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chuttenh  committed 07f61c4

[svn r410] Add missing PCLPlotter directory

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  • Parent commits 4dc3e95

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Files changed (6)

File tools/PCLPlotter/PCLPlotter.cpp

+/*****************************************************************************
+* This file is provided under the Creative Commons Attribution 3.0 license.
+*
+* You are free to share, copy, distribute, transmit, or adapt this work
+* PROVIDED THAT you attribute the work to the authors listed below.
+* For more information, please see the following web page:
+* http://creativecommons.org/licenses/by/3.0/
+*
+* This file is a component of the Sleipnir library for functional genomics,
+* authored by:
+* Curtis Huttenhower (chuttenh@princeton.edu)
+* Mark Schroeder
+* Maria D. Chikina
+* Olga G. Troyanskaya (ogt@princeton.edu, primary contact)
+*
+* If you use this library, the included executable tools, or any related
+* code in your work, please cite the following publication:
+* Curtis Huttenhower, Mark Schroeder, Maria D. Chikina, and
+* Olga G. Troyanskaya.
+* "The Sleipnir library for computational functional genomics"
+*****************************************************************************/
+#include "stdafx.h"
+#include "cmdline.h"
+
+int main( int iArgs, char** aszArgs ) {
+	gengetopt_args_info	sArgs;
+	CPCL				PCL;
+	vector<float>		vecdSumsIn, vecdSumSqsIn, vecdSumsOut, vecdSumSqsOut;
+	vector<size_t>		veciCountsIn, veciCountsOut;
+	size_t				i, j;
+	float				d;
+
+	if( cmdline_parser( iArgs, aszArgs, &sArgs ) ) {
+		cmdline_parser_print_help( );
+		return 1; }
+	CMeta Meta( sArgs.verbosity_arg );
+
+	if( !PCL.Open( sArgs.input_arg, sArgs.skip_arg ) ) {
+		cerr << "Could not open: " << ( sArgs.input_arg ? sArgs.input_arg : "stdin" ) << endl;
+		return 1; }
+
+	vecdSumsIn.resize( PCL.GetExperiments( ) );
+	vecdSumsOut.resize( PCL.GetExperiments( ) );
+	vecdSumSqsIn.resize( PCL.GetExperiments( ) );
+	vecdSumSqsOut.resize( PCL.GetExperiments( ) );
+	veciCountsIn.resize( PCL.GetExperiments( ) );
+	veciCountsOut.resize( PCL.GetExperiments( ) );
+	for( i = 0; i < PCL.GetGenes( ); ++i ) {
+		bool			fIn			= PCL.GetFeatures( ) && ( PCL.GetFeature( i, 1 )[ 0 ] == '*' );
+		vector<float>&	vecdSums	= fIn ? vecdSumsIn : vecdSumsOut;
+		vector<float>&	vecdSumSqs	= fIn ? vecdSumSqsIn : vecdSumSqsOut;
+		vector<size_t>&	veciCounts	= fIn ? veciCountsIn : veciCountsOut;
+
+		for( j = 0; j < PCL.GetExperiments( ); ++j )
+			if( !CMeta::IsNaN( d = PCL.Get( i, j ) ) ) {
+				veciCounts[ j ]++;
+				vecdSums[ j ] += d;
+				vecdSumSqs[ j ] += d * d; } }
+	for( i = 0; i < PCL.GetExperiments( ); ++i ) {
+		if( j = veciCountsIn[ i ] ) {
+			d = ( vecdSumsIn[ i ] /= j );
+			vecdSumSqsIn[ i ] = sqrt( ( vecdSumSqsIn[ i ] / j ) - ( d * d ) ); }
+		if( j = veciCountsOut[ i ] ) {
+			d = ( vecdSumsOut[ i ] /= j );
+			vecdSumSqsOut[ i ] = sqrt( ( vecdSumSqsOut[ i ] / j ) - ( d * d ) ); } }
+
+	for( i = 0; i < PCL.GetExperiments( ); ++i )
+		cout << ( i ? "\t" : "" ) << PCL.GetExperiment( i );
+	cout << endl;
+	for( i = 0; i < PCL.GetExperiments( ); ++i )
+		cout << ( i ? "\t" : "" ) << vecdSumsIn[ i ];
+	cout << endl;
+	for( i = 0; i < PCL.GetExperiments( ); ++i )
+		cout << ( i ? "\t" : "" ) << vecdSumSqsIn[ i ];
+	cout << endl;
+	for( i = 0; i < PCL.GetExperiments( ); ++i )
+		cout << ( i ? "\t" : "" ) << vecdSumsOut[ i ];
+	cout << endl;
+	for( i = 0; i < PCL.GetExperiments( ); ++i )
+		cout << ( i ? "\t" : "" ) << vecdSumSqsOut[ i ];
+	cout << endl;
+	
+
+	return 0; }

