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Anonymous committed f5a7ea7

[svn r425] Update Linux build

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Files changed (5)

 fi
 
 
-                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          ac_config_files="$ac_config_files Makefile src/Makefile tools/Makefile tools/Answerer/Makefile tools/Cliquer/Makefile tools/Clusterer/Makefile tools/Clusters2Dab/Makefile tools/COALESCE/Makefile tools/Combiner/Makefile tools/DChecker/Makefile tools/Dat2Dab/Makefile tools/Dat2Graph/Makefile tools/Data2Bnt/Makefile tools/Data2Features/Makefile tools/Data2Sql/Makefile tools/DataDumper/Makefile tools/Distancer/Makefile tools/Explainer/Makefile tools/Funcaeologist/Makefile tools/Funcifier/Makefile tools/Funcographer/Makefile tools/Hubber/Makefile tools/KNNImputer/Makefile tools/Mat2Txt/Makefile tools/MCluster/Makefile tools/Matcher/Makefile tools/MIer/Makefile tools/Netwalker/Makefile tools/Normalizer/Makefile tools/Orthologer/Makefile tools/Overlapper/Makefile tools/PCLPlotter/Makefile tools/Randomizer/Makefile tools/Seqs2Ngrams/Makefile tools/SVDer/Makefile tools/Synthesizer/Makefile tools/Txt2Bin/Makefile tools/BNConverter/Makefile tools/BNCreator/Makefile tools/BNEvaluator/Makefile tools/BNFunc/Makefile tools/BNTester/Makefile tools/BNTruster/Makefile tools/BNs2Txt/Makefile tools/BNUnraveler/Makefile tools/BNWeaver/Makefile tools/Contexter/Makefile tools/Counter/Makefile tools/Data2DB/Makefile tools/DSLConverter/Makefile tools/Dab2Dad/Makefile tools/Edges2Posteriors/Makefile tools/MEFIT/Makefile tools/Data2Svm/Makefile tools/SVMer/Makefile tools/OntoShell/Makefile tools/BNServer/Makefile"
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                ac_config_files="$ac_config_files Makefile src/Makefile tools/Makefile tools/Answerer/Makefile tools/Cliquer/Makefile tools/Clusterer/Makefile tools/Clusters2Dab/Makefile tools/COALESCE/Makefile tools/Combiner/Makefile tools/DChecker/Makefile tools/Dat2Dab/Makefile tools/Dat2Graph/Makefile tools/Data2Bnt/Makefile tools/Data2Features/Makefile tools/Data2Sql/Makefile tools/DataDumper/Makefile tools/Distancer/Makefile tools/Explainer/Makefile tools/Funcaeologist/Makefile tools/Funcifier/Makefile tools/Funcographer/Makefile tools/Hubber/Makefile tools/KNNImputer/Makefile tools/Mat2Txt/Makefile tools/MCluster/Makefile tools/Matcher/Makefile tools/MIer/Makefile tools/Normalizer/Makefile tools/Orthologer/Makefile tools/Overlapper/Makefile tools/PCLPlotter/Makefile tools/Randomizer/Makefile tools/Seqs2Ngrams/Makefile tools/SVDer/Makefile tools/Synthesizer/Makefile tools/Txt2Bin/Makefile tools/BNConverter/Makefile tools/BNCreator/Makefile tools/BNEvaluator/Makefile tools/BNFunc/Makefile tools/BNTester/Makefile tools/BNTruster/Makefile tools/BNs2Txt/Makefile tools/BNUnraveler/Makefile tools/BNWeaver/Makefile tools/Contexter/Makefile tools/Counter/Makefile tools/Data2DB/Makefile tools/DSLConverter/Makefile tools/Dab2Dad/Makefile tools/Edges2Posteriors/Makefile tools/MEFIT/Makefile tools/Data2Svm/Makefile tools/SVMer/Makefile tools/OntoShell/Makefile tools/BNServer/Makefile"
 
 
 
