortblk.c               |    4 
 blimps/translate.c             |    8 
 blimps/util.c                  |    3 
 fastaseqs.pod                  |   25 
 protomat/Makefile.Linux        |   61 +
 54 files changed, 426 insertions(+), 1492 deletions(-)

    
download this patch

Patch contents

* replaced gets() with fgets()
* fixes to blimps/Makefile.Linux
Index: blimps-3.9/blimps/addseqs.c
===================================================================
--- blimps-3.9.orig/blimps/addseqs.c	2012-02-03 21:58:55.968242949 +0100
+++ blimps-3.9/blimps/addseqs.c	2012-02-03 22:01:33.780367907 +0100
@@ -150,7 +150,7 @@
    else
    {
       printf("\nEnter name of file containing blocks: ");
-      gets(infile);
+      fgets(infile, MAXNAME, stdin);
    }
    if ( (fblk=fopen(infile, "r")) == NULL)
    {
@@ -164,7 +164,7 @@
    else
    {
       printf("\nEnter name of sequence file: ");
-      gets(seqsfile);
+      fgets(seqsfile, MAXNAME, stdin);
    }
    if ( (fseq=fopen(seqsfile, "r")) == NULL)
    {
@@ -177,7 +177,7 @@
    else
    {
       printf("\nEnter name of output seqs file: ");
-      gets(outfile);
+      fgets(outfile, MAXNAME, stdin);
    }
    if ( (fout=fopen(outfile, "w")) == NULL)
    {
Index: blimps-3.9/blimps/biassed_blocks_finder.c
===================================================================
--- blimps-3.9.orig/blimps/biassed_blocks_finder.c	2012-02-03 21:58:55.992242645 +0100
+++ blimps-3.9/blimps/biassed_blocks_finder.c	2012-02-03 22:02:36.760368069 +0100
@@ -25,6 +25,11 @@
 void unescape_url(char *url);
 void plustospace(char *str);
 */
+// lkajan: very nice but util.c does not have an interface defined
+// lkajan: can't figure out where this came from but it certainly picked up the wrong fmakeword
+char *fmakeword(FILE *f, char stop, int *cl);
+char *makeword(char *line, char stop);
+
  
 entry entries[10000];
 
@@ -124,7 +129,7 @@
 
 
   /* check that a block was specified */
-  if (BLOCK_Ptr->val[0] == NULL) 
+  if (BLOCK_Ptr->val[0] == 0)
     {
       printf("<H1>Error</H1>\n");
       printf("You need to enter a block by writing or pasting a block in the window.<P>\n");
@@ -139,7 +144,7 @@
 
 
   /* if block was pasted/written - */
-  if (BLOCK_Ptr->val[0] != NULL)
+  if (BLOCK_Ptr->val[0] != 0)
     {
       
       /* open up the block file to write to */
@@ -264,7 +269,7 @@
 
 /**********************************************************************/
 
-void main(int argc, char *argv[]) {
+int main(int argc, char *argv[]) {
 
   printf("Content-type: text/html\n\n\n");
 
@@ -301,6 +306,6 @@
 
   clean_temp_files() ;
 
-  exit(0) ;
+  return(0) ;
 }
 
Index: blimps-3.9/blimps/blalign.c
===================================================================
--- blimps-3.9.orig/blimps/blalign.c	2012-02-03 21:58:56.016242628 +0100
+++ blimps-3.9/blimps/blalign.c	2012-02-03 22:01:33.800368017 +0100
@@ -119,7 +119,7 @@
    else
    {
       printf("\nEnter name of file of blocks: ");
-      gets(bdbname);
+      fgets(bdbname, MAXNAME, stdin);
    }
    if ( (bfp=fopen(bdbname, "r")) == NULL)
    {
Index: blimps-3.9/blimps/bldist.c
===================================================================
--- blimps-3.9.orig/blimps/bldist.c	2012-02-03 21:58:56.040242492 +0100
+++ blimps-3.9/blimps/bldist.c	2012-02-03 22:01:33.808368122 +0100
@@ -70,7 +70,7 @@
    else
    {
       printf("\nEnter name of file of fasta multiple alignments: ");
-      gets(bdbname);
+      fgets(bdbname, MAXNAME, stdin);
    }
    if ( (ifp=fopen(bdbname, "r")) == NULL)
    {
@@ -94,7 +94,7 @@
    else
    {
       printf("\nEnter name of file containing substitution matrix: ");
-      gets(sijname);
+      fgets(sijname, MAXNAME, stdin);
    }
    if ( (sfp=fopen(sijname, "r")) == NULL)
    {
@@ -127,7 +127,7 @@
    else
    {
       printf("\nEnter name of output file: ");
-      gets(outname);
+      fgets(outname, MAXNAME, stdin);
    }
    if ( (ofp=fopen(outname, "w")) == NULL)
    {
@@ -140,7 +140,7 @@
    else
    {
       printf("\nEnter type (S=similarity, D=dissimilarity, C=correlation): ");
-      gets(ctemp);
+      fgets(ctemp, MAXNAME, stdin);
    }
    OutType = 1;			/* similarity is default */
    if      (ctemp[0] == 'd' || ctemp[0] == 'D' || ctemp[0] == '2') OutType = 2;
Index: blimps-3.9/blimps/blDR.c
===================================================================
--- blimps-3.9.orig/blimps/blDR.c	2012-02-03 21:58:56.064244662 +0100
+++ blimps-3.9/blimps/blDR.c	2012-02-03 22:01:33.812367892 +0100
@@ -56,7 +56,7 @@
    else
    {
       printf("\nEnter name of blocks database: ");
-      gets(bdbname);
+      fgets(bdbname, MAXNAME, stdin);
    }
    if ( (bfp=fopen(bdbname, "r")) == NULL)
    {
@@ -69,7 +69,7 @@
    {
       printf("\nSequence database must be in fasta format:");
       printf("\nEnter name of sequence database: ");
-      gets(sdbname);
+      fgets(sdbname, MAXNAME, stdin);
    }
    if ( (sfp=fopen(sdbname, "r")) == NULL)
    {
@@ -81,7 +81,7 @@
    else
    {
       printf("\nEnter name of new blocks database: ");
-      gets(outname);
+      fgets(outname, MAXNAME, stdin);
    }
    if ( (ofp=fopen(outname, "w")) == NULL)
    {
Index: blimps-3.9/blimps/blexplode.c
===================================================================
--- blimps-3.9.orig/blimps/blexplode.c	2012-02-03 21:58:56.088245006 +0100
+++ blimps-3.9/blimps/blexplode.c	2012-02-03 22:01:33.816367915 +0100
@@ -29,7 +29,7 @@
    else
    {
       printf("\nEnter name of blocks database: ");
-      gets(bdbname);
+      fgets(bdbname, MAXNAME, stdin);
    }
    if ( (bfp=fopen(bdbname, "r")) == NULL)
    {
Index: blimps-3.9/blimps/blk2DR.c
===================================================================
--- blimps-3.9.orig/blimps/blk2DR.c	2012-02-03 21:58:56.112246115 +0100
+++ blimps-3.9/blimps/blk2DR.c	2012-02-03 22:01:33.824367868 +0100
@@ -31,7 +31,7 @@
    else
    {
       printf("\nEnter name of blocks database: ");
-      gets(bdbname);
+      fgets(bdbname, MAXNAME, stdin);
    }
    if ( (bfp=fopen(bdbname, "r")) == NULL)
    {
Index: blimps-3.9/blimps/blk2GC.c
===================================================================
--- blimps-3.9.orig/blimps/blk2GC.c	2012-02-03 21:58:56.136242506 +0100
+++ blimps-3.9/blimps/blk2GC.c	2012-02-03 22:01:33.828368154 +0100
@@ -30,7 +30,7 @@
    else
    {
       printf("\nEnter name of blocks database: ");
-      gets(bdbname);
+      fgets(bdbname, MAXNAME, stdin);
    }
    if ( (bfp=fopen(bdbname, "r")) == NULL)
    {
Index: blimps-3.9/blimps/blk2lis.c
===================================================================
--- blimps-3.9.orig/blimps/blk2lis.c	2012-02-03 21:58:56.160242554 +0100
+++ blimps-3.9/blimps/blk2lis.c	2012-02-03 22:01:33.836367894 +0100
@@ -30,7 +30,7 @@
    else
    {
       printf("\nEnter name of blocks database: ");
-      gets(bdbname);
+      fgets(bdbname, MAXNAME, stdin);
    }
    if ( (bfp=fopen(bdbname, "r")) == NULL)
    {
Index: blimps-3.9/blimps/blk2mot.c
===================================================================
--- blimps-3.9.orig/blimps/blk2mot.c	2012-02-03 21:58:56.184244654 +0100
+++ blimps-3.9/blimps/blk2mot.c	2012-02-03 22:01:33.844367867 +0100
@@ -43,7 +43,7 @@
 char Seqname[MAXSEQS][SNAMELEN];
 
 /*=======================================================================*/
-void main(argc, argv)
+int main(argc, argv)
      int argc;
      char *argv[];
 {
@@ -71,7 +71,7 @@
    else
    {
       printf("\nEnter name of file containing sequences: ");
-      gets(seqfile);
+      fgets(seqfile, FNAMELEN, stdin);
    }
    if ( (fseq=fopen(seqfile, "r")) == NULL)
    {
@@ -92,7 +92,7 @@
    else
    {
       printf("\nEnter name of blocks file: ");
-      gets(blkfile);
+      fgets(blkfile, FNAMELEN, stdin);
    }
    if ( (fblk=fopen(blkfile, "r")) == NULL)
    {
@@ -126,7 +126,7 @@
    else
    {
       printf("\nEnter name of new motomat file: ");
-      gets(motfile);
+      fgets(motfile, FNAMELEN, stdin);
    }
    if ( (fmot=fopen(motfile, "wb")) == NULL)
    {
@@ -135,7 +135,7 @@
    }
    write_motifs(fmot, info, motif);
    fclose(fmot);
-   exit(0);
+   return(0);
 }   /* end of main */
 
 /*======================================================================
Index: blimps-3.9/blimps/blk2pssm.c
===================================================================
--- blimps-3.9.orig/blimps/blk2pssm.c	2012-02-03 21:58:56.208243132 +0100
+++ blimps-3.9/blimps/blk2pssm.c	2012-02-03 22:01:33.848367783 +0100
@@ -67,7 +67,8 @@
   Block *block;
   Matrix *matrix, *logodds;
   char bdbname[MAXNAME], conname[MAXNAME];
-  char ctemp[10];
+#define BLK2PSSM_CTEMPLEN 10
+  char ctemp[BLK2PSSM_CTEMPLEN];
   int format, type, itemp;
 
   ErrorLevelReport = 5;			/* No blimps errors reported */
@@ -87,7 +88,7 @@
    else
    {
       printf("\nEnter name of BLOCKS input file: ");
-      gets(bdbname);
+      fgets(bdbname, MAXNAME, stdin);
    }
    if ( (bfp=fopen(bdbname, "r")) == NULL)
    {
@@ -100,7 +101,7 @@
    else
    {
       printf("\nEnter name of PSSM output file: ");
-      gets(conname);
+      fgets(conname, MAXNAME, stdin);
    }
    if ( (ofp=fopen(conname, "w")) == NULL)
    {
@@ -115,7 +116,7 @@
    else
    {
       printf("\nEnter PSSM format type (B=blimps, M=mast, G=Gribskov, P=Psi-Blast) [B]:  ");
-      gets(ctemp);
+      fgets(ctemp, BLK2PSSM_CTEMPLEN, stdin );
    }
    if (strlen(ctemp) && (ctemp[0] == 'm' || ctemp[0] == 'M'))
    {       format = 1; type = 6;  }
Index: blimps-3.9/blimps/blk2slx.c
===================================================================
--- blimps-3.9.orig/blimps/blk2slx.c	2012-02-03 21:58:56.228242420 +0100
+++ blimps-3.9/blimps/blk2slx.c	2012-02-03 22:01:33.856367897 +0100
@@ -35,7 +35,7 @@
    else
    {
       printf("\nEnter name of blocks database: ");
-      gets(bdbname);
+      fgets(bdbname, MAXNAME, stdin);
    }
    if ( (bfp=fopen(bdbname, "r")) == NULL)
    {
@@ -48,7 +48,7 @@
    else
    {
       printf("\nEnter name of new slx database: ");
-      gets(conname);
+      fgets(conname, MAXNAME, stdin);
    }
    if ( (ofp=fopen(conname, "w")) == NULL)
    {
Index: blimps-3.9/blimps/blklis.c
===================================================================
--- blimps-3.9.orig/blimps/blklis.c	2012-02-03 21:58:56.252244950 +0100
+++ blimps-3.9/blimps/blklis.c	2012-02-03 22:01:33.860301362 +0100
@@ -34,7 +34,7 @@
    else
    {
       printf("\nEnter name of file of blocks: ");
-      gets(infile);
+      fgets(infile, 80, stdin);
    }
    if ( (fin=fopen(infile, "r")) == NULL)
    {
@@ -46,7 +46,7 @@
    else
    {
       printf("\nEnter name of output file: ");
-      gets(outfile);
+      fgets(outfile, 80, stdin );
    }
    if ( (fout=fopen(outfile, "w+")) == NULL)
    {
Index: blimps-3.9/blimps/blkprob.c
===================================================================
--- blimps-3.9.orig/blimps/blkprob.c	2012-02-03 21:58:56.276243207 +0100
+++ blimps-3.9/blimps/blkprob.c	2012-02-03 22:01:33.872367951 +0100
@@ -325,7 +325,7 @@
    {
       printf("\nEnter number of hits to report or ");
       printf("blimps configuration file name [%d]: ", MaxHit);
-      gets(ctemp);
+      fgets(ctemp, FNAMELEN, stdin);
    }
    if (!strlen(ctemp)) strcpy(ctemp, "0");
    for (i=0; i<strlen(ctemp); i++)
@@ -353,7 +353,7 @@
          else
          {
             printf("\nEnter name of file containing blocks search results: ");
-            gets(homfile);
+            fgets(homfile, FNAMELEN, stdin);
          }
          /*------------- arg 3:  blocks database file -----------------------*/
          db[0] = '\0';
@@ -362,7 +362,7 @@
          else
          {
             printf("\nEnter name of blocks database searched: ");
-            gets(datfile);
+            fgets(datfile, FNAMELEN, stdin);
          }
          if (strlen(datfile))
          {
Index: blimps-3.9/blimps/blocks.c
===================================================================
--- blimps-3.9.orig/blimps/blocks.c	2012-02-03 21:58:56.300243088 +0100
+++ blimps-3.9/blimps/blocks.c	2012-02-03 22:01:33.880367811 +0100
@@ -891,7 +891,7 @@
 	}
       }    
       else {
-	printf("??) \t");
+	printf("??" ") \t");
 	for(k=0; k<block->clusters[i].sequences[j].length; k++) {
 	  printf("%c", aa_btoa[block->clusters[i].sequences[j].sequence[k]]);
 	}
Index: blimps-3.9/blimps/blocks_search.c
===================================================================
--- blimps-3.9.orig/blimps/blocks_search.c	2012-02-03 21:58:56.324242665 +0100
+++ blimps-3.9/blimps/blocks_search.c	2012-02-03 22:03:02.608242149 +0100
@@ -302,8 +302,9 @@
         else if (!strncmp(entries[i].val, "pfam", 9))
         { Pfam_Flag = TRUE; }
       }
-      else if (!strncmp(entries[i].name, "bias", 4)) 
-      { strcpy(Minus_Flag, entries[i].val); }
+// lkajan: what was the intention here? Looks like this would copy entries[i].val to the value of boolean Minus_Flag interpreted as a pointer - trigger to segfault?
+//      else if (!strncmp(entries[i].name, "bias", 4))
+//      { strcpy(Minus_Flag, entries[i].val); }
       else if (!strncmp(entries[i].name, "ty", 2)) 
       { strcpy(type, entries[i].val); }
       else if (!strncmp(entries[i].name, "st", 2)) 
@@ -379,7 +380,7 @@
 
    cshp = fopen(csh_file, "w");
 