File tools/PCLPlotter/PCLPlotter.ggo

+package	"PCLPlotter"
+version	"1.0"
+purpose	"Plots summary information for PCL files/clusters."
+
+section "Main"
+option	"input"		i	"Input PCL file"
+						string	typestr="filename"
+
+section "Optional"
+option	"skip"		s	"Columns to skip in input PCL"
+						int	default="2"
+option	"verbosity"	v	"Message verbosity"
+						int	default="5"

File tools/PCLPlotter/cmdline.c

+/*
+  File autogenerated by gengetopt version 2.22
+  generated with the following command:
+  /r01/tergeo/chuttenh/sleipnir/trunk/../extlib/gengetopt-2.22/bin/gengetopt -iPCLPlotter.ggo --default-optional -u -N -e 
+
+  The developers of gengetopt consider the fixed text that goes in all
+  gengetopt output files to be in the public domain:
+  we make no copyright claims on it.
+*/
+
+/* If we use autoconf.  */
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "getopt.h"
+
+#include "cmdline.h"
+
+const char *gengetopt_args_info_purpose = "Plots summary information for PCL files/clusters.";
+
+const char *gengetopt_args_info_usage = "Usage: PCLPlotter [OPTIONS]... [FILES]...";
+
+const char *gengetopt_args_info_description = "";
+
+const char *gengetopt_args_info_help[] = {
+  "  -h, --help            Print help and exit",
+  "  -V, --version         Print version and exit",
+  "\nMain:",
+  "  -i, --input=filename  Input PCL file",
+  "\nOptional:",
+  "  -s, --skip=INT        Columns to skip in input PCL  (default=`2')",
+  "  -v, --verbosity=INT   Message verbosity  (default=`5')",
+    0
+};
+
+typedef enum {ARG_NO
+  , ARG_STRING
+  , ARG_INT
+} cmdline_parser_arg_type;
+
+static
+void clear_given (struct gengetopt_args_info *args_info);
+static
+void clear_args (struct gengetopt_args_info *args_info);
+
+static int
+cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
+                        struct cmdline_parser_params *params, const char *additional_error);
+
+
+static char *
+gengetopt_strdup (const char *s);
+
+static
+void clear_given (struct gengetopt_args_info *args_info)
+{
+  args_info->help_given = 0 ;
+  args_info->version_given = 0 ;
+  args_info->input_given = 0 ;
+  args_info->skip_given = 0 ;
+  args_info->verbosity_given = 0 ;
+}
+
+static
+void clear_args (struct gengetopt_args_info *args_info)
+{
+  args_info->input_arg = NULL;
+  args_info->input_orig = NULL;
+  args_info->skip_arg = 2;
+  args_info->skip_orig = NULL;
+  args_info->verbosity_arg = 5;
+  args_info->verbosity_orig = NULL;
+  
+}
+
+static
+void init_args_info(struct gengetopt_args_info *args_info)
+{
+
+
+  args_info->help_help = gengetopt_args_info_help[0] ;
+  args_info->version_help = gengetopt_args_info_help[1] ;
+  args_info->input_help = gengetopt_args_info_help[3] ;
+  args_info->skip_help = gengetopt_args_info_help[5] ;
+  args_info->verbosity_help = gengetopt_args_info_help[6] ;
+  
+}
+
+void
+cmdline_parser_print_version (void)
+{
+  printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
+}
+
+static void print_help_common(void) {
+  cmdline_parser_print_version ();
+
+  if (strlen(gengetopt_args_info_purpose) > 0)
+    printf("\n%s\n", gengetopt_args_info_purpose);
+
+  if (strlen(gengetopt_args_info_usage) > 0)
+    printf("\n%s\n", gengetopt_args_info_usage);
+
+  printf("\n");
+
+  if (strlen(gengetopt_args_info_description) > 0)
+    printf("%s\n", gengetopt_args_info_description);
+}
+
+void
+cmdline_parser_print_help (void)
+{
+  int i = 0;
+  print_help_common();
+  while (gengetopt_args_info_help[i])
+    printf("%s\n", gengetopt_args_info_help[i++]);
+}
+
+void
+cmdline_parser_init (struct gengetopt_args_info *args_info)
+{
+  clear_given (args_info);
+  clear_args (args_info);
+  init_args_info (args_info);
+
+  args_info->inputs = NULL;
+  args_info->inputs_num = 0;
+}
+
+void
+cmdline_parser_params_init(struct cmdline_parser_params *params)
