updated for windows compatibility

percolator · Apr 11, 2014 · aeb76d3 · aeb76d3
1 parent 87ca16a
commit aeb76d3
Show file tree

Hide file tree

Showing 4 changed files with 71 additions and 40 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -10,7 +10,7 @@ set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 
 set(POUT2MZIML_VERSION_MAJOR "0")
 set(POUT2MZIML_VERSION_MINOR "2")
-set(POUT2MZIML_VERSION_PATCH "6")
+set(POUT2MZIML_VERSION_PATCH "7")
 
 configure_file( version_config.h.in ${CMAKE_BINARY_DIR}/version_config.h )
 
@@ -41,7 +41,7 @@ include_directories(${XSD_INCLUDE_DIR})
 
 SET (Boost_ADDITIONAL_VERSIONS "1.36" "1.36.0" "1.41" "1.41.0" "1.39" "1.39.0" "1.42.0" "1.42" "1.43.0"
              "1.43." "1.44.0" "1.44.0" "1.45.0" "1.45" "1.46.0" "1.46" "1.47.0" "1.47")
-find_package(Boost COMPONENTS filesystem system REQUIRED)
+find_package(Boost COMPONENTS filesystem system program_options REQUIRED)
 if(Boost_FOUND)
   message(STATUS "Package Boost-${Boost_VERSION} found : ${Boost_INCLUDE_DIR}")
 else(Boost_FOUND)

diff --git a/global.h b/global.h
@@ -41,7 +41,37 @@ namespace global {
     }
   }
 //------------------------------------------------------------------------------
-// strings used for reporting error messages and status
+// strings used for options
+//------------------------------------------------------------------------------
+namespace CMDOPTIONS {
+  const char HELP_OPTION[]="help,h";
+  const char HELP_TEST[]="help";
+  const char HELP_TEXT[]="Displays available commands\n";
+  const char PERCOLATORFILE_OPTION[]="percolatorfile,p";
+  const char PERCOLATORFILE_TEST[]="percolatorfile";
+  const char PERCOLATORFILE_TEXT[]="Percolator Out XML result file\n";
+  const char MZIDFILE_OPTION[]="mzidfile,m";
+  const char MZIDFILE_TEST[]="mzidfile";
+  const char MZIDFILE_TEXT[]="MzIdentML input file\n";
+  const char MZIDOUTPUT_OPTION[]="output,o";
+  const char MZIDOUTPUT_TEST[]="output";
+  const char MZIDOUTPUT_TEXT[]="Outputs the results to original filename+[File]+.mzid.\n"
+                               "DEFAULT: output to stdout\n";
+  const char MZIDFILES_OPTION[]="filesmzid,f";
+  const char MZIDFILES_TEST[]="filesmzid";
+  const char MZIDFILES_TEXT[]="File containing a list of mzIdentML filenames\n";
+  const char DECOY_OPTION[]="decoy,d";
+  const char DECOY_TEST[]="decoy";
+  const char DECOY_TEXT[]="Only adds results to entries with decoy set to true. DEFAULT: false\n";
+  const char VALIDATION_OPTION[]="validate,v";
+  const char VALIDATION_TEST[]="validate";
+  const char VALIDATION_TEXT[]="Sets that validation of XML schema should not be performed. Faster parsing.\n";
+  const char WARNING_OPTION[]="warning,w";
+  const char WARNING_TEST[]="warning";
+  const char WARNING_TEXT[]="Sets that upon warning the software should terminate.\n";
+  }
+//------------------------------------------------------------------------------
+// strings used for reporting error messages, status
 //------------------------------------------------------------------------------
 namespace PRINT_TEXT {
   const char HELP[]="pout2mzid [OPTIONS]\n"

diff --git a/main.cpp b/main.cpp
@@ -17,8 +17,10 @@
 
 #include "version_config.h"
 #include "xmlio.h"
+#include "boost/program_options.hpp"
 
 //------------------------------------------------------------------------------
+namespace prgm_opt=boost::program_options;
 PercolatorOutI percolator;
 MzIDIO mzid;
 boost::unordered_map<PercolatorOutFeatures, string, PercolatorOutFeatures> pout_values;
@@ -30,44 +32,44 @@ void CleanUp(bool exitvalue) {
   }
 //------------------------------------------------------------------------------
 int main(int argc, char **argv) {
-  int opt;
+  prgm_opt::variables_map option_map;
+  prgm_opt::options_description options("Options");
 
