- added a fix to input params

diff --git a/src/colorvec.cpp b/src/colorvec.cpp
index d0159f8eba55c92595f8d8a95d60bfdc8e01fccc..0619b3171cc3a46a7875441d39fcbd3e6883b45a 100644 (file)
--- a/src/colorvec.cpp
+++ b/src/colorvec.cpp
@@ -314,9 +314,9 @@ class colorVec : public gmx::TrajectoryAnalysisModule
     private:
 
         gmx::SelectionList                                              sel_;
-        std::string                                                     fnOut;                  // selectable
-        std::string                                                     fnBetaListsDat;         // selectable
-        float                                                           effRad          {0.8};  // selectable
+        std::string                                                     fnOut           {"name"};   // selectable
+        std::string                                                     fnBetaListsDat;             // selectable
+        float                                                           effRad          {0.8};      // selectable
         std::vector< size_t >                                           index;
         std::vector< size_t >                                           indexCA;
         std::vector< std::vector< size_t > >                            aminoacidsIndex;
@@ -357,12 +357,13 @@ colorVec::initOptions(  gmx::IOptionsContainer          *options,
                             .storeVector(&sel_)
                             .required().dynamicMask().multiValue()
                             .description("select pepride and colors / -sf"));
+    // Add option for input file names
+    options->addOption(gmx::StringOption("dat")
+                            .store(&fnBetaListsDat)
+                            .description("a file to make dynamic beta lists"));
     // Add option for output file name
-    options->addOption(gmx::FileNameOption("dat").filetype(gmx::eftGenericData).inputFile()
-                            .store(&fnBetaListsDat).description("a file to make dynamic beta lists"));
-    // Add option for output file name
-    options->addOption(gmx::FileNameOption("out").filetype(gmx::eftGenericData).outputFile()
-                            .store(&fnOut).defaultBasename("colorAngles")
+    options->addOption(gmx::StringOption("out")
+                            .store(&fnOut)
                             .description("Index file for the algorithm output."));
     // Add option for effRad constant
     options->addOption(gmx::FloatOption("efRad")