+{
+  if (params)
+    { 
+      params->override = 0;
+      params->initialize = 1;
+      params->check_required = 1;
+      params->check_ambiguity = 0;
+      params->print_errors = 1;
+    }
+}
+
+struct cmdline_parser_params *
+cmdline_parser_params_create(void)
+{
+  struct cmdline_parser_params *params = 
+    (struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
+  cmdline_parser_params_init(params);  
+  return params;
+}
+
+static void
+free_string_field (char **s)
+{
+  if (*s)
+    {
+      free (*s);
+      *s = 0;
+    }
+}
+
+
+static void
+cmdline_parser_release (struct gengetopt_args_info *args_info)
+{
+  unsigned int i;
+  free_string_field (&(args_info->input_arg));
+  free_string_field (&(args_info->input_orig));
+  free_string_field (&(args_info->skip_orig));
+  free_string_field (&(args_info->verbosity_orig));
+  
+  
+  for (i = 0; i < args_info->inputs_num; ++i)
+    free (args_info->inputs [i]);
+
+  if (args_info->inputs_num)
+    free (args_info->inputs);
+
+  clear_given (args_info);
+}
+
+
+static void
+write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
+{
+  if (arg) {
+    fprintf(outfile, "%s=\"%s\"\n", opt, arg);
+  } else {
+    fprintf(outfile, "%s\n", opt);
+  }
+}
+
+
+int
+cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
+{
+  int i = 0;
+
+  if (!outfile)
+    {
+      fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
+      return EXIT_FAILURE;
+    }
+
+  if (args_info->help_given)
+    write_into_file(outfile, "help", 0, 0 );
+  if (args_info->version_given)
+    write_into_file(outfile, "version", 0, 0 );
+  if (args_info->input_given)
+    write_into_file(outfile, "input", args_info->input_orig, 0);
+  if (args_info->skip_given)
+    write_into_file(outfile, "skip", args_info->skip_orig, 0);
+  if (args_info->verbosity_given)
+    write_into_file(outfile, "verbosity", args_info->verbosity_orig, 0);
+  
+
+  i = EXIT_SUCCESS;
+  return i;
+}
+
+int
+cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
+{
+  FILE *outfile;
+  int i = 0;
+
+  outfile = fopen(filename, "w");
+
+  if (!outfile)
+    {
+      fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
+      return EXIT_FAILURE;
+    }
+
+  i = cmdline_parser_dump(outfile, args_info);
+  fclose (outfile);
+
+  return i;
+}
+
+void
+cmdline_parser_free (struct gengetopt_args_info *args_info)
+{
+  cmdline_parser_release (args_info);
+}
+
+/** @brief replacement of strdup, which is not standard */
+char *
+gengetopt_strdup (const char *s)
+{
+  char *result = NULL;
+  if (!s)
+    return result;
+
+  result = (char*)malloc(strlen(s) + 1);
+  if (result == (char*)0)
+    return (char*)0;
+  strcpy(result, s);
+  return result;
+}
+
+int
+cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
+{
+  return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
+}
+
+int
+cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info,
+                   struct cmdline_parser_params *params)
+{
+  int result;
+  result = cmdline_parser_internal (argc, argv, args_info, params, NULL);
+
+  return result;
+}
+
+int
+cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
+{
+  int result;
+  struct cmdline_parser_params params;
+  
+  params.override = override;
+  params.initialize = initialize;
+  params.check_required = check_required;
+  params.check_ambiguity = 0;
+  params.print_errors = 1;
+
+  result = cmdline_parser_internal (argc, argv, args_info, &params, NULL);
+
+  return result;
+}
+
+int
+cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
+{
+  return EXIT_SUCCESS;
+}
+
+
+static char *package_name = 0;
+
+/**
+ * @brief updates an option
+ * @param field the generic pointer to the field to update
+ * @param orig_field the pointer to the orig field
+ * @param field_given the pointer to the number of occurrence of this option