-   fprintf(cshp, "\#\!/bin/csh\n");
+   fprintf(cshp, "#!/bin/csh\n");
    fprintf(cshp, "unalias mv\n");
    fprintf(cshp, "%s %s >& /dev/null\n", blimps, cs_file);
    if (Title_Ptr != NULL)
@@ -419,7 +420,7 @@
               mailprog, email_addr, buf, Address_Ptr->val, blksort_output);
        }
    }
-   fprintf(cshp, "exit\(0\)\n");
+   fprintf(cshp, "exit(0)\n");
    fclose(cshp);
    sprintf(buf, "chmod a+x %s", csh_file);
    system(buf);
@@ -433,7 +434,7 @@
   Boolean loop = TRUE;
   int tot, sum;
 
-  if (Sequence_Ptr->val[0] == NULL) {
+  if (Sequence_Ptr->val[0] == 0) {
     printf("<H1>Search Error</H1>\n");
     printf("You need to enter a sequence to search with.<P>\n");
     exit(0);
@@ -590,7 +591,7 @@
 
 
 /*=======================================================================*/
-void main(int argc, char *argv[]) {
+int main(int argc, char *argv[]) {
 
 
 /*
@@ -655,5 +656,5 @@
 /*
   fclose(jgh);
 */
-  exit(0);
+  return(0);
 }  /* end of main */
Index: blimps-3.9/blimps/block_vis.c
===================================================================
--- blimps-3.9.orig/blimps/block_vis.c	2012-02-03 21:58:56.348242549 +0100
+++ blimps-3.9/blimps/block_vis.c	2012-02-03 22:01:33.896367700 +0100
@@ -868,7 +868,7 @@
  * each input file. The only actual work done here is interpreting
  * '*' in the output filename.
  */
-void main(int argc, char *argv[])
+int main(int argc, char *argv[])
 {
   int i1, i2, i3, i4;
   char out_filename[80];
@@ -910,5 +910,7 @@
   /* No arguments? Give the user some help (and skip the warning above) */
   if (argc == 1)
     do_help();
+
+  return(0);
 }
 
Index: blimps-3.9/blimps/blpssm.c
===================================================================
--- blimps-3.9.orig/blimps/blpssm.c	2012-02-03 21:58:56.372242140 +0100
+++ blimps-3.9/blimps/blpssm.c	2012-02-03 22:01:33.904367947 +0100
@@ -241,7 +241,7 @@
    else
    {
       printf("\nEnter name of configuration file: ");
-      gets(cfname);
+      fgets(cfname, FNAMELEN, stdin);
    }
    if ( (cfp=fopen(cfname, "r")) == NULL)
    {
Index: blimps-3.9/blimps/blweight.c
===================================================================
--- blimps-3.9.orig/blimps/blweight.c	2012-02-03 21:58:56.396242171 +0100
+++ blimps-3.9/blimps/blweight.c	2012-02-03 22:01:33.916367894 +0100
@@ -92,7 +92,8 @@
   FILE *bfp, *ofp;
   Block *block, *cblock;
   int wtype, clus, stype;
-  char bdbname[MAXNAME], conname[MAXNAME], ctemp[10];
+#define BLWEIGHT_CTEMPLEN 10
+  char bdbname[MAXNAME], conname[MAXNAME], ctemp[BLWEIGHT_CTEMPLEN];
   struct timeval tv;
 
   ErrorLevelReport = 5;			/* don't want to see them */
@@ -119,7 +120,7 @@
    else
    {
       printf("\nEnter name of blocks database: ");
-      gets(bdbname);
+      fgets( bdbname, MAXNAME, stdin );
    }
    if ( (bfp=fopen(bdbname, "r")) == NULL)
    {
@@ -132,7 +133,7 @@
    else
    {
       printf("\nEnter name of new weighted blocks database: ");
-      gets(conname);
+      fgets( conname, MAXNAME, stdin );
    }
    if ( (ofp=fopen(conname, "w")) == NULL)
    {
@@ -149,7 +150,7 @@
    {
       printf("\nEnter weighting scheme (P=position-based, V=Voronoi, ");
       printf("\n A=Vingron & Argos, Cn = n-percent cluster [P]: ");
-      gets(ctemp);
+      fgets( ctemp, BLWEIGHT_CTEMPLEN, stdin );
    }
    if (strlen(ctemp))
    {
@@ -187,7 +188,7 @@
    else
    {
       printf("\nEnter scale (M=>max=100, N=>sum=#seq, ###=>sum=###) [M]: ");
-      gets(ctemp);
+      fgets( ctemp, BLWEIGHT_CTEMPLEN, stdin );
    }
    if (strlen(ctemp))
    {
Index: blimps-3.9/blimps/cobbler.c
===================================================================
--- blimps-3.9.orig/blimps/cobbler.c	2012-02-03 21:58:56.436242699 +0100
+++ blimps-3.9/blimps/cobbler.c	2012-02-03 22:01:33.928367965 +0100
@@ -256,7 +256,7 @@
    else
    {
       printf("\nEnter name of configuration file: ");
-      gets(cfname);
+      fgets(cfname, MAXNAME, stdin);
    }
    if ( (cfp=fopen(cfname, "r")) == NULL)
    {
Index: blimps-3.9/blimps/coduse.c
===================================================================
--- blimps-3.9.orig/blimps/coduse.c	2012-02-03 21:58:56.460292853 +0100
+++ blimps-3.9/blimps/coduse.c	2012-02-03 22:01:33.932368014 +0100
@@ -65,7 +65,7 @@
    else
    {
       printf("\nEnter name of CUTG spsum file: ");
-      gets(infile);
+      fgets(infile, MAXNAME, stdin );
    }
    if ( (fin=fopen(infile, "r")) == NULL)
    {
@@ -78,7 +78,7 @@
    else
    {
       printf("Enter organism name (leave blank for first organism in file): ");
-      gets(organism);
+      fgets(organism, MAXNAME, stdin);
    }
    if (strlen(organism))
    {
@@ -95,7 +95,7 @@
    else
    {
       printf("\nEnter name of Blimps codon usage output file: ");
-      gets(outfile);
+      fgets(outfile, MAXNAME, stdin);
    }
    if ( (fout=fopen(outfile, "w")) == NULL)
    {
Index: blimps-3.9/blimps/email.c
===================================================================
--- blimps-3.9.orig/blimps/email.c	2012-02-03 21:58:56.484242590 +0100
+++ blimps-3.9/blimps/email.c	2012-02-03 22:01:33.940368038 +0100
@@ -35,7 +35,7 @@
    else
    {
       printf("\nEnter name of sequence file: ");
-      gets(filename);
+      fgets(filename, MAXNAME, stdin);
    }
    if ( (bfp=fopen(filename, "r")) == NULL)
    {
Index: blimps-3.9/blimps/fastaseqs.c
===================================================================
--- blimps-3.9.orig/blimps/fastaseqs.c	2012-02-03 21:58:56.508245227 +0100
+++ blimps-3.9/blimps/fastaseqs.c	2012-02-03 22:01:33.944367858 +0100
@@ -39,7 +39,7 @@
    else
    {
       printf("\nEnter name of input sequence file: ");
-      gets(infile);
+      fgets(infile, MAXNAME, stdin);
    }
    if ( (fin=fopen(infile, "r")) == NULL)
    {
@@ -52,7 +52,7 @@
    else
    {
       printf("\nEnter name of output file: ");
-      gets(outfile);
+      fgets(outfile, MAXNAME, stdin);
    }
    if ( (fout=fopen(outfile, "w")) == NULL)
    {
Index: blimps-3.9/blimps/find_biassed_blocks.c
===================================================================
--- blimps-3.9.orig/blimps/find_biassed_blocks.c	2012-02-03 21:58:56.532242527 +0100
+++ blimps-3.9/blimps/find_biassed_blocks.c	2012-02-03 22:01:33.952367787 +0100
@@ -290,7 +290,7 @@
    else                                   /* get input file interactively */
       {
       printf("\nEnter name of a file with blocks or block matrices: ");
-      gets(bdbname);
+      fgets(bdbname, MAXNAME, stdin);
       }
 
    if ( (*bfp=fopen(bdbname, "r")) == NULL)
Index: blimps-3.9/blimps/format_block.c
===================================================================
--- blimps-3.9.orig/blimps/format_block.c	2012-02-03 21:58:56.552242598 +0100
+++ blimps-3.9/blimps/format_block.c	2012-02-03 22:04:33.268242693 +0100
@@ -242,14 +242,14 @@
 }
 
 /* 
- * resize_block_sequences
+ * fb_resize_block_sequences
  *   Increases the memory for the storage of the sequences of a block.
  *   Parameter:
  *     Block *block: the block to resize
  *   Error codes: none
  */
 
-static void resize_block_sequences(block)
+static void fb_resize_block_sequences(block)
      Block *block;
 {
   int i;
@@ -315,13 +315,13 @@
   /* check that obligatory fields have something */
 
 /* Note if sequence names and start positions not supplied */
-  if (SEQ_NAMES_Ptr->val[0] == NULL) no_seq_names = 1 ;
+  if (SEQ_NAMES_Ptr->val[0] == 0) no_seq_names = 1 ;
   else                               no_seq_names = 0 ; 
 
-  if (SEQ_POS_Ptr->val[0] == NULL) no_seq_pos = 1 ;
+  if (SEQ_POS_Ptr->val[0] == 0) no_seq_pos = 1 ;
   else                             no_seq_pos = 0 ; 
 
-  if (SEQS_Ptr->val[0] == NULL) 
+  if (SEQS_Ptr->val[0] == 0)
     {
       printf("<H1>Error</H1>\n");
       printf("No sequences specified.<P>\n");
@@ -403,7 +403,7 @@
        exit(0);
        }
 
-    if (MA_WIDTH_Ptr->val[0] != NULL && 
+    if (MA_WIDTH_Ptr->val[0] != 0 &&
         block->width != atoi (MA_WIDTH_Ptr->val))
        {
        printf("<H2>Warning</H2>\n");
@@ -470,15 +470,15 @@
       if (seq_header)
 	 {
                                                             /* skip blanks */
-         for(; isspace(SEQS_Ptr->val[i]) && SEQS_Ptr->val[i] != '/n' && 
-               SEQS_Ptr->val[i] != '/0'; i++) ;
-         if (SEQS_Ptr->val[i] == '/n')      /* no name is found in line */
+         for(; isspace(SEQS_Ptr->val[i]) && SEQS_Ptr->val[i] != '\n' &&
+               SEQS_Ptr->val[i] != '\0'; i++) ;
+         if (SEQS_Ptr->val[i] == '\n')      /* no name is found in line */
              sprintf(block->sequences[block->num_sequences].name, 
                      "%s%d", UNKNOWN_SEQ_NAME, block->num_sequences+1) ;
          else
                         /* copy first 20 chars or until a space is reached */
          for(k=0; !(isspace(SEQS_Ptr->val[i])) && k<20 &&
-                  SEQS_Ptr->val[i] != '/n' ; i++, k++) 
+                  SEQS_Ptr->val[i] != '\n' ; i++, k++)
             block->sequences[block->num_sequences].name[k] = SEQS_Ptr->val[i];
 
                                                             /* end string */
@@ -520,7 +520,7 @@
          string[j] = '\0' ;
 
          if (block->max_sequences <= block->num_sequences+1) 
-            resize_block_sequences(block) ;
+            fb_resize_block_sequences(block) ;
 
 	                                            /* process the sequence */
 
@@ -623,7 +623,7 @@
             string[j] = '\0' ;
 
             if (block->max_sequences <= k) 
-               resize_block_sequences(block) ;
+               fb_resize_block_sequences(block) ;
 
                                        /* copy up to first 20 chars of name */
             strncpy(block->sequences[k].name,string,20) ;
@@ -681,7 +681,7 @@
                }
             string[j] = '\0' ;
 
-            if (block->max_sequences <= k+1) resize_block_sequences(block) ;
+            if (block->max_sequences <= k+1) fb_resize_block_sequences(block) ;
 
             block->sequences[k].position = atoi(string) ;
 
@@ -703,7 +703,7 @@
 
                        /* check that actual number of sequences is equal to 
                           what the user gave */
-    if (MA_SEQS_Ptr->val[0] != NULL && 
+    if (MA_SEQS_Ptr->val[0] != 0 &&
         block->num_sequences != atoi (MA_SEQS_Ptr->val))
        {
        printf("<H2>Warning</H2>\n");
@@ -719,7 +719,7 @@
 
  /* get block header data */
 
-    if (ID_Ptr->val[0] == NULL) 
+    if (ID_Ptr->val[0] == 0)
        strcpy(block->id, "None") ;
     else
        strncpy(block->id,ID_Ptr->val, SMALL_BUFF_LENGTH) ;
@@ -727,7 +727,7 @@
     strcat(block->id, "; BLOCK") ;
 
 
-    if (AC_Ptr->val[0] == NULL) 
+    if (AC_Ptr->val[0] == 0)
     {
        strncpy(block->number, block->sequences[0].name, MAXAC) ;
     }
@@ -746,7 +746,7 @@
 
     strcpy(block->ac,block->number) ;
 
-    if (MIN_DIST_Ptr->val[0] == NULL) 
+    if (MIN_DIST_Ptr->val[0] == 0)
        {
        j = 10000 ;
        for(i=0; i<block->num_sequences; i++) 
@@ -758,7 +758,7 @@
             block->ac, j) ;
 
 
-    if (MAX_DIST_Ptr->val[0] == NULL) 
+    if (MAX_DIST_Ptr->val[0] == 0)
        {
        j = 0 ;
        for(i=0; i<block->num_sequences; i++) 
@@ -769,12 +769,12 @@
     sprintf(block->ac, "%s,%d)",
             block->ac, j) ;
   
-    if (DE_Ptr->val[0] == NULL) 
+    if (DE_Ptr->val[0] == 0)
        strcpy(block->de, "None") ;
     else
        strncpy(block->de,DE_Ptr->val, SMALL_BUFF_LENGTH) ;
 
-    if (MA_METH_Ptr->val[0] != NULL) 
+    if (MA_METH_Ptr->val[0] != 0)
        strncpy(block->bl,MA_METH_Ptr->val, SMALL_BUFF_LENGTH-25) ;
     else
        strcpy(block->bl,"Method unspecified") ;
@@ -881,7 +881,7 @@
 }
 
 
-void main(int argc, char *argv[]) {
+int main(int argc, char *argv[]) {
 
   printf("Content-type: text/html\n\n\n");
 
@@ -918,6 +918,6 @@
 
   clean_temp_files() ;
 
-  exit(0) ;
+  return(0) ;
 }
 
Index: blimps-3.9/blimps/htmlize-codehop.c
===================================================================
--- blimps-3.9.orig/blimps/htmlize-codehop.c	2012-02-03 21:58:56.576245371 +0100
+++ blimps-3.9/blimps/htmlize-codehop.c	2012-02-03 22:01:33.964368000 +0100
@@ -47,7 +47,7 @@
 void condense();
 
 /*======================================================================*/
-void main(argc, argv)
+int main(argc, argv)
 int argc;
 char *argv[];
 {
@@ -250,7 +250,7 @@
    printf("\n%d blocks, %d oligos processed\n", nblock, noligo);
 */
 
-   exit(0);
+   return(0);
 }  /* end of main */
 /*=========================================================================*/
 struct olist *make_olist()
Index: blimps-3.9/blimps/htmlize-LAMA.c
===================================================================
--- blimps-3.9.orig/blimps/htmlize-LAMA.c	2012-02-03 21:58:56.600245084 +0100
+++ blimps-3.9/blimps/htmlize-LAMA.c	2012-02-03 22:01:33.972368017 +0100
@@ -13,6 +13,7 @@
 