   "tools/MCluster/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/MCluster/Makefile" ;;
   "tools/Matcher/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/Matcher/Makefile" ;;
   "tools/MIer/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/MIer/Makefile" ;;
-  "tools/Netwalker/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/Netwalker/Makefile" ;;
   "tools/Normalizer/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/Normalizer/Makefile" ;;
   "tools/Orthologer/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/Orthologer/Makefile" ;;
   "tools/Overlapper/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/Overlapper/Makefile" ;;
 		 tools/MCluster/Makefile \
 		 tools/Matcher/Makefile \
 		 tools/MIer/Makefile \
-		 tools/Netwalker/Makefile \
 		 tools/Normalizer/Makefile \
 		 tools/Orthologer/Makefile \
 		 tools/Overlapper/Makefile \

tools/COALESCE/cmdline.c

   "  -E, --size_merge=INT          Maximum motif count for realtime merging  \n                                  (default=`100')",
   "  -Z, --size_maximum=INT        Maximum motif count to consider a cluster \n                                  saturated  (default=`1000')",
   "\nPostprocessing Parameters:",
-  "  -j, --postprocess=directory   Input directory of clusters to postprocess",
+  "  -j, --postprocess=directory   Input file/directory of clusters to postprocess",
   "  -K, --known_motifs=filename   File containing known motifs",
   "  -F, --known_cutoff=DOUBLE     Score cutoff for known motif labeling  \n                                  (default=`0.05')",
   "  -S, --known_type=STRING       Type of known motif matching  (possible \n                                  values=\"pvalue\", \"rmse\", \"js\" \n                                  default=`pvalue')",
   "  -u, --min_info=DOUBLE         Uninformative motif threshhold (bits)  \n                                  (default=`0.3')",
   "  -x, --max_motifs=INT          Maximum motifs to merge exactly  \n                                  (default=`2500')",
   "\nMiscellaneous:",
-  "  -e, --cache=filename          Cache file for sequence analysis",
+  "  -e, --normalize               Automatically detect/normalize single channel \n                                  data  (default=off)",
   "  -O, --progressive             Generate output progressively  (default=on)",
   "\nOptional:",
   "  -t, --threads=INT             Maximum number of concurrent threads  \n                                  (default=`1')",
   args_info->remove_rcs_given = 0 ;
   args_info->min_info_given = 0 ;
   args_info->max_motifs_given = 0 ;
-  args_info->cache_given = 0 ;
+  args_info->normalize_given = 0 ;
   args_info->progressive_given = 0 ;
   args_info->threads_given = 0 ;
   args_info->skip_given = 0 ;
   args_info->min_info_orig = NULL;
   args_info->max_motifs_arg = 2500;
   args_info->max_motifs_orig = NULL;
-  args_info->cache_arg = NULL;
-  args_info->cache_orig = NULL;
+  args_info->normalize_flag = 0;
   args_info->progressive_flag = 1;
   args_info->threads_arg = 1;
   args_info->threads_orig = NULL;
   args_info->remove_rcs_help = gengetopt_args_info_help[35] ;
   args_info->min_info_help = gengetopt_args_info_help[36] ;
   args_info->max_motifs_help = gengetopt_args_info_help[37] ;
-  args_info->cache_help = gengetopt_args_info_help[39] ;
+  args_info->normalize_help = gengetopt_args_info_help[39] ;
   args_info->progressive_help = gengetopt_args_info_help[40] ;
   args_info->threads_help = gengetopt_args_info_help[42] ;
   args_info->skip_help = gengetopt_args_info_help[43] ;
   free_string_field (&(args_info->cutoff_trim_orig));
   free_string_field (&(args_info->min_info_orig));
   free_string_field (&(args_info->max_motifs_orig));
-  free_string_field (&(args_info->cache_arg));
-  free_string_field (&(args_info->cache_orig));
   free_string_field (&(args_info->threads_orig));
   free_string_field (&(args_info->skip_orig));
   free_string_field (&(args_info->random_orig));
     write_into_file(outfile, "min_info", args_info->min_info_orig, 0);
   if (args_info->max_motifs_given)
     write_into_file(outfile, "max_motifs", args_info->max_motifs_orig, 0);
-  if (args_info->cache_given)
-    write_into_file(outfile, "cache", args_info->cache_orig, 0);
+  if (args_info->normalize_given)
+    write_into_file(outfile, "normalize", 0, 0 );
   if (args_info->progressive_given)
     write_into_file(outfile, "progressive", 0, 0 );
   if (args_info->threads_given)
         { "remove_rcs",	0, NULL, 'R' },
         { "min_info",	1, NULL, 'u' },
         { "max_motifs",	1, NULL, 'x' },
-        { "cache",	1, NULL, 'e' },
+        { "normalize",	0, NULL, 'e' },
         { "progressive",	0, NULL, 'O' },
         { "threads",	1, NULL, 't' },
         { "skip",	1, NULL, 's' },
         { NULL,	0, NULL, 0 }
       };
 