+ * @param prev_given the pointer to the number of occurrence already seen
+ * @param value the argument for this option (if null no arg was specified)
+ * @param possible_values the possible values for this option (if specified)
+ * @param default_value the default value (in case the option only accepts fixed values)
+ * @param arg_type the type of this option
+ * @param check_ambiguity @see cmdline_parser_params.check_ambiguity
+ * @param override @see cmdline_parser_params.override
+ * @param no_free whether to free a possible previous value
+ * @param multiple_option whether this is a multiple option
+ * @param long_opt the corresponding long option
+ * @param short_opt the corresponding short option (or '-' if none)
+ * @param additional_error possible further error specification
+ */
+static
+int update_arg(void *field, char **orig_field,
+               unsigned int *field_given, unsigned int *prev_given, 
+               char *value, char *possible_values[], const char *default_value,
+               cmdline_parser_arg_type arg_type,
+               int check_ambiguity, int override,
+               int no_free, int multiple_option,
+               const char *long_opt, char short_opt,
+               const char *additional_error)
+{
+  char *stop_char = 0;
+  const char *val = value;
+  int found;
+  char **string_field;
+
+  stop_char = 0;
+  found = 0;
+
+  if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
+    {
+      if (short_opt != '-')
+        fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n", 
+               package_name, long_opt, short_opt,
+               (additional_error ? additional_error : ""));
+      else
+        fprintf (stderr, "%s: `--%s' option given more than once%s\n", 
+               package_name, long_opt,
+               (additional_error ? additional_error : ""));
+      return 1; /* failure */
+    }
+
+    
+  if (field_given && *field_given && ! override)
+    return 0;
+  if (prev_given)
+    (*prev_given)++;
+  if (field_given)
+    (*field_given)++;
+  if (possible_values)
+    val = possible_values[found];
+
+  switch(arg_type) {
+  case ARG_INT:
+    if (val) *((int *)field) = strtol (val, &stop_char, 0);
+    break;
+  case ARG_STRING:
+    if (val) {
+      string_field = (char **)field;
+      if (!no_free && *string_field)
+        free (*string_field); /* free previous string */
+      *string_field = gengetopt_strdup (val);
+    }
+    break;
+  default:
+    break;
+  };
+
+  /* check numeric conversion */
+  switch(arg_type) {
+  case ARG_INT:
+    if (val && !(stop_char && *stop_char == '\0')) {
+      fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
+      return 1; /* failure */
+    }
+    break;
+  default:
+    ;
+  };
+
+  /* store the original value */
+  switch(arg_type) {
+  case ARG_NO:
+    break;
+  default:
+    if (value && orig_field) {
+      if (no_free) {
+        *orig_field = value;
+      } else {
+        if (*orig_field)
+          free (*orig_field); /* free previous string */
+        *orig_field = gengetopt_strdup (value);
+      }
+    }
+  };
+
+  return 0; /* OK */
+}
+
+
+int
+cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
+                        struct cmdline_parser_params *params, const char *additional_error)
+{
+  int c;	/* Character of the parsed option.  */
+
+  int error = 0;
+  struct gengetopt_args_info local_args_info;
+  
+  int override;
+  int initialize;
+  int check_required;
+  int check_ambiguity;
+  
+  package_name = argv[0];
+  
+  override = params->override;
+  initialize = params->initialize;
+  check_required = params->check_required;
+  check_ambiguity = params->check_ambiguity;
+
+  if (initialize)
+    cmdline_parser_init (args_info);
+
+  cmdline_parser_init (&local_args_info);
+
+  optarg = 0;
+  optind = 0;