 #include <stdlib.h>
 #include <stdio.h>
+#include <string.h>
 
 
 #define TRUE 1
Index: blimps-3.9/blimps/interpro.c
===================================================================
--- blimps-3.9.orig/blimps/interpro.c	2012-02-03 21:58:56.624245384 +0100
+++ blimps-3.9/blimps/interpro.c	2012-02-03 22:01:33.976367852 +0100
@@ -94,7 +94,7 @@
    else
    {
       printf("\nEnter name of interpro xml file: ");
-      gets(iprfile);
+      fgets(iprfile, MAXNAME, stdin);
    }
    if ( (fip=fopen(iprfile, "r")) == NULL)
    {
@@ -108,7 +108,7 @@
    else
    {
       printf("\nEnter name of interpro entry or all : ");
-      gets(iprname);
+      fgets(iprname, MAXAC, stdin);
    }
    if (!strlen(iprname)) strcpy(iprname, "all");
    All = NO;
Index: blimps-3.9/blimps/LAMA.c
===================================================================
--- blimps-3.9.orig/blimps/LAMA.c	2012-02-03 21:58:56.648243282 +0100
+++ blimps-3.9/blimps/LAMA.c	2012-02-03 22:01:33.984368213 +0100
@@ -400,12 +400,12 @@
    else                                   /* get input file(s) interactively */
       {
       printf("\nEnter name of a file with blocks or block matrices: ");
-      gets(bdbname[0]);
+      fgets(bdbname[0], MAXNAME, stdin);
 
       printf("\nThe blocks/matrices in this file will be intercompared.\n");
       printf("If you wish to compare them against blocks/matrices in\n");
       printf("another file enter that file name (else just hit <ENTER>).\n");
-      gets(bdbname[1]);
+      fgets(bdbname[1], MAXNAME, stdin);
 
       if (bdbname[1][0] == '\0') *inpfiles = 1 ;
       else                       *inpfiles = 2 ;
@@ -426,7 +426,7 @@
    else
       {
       printf("\nEnter name of output file: ");
-      gets(outname);
+      fgets(outname, MAXNAME, stdin);
       }
 
    if ( (*out=fopen(outname, "w")) == NULL)
Index: blimps-3.9/blimps/LAMA_search.c
===================================================================
--- blimps-3.9.orig/blimps/LAMA_search.c	2012-02-03 21:58:56.672242748 +0100
+++ blimps-3.9/blimps/LAMA_search.c	2012-02-03 22:02:47.176242818 +0100
@@ -281,7 +281,7 @@
 
 
   /* check that a block was specified */
-  if (Qblock_Ptr->val[0] == NULL) 
+  if (Qblock_Ptr->val[0] == 0)
     {
       printf("<H1>Search Error</H1>\n");
       printf("You need to enter a block to search with by writing or pasting a block in the query block window.<P>\n");
@@ -296,7 +296,7 @@
 
 
   /* if block was pasted/written - */
-  if (Qblock_Ptr->val[0] != NULL)
+  if (Qblock_Ptr->val[0] != 0)
     {
       
       /* open up the block file to write to */
@@ -579,7 +579,7 @@
   /*    mail the person the results */
   /*    NOTE: need to echo the header lines for the LAMA output :P */
   /*    NOTE: all this should need to do is to cat the ouput file. */
-  sprintf(buf, "%s %s '(cat %s) | /usr/bin/mailx -s \"LAMA Results\" -r \"blocks\@fhcrc.org\" %s'", add_queue_entry, LAMA_queue, LAMA_output, Address_Ptr->val);
+  sprintf(buf, "%s %s '(cat %s) | /usr/bin/mailx -s \"LAMA Results\" -r \"blocks@fhcrc.org\" %s'", add_queue_entry, LAMA_queue, LAMA_output, Address_Ptr->val);
   system(buf);
   
 
@@ -666,7 +666,7 @@
 
 } /* end of run Cyrca */
 
-void main(int argc, char *argv[]) {
+int main(int argc, char *argv[]) {
 
   printf("Content-type: text/html\n\n\n");
 
@@ -715,5 +715,5 @@
 
   clean_temp_files() ;
 
-  exit(0) ;
+  return(0) ;
 }
Index: blimps-3.9/blimps/lisblk.c
===================================================================
--- blimps-3.9.orig/blimps/lisblk.c	2012-02-03 21:58:56.856367328 +0100
+++ blimps-3.9/blimps/lisblk.c	2012-02-03 22:01:34.028368291 +0100
@@ -33,7 +33,7 @@
 char Title[MAXLINE];
 
 /*======================================================================*/
-void main(argc, argv)
+int main(argc, argv)
 int argc;
 char *argv[];
 {
@@ -53,7 +53,7 @@
    else
    {
       printf("\nEnter name of file containing list of sequences: ");
-      gets(lisfile);
+      fgets(lisfile, FNAMELEN, stdin);
    }
    if ( (flis=fopen(lisfile, "r")) == NULL)
    {
@@ -69,7 +69,7 @@
    else
    {
       printf("\nEnter name of block file: ");
-      gets(blkfile);
+      fgets(blkfile, FNAMELEN, stdin);
    }
 
    if ((fblk=fopen(blkfile, "r")) == NULL)
@@ -85,7 +85,7 @@
       if ((fblk=fopen(blkfile, "r")) == NULL)
       {
 	    printf("\nEnter name of block file: ");
-	    gets(blkfile);
+	    fgets(blkfile, FNAMELEN, stdin);
       }
    }
    if (fblk == NULL)
@@ -147,7 +147,7 @@
    fclose(fout);
 
    printf("\n");
-   exit(0);
+   return(0);
 }  /*  end of main */
 /*================================================================*/
 int flag_ids(block, ids)
Index: blimps-3.9/blimps/mablock.c
===================================================================
--- blimps-3.9.orig/blimps/mablock.c	2012-02-03 21:58:56.880439022 +0100
+++ blimps-3.9/blimps/mablock.c	2012-02-03 22:01:34.040367995 +0100
@@ -102,7 +102,8 @@
 {
    FILE *ifp, *bfp, *sfp;
    Sequence *seqs[MAXSEQ];
-   char ctemp[MAXNAME], bdbname[MAXNAME], outtype[10], *ptr;
+#define MABLOCK_OUTTYPELEN 10
+   char ctemp[MAXNAME], bdbname[MAXNAME], outtype[MABLOCK_OUTTYPELEN], *ptr;
    int db_type, seq_type, nseq, i, bflag, ftype;
    struct blocks_list *blocks;
    Block *block;
@@ -127,7 +128,7 @@
    else
    {
       printf("\nEnter name of blocks database: ");
-      gets(bdbname);
+      fgets( bdbname, MAXNAME, stdin );
    }
    if ( (ifp=fopen(bdbname, "r")) == NULL)
    {
@@ -157,7 +158,7 @@
    else
    {
       printf("\nEnter name of output file: ");
-      gets(OutName);
+      fgets( OutName, MAXNAME, stdin );
    }
    strcpy(ctemp, OutName); strcat(ctemp, ".blks");
    if ( (bfp=fopen(ctemp, "w")) == NULL)
@@ -177,7 +178,7 @@
    else
    {
       printf("\nEnter type of output file [B=blocks|F=fasta]: ");
-      gets(outtype);
+      fgets( outtype, MABLOCK_OUTTYPELEN, stdin );
    }
    if (outtype[0] == 'F' || outtype[0] == 'f') ftype = 1;
 /* ------------4th arg = optional min trimming size--------------------*/
Index: blimps-3.9/blimps/Makefile.Linux
===================================================================
--- blimps-3.9.orig/blimps/Makefile.Linux	2012-02-03 21:58:56.904242649 +0100
+++ blimps-3.9/blimps/Makefile.Linux	2012-02-03 22:01:34.264242740 +0100
@@ -44,19 +44,25 @@
 #	so the Makefile continues to work.
 
 # Linux
+VERSION := 3.9
+SOVERSION := 3.0.0
+SHORTSOVERSION := 3
+
 DEFINES = 
 SYSTEM  = 
-OPTIMIZ = -Wall -O2
+#OPTIMIZ = -Wall -O2
+OPTIMIZ = -Wuninitialized -O2
+#OPTIMIZ = -Werror -O2
 RANLIB = ls
 
 MAKE = make
-DEPEND = makedepend
+DEPEND = $(CC)
 
 #	ar -t libpssm.a for table of contents
 AR = ar
 RM = rm -f
 MV = mv -f 
-CP = cp
+CP = cp -af
 
 
 # C compiler
@@ -106,12 +112,12 @@
 
 # C Flags to compiler
 #CFLAGS = `getconf LFS_CFLAGS` $(OPTIMIZ) $(DEFINES) $(INCLUDES)
-CFLAGS = $(OPTIMIZ) $(DEFINES) $(INCLUDES)
+CFLAGS = $(OPTIMIZ) $(DEFINES) $(INCLUDES) -fpic
 
 
 # Linker Flags
 LDFLAGS = $(CFLAGS)
-LDLIBS = -lblimps -ly -lm
+LDLIBS = -lblimps -lm
 LDOPTIONS = $(LDFLAGS) $(LDDIR)
 # cc ld options
 
@@ -120,6 +126,9 @@
 LIBRARY_DIR = ./
 LDDIR = -L$(LIBRARY_DIR)
 
+#SHARED_LIB_DIR := ./.libs
+SHARED_LIB_DIR := .
+
 
 # source files
 SRCS =  blimps-mem.c \
@@ -197,34 +206,36 @@
 OTHER_OBJS_DEBUG =	/usr/lib/debug/malloc.o \
 		/usr/lib/debug/mallocmap.o
 
-LIBOBJS = pattern.o \
-	files.o \
-	frequency.o \
-	convert.o \
+LIBOBJS = \
+	blimps.o \
+	blimps-mem.o \
 	blocks.o \
+	config.o \
+	convert.o \
 	errors.o \
+	files.o \
+	frequency.o \
 	gcode.o \
+	lists.o \
 	matrix.o \
 	memory.o \
-	sequences.o \
-	strutil.o \
-	sl.o \
-	version.o \
 	options.o \
-	blimps-mem.o \
-	config.o \
-	lists.o \
+	p2clib.o \
+	pattern.o \
+        protomat.o \
 	scores.o \
 	scoring.o \
-	p2clib.o \
+	sequences.o \
+	sl.o \
+	strutil.o \
 	util.o \
-        protomat.o
+	version.o
 
 
 # need malloc.o for malloc_debug() which will have free() raise SIGABRT
 # if it is unable to free the space.
 
-LIBRARIES = libblimps.a
+LIBRARIES = libblimps.a $(SHARED_LIB_DIR)/libblimps.so.$(SOVERSION)
 
 
 ########################################################################
@@ -235,10 +246,10 @@
 ########################################################################
 ########################################################################
 
-install: clean all move-lib move-bin
-
 all: lib blimps blweight blalign bldist blk2pssm rank_matrix retblock codehop htmlize-codehop oligo_melt mablock cobbler addseqs fastaseqs LAMA find_biassed_blocks makeblockmap prints2blocks lisblk coduse narrow blk2slx blkprob interpro pssmdist pssmBL papssm matrix_logob makelogob blocks_search LAMA_search block_vis format_block biassed_blocks_finder htmlize-LAMA show_aligned_blocks makelis blk2mot 
 
+install: clean all move-lib move-bin
+
 blimps: $(LIBRARIES) blimps.o $(LIBOBJS) 
 	$(RM) $@
 	$(CC) -o $@  blimps.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS) 
@@ -427,7 +438,15 @@
 #
 
 libblimps.a: $(LIBOBJS)
-	$(AR) cr $@ $(LIBOBJS) ; $(RANLIB) $@
+	$(AR) cr $@ $(LIBOBJS)
+
+$(SHARED_LIB_DIR):
+	mkdir -p $@
+
+$(SHARED_LIB_DIR)/libblimps.so.$(SOVERSION): $(LIBOBJS) | $(SHARED_LIB_DIR)
+	$(CC) $(LDFLAGS) -shared -Wl,-soname,libblimps.so.$(SHORTSOVERSION) -o $@ -lm $(LIBOBJS)
+	/sbin/ldconfig -n $(SHARED_LIB_DIR)
+	rm -f $(SHARED_LIB_DIR)/libblimps.so && ln -sf libblimps.so.$(SOVERSION) $(SHARED_LIB_DIR)/libblimps.so
 
 ########################################################################
 ########################################################################
@@ -480,57 +499,61 @@
 	etags ./*.[ch] $(INCLUDE_DIR)/*.[ch]
 
 
-depend: 
-	 $(DEPEND) -- $(CFLAGS) -- -s "# DO NOT DELETE" -- $(SRCS)
+depend: deps.mk
 
 
-clean::
+clean:
 	$(RM) blimps blweight blalign bldist blk2pssm rank_matrix retblock codehop htmlize-codehop oligo_melt mablock makeblockmap prints2blocks lisblk coduse narrow blkprob blk2slx LAMA find_biassed_blocks fastaseqs addseqs cobbler interpro pssmdist pssmBL papssm matrix_logob makelogob blocks_search LAMA_search block_vis format_block biassed_blocks_finder htmlize-LAMA show_aligned_blocks makelis blk2mot 
 	$(RM) *.a *.o *~ 
+	if [ "$(SHARED_LIB_DIR)" != "." ]; then $(RM) -r $(SHARED_LIB_DIR); fi
+	rm -f $(SHARED_LIB_DIR)/libblimps.so*
 	@echo " "
 
+distclean: clean
+	$(RM) deps.mk
+
 move-lib:
-	$(MV) lib*.a ../lib
+	$(CP) lib*.a $(SHARED_LIB_DIR)/*.so ../lib
 
 move-bin:
-	$(MV) blimps ../bin
-	$(MV) blweight ../bin
-	$(MV) blalign ../bin
-	$(MV) bldist ../bin
-	$(MV) blk2pssm ../bin
-	$(MV) rank_matrix ../bin
-	$(MV) retblock ../bin
-	$(MV) codehop ../bin
-	$(MV) htmlize-codehop ../bin
-	$(MV) oligo_melt ../bin
-	$(MV) mablock ../bin
-	$(MV) makeblockmap ../bin
-	$(MV) prints2blocks ../bin
-	$(MV) lisblk ../bin
-	$(MV) coduse ../bin
-	$(MV) narrow ../bin
-	$(MV) blkprob ../bin
-	$(MV) blk2slx ../bin
-	$(MV) LAMA ../bin
-	$(MV) find_biassed_blocks ../bin
-	$(MV) fastaseqs ../bin
-	$(MV) addseqs ../bin
-	$(MV) cobbler ../bin
-	$(MV) interpro ../bin
-	$(MV) pssmdist ../bin
-	$(MV) pssmBL ../bin
-	$(MV) papssm ../bin
-	$(MV) matrix_logob ../bin
-	$(MV) makelogob ../bin
-	$(MV) blocks_search ../bin
-	$(MV) LAMA_search ../bin
-	$(MV) block_vis ../bin
-	$(MV) format_block ../bin
-	$(MV) biassed_blocks_finder ../bin
-	$(MV) htmlize-LAMA ../bin
-	$(MV) show_aligned_blocks ../bin
-	$(MV) makelis ../bin
-	$(MV) blk2mot ../bin
+	$(CP) blimps ../bin
+	$(CP) blweight ../bin
+	$(CP) blalign ../bin
+	$(CP) bldist ../bin
+	$(CP) blk2pssm ../bin
+	$(CP) rank_matrix ../bin
+	$(CP) retblock ../bin
+	$(CP) codehop ../bin
+	$(CP) htmlize-codehop ../bin
+	$(CP) oligo_melt ../bin
+	$(CP) mablock ../bin
+	$(CP) makeblockmap ../bin
+	$(CP) prints2blocks ../bin
+	$(CP) lisblk ../bin
+	$(CP) coduse ../bin
+	$(CP) narrow ../bin
+	$(CP) blkprob ../bin
+	$(CP) blk2slx ../bin
+	$(CP) LAMA ../bin
+	$(CP) find_biassed_blocks ../bin
+	$(CP) fastaseqs ../bin
+	$(CP) addseqs ../bin
+	$(CP) cobbler ../bin
+	$(CP) interpro ../bin
+	$(CP) pssmdist ../bin
+	$(CP) pssmBL ../bin
+	$(CP) papssm ../bin
+	$(CP) matrix_logob ../bin
+	$(CP) makelogob ../bin
+	$(CP) blocks_search ../bin
+	$(CP) LAMA_search ../bin
+	$(CP) block_vis ../bin
+	$(CP) format_block ../bin
+	$(CP) biassed_blocks_finder ../bin
+	$(CP) htmlize-LAMA ../bin
+	$(CP) show_aligned_blocks ../bin
+	$(CP) makelis ../bin
+	$(CP) blk2mot ../bin
 
