minor bugs fixes and added line and label options to read.otu's parselist and shared...

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index 9b740a68c1a6b945d4f12789a5ee125e308f2c8c..eeb1f4d5c51d36d5f38942f6c0b328a7386eb20b 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -67,7 +67,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                allLines = 1;
                commandName = commandString; //save command name to be used by other classes
                
-               //set all non filename paramters to default values
+               //set all non filename paramters to default
                reset();
                
                //clears out data from previous read
@@ -75,6 +75,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        clear();
                        gGroupmap = NULL;
                        gTree.clear();
+                       labels.clear(); lines.clear(); groups.clear();
+                       
                }
                
                //saves help request
@@ -107,7 +109,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                if (key == "freq" )                     { freq = value;                 }
                                if (key == "method" )           { method = value;               }
                                if (key == "fileroot" )         { fileroot = value;             }
-                               if (key == "randomtree" )       { randomtree = value;   }
+                               if (key == "random" )           { randomtree = value;   }
                                if (key == "groups" )           { groups = value;       }
                                if (key == "calc")                      { calc = value;         }
                                
@@ -153,7 +155,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        if (key == "freq" )                     { freq = value;                 }
                        if (key == "method" )           { method = value;               }
                        if (key == "fileroot" )         { fileroot = value;             }
-                       if (key == "randomtree" )       { randomtree = value;   }
+                       if (key == "random" )           { randomtree = value;   }
                        if (key == "groups" )           { groups = value;       }
                        if (key == "calc")                      { calc = value;         }
 
@@ -296,7 +298,7 @@ void GlobalData::clear() {
        label                   =       "";
        groups                  =       "";
        jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
-       randomtree              =       "0";  //0 means user will enter some user trees, 1 means they just want the random tree distribution.
+       randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
        freq                    =       "100";
        method                  =       "furthest";
        fileroot                =       "";
@@ -313,7 +315,7 @@ void GlobalData::reset() {
        label                   =       "";
        groups                  =       "";
        jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
-       randomtree              =       "0";  //0 means user will enter some user trees, 1 means they just want the random tree distribution.
+       randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
        freq                    =       "100";
        method                  =       "furthest";
        calc                    =       "";