+  opterr = params->print_errors;
+  optopt = '?';
+
+  while (1)
+    {
+      int option_index = 0;
+
+      static struct option long_options[] = {
+        { "help",	0, NULL, 'h' },
+        { "version",	0, NULL, 'V' },
+        { "input",	1, NULL, 'i' },
+        { "skip",	1, NULL, 's' },
+        { "verbosity",	1, NULL, 'v' },
+        { NULL,	0, NULL, 0 }
+      };
+
+      c = getopt_long (argc, argv, "hVi:s:v:", long_options, &option_index);
+
+      if (c == -1) break;	/* Exit from `while (1)' loop.  */
+
+      switch (c)
+        {
+        case 'h':	/* Print help and exit.  */
+          cmdline_parser_print_help ();
+          cmdline_parser_free (&local_args_info);
+          exit (EXIT_SUCCESS);
+
+        case 'V':	/* Print version and exit.  */
+        
+        
+          if (update_arg( 0 , 
+               0 , &(args_info->version_given),
+              &(local_args_info.version_given), optarg, 0, 0, ARG_NO,
+              check_ambiguity, override, 0, 0,
+              "version", 'V',
+              additional_error))
+            goto failure;
+          cmdline_parser_free (&local_args_info);
+          return 0;
+        
+          break;
+        case 'i':	/* Input PCL file.  */
+        
+        
+          if (update_arg( (void *)&(args_info->input_arg), 
+               &(args_info->input_orig), &(args_info->input_given),
+              &(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
+              check_ambiguity, override, 0, 0,
+              "input", 'i',
+              additional_error))
+            goto failure;
+        
+          break;
+        case 's':	/* Columns to skip in input PCL.  */
+        
+        
+          if (update_arg( (void *)&(args_info->skip_arg), 
+               &(args_info->skip_orig), &(args_info->skip_given),
+              &(local_args_info.skip_given), optarg, 0, "2", ARG_INT,
+              check_ambiguity, override, 0, 0,
+              "skip", 's',
+              additional_error))
+            goto failure;
+        
+          break;
+        case 'v':	/* Message verbosity.  */
+        
+        
+          if (update_arg( (void *)&(args_info->verbosity_arg), 
+               &(args_info->verbosity_orig), &(args_info->verbosity_given),
+              &(local_args_info.verbosity_given), optarg, 0, "5", ARG_INT,
+              check_ambiguity, override, 0, 0,
+              "verbosity", 'v',
+              additional_error))
+            goto failure;
+        
+          break;
+
+        case 0:	/* Long option with no short option */
+        case '?':	/* Invalid option.  */
+          /* `getopt_long' already printed an error message.  */
+          goto failure;
+
+        default:	/* bug: option not considered.  */
+          fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
+          abort ();
+        } /* switch */
+    } /* while */
+
+
+
+
+  cmdline_parser_release (&local_args_info);
+
+  if ( error )
+    return (EXIT_FAILURE);
+
+  if (optind < argc)
+    {
+      int i = 0 ;
+      int found_prog_name = 0;
+      /* whether program name, i.e., argv[0], is in the remaining args
+         (this may happen with some implementations of getopt,
+          but surely not with the one included by gengetopt) */
+
+      i = optind;
+      while (i < argc)
+        if (argv[i++] == argv[0]) {
+          found_prog_name = 1;
+          break;
+        }
+      i = 0;
+
+      args_info->inputs_num = argc - optind - found_prog_name;
+      args_info->inputs =
+        (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
+      while (optind < argc)
+        if (argv[optind++] != argv[0])
+          args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
+    }
+
+  return 0;
+
+failure:
+  
+  cmdline_parser_release (&local_args_info);
+  return (EXIT_FAILURE);
+}