 
 ##########
@@ -687,1272 +710,14 @@
 	  $(VERSIONDISTRIB)/blimps.$(TXTVER)/docs/INSTALL $(FTPDIR)
 	@echo " "
 
-
+deps.mk:
+	$(DEPEND) -MM $(CFLAGS) $(SRCS) > $@
 
 ###########################################################################
 
+.PHONY: depend all clean distclean dist
  
 ###########################################################################
-# dependencies generated by makedepend
- 
-# DO NOT DELETE
+# dependencies
+include deps.mk
 
-blimps-mem.o: ../include/global.h /usr/include/stdlib.h
-blimps-mem.o: /usr/include/features.h /usr/include/sys/cdefs.h
-blimps-mem.o: /usr/include/gnu/stubs.h
-blimps-mem.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-blimps-mem.o: /usr/include/stdio.h /usr/include/bits/types.h
-blimps-mem.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-blimps-mem.o: /usr/include/libio.h /usr/include/_G_config.h
-blimps-mem.o: /usr/include/wchar.h /usr/include/bits/wchar.h
-blimps-mem.o: /usr/include/gconv.h
-blimps-mem.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-blimps-mem.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-blimps-mem.o: /usr/include/string.h /usr/include/ctype.h
-blimps-mem.o: /usr/include/endian.h /usr/include/bits/endian.h
-blimps-mem.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
-blimps-mem.o: ../include/errors.h ../include/memory.h blimps-mem.h blimps.h
-blimps-mem.o: lists.h ../include/skiplist.h
-blimps.o: /usr/include/math.h /usr/include/features.h
-blimps.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
-blimps.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-blimps.o: /usr/include/bits/mathcalls.h /usr/include/signal.h
-blimps.o: /usr/include/bits/sigset.h /usr/include/bits/types.h
-blimps.o: /usr/include/bits/wordsize.h
-blimps.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-blimps.o: /usr/include/bits/typesizes.h /usr/include/bits/signum.h
-blimps.o: ../include/global.h /usr/include/stdlib.h /usr/include/stdio.h
-blimps.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-blimps.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-blimps.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-blimps.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-blimps.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
-blimps.o: /usr/include/bits/endian.h /usr/include/malloc.h
-blimps.o: ../include/license.h ../include/strutil.h ../include/errors.h
-blimps.o: ../include/memory.h ../include/version.h ../include/residues.h
-blimps.o: ../include/blastapp.h /usr/include/limits.h
-blimps.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-blimps.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-blimps.o: ../include/gcode.h ../include/files.h ../include/blocks.h
-blimps.o: ../include/output.h ../include/sequences.h ../include/matrix.h
-blimps.o: ../include/pattern.h ../include/convert.h ../include/frequency.h
-blimps.o: ../include/options.h blimps.h blimps-mem.h config.h scores.h
-blimps.o: scoring.h lists.h ../include/skiplist.h
-blweight.o: ../include/blocksprogs.h /usr/include/stdlib.h
-blweight.o: /usr/include/features.h /usr/include/sys/cdefs.h
-blweight.o: /usr/include/gnu/stubs.h
-blweight.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-blweight.o: /usr/include/stdio.h /usr/include/bits/types.h
-blweight.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-blweight.o: /usr/include/libio.h /usr/include/_G_config.h
-blweight.o: /usr/include/wchar.h /usr/include/bits/wchar.h
-blweight.o: /usr/include/gconv.h
-blweight.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-blweight.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-blweight.o: /usr/include/string.h /usr/include/math.h
-blweight.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-blweight.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
-blweight.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
-blweight.o: /usr/include/ctype.h /usr/include/endian.h
-blweight.o: /usr/include/bits/endian.h ../include/global.h
-blweight.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
-blweight.o: ../include/errors.h ../include/memory.h ../include/residues.h
-blweight.o: ../include/blastapp.h /usr/include/limits.h
-blweight.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-blweight.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-blweight.o: ../include/gcode.h ../include/blocks.h ../include/output.h
-blweight.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
-blweight.o: ../include/convert.h ../include/frequency.h ../include/files.h
-blweight.o: ../include/protomat.h /usr/include/sys/time.h /usr/include/time.h
-blweight.o: /usr/include/bits/time.h /usr/include/sys/select.h
-blweight.o: /usr/include/bits/select.h /usr/include/bits/sigset.h
-blalign.o: ../include/blocksprogs.h /usr/include/stdlib.h
-blalign.o: /usr/include/features.h /usr/include/sys/cdefs.h
-blalign.o: /usr/include/gnu/stubs.h
-blalign.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-blalign.o: /usr/include/stdio.h /usr/include/bits/types.h
-blalign.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-blalign.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-blalign.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-blalign.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-blalign.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-blalign.o: /usr/include/string.h /usr/include/math.h
-blalign.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-blalign.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
-blalign.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
-blalign.o: /usr/include/ctype.h /usr/include/endian.h
-blalign.o: /usr/include/bits/endian.h ../include/global.h
-blalign.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
-blalign.o: ../include/errors.h ../include/memory.h ../include/residues.h
-blalign.o: ../include/blastapp.h /usr/include/limits.h
-blalign.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-blalign.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-blalign.o: ../include/gcode.h ../include/blocks.h ../include/output.h
-blalign.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
-blalign.o: ../include/convert.h ../include/frequency.h ../include/files.h
-blalign.o: ../include/protomat.h
-bldist.o: ../include/blocksprogs.h /usr/include/stdlib.h
-bldist.o: /usr/include/features.h /usr/include/sys/cdefs.h
-bldist.o: /usr/include/gnu/stubs.h
-bldist.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-bldist.o: /usr/include/stdio.h /usr/include/bits/types.h
-bldist.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-bldist.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-bldist.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-bldist.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-bldist.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-bldist.o: /usr/include/string.h /usr/include/math.h
-bldist.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-bldist.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
-bldist.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
-bldist.o: /usr/include/ctype.h /usr/include/endian.h
-bldist.o: /usr/include/bits/endian.h ../include/global.h
-bldist.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
-bldist.o: ../include/errors.h ../include/memory.h ../include/residues.h
-bldist.o: ../include/blastapp.h /usr/include/limits.h
-bldist.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-bldist.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-bldist.o: ../include/gcode.h ../include/blocks.h ../include/output.h
-bldist.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
-bldist.o: ../include/convert.h ../include/frequency.h ../include/files.h
-bldist.o: ../include/protomat.h
-blk2pssm.o: ../include/blocksprogs.h /usr/include/stdlib.h
-blk2pssm.o: /usr/include/features.h /usr/include/sys/cdefs.h
-blk2pssm.o: /usr/include/gnu/stubs.h
-blk2pssm.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-blk2pssm.o: /usr/include/stdio.h /usr/include/bits/types.h
-blk2pssm.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-blk2pssm.o: /usr/include/libio.h /usr/include/_G_config.h
-blk2pssm.o: /usr/include/wchar.h /usr/include/bits/wchar.h
-blk2pssm.o: /usr/include/gconv.h
-blk2pssm.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-blk2pssm.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-blk2pssm.o: /usr/include/string.h /usr/include/math.h
-blk2pssm.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-blk2pssm.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
-blk2pssm.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
-blk2pssm.o: /usr/include/ctype.h /usr/include/endian.h
-blk2pssm.o: /usr/include/bits/endian.h ../include/global.h
-blk2pssm.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
-blk2pssm.o: ../include/errors.h ../include/memory.h ../include/residues.h
-blk2pssm.o: ../include/blastapp.h /usr/include/limits.h
-blk2pssm.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-blk2pssm.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-blk2pssm.o: ../include/gcode.h ../include/blocks.h ../include/output.h
-blk2pssm.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
-blk2pssm.o: ../include/convert.h ../include/frequency.h ../include/files.h
-blk2pssm.o: ../include/protomat.h
-rank_matrix.o: ../include/blocksprogs.h /usr/include/stdlib.h
-rank_matrix.o: /usr/include/features.h /usr/include/sys/cdefs.h
-rank_matrix.o: /usr/include/gnu/stubs.h
-rank_matrix.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-rank_matrix.o: /usr/include/stdio.h /usr/include/bits/types.h
-rank_matrix.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-rank_matrix.o: /usr/include/libio.h /usr/include/_G_config.h
-rank_matrix.o: /usr/include/wchar.h /usr/include/bits/wchar.h
-rank_matrix.o: /usr/include/gconv.h
-rank_matrix.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-rank_matrix.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-rank_matrix.o: /usr/include/string.h /usr/include/math.h
-rank_matrix.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-rank_matrix.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
-rank_matrix.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
-rank_matrix.o: /usr/include/ctype.h /usr/include/endian.h
-rank_matrix.o: /usr/include/bits/endian.h ../include/global.h
-rank_matrix.o: /usr/include/malloc.h ../include/license.h
-rank_matrix.o: ../include/strutil.h ../include/errors.h ../include/memory.h
-rank_matrix.o: ../include/residues.h ../include/blastapp.h
-rank_matrix.o: /usr/include/limits.h
-rank_matrix.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-rank_matrix.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-rank_matrix.o: ../include/gcode.h ../include/blocks.h ../include/output.h
-rank_matrix.o: ../include/sequences.h ../include/matrix.h
-rank_matrix.o: ../include/pattern.h ../include/convert.h
-rank_matrix.o: ../include/frequency.h ../include/files.h
-rank_matrix.o: ../include/protomat.h
-retblock.o: ../include/blocksprogs.h /usr/include/stdlib.h
-retblock.o: /usr/include/features.h /usr/include/sys/cdefs.h
-retblock.o: /usr/include/gnu/stubs.h
-retblock.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-retblock.o: /usr/include/stdio.h /usr/include/bits/types.h
-retblock.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-retblock.o: /usr/include/libio.h /usr/include/_G_config.h
-retblock.o: /usr/include/wchar.h /usr/include/bits/wchar.h
-retblock.o: /usr/include/gconv.h
-retblock.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-retblock.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-retblock.o: /usr/include/string.h /usr/include/math.h
-retblock.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-retblock.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
-retblock.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
-retblock.o: /usr/include/ctype.h /usr/include/endian.h
-retblock.o: /usr/include/bits/endian.h ../include/global.h
-retblock.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
-retblock.o: ../include/errors.h ../include/memory.h ../include/residues.h
-retblock.o: ../include/blastapp.h /usr/include/limits.h
-retblock.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-retblock.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-retblock.o: ../include/gcode.h ../include/blocks.h ../include/output.h
-retblock.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
-retblock.o: ../include/convert.h ../include/frequency.h ../include/files.h
-retblock.o: ../include/protomat.h
-codehop.o: ../include/blocksprogs.h /usr/include/stdlib.h
-codehop.o: /usr/include/features.h /usr/include/sys/cdefs.h
-codehop.o: /usr/include/gnu/stubs.h
-codehop.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-codehop.o: /usr/include/stdio.h /usr/include/bits/types.h
-codehop.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-codehop.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-codehop.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-codehop.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-codehop.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-codehop.o: /usr/include/string.h /usr/include/math.h
-codehop.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-codehop.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
-codehop.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
-codehop.o: /usr/include/ctype.h /usr/include/endian.h
-codehop.o: /usr/include/bits/endian.h ../include/global.h
-codehop.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
-codehop.o: ../include/errors.h ../include/memory.h ../include/residues.h
-codehop.o: ../include/blastapp.h /usr/include/limits.h
-codehop.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-codehop.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-codehop.o: ../include/gcode.h ../include/blocks.h ../include/output.h
-codehop.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
-codehop.o: ../include/convert.h ../include/frequency.h ../include/files.h
-codehop.o: ../include/protomat.h codehop.h /usr/include/sys/time.h
-codehop.o: /usr/include/time.h /usr/include/bits/time.h
-codehop.o: /usr/include/sys/select.h /usr/include/bits/select.h
-codehop.o: /usr/include/bits/sigset.h
-htmlize-codehop.o: /usr/include/stdio.h /usr/include/features.h
-htmlize-codehop.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
-htmlize-codehop.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-htmlize-codehop.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
-htmlize-codehop.o: /usr/include/bits/typesizes.h /usr/include/libio.h
-htmlize-codehop.o: /usr/include/_G_config.h /usr/include/wchar.h
-htmlize-codehop.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-htmlize-codehop.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-htmlize-codehop.o: /usr/include/bits/stdio_lim.h
-htmlize-codehop.o: /usr/include/bits/sys_errlist.h /usr/include/string.h
-htmlize-codehop.o: /usr/include/stdlib.h
-oligo_melt.o: ../include/blocksprogs.h /usr/include/stdlib.h
-oligo_melt.o: /usr/include/features.h /usr/include/sys/cdefs.h
-oligo_melt.o: /usr/include/gnu/stubs.h
-oligo_melt.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-oligo_melt.o: /usr/include/stdio.h /usr/include/bits/types.h
-oligo_melt.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-oligo_melt.o: /usr/include/libio.h /usr/include/_G_config.h
-oligo_melt.o: /usr/include/wchar.h /usr/include/bits/wchar.h
-oligo_melt.o: /usr/include/gconv.h
-oligo_melt.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-oligo_melt.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-oligo_melt.o: /usr/include/string.h /usr/include/math.h
-oligo_melt.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-oligo_melt.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
-oligo_melt.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
-oligo_melt.o: /usr/include/ctype.h /usr/include/endian.h
-oligo_melt.o: /usr/include/bits/endian.h ../include/global.h
-oligo_melt.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
-oligo_melt.o: ../include/errors.h ../include/memory.h ../include/residues.h
-oligo_melt.o: ../include/blastapp.h /usr/include/limits.h
-oligo_melt.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-oligo_melt.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-oligo_melt.o: ../include/gcode.h ../include/blocks.h ../include/output.h
-oligo_melt.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
-oligo_melt.o: ../include/convert.h ../include/frequency.h ../include/files.h
-oligo_melt.o: ../include/protomat.h
-mablock.o: ../include/blocksprogs.h /usr/include/stdlib.h
-mablock.o: /usr/include/features.h /usr/include/sys/cdefs.h
-mablock.o: /usr/include/gnu/stubs.h
-mablock.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-mablock.o: /usr/include/stdio.h /usr/include/bits/types.h
-mablock.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-mablock.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-mablock.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-mablock.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-mablock.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-mablock.o: /usr/include/string.h /usr/include/math.h
-mablock.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-mablock.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
-mablock.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
-mablock.o: /usr/include/ctype.h /usr/include/endian.h
-mablock.o: /usr/include/bits/endian.h ../include/global.h
-mablock.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
-mablock.o: ../include/errors.h ../include/memory.h ../include/residues.h
-mablock.o: ../include/blastapp.h /usr/include/limits.h
-mablock.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-mablock.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-mablock.o: ../include/gcode.h ../include/blocks.h ../include/output.h
-mablock.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
-mablock.o: ../include/convert.h ../include/frequency.h ../include/files.h
-mablock.o: ../include/protomat.h
-cobbler.o: ../include/blocksprogs.h /usr/include/stdlib.h
-cobbler.o: /usr/include/features.h /usr/include/sys/cdefs.h
-cobbler.o: /usr/include/gnu/stubs.h
-cobbler.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-cobbler.o: /usr/include/stdio.h /usr/include/bits/types.h
-cobbler.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-cobbler.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-cobbler.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-cobbler.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-cobbler.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-cobbler.o: /usr/include/string.h /usr/include/math.h
-cobbler.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-cobbler.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
-cobbler.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
-cobbler.o: /usr/include/ctype.h /usr/include/endian.h
-cobbler.o: /usr/include/bits/endian.h ../include/global.h
-cobbler.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
-cobbler.o: ../include/errors.h ../include/memory.h ../include/residues.h
-cobbler.o: ../include/blastapp.h /usr/include/limits.h
-cobbler.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-cobbler.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-cobbler.o: ../include/gcode.h ../include/blocks.h ../include/output.h
-cobbler.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
-cobbler.o: ../include/convert.h ../include/frequency.h ../include/files.h
-cobbler.o: ../include/protomat.h /usr/include/sys/time.h /usr/include/time.h
-cobbler.o: /usr/include/bits/time.h /usr/include/sys/select.h
-cobbler.o: /usr/include/bits/select.h /usr/include/bits/sigset.h
-addseqs.o: ../include/blocksprogs.h /usr/include/stdlib.h
-addseqs.o: /usr/include/features.h /usr/include/sys/cdefs.h
-addseqs.o: /usr/include/gnu/stubs.h
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-addseqs.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-addseqs.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-addseqs.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-addseqs.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-addseqs.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-addseqs.o: /usr/include/string.h /usr/include/math.h
-addseqs.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-addseqs.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
-addseqs.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
-addseqs.o: /usr/include/ctype.h /usr/include/endian.h
-addseqs.o: /usr/include/bits/endian.h ../include/global.h
-addseqs.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
-addseqs.o: ../include/errors.h ../include/memory.h ../include/residues.h
-addseqs.o: ../include/blastapp.h /usr/include/limits.h
-addseqs.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-addseqs.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-addseqs.o: ../include/gcode.h ../include/blocks.h ../include/output.h
-addseqs.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
-addseqs.o: ../include/convert.h ../include/frequency.h ../include/files.h
-addseqs.o: ../include/protomat.h
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-fastaseqs.o: /usr/include/features.h /usr/include/sys/cdefs.h
-fastaseqs.o: /usr/include/gnu/stubs.h
-fastaseqs.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-fastaseqs.o: /usr/include/stdio.h /usr/include/bits/types.h
-fastaseqs.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-fastaseqs.o: /usr/include/libio.h /usr/include/_G_config.h
-fastaseqs.o: /usr/include/wchar.h /usr/include/bits/wchar.h
-fastaseqs.o: /usr/include/gconv.h
-fastaseqs.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-fastaseqs.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-fastaseqs.o: /usr/include/string.h /usr/include/math.h
-fastaseqs.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-fastaseqs.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
-fastaseqs.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
-fastaseqs.o: /usr/include/ctype.h /usr/include/endian.h
-fastaseqs.o: /usr/include/bits/endian.h ../include/global.h
-fastaseqs.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
-fastaseqs.o: ../include/errors.h ../include/memory.h ../include/residues.h
-fastaseqs.o: ../include/blastapp.h /usr/include/limits.h
