fixed bug with line and label parameters and added all as option for both

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index 3ddd02e5c24dc03cd8ff7549b6b03a32982562e9..17b4908515179211b792a6d06801d2dc878a7bca 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -20,7 +20,6 @@ GlobalData* GlobalData::getInstance() {
 //This function parses through the option string of the command to remove its parameters
 void GlobalData::parseGlobalData(string commandString, string optionText){
        try {
-               allLines = 1;
                commandName = commandString; //save command name to be used by other classes
                
                //set all non filename paramters to default
@@ -32,6 +31,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        gGroupmap = NULL;
                        gTree.clear();
                        labels.clear(); lines.clear(); groups.clear();
+                       allLines = 1;
                }
                
                //saves help request
@@ -122,16 +122,17 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                lines.clear();
                                line = value;
                                label = "";
-                               splitAtDash(value, lines);
-                               allLines = 0;
+                               if (line != "all") {  splitAtDash(value, lines);  allLines = 0;  }
+                               else { allLines = 1;  }
                        }
                        if (key == "label") {//stores lines to be used in a vector
                                labels.clear();
                                label = value;
                                line = "";
-                               splitAtDash(value, labels);
-                               allLines = 0;
+                               if (label != "all") {  splitAtDash(value, labels);  allLines = 0;  }
+                               else { allLines = 1;  }
                        }
+                       
                        if (key == "groups") {//stores groups to be used in a vector
                                        Groups.clear();
                                        groups = value;
@@ -274,8 +275,6 @@ void GlobalData::reset() {
        cutoff                  =       "10.00";
        precision               =       "100";
        iters                   =       "1000"; 
-       line                    =   "";
-       label                   =       "";
        groups                  =       "";
        jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
        randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.