File tools/PCLPlotter/cmdline.h

+/** @file cmdline.h
+ *  @brief The header file for the command line option parser
+ *  generated by GNU Gengetopt version 2.22
+ *  http://www.gnu.org/software/gengetopt.
+ *  DO NOT modify this file, since it can be overwritten
+ *  @author GNU Gengetopt by Lorenzo Bettini */
+
+#ifndef CMDLINE_H
+#define CMDLINE_H
+
+/* If we use autoconf.  */
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h> /* for FILE */
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+#ifndef CMDLINE_PARSER_PACKAGE
+/** @brief the program name */
+#define CMDLINE_PARSER_PACKAGE "PCLPlotter"
+#endif
+
+#ifndef CMDLINE_PARSER_VERSION
+/** @brief the program version */
+#define CMDLINE_PARSER_VERSION "1.0"
+#endif
+
+/** @brief Where the command line options are stored */
+struct gengetopt_args_info
+{
+  const char *help_help; /**< @brief Print help and exit help description.  */
+  const char *version_help; /**< @brief Print version and exit help description.  */
+  char * input_arg;	/**< @brief Input PCL file.  */
+  char * input_orig;	/**< @brief Input PCL file original value given at command line.  */
+  const char *input_help; /**< @brief Input PCL file help description.  */
+  int skip_arg;	/**< @brief Columns to skip in input PCL (default='2').  */
+  char * skip_orig;	/**< @brief Columns to skip in input PCL original value given at command line.  */
+  const char *skip_help; /**< @brief Columns to skip in input PCL help description.  */
+  int verbosity_arg;	/**< @brief Message verbosity (default='5').  */
+  char * verbosity_orig;	/**< @brief Message verbosity original value given at command line.  */
+  const char *verbosity_help; /**< @brief Message verbosity help description.  */
+  
+  unsigned int help_given ;	/**< @brief Whether help was given.  */
+  unsigned int version_given ;	/**< @brief Whether version was given.  */
+  unsigned int input_given ;	/**< @brief Whether input was given.  */
+  unsigned int skip_given ;	/**< @brief Whether skip was given.  */
+  unsigned int verbosity_given ;	/**< @brief Whether verbosity was given.  */
+
+  char **inputs ; /**< @brief unamed options (options without names) */
+  unsigned inputs_num ; /**< @brief unamed options number */
+} ;
+
+/** @brief The additional parameters to pass to parser functions */
+struct cmdline_parser_params
+{
+  int override; /**< @brief whether to override possibly already present options (default 0) */
+  int initialize; /**< @brief whether to initialize the option structure gengetopt_args_info (default 1) */
+  int check_required; /**< @brief whether to check that all required options were provided (default 1) */
+  int check_ambiguity; /**< @brief whether to check for options already specified in the option structure gengetopt_args_info (default 0) */
+  int print_errors; /**< @brief whether getopt_long should print an error message for a bad option (default 1) */
+} ;
+
+/** @brief the purpose string of the program */
+extern const char *gengetopt_args_info_purpose;
+/** @brief the usage string of the program */
+extern const char *gengetopt_args_info_usage;
+/** @brief all the lines making the help output */
+extern const char *gengetopt_args_info_help[];
+
+/**
+ * The command line parser
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser (int argc, char * const *argv,
+  struct gengetopt_args_info *args_info);
+
+/**
+ * The command line parser (version with additional parameters - deprecated)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use cmdline_parser_ext() instead
+ */
+int cmdline_parser2 (int argc, char * const *argv,
+  struct gengetopt_args_info *args_info,
+  int override, int initialize, int check_required);
+
+/**
+ * The command line parser (version with additional parameters)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_ext (int argc, char * const *argv,
+  struct gengetopt_args_info *args_info,
+  struct cmdline_parser_params *params);
+
+/**
+ * Save the contents of the option struct into an already open FILE stream.
+ * @param outfile the stream where to dump options
+ * @param args_info the option struct to dump
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_dump(FILE *outfile,
+  struct gengetopt_args_info *args_info);
+
+/**
+ * Save the contents of the option struct into a (text) file.
+ * This file can be read by the config file parser (if generated by gengetopt)
+ * @param filename the file where to save
+ * @param args_info the option struct to save
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_file_save(const char *filename,
+  struct gengetopt_args_info *args_info);
+
+/**
+ * Print the help
+ */
+void cmdline_parser_print_help(void);
+/**
+ * Print the version
+ */
+void cmdline_parser_print_version(void);
+
+/**
+ * Initializes all the fields a cmdline_parser_params structure 
+ * to their default values
+ * @param params the structure to initialize
+ */
+void cmdline_parser_params_init(struct cmdline_parser_params *params);
+
+/**
+ * Allocates dynamically a cmdline_parser_params structure and initializes
+ * all its fields to their default values
+ * @return the created and initialized cmdline_parser_params structure
+ */
+struct cmdline_parser_params *cmdline_parser_params_create(void);
+
+/**
+ * Initializes the passed gengetopt_args_info structure's fields
+ * (also set default values for options that have a default)
+ * @param args_info the structure to initialize
+ */
+void cmdline_parser_init (struct gengetopt_args_info *args_info);
+/**
+ * Deallocates the string fields of the gengetopt_args_info structure
+ * (but does not deallocate the structure itself)
+ * @param args_info the structure to deallocate
+ */
+void cmdline_parser_free (struct gengetopt_args_info *args_info);
+
+/**
+ * Checks that all the required options were specified
+ * @param args_info the structure to check
+ * @param prog_name the name of the program that will be used to print
+ *   possible errors
+ * @return
+ */
+int cmdline_parser_required (struct gengetopt_args_info *args_info,
+  const char *prog_name);
+
+
+#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+#endif /* CMDLINE_H */