-fastaseqs.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-fastaseqs.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-fastaseqs.o: ../include/gcode.h ../include/blocks.h ../include/output.h
-fastaseqs.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
-fastaseqs.o: ../include/convert.h ../include/frequency.h ../include/files.h
-fastaseqs.o: ../include/protomat.h
-LAMA.o: ../include/blocksprogs.h /usr/include/stdlib.h
-LAMA.o: /usr/include/features.h /usr/include/sys/cdefs.h
-LAMA.o: /usr/include/gnu/stubs.h
-LAMA.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-LAMA.o: /usr/include/stdio.h /usr/include/bits/types.h
-LAMA.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-LAMA.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-LAMA.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-LAMA.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-LAMA.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-LAMA.o: /usr/include/string.h /usr/include/math.h
-LAMA.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-LAMA.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
-LAMA.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
-LAMA.o: /usr/include/ctype.h /usr/include/endian.h /usr/include/bits/endian.h
-LAMA.o: ../include/global.h /usr/include/malloc.h ../include/license.h
-LAMA.o: ../include/strutil.h ../include/errors.h ../include/memory.h
-LAMA.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
-LAMA.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-LAMA.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-LAMA.o: ../include/gcode.h ../include/blocks.h ../include/output.h
-LAMA.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
-LAMA.o: ../include/convert.h ../include/frequency.h ../include/files.h
-LAMA.o: ../include/protomat.h LAMA.h
-find_biassed_blocks.o: ../include/blocksprogs.h /usr/include/stdlib.h
-find_biassed_blocks.o: /usr/include/features.h /usr/include/sys/cdefs.h
-find_biassed_blocks.o: /usr/include/gnu/stubs.h
-find_biassed_blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-find_biassed_blocks.o: /usr/include/stdio.h /usr/include/bits/types.h
-find_biassed_blocks.o: /usr/include/bits/wordsize.h
-find_biassed_blocks.o: /usr/include/bits/typesizes.h /usr/include/libio.h
-find_biassed_blocks.o: /usr/include/_G_config.h /usr/include/wchar.h
-find_biassed_blocks.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-find_biassed_blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-find_biassed_blocks.o: /usr/include/bits/stdio_lim.h
-find_biassed_blocks.o: /usr/include/bits/sys_errlist.h /usr/include/string.h
-find_biassed_blocks.o: /usr/include/math.h /usr/include/bits/huge_val.h
-find_biassed_blocks.o: /usr/include/bits/mathdef.h
-find_biassed_blocks.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
-find_biassed_blocks.o: /usr/include/bits/posix_opt.h
-find_biassed_blocks.o: /usr/include/bits/confname.h /usr/include/ctype.h
-find_biassed_blocks.o: /usr/include/endian.h /usr/include/bits/endian.h
-find_biassed_blocks.o: ../include/global.h /usr/include/malloc.h
-find_biassed_blocks.o: ../include/license.h ../include/strutil.h
-find_biassed_blocks.o: ../include/errors.h ../include/memory.h
-find_biassed_blocks.o: ../include/residues.h ../include/blastapp.h
-find_biassed_blocks.o: /usr/include/limits.h
-find_biassed_blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-find_biassed_blocks.o: ../include/alphabet.h ../include/aabet.h
-find_biassed_blocks.o: ../include/ntbet.h ../include/gcode.h
-find_biassed_blocks.o: ../include/blocks.h ../include/output.h
-find_biassed_blocks.o: ../include/sequences.h ../include/matrix.h
-find_biassed_blocks.o: ../include/pattern.h ../include/convert.h
-find_biassed_blocks.o: ../include/frequency.h ../include/files.h
-find_biassed_blocks.o: ../include/protomat.h blkvblk.h
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-makeblockmap.o: /usr/include/features.h /usr/include/sys/cdefs.h
-makeblockmap.o: /usr/include/gnu/stubs.h
-makeblockmap.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-makeblockmap.o: /usr/include/stdio.h /usr/include/bits/types.h
-makeblockmap.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-makeblockmap.o: /usr/include/libio.h /usr/include/_G_config.h
-makeblockmap.o: /usr/include/wchar.h /usr/include/bits/wchar.h
-makeblockmap.o: /usr/include/gconv.h
-makeblockmap.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-makeblockmap.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-makeblockmap.o: /usr/include/string.h /usr/include/math.h
-makeblockmap.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-makeblockmap.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
-makeblockmap.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
-makeblockmap.o: /usr/include/ctype.h /usr/include/endian.h
-makeblockmap.o: /usr/include/bits/endian.h ../include/global.h
-makeblockmap.o: /usr/include/malloc.h ../include/license.h
-makeblockmap.o: ../include/strutil.h ../include/errors.h ../include/memory.h
-makeblockmap.o: ../include/residues.h ../include/blastapp.h
-makeblockmap.o: /usr/include/limits.h
-makeblockmap.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-makeblockmap.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-makeblockmap.o: ../include/gcode.h ../include/blocks.h ../include/output.h
-makeblockmap.o: ../include/sequences.h ../include/matrix.h
-makeblockmap.o: ../include/pattern.h ../include/convert.h
-makeblockmap.o: ../include/frequency.h ../include/files.h
-makeblockmap.o: ../include/protomat.h blockmap.h
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-prints2blocks.o: /usr/include/features.h /usr/include/sys/cdefs.h
-prints2blocks.o: /usr/include/gnu/stubs.h
-prints2blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-prints2blocks.o: /usr/include/stdio.h /usr/include/bits/types.h
-prints2blocks.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-prints2blocks.o: /usr/include/libio.h /usr/include/_G_config.h
-prints2blocks.o: /usr/include/wchar.h /usr/include/bits/wchar.h
-prints2blocks.o: /usr/include/gconv.h
-prints2blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-prints2blocks.o: /usr/include/bits/stdio_lim.h
-prints2blocks.o: /usr/include/bits/sys_errlist.h /usr/include/string.h
-prints2blocks.o: /usr/include/math.h /usr/include/bits/huge_val.h
-prints2blocks.o: /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h
-prints2blocks.o: /usr/include/unistd.h /usr/include/bits/posix_opt.h
-prints2blocks.o: /usr/include/bits/confname.h /usr/include/ctype.h
-prints2blocks.o: /usr/include/endian.h /usr/include/bits/endian.h
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-prints2blocks.o: ../include/errors.h ../include/memory.h
-prints2blocks.o: ../include/residues.h ../include/blastapp.h
-prints2blocks.o: /usr/include/limits.h
-prints2blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-prints2blocks.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-prints2blocks.o: ../include/gcode.h ../include/blocks.h ../include/output.h
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-prints2blocks.o: ../include/pattern.h ../include/convert.h
-prints2blocks.o: ../include/frequency.h ../include/files.h
-prints2blocks.o: ../include/protomat.h
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-lisblk.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
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-lisblk.o: /usr/include/string.h /usr/include/math.h
-lisblk.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-lisblk.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
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-lisblk.o: /usr/include/ctype.h /usr/include/endian.h
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-coduse.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
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-coduse.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-coduse.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-coduse.o: /usr/include/bits/wchar.h /usr/include/gconv.h
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-coduse.o: /usr/include/string.h /usr/include/math.h
-coduse.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-coduse.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
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-coduse.o: /usr/include/ctype.h /usr/include/endian.h
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-coduse.o: ../include/errors.h ../include/memory.h ../include/residues.h
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-narrow.o: /usr/include/string.h /usr/include/math.h
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-narrow.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
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-narrow.o: /usr/include/ctype.h /usr/include/endian.h
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-narrow.o: ../include/protomat.h
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-blk2slx.o: /usr/include/gnu/stubs.h
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-blk2slx.o: /usr/include/stdio.h /usr/include/bits/types.h
-blk2slx.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-blk2slx.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-blk2slx.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-blk2slx.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-blk2slx.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-blk2slx.o: /usr/include/string.h /usr/include/math.h
-blk2slx.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-blk2slx.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
-blk2slx.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
-blk2slx.o: /usr/include/ctype.h /usr/include/endian.h
-blk2slx.o: /usr/include/bits/endian.h ../include/global.h
-blk2slx.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
-blk2slx.o: ../include/errors.h ../include/memory.h ../include/residues.h
-blk2slx.o: ../include/blastapp.h /usr/include/limits.h
-blk2slx.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-blk2slx.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-blk2slx.o: ../include/gcode.h ../include/blocks.h ../include/output.h
-blk2slx.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
-blk2slx.o: ../include/convert.h ../include/frequency.h ../include/files.h
-blk2slx.o: ../include/protomat.h
-blkprob.o: ../include/blocksprogs.h /usr/include/stdlib.h
-blkprob.o: /usr/include/features.h /usr/include/sys/cdefs.h
-blkprob.o: /usr/include/gnu/stubs.h
-blkprob.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-blkprob.o: /usr/include/stdio.h /usr/include/bits/types.h
-blkprob.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-blkprob.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-blkprob.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-blkprob.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-blkprob.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-blkprob.o: /usr/include/string.h /usr/include/math.h
-blkprob.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-blkprob.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
-blkprob.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
-blkprob.o: /usr/include/ctype.h /usr/include/endian.h
-blkprob.o: /usr/include/bits/endian.h ../include/global.h
-blkprob.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
-blkprob.o: ../include/errors.h ../include/memory.h ../include/residues.h
-blkprob.o: ../include/blastapp.h /usr/include/limits.h
-blkprob.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-blkprob.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-blkprob.o: ../include/gcode.h ../include/blocks.h ../include/output.h
-blkprob.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
-blkprob.o: ../include/convert.h ../include/frequency.h ../include/files.h
-blkprob.o: ../include/protomat.h
-blocks.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h
-blocks.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
-blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-blocks.o: /usr/include/stdio.h /usr/include/bits/types.h
-blocks.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-blocks.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-blocks.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-blocks.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-blocks.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
-blocks.o: /usr/include/bits/endian.h /usr/include/malloc.h
-blocks.o: ../include/license.h ../include/strutil.h ../include/errors.h
-blocks.o: ../include/memory.h ../include/blocks.h ../include/output.h
-blocks.o: ../include/sequences.h ../include/residues.h ../include/blastapp.h
-blocks.o: /usr/include/limits.h
-blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-blocks.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-blocks.o: ../include/gcode.h
-config.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h
-config.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
-config.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-config.o: /usr/include/stdio.h /usr/include/bits/types.h
-config.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-config.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-config.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-config.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-config.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-config.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
-config.o: /usr/include/bits/endian.h /usr/include/malloc.h
-config.o: ../include/license.h ../include/strutil.h ../include/errors.h
-config.o: ../include/memory.h ../include/files.h ../include/sequences.h
-config.o: ../include/pattern.h ../include/options.h config.h blimps.h
-config.o: scoring.h lists.h ../include/skiplist.h
-convert.o: /usr/include/assert.h /usr/include/features.h
-convert.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
-convert.o: /usr/include/math.h /usr/include/bits/huge_val.h
-convert.o: /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h
-convert.o: ../include/global.h /usr/include/stdlib.h
-convert.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-convert.o: /usr/include/stdio.h /usr/include/bits/types.h
-convert.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-convert.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-convert.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-convert.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-convert.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-convert.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
-convert.o: /usr/include/bits/endian.h /usr/include/malloc.h
-convert.o: ../include/license.h ../include/strutil.h ../include/errors.h
-convert.o: ../include/memory.h ../include/options.h ../include/blocks.h
-convert.o: ../include/output.h ../include/sequences.h ../include/matrix.h
-convert.o: ../include/pattern.h ../include/residues.h ../include/blastapp.h
-convert.o: /usr/include/limits.h
-convert.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-convert.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-convert.o: ../include/gcode.h ../include/frequency.h ../include/protomat.h
-convert.o: ../include/convert.h blimps.h
-errors.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h
-errors.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
-errors.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-errors.o: /usr/include/stdio.h /usr/include/bits/types.h
-errors.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-errors.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-errors.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-errors.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-errors.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-errors.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
-errors.o: /usr/include/bits/endian.h /usr/include/malloc.h
-errors.o: ../include/license.h ../include/strutil.h ../include/errors.h
-errors.o: ../include/memory.h
-files.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h
-files.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
-files.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-files.o: /usr/include/stdio.h /usr/include/bits/types.h
-files.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-files.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-files.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-files.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-files.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-files.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
-files.o: /usr/include/bits/endian.h /usr/include/malloc.h
-files.o: ../include/license.h ../include/strutil.h ../include/errors.h
-files.o: ../include/memory.h ../include/files.h ../include/sequences.h
-frequency.o: ../include/global.h /usr/include/stdlib.h
-frequency.o: /usr/include/features.h /usr/include/sys/cdefs.h
-frequency.o: /usr/include/gnu/stubs.h
-frequency.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-frequency.o: /usr/include/stdio.h /usr/include/bits/types.h
-frequency.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-frequency.o: /usr/include/libio.h /usr/include/_G_config.h
-frequency.o: /usr/include/wchar.h /usr/include/bits/wchar.h
-frequency.o: /usr/include/gconv.h
-frequency.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-frequency.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-frequency.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
-frequency.o: /usr/include/bits/endian.h /usr/include/malloc.h
-frequency.o: ../include/license.h ../include/strutil.h ../include/errors.h
-frequency.o: ../include/memory.h ../include/blocks.h ../include/output.h
-frequency.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
-frequency.o: ../include/frequency.h ../include/convert.h ../include/files.h
-frequency.o: ../include/residues.h ../include/blastapp.h
-frequency.o: /usr/include/limits.h
-frequency.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-frequency.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-frequency.o: ../include/gcode.h
-gcode.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h
-gcode.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
-gcode.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-gcode.o: /usr/include/stdio.h /usr/include/bits/types.h
-gcode.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-gcode.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-gcode.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-gcode.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-gcode.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-gcode.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
-gcode.o: /usr/include/bits/endian.h /usr/include/malloc.h
-gcode.o: ../include/license.h ../include/strutil.h ../include/errors.h
-gcode.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
-gcode.o: /usr/include/limits.h
-gcode.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-gcode.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-gcode.o: ../include/gcode.h ../include/sequences.h
-lists.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h
-lists.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
-lists.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-lists.o: /usr/include/stdio.h /usr/include/bits/types.h
-lists.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-lists.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-lists.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-lists.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-lists.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-lists.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
-lists.o: /usr/include/bits/endian.h /usr/include/malloc.h
-lists.o: ../include/license.h ../include/strutil.h ../include/errors.h
-lists.o: ../include/memory.h ../include/blocks.h ../include/output.h
-lists.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
-lists.o: lists.h ../include/skiplist.h blimps.h scores.h
-matrix.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h
-matrix.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
-matrix.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-matrix.o: /usr/include/stdio.h /usr/include/bits/types.h
-matrix.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-matrix.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-matrix.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-matrix.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-matrix.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-matrix.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
-matrix.o: /usr/include/bits/endian.h /usr/include/malloc.h
-matrix.o: ../include/license.h ../include/strutil.h ../include/errors.h
-matrix.o: ../include/memory.h ../include/blocks.h ../include/output.h
-matrix.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
-matrix.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
-matrix.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-matrix.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-matrix.o: ../include/gcode.h
-memory.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h
-memory.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
-memory.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-memory.o: /usr/include/stdio.h /usr/include/bits/types.h
-memory.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-memory.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-memory.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-memory.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-memory.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-memory.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
-memory.o: /usr/include/bits/endian.h /usr/include/malloc.h
-memory.o: ../include/license.h ../include/strutil.h ../include/errors.h
-memory.o: ../include/memory.h
-pattern.o: /usr/include/assert.h /usr/include/features.h
-pattern.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
-pattern.o: ../include/global.h /usr/include/stdlib.h
-pattern.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-pattern.o: /usr/include/stdio.h /usr/include/bits/types.h
-pattern.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-pattern.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-pattern.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-pattern.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-pattern.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-pattern.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