   try {
-    while ((opt=getopt(argc,argv,"o::m:p:f:vdhw")) != EOF)
-      switch(opt) {
-        case 'd':
-          percolator.setDecoy();
-          break;
-        case 'v':
-          percolator.unsetValidation();
-          mzid.unsetValidation();
-          break;
-        case 'o':
-          mzid.setOutputFileEnding(optarg?optarg:MZID_PARAM::FILE_END_DEFAULT);
-          break;
-        case 'p':
-          if (!percolator.setFilename(optarg))
-            THROW_ERROR_VALUE(PRINT_TEXT::NO_PERCOLATOR_FILE,optarg);
-          break;
-        case 'm':
-          mzid.setFilename(optarg);
-          break;
-        case 'f':
-          if (!mzid.addFilenames(optarg))
-            THROW_ERROR_VALUE(PRINT_TEXT::NO_MZID_FILE,optarg);
-          break;
-        case 'w':
-          mzid.unsetWarningFlag();
-          break;
-        case 'h':
-        case '?':
-          printVersion();
-          cout << PRINT_TEXT::HELP << endl;
-          CleanUp(EXIT_SUCCESS);
-          break;
-        default:
-          CleanUp(EXIT_SUCCESS);
-        }
+    prgm_opt::arg="[File]";
+    options.add_options()
+      (CMDOPTIONS::HELP_OPTION,CMDOPTIONS::HELP_TEXT)
+      (CMDOPTIONS::PERCOLATORFILE_OPTION,prgm_opt::value<string>()->required(),CMDOPTIONS::PERCOLATORFILE_TEXT)
+      (CMDOPTIONS::MZIDFILE_OPTION,prgm_opt::value<string>()->required(),CMDOPTIONS::MZIDFILE_TEXT)
+      (CMDOPTIONS::MZIDOUTPUT_OPTION,prgm_opt::value<string>()->required(),CMDOPTIONS::MZIDOUTPUT_TEXT)
+      (CMDOPTIONS::MZIDFILES_OPTION,prgm_opt::value<string>()->required(),CMDOPTIONS::MZIDFILES_TEXT)
+      (CMDOPTIONS::DECOY_OPTION,CMDOPTIONS::DECOY_TEXT)
+      (CMDOPTIONS::VALIDATION_OPTION,CMDOPTIONS::VALIDATION_TEXT)
+      (CMDOPTIONS::WARNING_OPTION,CMDOPTIONS::WARNING_TEXT);
+    prgm_opt::store(prgm_opt::parse_command_line(argc,argv,options),option_map);
+    if (option_map.count(CMDOPTIONS::HELP_TEST)) {
+      printVersion();
+      cout << options;
+      CleanUp(EXIT_SUCCESS);
+      }
+    if (option_map.count(CMDOPTIONS::DECOY_TEST))
+      percolator.setDecoy();
+    if (option_map.count(CMDOPTIONS::VALIDATION_TEST)) {
+      percolator.unsetValidation();
+      mzid.unsetValidation();
+      }
+    if (option_map.count(CMDOPTIONS::MZIDOUTPUT_TEST))
+      mzid.setOutputFileEnding(option_map[CMDOPTIONS::MZIDOUTPUT_TEST].as<string>());
+    if (option_map.count(CMDOPTIONS::PERCOLATORFILE_TEST))
+      if (!percolator.setFilename(option_map[CMDOPTIONS::PERCOLATORFILE_TEST].as<string>()))
+        THROW_ERROR_VALUE(PRINT_TEXT::NO_PERCOLATOR_FILE,option_map[CMDOPTIONS::PERCOLATORFILE_TEST].as<string>());
+    if (option_map.count(CMDOPTIONS::MZIDFILE_TEST))
+      mzid.setFilename(option_map[CMDOPTIONS::MZIDFILE_TEST].as<string>());
+    if (option_map.count(CMDOPTIONS::MZIDFILES_TEST))
+      if (!mzid.addFilenames(option_map[CMDOPTIONS::MZIDFILES_TEST].as<string>()))
+        THROW_ERROR_VALUE(PRINT_TEXT::NO_MZID_FILE,option_map[CMDOPTIONS::MZIDFILES_TEST].as<string>());
+    if (option_map.count(CMDOPTIONS::WARNING_TEST))
+       mzid.unsetWarningFlag();
     if (!mzid.checkFilenames())
       CleanUp(EXIT_FAILURE);
     if (percolator.noFilename())

diff --git a/xmlio.h b/xmlio.h
@@ -43,7 +43,6 @@ using namespace std;
 namespace MZID_PARAM {
   const char SCHEMA_NAME[]="http://psidev.info/psi/pi/mzIdentML/1.1";
   const char SCHEMA[]="mzIdentML1.1.0.xsd";
-  const char FILE_END_DEFAULT[]="_output";
   enum ELEMENT_TYPE { USERPARAM,CVPARAM };
 
   namespace ELEMENT_DATA {