File tools/PCLPlotter/stdafx.cpp

+/*****************************************************************************
+* This file is provided under the Creative Commons Attribution 3.0 license.
+*
+* You are free to share, copy, distribute, transmit, or adapt this work
+* PROVIDED THAT you attribute the work to the authors listed below.
+* For more information, please see the following web page:
+* http://creativecommons.org/licenses/by/3.0/
+*
+* This file is a component of the Sleipnir library for functional genomics,
+* authored by:
+* Curtis Huttenhower (chuttenh@princeton.edu)
+* Mark Schroeder
+* Maria D. Chikina
+* Olga G. Troyanskaya (ogt@princeton.edu, primary contact)
+*
+* If you use this library, the included executable tools, or any related
+* code in your work, please cite the following publication:
+* Curtis Huttenhower, Mark Schroeder, Maria D. Chikina, and
+* Olga G. Troyanskaya.
+* "The Sleipnir library for computational functional genomics"
+*****************************************************************************/
+#include "stdafx.h"
+
+/*!
+ * \page Clusters2Dab Clusters2Dab
+ * 
+ * Clusters2Dab converts the output of many common non-hierarchical clustering algorithms into pairwise
+ * scores based on the frequency or confidence of coclustering.  For example, if two genes are scored by
+ * the number of times they cocluster over many random seeds, then high scores will be indicative of a
+ * stronger pairwise relationship than low scores.
+ * 
+ * \section sec_usage Usage
+ * 
+ * \subsection ssec_usage_basic Basic Usage
+ * 
+ * \code
+ * Clusters2Dab -i <clusters.txt> -o <coclusters.dab>
+ * \endcode
+ * 
+ * Create a new DAT/DAB file \c coclusters.dab in which each gene pair is given a score of one if they
+ * cluster together in the hard clustering \c clusters.txt and a score of zero if they do not.
+ * 
+ * \code
+ * Clusters2Dab -t samba -i <clusters.txt> -o <coclusters.dab>
+ * \endcode
+ * 
+ * Create a new DAT/DAB file \c coclusters.dab in which each gene pair is given a score equal to the
+ * confidence of their strongest shared SAMBA bicluster in \c clusters.txt if one exists or zero if it
+ * does not.
+ * 
+ * \code
+ * Clusters2Dab -t param -i <clusters.txt> -o <coclusters.dab>
+ * \endcode
+ * 
+ * Create a new DAT/DAB file \c coclusters.dab in which each gene pair is given a score equal to the
+ * maximum parameter value in \c clusters.txt at which they cocluster.
+ * 
+ * \subsection ssec_usage_detailed Detailed Usage
+ * 
+ * \include Clusters2Dab/Clusters2Dab.ggo
+ * 
+ * <table><tr>
+ *	<th>Flag</th>
+ *	<th>Default</th>
+ *	<th>Type</th>