-pattern.o: /usr/include/bits/endian.h /usr/include/malloc.h
-pattern.o: ../include/license.h ../include/strutil.h ../include/errors.h
-pattern.o: ../include/memory.h ../include/files.h ../include/blocks.h
-pattern.o: ../include/output.h ../include/sequences.h ../include/matrix.h
-pattern.o: ../include/pattern.h ../include/residues.h ../include/blastapp.h
-pattern.o: /usr/include/limits.h
-pattern.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-pattern.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-pattern.o: ../include/gcode.h ../include/skiplist.h
-scores.o: /usr/include/math.h /usr/include/features.h
-scores.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
-scores.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-scores.o: /usr/include/bits/mathcalls.h ../include/global.h
-scores.o: /usr/include/stdlib.h
-scores.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-scores.o: /usr/include/stdio.h /usr/include/bits/types.h
-scores.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-scores.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-scores.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-scores.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-scores.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-scores.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
-scores.o: /usr/include/bits/endian.h /usr/include/malloc.h
-scores.o: ../include/license.h ../include/strutil.h ../include/errors.h
-scores.o: ../include/memory.h ../include/blocks.h ../include/output.h
-scores.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
-scores.o: scores.h blimps.h scoring.h lists.h ../include/skiplist.h
-scoring.o: /usr/include/math.h /usr/include/features.h
-scoring.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
-scoring.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-scoring.o: /usr/include/bits/mathcalls.h ../include/global.h
-scoring.o: /usr/include/stdlib.h
-scoring.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-scoring.o: /usr/include/stdio.h /usr/include/bits/types.h
-scoring.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-scoring.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-scoring.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-scoring.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-scoring.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-scoring.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
-scoring.o: /usr/include/bits/endian.h /usr/include/malloc.h
-scoring.o: ../include/license.h ../include/strutil.h ../include/errors.h
-scoring.o: ../include/memory.h ../include/blocks.h ../include/output.h
-scoring.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
-scoring.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
-scoring.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-scoring.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-scoring.o: ../include/gcode.h scoring.h blimps.h scores.h lists.h
-scoring.o: ../include/skiplist.h
-sequences.o: ../include/global.h /usr/include/stdlib.h
-sequences.o: /usr/include/features.h /usr/include/sys/cdefs.h
-sequences.o: /usr/include/gnu/stubs.h
-sequences.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-sequences.o: /usr/include/stdio.h /usr/include/bits/types.h
-sequences.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-sequences.o: /usr/include/libio.h /usr/include/_G_config.h
-sequences.o: /usr/include/wchar.h /usr/include/bits/wchar.h
-sequences.o: /usr/include/gconv.h
-sequences.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-sequences.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-sequences.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
-sequences.o: /usr/include/bits/endian.h /usr/include/malloc.h
-sequences.o: ../include/license.h ../include/strutil.h ../include/errors.h
-sequences.o: ../include/memory.h ../include/sequences.h ../include/residues.h
-sequences.o: ../include/blastapp.h /usr/include/limits.h
-sequences.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-sequences.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-sequences.o: ../include/gcode.h
-sl.o: /usr/include/assert.h /usr/include/features.h /usr/include/sys/cdefs.h
-sl.o: /usr/include/gnu/stubs.h /usr/include/time.h /usr/include/bits/types.h
-sl.o: /usr/include/bits/wordsize.h
-sl.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-sl.o: /usr/include/bits/typesizes.h ../include/global.h /usr/include/stdlib.h
-sl.o: /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h
-sl.o: /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h
-sl.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-sl.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-sl.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
-sl.o: /usr/include/bits/endian.h /usr/include/malloc.h ../include/license.h
-sl.o: ../include/strutil.h ../include/errors.h ../include/memory.h
-sl.o: ../include/skiplist.h
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-strutil.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
-strutil.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-strutil.o: /usr/include/stdio.h /usr/include/bits/types.h
-strutil.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-strutil.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-strutil.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-strutil.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-strutil.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-strutil.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
-strutil.o: /usr/include/bits/endian.h /usr/include/malloc.h
-strutil.o: ../include/license.h ../include/strutil.h ../include/errors.h
-strutil.o: ../include/memory.h
-version.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h
-version.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
-version.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-version.o: /usr/include/stdio.h /usr/include/bits/types.h
-version.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-version.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-version.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-version.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-version.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-version.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
-version.o: /usr/include/bits/endian.h /usr/include/malloc.h
-version.o: ../include/license.h ../include/strutil.h ../include/errors.h
-version.o: ../include/memory.h ../include/version.h
-options.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h
-options.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
-options.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
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-options.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-options.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-options.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-options.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-options.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-options.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
-options.o: /usr/include/bits/endian.h /usr/include/malloc.h
-options.o: ../include/license.h ../include/strutil.h ../include/errors.h
-options.o: ../include/memory.h ../include/options.h
-protomat.o: /usr/include/sys/types.h /usr/include/features.h
-protomat.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
-protomat.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
-protomat.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-protomat.o: /usr/include/bits/typesizes.h /usr/include/time.h
-protomat.o: /usr/include/dirent.h /usr/include/bits/dirent.h
-protomat.o: /usr/include/ctype.h /usr/include/endian.h
-protomat.o: /usr/include/bits/endian.h ../include/protomat.h
-protomat.o: /usr/include/stdlib.h /usr/include/stdio.h /usr/include/libio.h
-protomat.o: /usr/include/_G_config.h /usr/include/wchar.h
-protomat.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-protomat.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-protomat.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-protomat.o: /usr/include/string.h
-interpro.o: ../include/blocksprogs.h /usr/include/stdlib.h
-interpro.o: /usr/include/features.h /usr/include/sys/cdefs.h
-interpro.o: /usr/include/gnu/stubs.h
-interpro.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-interpro.o: /usr/include/stdio.h /usr/include/bits/types.h
-interpro.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-interpro.o: /usr/include/libio.h /usr/include/_G_config.h
-interpro.o: /usr/include/wchar.h /usr/include/bits/wchar.h
-interpro.o: /usr/include/gconv.h
-interpro.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-interpro.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-interpro.o: /usr/include/string.h /usr/include/math.h
-interpro.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-interpro.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
-interpro.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
-interpro.o: /usr/include/ctype.h /usr/include/endian.h
-interpro.o: /usr/include/bits/endian.h ../include/global.h
-interpro.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
-interpro.o: ../include/errors.h ../include/memory.h ../include/residues.h
-interpro.o: ../include/blastapp.h /usr/include/limits.h
-interpro.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-interpro.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-interpro.o: ../include/gcode.h ../include/blocks.h ../include/output.h
-interpro.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
-interpro.o: ../include/convert.h ../include/frequency.h ../include/files.h
-interpro.o: ../include/protomat.h
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-pssmdist.o: /usr/include/wchar.h /usr/include/bits/wchar.h
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-pssmdist.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
-pssmdist.o: ../include/errors.h ../include/memory.h ../include/residues.h
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-pssmBL.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
-pssmBL.o: ../include/errors.h ../include/memory.h ../include/residues.h
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-papssm.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
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-papssm.o: ../include/convert.h ../include/frequency.h ../include/files.h
-papssm.o: ../include/protomat.h blimps.h
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-matrix_logob.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
-matrix_logob.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
-matrix_logob.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-matrix_logob.o: /usr/include/bits/typesizes.h /usr/include/time.h
-matrix_logob.o: /usr/include/sys/stat.h /usr/include/bits/stat.h
-matrix_logob.o: ../include/blocksprogs.h /usr/include/stdlib.h
-matrix_logob.o: /usr/include/stdio.h /usr/include/libio.h
-matrix_logob.o: /usr/include/_G_config.h /usr/include/wchar.h
-matrix_logob.o: /usr/include/bits/wchar.h /usr/include/gconv.h
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-matrix_logob.o: /usr/include/string.h /usr/include/math.h
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-matrix_logob.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
-matrix_logob.o: /usr/include/ctype.h /usr/include/endian.h
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-matrix_logob.o: ../include/strutil.h ../include/errors.h ../include/memory.h
-matrix_logob.o: ../include/residues.h ../include/blastapp.h
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-matrix_logob.o: ../include/pattern.h ../include/convert.h
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-makelogob.o: /usr/include/setjmp.h /usr/include/bits/setjmp.h
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-blocks_search.o: /usr/include/bits/confname.h
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-LAMA_search.o: /usr/include/gnu/stubs.h
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-LAMA_search.o: /usr/include/stdio.h /usr/include/bits/types.h
-LAMA_search.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-LAMA_search.o: /usr/include/libio.h /usr/include/_G_config.h
-LAMA_search.o: /usr/include/wchar.h /usr/include/bits/wchar.h
-LAMA_search.o: /usr/include/gconv.h
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-LAMA_search.o: /usr/include/string.h /usr/include/math.h
-LAMA_search.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-LAMA_search.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
-LAMA_search.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
-LAMA_search.o: /usr/include/ctype.h /usr/include/endian.h
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-LAMA_search.o: ../include/residues.h ../include/blastapp.h
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-LAMA_search.o: ../include/frequency.h ../include/files.h
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-block_vis.o: ../include/blastapp.h /usr/include/limits.h
-block_vis.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-block_vis.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-block_vis.o: ../include/gcode.h ../include/blocks.h ../include/output.h
-block_vis.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
-block_vis.o: ../include/convert.h ../include/frequency.h ../include/files.h
-block_vis.o: ../include/protomat.h blockmap.h
-format_block.o: ../include/blocksprogs.h /usr/include/stdlib.h
-format_block.o: /usr/include/features.h /usr/include/sys/cdefs.h
-format_block.o: /usr/include/gnu/stubs.h
-format_block.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-format_block.o: /usr/include/stdio.h /usr/include/bits/types.h
-format_block.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-format_block.o: /usr/include/libio.h /usr/include/_G_config.h
-format_block.o: /usr/include/wchar.h /usr/include/bits/wchar.h
-format_block.o: /usr/include/gconv.h
-format_block.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-format_block.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-format_block.o: /usr/include/string.h /usr/include/math.h
-format_block.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-format_block.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
-format_block.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
-format_block.o: /usr/include/ctype.h /usr/include/endian.h
-format_block.o: /usr/include/bits/endian.h ../include/global.h
-format_block.o: /usr/include/malloc.h ../include/license.h
-format_block.o: ../include/strutil.h ../include/errors.h ../include/memory.h
-format_block.o: ../include/residues.h ../include/blastapp.h
-format_block.o: /usr/include/limits.h
-format_block.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-format_block.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-format_block.o: ../include/gcode.h ../include/blocks.h ../include/output.h
-format_block.o: ../include/sequences.h ../include/matrix.h
-format_block.o: ../include/pattern.h ../include/convert.h
-format_block.o: ../include/frequency.h ../include/files.h
-format_block.o: ../include/protomat.h
-biassed_blocks_finder.o: ../include/blocksprogs.h /usr/include/stdlib.h
-biassed_blocks_finder.o: /usr/include/features.h /usr/include/sys/cdefs.h
-biassed_blocks_finder.o: /usr/include/gnu/stubs.h
-biassed_blocks_finder.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-biassed_blocks_finder.o: /usr/include/stdio.h /usr/include/bits/types.h
-biassed_blocks_finder.o: /usr/include/bits/wordsize.h
-biassed_blocks_finder.o: /usr/include/bits/typesizes.h /usr/include/libio.h
-biassed_blocks_finder.o: /usr/include/_G_config.h /usr/include/wchar.h
-biassed_blocks_finder.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-biassed_blocks_finder.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-biassed_blocks_finder.o: /usr/include/bits/stdio_lim.h
-biassed_blocks_finder.o: /usr/include/bits/sys_errlist.h
-biassed_blocks_finder.o: /usr/include/string.h /usr/include/math.h
-biassed_blocks_finder.o: /usr/include/bits/huge_val.h
-biassed_blocks_finder.o: /usr/include/bits/mathdef.h
-biassed_blocks_finder.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
-biassed_blocks_finder.o: /usr/include/bits/posix_opt.h
-biassed_blocks_finder.o: /usr/include/bits/confname.h /usr/include/ctype.h
-biassed_blocks_finder.o: /usr/include/endian.h /usr/include/bits/endian.h
-biassed_blocks_finder.o: ../include/global.h /usr/include/malloc.h
-biassed_blocks_finder.o: ../include/license.h ../include/strutil.h
-biassed_blocks_finder.o: ../include/errors.h ../include/memory.h
-biassed_blocks_finder.o: ../include/residues.h ../include/blastapp.h
-biassed_blocks_finder.o: /usr/include/limits.h
-biassed_blocks_finder.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-biassed_blocks_finder.o: ../include/alphabet.h ../include/aabet.h
-biassed_blocks_finder.o: ../include/ntbet.h ../include/gcode.h
-biassed_blocks_finder.o: ../include/blocks.h ../include/output.h
-biassed_blocks_finder.o: ../include/sequences.h ../include/matrix.h
-biassed_blocks_finder.o: ../include/pattern.h ../include/convert.h
-biassed_blocks_finder.o: ../include/frequency.h ../include/files.h
-biassed_blocks_finder.o: ../include/protomat.h
-htmlize-LAMA.o: /usr/include/stdlib.h /usr/include/features.h
-htmlize-LAMA.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
-htmlize-LAMA.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-htmlize-LAMA.o: /usr/include/stdio.h /usr/include/bits/types.h
-htmlize-LAMA.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-htmlize-LAMA.o: /usr/include/libio.h /usr/include/_G_config.h
-htmlize-LAMA.o: /usr/include/wchar.h /usr/include/bits/wchar.h
-htmlize-LAMA.o: /usr/include/gconv.h
-htmlize-LAMA.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-htmlize-LAMA.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-show_aligned_blocks.o: ../include/blocksprogs.h /usr/include/stdlib.h
-show_aligned_blocks.o: /usr/include/features.h /usr/include/sys/cdefs.h
-show_aligned_blocks.o: /usr/include/gnu/stubs.h
-show_aligned_blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-show_aligned_blocks.o: /usr/include/stdio.h /usr/include/bits/types.h
-show_aligned_blocks.o: /usr/include/bits/wordsize.h
-show_aligned_blocks.o: /usr/include/bits/typesizes.h /usr/include/libio.h
-show_aligned_blocks.o: /usr/include/_G_config.h /usr/include/wchar.h
-show_aligned_blocks.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-show_aligned_blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-show_aligned_blocks.o: /usr/include/bits/stdio_lim.h
-show_aligned_blocks.o: /usr/include/bits/sys_errlist.h /usr/include/string.h
-show_aligned_blocks.o: /usr/include/math.h /usr/include/bits/huge_val.h
-show_aligned_blocks.o: /usr/include/bits/mathdef.h
-show_aligned_blocks.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
-show_aligned_blocks.o: /usr/include/bits/posix_opt.h
-show_aligned_blocks.o: /usr/include/bits/confname.h /usr/include/ctype.h
-show_aligned_blocks.o: /usr/include/endian.h /usr/include/bits/endian.h
-show_aligned_blocks.o: ../include/global.h /usr/include/malloc.h
-show_aligned_blocks.o: ../include/license.h ../include/strutil.h
-show_aligned_blocks.o: ../include/errors.h ../include/memory.h
-show_aligned_blocks.o: ../include/residues.h ../include/blastapp.h
-show_aligned_blocks.o: /usr/include/limits.h
-show_aligned_blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-show_aligned_blocks.o: ../include/alphabet.h ../include/aabet.h
-show_aligned_blocks.o: ../include/ntbet.h ../include/gcode.h
-show_aligned_blocks.o: ../include/blocks.h ../include/output.h
-show_aligned_blocks.o: ../include/sequences.h ../include/matrix.h
-show_aligned_blocks.o: ../include/pattern.h ../include/convert.h
-show_aligned_blocks.o: ../include/frequency.h ../include/files.h
-show_aligned_blocks.o: ../include/protomat.h
-blk2mot.o: ../include/blocksprogs.h /usr/include/stdlib.h
-blk2mot.o: /usr/include/features.h /usr/include/sys/cdefs.h
-blk2mot.o: /usr/include/gnu/stubs.h
-blk2mot.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
-blk2mot.o: /usr/include/stdio.h /usr/include/bits/types.h
-blk2mot.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
-blk2mot.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
-blk2mot.o: /usr/include/bits/wchar.h /usr/include/gconv.h
-blk2mot.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
-blk2mot.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
-blk2mot.o: /usr/include/string.h /usr/include/math.h
-blk2mot.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
-blk2mot.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
-blk2mot.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
-blk2mot.o: /usr/include/ctype.h /usr/include/endian.h
-blk2mot.o: /usr/include/bits/endian.h ../include/global.h
-blk2mot.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
-blk2mot.o: ../include/errors.h ../include/memory.h ../include/residues.h
-blk2mot.o: ../include/blastapp.h /usr/include/limits.h
-blk2mot.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
-blk2mot.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
-blk2mot.o: ../include/gcode.h ../include/blocks.h ../include/output.h
-blk2mot.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
-blk2mot.o: ../include/convert.h ../include/frequency.h ../include/files.h
-blk2mot.o: ../include/protomat.h
Index: blimps-3.9/blimps/makelogob.c
===================================================================
--- blimps-3.9.orig/blimps/makelogob.c	2012-02-03 21:58:56.928242561 +0100
+++ blimps-3.9/blimps/makelogob.c	2012-02-03 22:01:34.060367844 +0100
@@ -797,7 +797,7 @@
     *w = NULL;
     return;
   }
-  *w = (waveparam *)Malloc(sizeof(waveparam));
+  *w = (waveparam *)malloc(sizeof(waveparam));
   p = *w;
   while (!BUFEOF(afile->f)) {
     fscanf(afile->f, "%c%*[^\n]", &p->extreme);
@@ -831,7 +831,7 @@
       }
     }
     if (!BUFEOF(afile->f)) {
-      p->next = (waveparam *)Malloc(sizeof(waveparam));
+      p->next = (waveparam *)malloc(sizeof(waveparam));
       p = p->next;
     } else
       p->next = NULL;
@@ -2007,7 +2007,7 @@
     return;
   }
 