-      c = getopt_long (argc, argv, "hVi:f:d:o:p:c:m:C:M:k:g:G:y:Y:n:N:q:b:z:E:Z:j:K:F:S:J:L:T:Ru:x:e:Ot:s:r:v:", long_options, &option_index);
+      c = getopt_long (argc, argv, "hVi:f:d:o:p:c:m:C:M:k:g:G:y:Y:n:N:q:b:z:E:Z:j:K:F:S:J:L:T:Ru:x:eOt:s:r:v:", long_options, &option_index);
 
       if (c == -1) break;	/* Exit from `while (1)' loop.  */
 
             goto failure;
         
           break;
-        case 'j':	/* Input directory of clusters to postprocess.  */
+        case 'j':	/* Input file/directory of clusters to postprocess.  */
         
         
           if (update_arg( (void *)&(args_info->postprocess_arg), 
             goto failure;
         
           break;
-        case 'e':	/* Cache file for sequence analysis.  */
+        case 'e':	/* Automatically detect/normalize single channel data.  */
         
         
-          if (update_arg( (void *)&(args_info->cache_arg), 
-               &(args_info->cache_orig), &(args_info->cache_given),
-              &(local_args_info.cache_given), optarg, 0, 0, ARG_STRING,
-              check_ambiguity, override, 0, 0,
-              "cache", 'e',
+          if (update_arg((void *)&(args_info->normalize_flag), 0, &(args_info->normalize_given),
+              &(local_args_info.normalize_given), optarg, 0, 0, ARG_FLAG,
+              check_ambiguity, override, 1, 0, "normalize", 'e',
               additional_error))
             goto failure;
         

tools/COALESCE/cmdline.h

   int size_maximum_arg;	/**< @brief Maximum motif count to consider a cluster saturated (default='1000').  */
   char * size_maximum_orig;	/**< @brief Maximum motif count to consider a cluster saturated original value given at command line.  */
   const char *size_maximum_help; /**< @brief Maximum motif count to consider a cluster saturated help description.  */
-  char * postprocess_arg;	/**< @brief Input directory of clusters to postprocess.  */
-  char * postprocess_orig;	/**< @brief Input directory of clusters to postprocess original value given at command line.  */
-  const char *postprocess_help; /**< @brief Input directory of clusters to postprocess help description.  */
+  char * postprocess_arg;	/**< @brief Input file/directory of clusters to postprocess.  */
+  char * postprocess_orig;	/**< @brief Input file/directory of clusters to postprocess original value given at command line.  */
+  const char *postprocess_help; /**< @brief Input file/directory of clusters to postprocess help description.  */
   char * known_motifs_arg;	/**< @brief File containing known motifs.  */
   char * known_motifs_orig;	/**< @brief File containing known motifs original value given at command line.  */
   const char *known_motifs_help; /**< @brief File containing known motifs help description.  */
   int max_motifs_arg;	/**< @brief Maximum motifs to merge exactly (default='2500').  */
   char * max_motifs_orig;	/**< @brief Maximum motifs to merge exactly original value given at command line.  */
   const char *max_motifs_help; /**< @brief Maximum motifs to merge exactly help description.  */
-  char * cache_arg;	/**< @brief Cache file for sequence analysis.  */
-  char * cache_orig;	/**< @brief Cache file for sequence analysis original value given at command line.  */
-  const char *cache_help; /**< @brief Cache file for sequence analysis help description.  */
+  int normalize_flag;	/**< @brief Automatically detect/normalize single channel data (default=off).  */
+  const char *normalize_help; /**< @brief Automatically detect/normalize single channel data help description.  */
   int progressive_flag;	/**< @brief Generate output progressively (default=on).  */
   const char *progressive_help; /**< @brief Generate output progressively help description.  */
   int threads_arg;	/**< @brief Maximum number of concurrent threads (default='1').  */
   unsigned int remove_rcs_given ;	/**< @brief Whether remove_rcs was given.  */
   unsigned int min_info_given ;	/**< @brief Whether min_info was given.  */
   unsigned int max_motifs_given ;	/**< @brief Whether max_motifs was given.  */
-  unsigned int cache_given ;	/**< @brief Whether cache was given.  */
+  unsigned int normalize_given ;	/**< @brief Whether normalize was given.  */
   unsigned int progressive_given ;	/**< @brief Whether progressive was given.  */
   unsigned int threads_given ;	/**< @brief Whether threads was given.  */
   unsigned int skip_given ;	/**< @brief Whether skip was given.  */

tools/Makefile.am

 	  MCluster \
 	  Matcher \
 	  MIer \
-	  Netwalker \
 	  Normalizer \
 	  Orthologer \
 	  Overlapper \