+ *	<th>Description</th>
+ * </tr><tr>
+ *	<td>-i</td>
+ *	<td>stdin</td>
+ *	<td>Text file</td>
+ *	<td>Input cluster file in one of the text formats supported by \c -t.</td>
+ * </tr><tr>
+ *	<td>-o</td>
+ *	<td>stdout</td>
+ *	<td>DAT/DAB file</td>
+ *	<td>Output DAT/DAB file containing pairwise scores appropriate to the input cluster type.</td>
+ * </tr><tr>
+ *	<td>-t</td>
+ *	<td>list</td>
+ *	<td>list, samba, param, or fuzzy</td>
+ *	<td>Type of cluster file provided to \c -i.  \c list assumes that each line contains a gene ID and a
+ *		cluster index separated by a tab, \c samba reads biclustering output from the EXPANDER program by
+ *		Sharan, Shamir, et al, \c param reads hard clustering output from EXPANDER, and \c fuzzy reads
+ *		output from the Aerie fuzzy k-means program by Gasch, Eisen, et al.</td>
+ * </tr><tr>
+ *	<td>-c</td>
+ *	<td>off</td>
+ *	<td>Flag</td>
+ *	<td>If on, calculate pairwise scores solely by cocluster frequency (counts); otherwise, pairwise scores
+ *		are weighted by cluster confidence.</td>
+ * </tr><tr>
+ *	<td>-s</td>
+ *	<td>2</td>
+ *	<td>Integer</td>
+ *	<td>Number of columns to skip between the initial ID column and the first experimental (data) column
+ *		in the input PCL.</td>
+ * </tr></table>
+ */

File tools/PCLPlotter/stdafx.h

+/*****************************************************************************
+* This file is provided under the Creative Commons Attribution 3.0 license.
+*
+* You are free to share, copy, distribute, transmit, or adapt this work
+* PROVIDED THAT you attribute the work to the authors listed below.
+* For more information, please see the following web page:
+* http://creativecommons.org/licenses/by/3.0/
+*
+* This file is a component of the Sleipnir library for functional genomics,
+* authored by:
+* Curtis Huttenhower (chuttenh@princeton.edu)
+* Mark Schroeder
+* Maria D. Chikina
+* Olga G. Troyanskaya (ogt@princeton.edu, primary contact)
+*
+* If you use this library, the included executable tools, or any related
+* code in your work, please cite the following publication:
+* Curtis Huttenhower, Mark Schroeder, Maria D. Chikina, and
+* Olga G. Troyanskaya.
+* "The Sleipnir library for computational functional genomics"
+*****************************************************************************/
+#ifndef STDAFX_H
+#define STDAFX_H
+
+#include <float.h>
+#include <math.h>
+
+#include <algorithm>
+#include <fstream>
+using namespace std;
+
+#include "dat.h"
+#include "genome.h"
+#include "measure.h"
+#include "meta.h"
+#include "pcl.h"
+#include "statistics.h"
+using namespace Sleipnir;
+
+#endif // STDAFX_H