-  *thestrings = (strings *)Malloc(sizeof(strings));
+  *thestrings = (strings *)malloc(sizeof(strings));
   stringspot = *thestrings;
   for (n = 1; n <= numberstrings; n++) {
     if (BUFEOF(theplace->f)) {
@@ -2023,7 +2023,7 @@
       halt();
     }
     if (n < numberstrings) {
-      stringspot->next = (strings *)Malloc(sizeof(strings));
+      stringspot->next = (strings *)malloc(sizeof(strings));
       stringspot = stringspot->next;
     } else
       stringspot->next = NULL;
Index: blimps-3.9/blimps/matrix_logob.c
===================================================================
--- blimps-3.9.orig/blimps/matrix_logob.c	2012-02-03 21:58:56.952242669 +0100
+++ blimps-3.9/blimps/matrix_logob.c	2012-02-03 22:01:34.068367778 +0100
@@ -331,7 +331,7 @@
    else                               
       {
       printf("\nEnter name of BLOCK or MATRIX file: ");
-      gets(bdbname);
+      fgets(bdbname, MAXNAME, stdin);
       }
 
    /*   Read stdin if the filename starts with '-'   */
@@ -347,7 +347,7 @@
    else                                   /* get input file(s) interactively */
       {
       printf("\nEnter AC in %s or - to make logos for all: ", bdbname);
-      gets(blockAC);
+      fgets(blockAC, MAXNAME, stdin);
       }
 
 /* ------------3rd arg = file name suffix ------------------------------JGH*/
@@ -356,7 +356,7 @@
    else
       {
       printf("\nEnter file name suffix: ");
-      gets(suffix);
+      fgets(suffix, MAXNAME, stdin);
       printf("Logos will be written to logo.%s\n", suffix);
       }
 
@@ -588,7 +588,7 @@
       printf("     after viewing you can also choose to print,\n") ;
       printf("   P to print logo (%s %s).)\n", PSprint, outname) ;
 
-      gets(ans) ;
+      fgets(ans, 2, stdin) ;
 
       switch (toupper(ans[0]))
 	 {
Index: blimps-3.9/blimps/narrow.c
===================================================================
--- blimps-3.9.orig/blimps/narrow.c	2012-02-03 21:58:56.992242661 +0100
+++ blimps-3.9/blimps/narrow.c	2012-02-03 22:01:34.080368098 +0100
@@ -93,7 +93,7 @@
    else
    {
       printf("\nEnter type of input file (Block|Frequencies|Weights): ");
-      gets(ctemp);
+      fgets(ctemp, 80, stdin);
    }
    if (ctemp[0] == 'F' || ctemp[0] == 'f') type = 1; 
    else if (ctemp[0] == 'W' || ctemp[0] == 'w') type = 2; 
@@ -104,7 +104,7 @@
    else
    {
       printf("\nEnter name of input file: ");
-      gets(chkname);
+      fgets(chkname, 80, stdin);
    }
    if ( (chk=fopen(chkname, "r")) == NULL)
    {
Index: blimps-3.9/blimps/oligo_melt.c
===================================================================
--- blimps-3.9.orig/blimps/oligo_melt.c	2012-02-03 21:58:57.016242811 +0100
+++ blimps-3.9/blimps/oligo_melt.c	2012-02-03 22:01:34.084367826 +0100
@@ -75,7 +75,7 @@
    else
    {
       printf("Enter name of file containing oligos: ");
-      gets(fname);
+      fgets(fname, 80, stdin);
    }
    if (!strlen(fname) ) inpf = stdin;
    else if ((inpf=fopen(fname, "r")) == NULL)
Index: blimps-3.9/blimps/papssm.c
===================================================================
--- blimps-3.9.orig/blimps/papssm.c	2012-02-03 21:58:57.040242995 +0100
+++ blimps-3.9/blimps/papssm.c	2012-02-03 22:01:34.096367794 +0100
@@ -163,7 +163,7 @@
 
 int read_cf();
 int load_frequencies();
-double read_freq();
+static double read_freq();
 void load_subst();
 double nrgamma();
 double addlogs();
@@ -250,7 +250,7 @@
    else
    {
       printf("\nEnter name of configuration file: ");
-      gets(cfname);
+      fgets(cfname, FNAMELEN, stdin);
    }
    if ( (cfp=fopen(cfname, "r")) == NULL)
    {
Index: blimps-3.9/blimps/prints2blocks.c
===================================================================
--- blimps-3.9.orig/blimps/prints2blocks.c	2012-02-03 21:58:57.064243161 +0100
+++ blimps-3.9/blimps/prints2blocks.c	2012-02-03 22:01:34.112370260 +0100
@@ -63,7 +63,7 @@
       {
       printf(
        "\nEnter name of input file (Prints protein motifs database): ");
-      gets(inpfname);
+      fgets(inpfname, MAXNAME, stdin);
       }
 
    if ( (inpf=fopen(inpfname, "r")) == NULL)
Index: blimps-3.9/blimps/protomat.c
===================================================================
--- blimps-3.9.orig/blimps/protomat.c	2012-02-03 21:58:57.088242308 +0100
+++ blimps-3.9/blimps/protomat.c	2012-02-03 22:01:34.120367726 +0100
@@ -438,7 +438,8 @@
 char *dir_unix(line)
 char *line;
 {
-   char tname[FNAMELEN], mem[MAXLINE], pros[FNAMELEN], *ptr;
+   char tname[FNAMELEN], mem[MAXLINE], *ptr;
+   static char pros[FNAMELEN];
    int test;
    DIR *dp;
 
Index: blimps-3.9/blimps/protxblk.c
===================================================================
--- blimps-3.9.orig/blimps/protxblk.c	2012-02-03 21:58:57.112250471 +0100
+++ blimps-3.9/blimps/protxblk.c	2012-02-03 22:01:34.124367836 +0100
@@ -37,7 +37,7 @@
    else
    {
       printf("\nEnter name of blocks database: ");
-      gets(bdbname);
+      fgets(bdbname, MAXNAME, stdin);
    }
    if ( (bfp=fopen(bdbname, "r")) == NULL)
    {
@@ -50,7 +50,7 @@
    else
    {
       printf("\nEnter name of output file: ");
-      gets(conname);
+      fgets(conname, MAXNAME, stdin);
    }
    if ( (ofp=fopen(conname, "w")) == NULL)
    {
Index: blimps-3.9/blimps/pssmBL.c
===================================================================
--- blimps-3.9.orig/blimps/pssmBL.c	2012-02-03 21:58:57.136245051 +0100
+++ blimps-3.9/blimps/pssmBL.c	2012-02-03 22:01:34.128368059 +0100
@@ -29,7 +29,7 @@
    else
    {
       printf("\nEnter name of pssmdist.dat file: ");
-      gets(pssmname);
+      fgets(pssmname, MAXNAME, stdin);
    }
    if ( (pfp=fopen(pssmname, "r")) == NULL)
    {
@@ -42,7 +42,7 @@
    else
    {
       printf("\nEnter name of blocks database: ");
-      gets(bdbname);
+      fgets(bdbname, MAXNAME, stdin);
    }
    if ( (bfp=fopen(bdbname, "r")) == NULL)
    {
@@ -55,7 +55,7 @@
    else
    {
       printf("\nEnter name of new blocks database: ");
-      gets(conname);
+      fgets(conname, MAXNAME, stdin);
    }
    if ( (ofp=fopen(conname, "a")) == NULL)
    {
Index: blimps-3.9/blimps/pssmdist.c
===================================================================
--- blimps-3.9.orig/blimps/pssmdist.c	2012-02-03 21:58:57.160242689 +0100
+++ blimps-3.9/blimps/pssmdist.c	2012-02-03 22:01:34.136422451 +0100
@@ -81,7 +81,7 @@
 
 int compute();
 int load_freqs();
-double read_a_freq();
+static double read_a_freq();
 void fix_freqs();
 int count_tps();
 
@@ -113,7 +113,7 @@
    else
    {
       printf("\nEnter name of matrix database: ");
-      gets(mname);
+      fgets(mname, MAXNAME, stdin);
    }
    if ( (mfp=fopen(mname, "r")) == NULL)
    {
@@ -126,7 +126,7 @@
    else
    {
       printf("\nEnter name of observed frequencies database: ");
-      gets(oname);
+      fgets(oname, MAXNAME, stdin);
    }
    if ( (ofp=fopen(oname, "r")) == NULL)
    {
@@ -138,7 +138,7 @@
    else
    {
       printf("\nEnter name of frequency file: ");
-      gets(fname);
+      fgets(fname, MAXNAME,stdin);
    }
    if ( (ffp=fopen(fname, "r")) == NULL)
    {
@@ -155,7 +155,7 @@
    {
       printf("\nEnter number of sequences in a typical search [%.0f]: ",
 		 Search);
-      gets(ctemp);
+      fgets(ctemp, MAXNAME, stdin);
    }
    if (strlen(ctemp)) Search = atof(ctemp);
 /* ------------5th arg = #aas in a search--------------------*/
@@ -166,7 +166,7 @@
    {
       printf("\nEnter number of amino acids in a typical database [%.0f]: ",
 		SearchAA);
-      gets(ctemp);
+      fgets(ctemp, MAXNAME, stdin);
    }
    if (strlen(ctemp)) SearchAA = atof(ctemp);
    printf ("Assuming %.0f sequences, %.0f amino acids in a search\n",
Index: blimps-3.9/blimps/rank_matrix.c
===================================================================
--- blimps-3.9.orig/blimps/rank_matrix.c	2012-02-03 21:58:57.184242671 +0100
+++ blimps-3.9/blimps/rank_matrix.c	2012-02-03 22:01:34.140418430 +0100
@@ -39,7 +39,7 @@
    else
    {
       printf("\nEnter name of scoring matrix: ");
-      gets(matname);
+      fgets(matname, MAXNAME, stdin);
    }
    if ( (fmat=fopen(matname, "r")) == NULL)
    {
Index: blimps-3.9/blimps/readchk.c
===================================================================
--- blimps-3.9.orig/blimps/readchk.c	2012-02-03 21:58:57.208242554 +0100
+++ blimps-3.9/blimps/readchk.c	2012-02-03 22:01:34.148318588 +0100
@@ -20,7 +20,7 @@
    else
    {
       printf("\nEnter name of configuration file: ");
-      gets(chkname);
+      fgets(chkname, 80, stdin);
    }
    if ( (chk=fopen(chkname, "r")) == NULL)
    {
Index: blimps-3.9/blimps/readmast.c
===================================================================
--- blimps-3.9.orig/blimps/readmast.c	2012-02-03 21:58:57.232242646 +0100
+++ blimps-3.9/blimps/readmast.c	2012-02-03 22:01:34.160367725 +0100
@@ -26,7 +26,7 @@
    else
    {
       printf("\nEnter name of configuration file: ");
-      gets(chkname);
+      fgets(chkname, 80, stdin);
    }
    if ( (chk=fopen(chkname, "r")) == NULL)
    {
Index: blimps-3.9/blimps/retblock.c
===================================================================
--- blimps-3.9.orig/blimps/retblock.c	2012-02-03 21:58:57.256245156 +0100
+++ blimps-3.9/blimps/retblock.c	2012-02-03 22:01:34.164367729 +0100
@@ -50,7 +50,7 @@
    else
    {
       printf("\nEnter name of blocks database: ");
-      gets(bdbname);
+      fgets(bdbname, MAXNAME, stdin);
    }
    if ( (bfp=fopen(bdbname, "r")) == NULL)
    {
@@ -66,7 +66,7 @@
    {
       strcpy(acname, "all");
       printf("\nEnter AC of blocks to extract, or all [%s]: ", acname);
-      gets(acname);
+      fgets(acname, MAXNAME, stdin);
    }
    if (strcasecmp(acname, "all") == 0) allflag = TRUE;
 
Index: blimps-3.9/blimps/sequences.c
===================================================================
--- blimps-3.9.orig/blimps/sequences.c	2012-02-03 21:58:57.280242598 +0100
+++ blimps-3.9/blimps/sequences.c	2012-02-03 22:01:34.172367940 +0100
@@ -665,7 +665,7 @@
       stemp is a huge negative number ...
   */
   if (seq_type == AA_SEQ) {
-    while ( (c != NULL) && (c != '\0') && (num_seen < room_left) ) {
+    while ( (c != 0) && (c != '\0') && (num_seen < room_left) ) {
       stemp = aa_atob[c];
       if (stemp < 0 || stemp > AAID_MAX) stemp = AAID_MAX + 1;
       if ( stemp <= AAID_MAX ) {
@@ -1201,7 +1201,7 @@
     }
   }    
   else {
-    printf("??) \t");
+    printf("??"") \t");
 printf("\n");
     for(k=0; k<seq->length; k++) {
       printf("%c", aa_btoa[seq->sequence[k]]);
Index: blimps-3.9/blimps/sortblk.c
===================================================================
--- blimps-3.9.orig/blimps/sortblk.c	2012-02-03 21:58:57.304243124 +0100
+++ blimps-3.9/blimps/sortblk.c	2012-02-03 22:01:34.176367755 +0100
@@ -58,7 +58,7 @@
    else
    {
       printf("\nEnter name of blocks database: ");
-      gets(bdbname);
+      fgets(bdbname, MAXNAME, stdin);
    }
    if ( (bfp=fopen(bdbname, "r")) == NULL)
    {
@@ -71,7 +71,7 @@
    else
    {
       printf("\nEnter name of new sorted blocks database: ");
-      gets(conname);
+      fgets(conname, MAXNAME, stdin);
    }
    if ( (ofp=fopen(conname, "w")) == NULL)
    {
Index: blimps-3.9/blimps/translate.c
===================================================================
--- blimps-3.9.orig/blimps/translate.c	2012-02-03 21:58:57.344242740 +0100
+++ blimps-3.9/blimps/translate.c	2012-02-03 22:01:34.184367687 +0100
@@ -29,7 +29,7 @@
    else
    {
       printf("\nEnter name of sequence database: ");
-      gets(sname);
+      fgets(sname, MAXNAME, stdin);
    }
    if ( (bfp=fopen(sname, "r")) == NULL)
    {
@@ -50,7 +50,7 @@
    else
    {
       printf("\nEnter name of new translated sequence database: ");
-      gets(outname);
+      fgets(outname, MAXNAME, stdin);
    }
    if ( (ofp=fopen(outname, "w")) == NULL)
    {
@@ -62,7 +62,7 @@
    else
    {
       printf("\nEnter translation frame: ");
-      gets(ctemp);
+      fgets(ctemp, MAXNAME, stdin);
       frame = atoi(ctemp);
    }
    if (frame == 0 || frame < -3 || frame > 3) frame = 1;
@@ -74,7 +74,7 @@
       for (code = 0; code < NUMBER_OF_GENETIC_CODES; code++)
           printf("\n %d %s", code, gcodes[code].name);
       printf("\nEnter genetic code: ");
-      gets(ctemp);
+      fgets(ctemp, MAXNAME, stdin);
       code = atoi(ctemp);
    }
    if (code < 0 || code > 8) code = 0;
Index: blimps-3.9/blimps/util.c
===================================================================
--- blimps-3.9.orig/blimps/util.c	2012-02-03 21:58:57.368242612 +0100
+++ blimps-3.9/blimps/util.c	2012-02-03 22:01:34.192367708 +0100
@@ -1,5 +1,6 @@
 #include <stdlib.h>
 #include <stdio.h>
+#include <string.h>
 
 #define LF 10
 #define CR 13
@@ -92,7 +93,7 @@
     return -1;
 }
 
-int getline(char *s, int n, FILE *f) {
+int blimps_getline(char *s, int n, FILE *f) {
     register int i=0;
 
     while(1) {
Index: blimps-3.9/protomat/Makefile.Linux
===================================================================
--- blimps-3.9.orig/protomat/Makefile.Linux	2012-02-03 21:58:57.400242558 +0100
+++ blimps-3.9/protomat/Makefile.Linux	2012-02-03 22:02:24.588297986 +0100
@@ -3,52 +3,65 @@
 #   Type  "make blksort" to compile blksort program 
 CC = gcc
 CFLAGS = -Wall -O2 -c
-CL = gcc
-LFLAGS = -lm -o
+LDFLAGS = -lm -o
 RM = /bin/rm -f
 MV = /bin/mv -f
+CP = cp -af
+
+BIN := blksort getblock getseq multimat motifj motomat uextract blosum blastdat
 #
-install:	clean all
-clean:		
-	$(RM) *.o blksort getblock getseq multimat motifj motomat uextract blosum blastdat
-all:		blksort getblock getseq multimat motifj motomat uextract blosum blastdat
+all:	$(BIN)
 #
+install: $(BIN)
+		$(CP) blksort ../bin
+		$(CP) getblock ../bin
+		$(CP) getseq ../bin
+		$(CP) multimat ../bin
+		$(CP) motifj ../bin
+		$(CP) motomat ../bin
+		$(CP) uextract ../bin
+		$(CP) blosum ../bin
+		$(CP) blastdat ../bin
+
+clean:
+	$(RM) *.o $(BIN)
+
 #	blksort: Analyze results of a BLOCKS search
 blksort:	blksort.o motmisc.o
-		$(CL) blksort.o motmisc.o $(LFLAGS) blksort
-		mv blksort ../bin
+		$(CC) blksort.o motmisc.o $(LDFLAGS) blksort
+
 #	getblock: Retrieve BLOCKs
 getblock:	getblock.o motmisc.o
-		$(CL) getblock.o motmisc.o $(LFLAGS) getblock
-		mv getblock ../bin
+		$(CC) getblock.o motmisc.o $(LDFLAGS) getblock
+
 #	getseq: Retrieve a sequence
 getseq:		getseq.o motmisc.o
-		$(CL) getseq.o motmisc.o $(LFLAGS) getseq
-		mv getseq ../bin
+		$(CC) getseq.o motmisc.o $(LDFLAGS) getseq
+
 #	multimat: Analyze results of a MATRIX search
 multimat:	multimat.o motmisc.o
-		$(CL) multimat.o motmisc.o $(LFLAGS) multimat
-		mv multimat ../bin
+		$(CC) multimat.o motmisc.o $(LDFLAGS) multimat
+
 #	motifj: Make blocks using Ham Smith's motif algorithm
 motifj:		motifj.o motmisc.o
-		$(CL) motifj.o motmisc.o $(LFLAGS) motifj
-		mv motifj ../bin
+		$(CC) motifj.o motmisc.o $(LDFLAGS) motifj
+
 #	motomat: Assemble blocks from motifj
 motomat:	motomat.o motmisc.o
-		$(CL) motomat.o motmisc.o $(LFLAGS) motomat
-		mv motomat ../bin
+		$(CC) motomat.o motmisc.o $(LDFLAGS) motomat
+
 #	uextract: Extract protein families from prosite.dat
 uextract:	uextract.o motmisc.o
-		$(CL) uextract.o motmisc.o $(LFLAGS) uextract
-		mv uextract ../bin
+		$(CC) uextract.o motmisc.o $(LDFLAGS) uextract
+
 #	blosum: Make substitution matrices from blocks
 blosum:		blosum.o motmisc.o
-		$(CL) blosum.o motmisc.o $(LFLAGS) blosum
-		mv blosum ../bin
+		$(CC) blosum.o motmisc.o $(LDFLAGS) blosum
+
 #	blastdat: Read blast output
 blastdat:	blastdat.o motmisc.o
-		$(CL) blastdat.o motmisc.o $(LFLAGS) blastdat
-		mv blastdat ../bin
+		$(CC) blastdat.o motmisc.o $(LDFLAGS) blastdat
+
 #
 blksort.o:	blksort.c motifj.h
 		$(CC) $(CFLAGS) blksort.c
Index: blimps-3.9/Makefile
===================================================================
--- /dev/null	1970-01-01 00:00:00.000000000 +0000
+++ blimps-3.9/Makefile	2012-02-03 22:01:34.208367543 +0100
@@ -0,0 +1,117 @@
+PACKAGE := blimps
+VERSION := 3.9
+DISTDIR := $(PACKAGE)-$(VERSION)
+
+BLIMPSDIR := blimps
+DOCSDIR := docs
+INCLUDEDIR := include
+PROTOMATDIR := protomat
+
+MAN1POD := fastaseqs.pod
+MAN1GZ := $(MAN1POD:%.pod=%.1.gz)
+
+libdir ?= $(prefix)/lib
+
+# export LD_LIBRARY_PATH=/mnt/home/lkajan/project/rostlab/blimps/blimps-3.9/blimps
+
+all: blimps protomat man
+
+blimps:
+	$(MAKE) -C $(BLIMPSDIR) -f Makefile.Linux VERSION=$(VERSION)
+
+protomat:
+	$(MAKE) -C $(PROTOMATDIR) -f Makefile.Linux VERSION=$(VERSION)
+
+man:	$(MAN1GZ)
+
+$(MAN1GZ) : %.1.gz : %.pod
+	pod2man -c 'User Commands' -r "$(VERSION)" $< | gzip -c > $@
+
+# The sift package does not provide fastaseqs but expects it to exist. Fortunately this package provides it.
+install: install-utils install-lib-dev install-lib install-data install-doc
+
+install-data:
+	mkdir -p $(DESTDIR)$(prefix)/share/$(PACKAGE) && \
+		cp -a $(DOCSDIR) \
+			$(DESTDIR)$(prefix)/share/$(PACKAGE)/
+
+install-utils:
+	mkdir -p $(DESTDIR)$(prefix)/bin && \
+		cp -a $(BLIMPSDIR)/fastaseqs \
+			$(DESTDIR)$(prefix)/bin/
+	mkdir -p $(DESTDIR)$(prefix)/share/man/man1 && cp $(MAN1GZ) $(DESTDIR)$(prefix)/share/man/man1/
+
+install-lib-dev:
+	mkdir -p $(DESTDIR)$(prefix)/include/$(PACKAGE) && \
+		cp $(INCLUDEDIR)/*.h $(DESTDIR)$(prefix)/include/$(PACKAGE)/
+	mkdir -p $(DESTDIR)$(libdir) && \
+		cp -a $(BLIMPSDIR)/*.a $(BLIMPSDIR)/*.so \
+			$(DESTDIR)$(libdir)/
+
+install-lib:
+	mkdir -p $(DESTDIR)$(prefix)/lib && \
+		cp -a $(BLIMPSDIR)/*.so.* \
+			$(DESTDIR)$(libdir)/
+
+.PHONY: install-doc
+install-doc:
+	mkdir -p $(DESTDIR)$(prefix)/share/doc/$(PACKAGE) && \
+		cp -a LICENSE README UPDATES \
+			$(DESTDIR)$(prefix)/share/doc/$(PACKAGE)/
+
+clean: clean-blimps clean-protomat
+	rm -f *.[12345678].gz
+
+clean-blimps:
+	-if [ -d $(BLIMPSDIR) ]; then $(MAKE) -C $(BLIMPSDIR) -f Makefile.Linux clean; fi
+
+clean-protomat:
+	-if [ -d $(PROTOMATDIR) ]; then $(MAKE) -C $(PROTOMATDIR) -f Makefile.Linux clean; fi
+
+distclean: clean
+	-if [ -d "$(DISTDIR)" ]; then rm -rf $(DISTDIR); fi
+	rm -rf	\
+		$(DISTDIR) \
+		$(DISTDIR).tar.gz
+
+dist: distdir
+	tar chof - "$(DISTDIR)" | gzip -c >$(DISTDIR).tar.gz
+	rm -rf $(DISTDIR)
+
+distdir:
+	rm -rf $(DISTDIR) && mkdir -p $(DISTDIR) && \
+	rsync -avCR \
+		--exclude /*-stamp \
+		--exclude .*.swp \
+		--exclude debian \
+		ChangeLog \
+		Makefile \
+		$(PACKAGE).spec \
+		$(MAN1POD) \
+		$(DISTDIR)/;
+
+help:
+	@echo "Rules:"
+	@echo "all*"
+	@echo "*blimps"
+	@echo "install+"
+	@echo "+install-data"
+	@echo "+install-lib"
+	@echo "+install-lib-dev"
+	@echo "+install-utils"
+	@echo "clean"
+	@echo "distclean"
+	@echo "dist"
+	@echo "help"
+	@echo "*man"
+	@echo "*protomat"
+	@echo
+	@echo "Variables:"
+	@echo "DESTDIR - install to DESTDIR"
+	@echo "prefix - common installation prefix for all files"
+	@echo "libdir - install libraries here, default: /$$(prefix)/lib"
+	@echo "  use prefix=$$HOME to build for personal use"
+
+.PHONY: all bin clean-blimps clean diff dist distclean distdir help install install-data install-lib install-lib-dev install-utils man untar blimps protomat clean-protomat
+
+# vim:ai:
Index: blimps-3.9/fastaseqs.pod
===================================================================
--- /dev/null	1970-01-01 00:00:00.000000000 +0000
+++ blimps-3.9/fastaseqs.pod	2012-02-03 22:01:34.372247697 +0100
@@ -0,0 +1,25 @@
+=head1 NAME
+
+fastaseqs - converts a file of sequences to FASTA format
+
+=head1 SYNOPSIS
+
+fastaseqs <INPUTFILE> <OUTPUTFILE>
+
+=head1 DESCRIPTION
+
+fastaseqs converts a file of sequences to FASTA format.
+
+=head1 AUTHOR
+
+J. Henikoff
+
+=head1 COPYRIGHT AND LICENSE
+
+Copyright 1998, Fred Hutchinson Cancer Research Center
+
+Please refer to /usr/share/doc/*blimps*/copyright for the license.
+
+=head1 SEE ALSO
+
+L<http://blocks.fhcrc.org/blocks/uploads/blimps/>