added errorchecking and help info on new unifrac and treeclimber code

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index bc836e854cb3c4f1b7cc184789b0d49d6e8e3f45..d4eb9980c9051919eecb25e18a0c7b685dae65a1 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -103,7 +103,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
                                if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       } 
                                if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         } 
-                               if (key == "treefile" )         { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
+                               if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
                                if (key == "name" )             { namefile = value;             }
                                if (key == "order" )    { orderfile = value;    }
                                if (key == "group" )    { groupfile = value;    }
@@ -154,14 +154,14 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                        splitAtDash(value, lines);
                                        allLines = 0;
                                }
-                               if (key == "label") {//stores lines to be used in a set
+                               if (key == "label") {//stores labels to be used in a set
                                        labels.clear();
                                        label = value;
                                        line = "";
                                        splitAtDash(value, labels);
                                        allLines = 0;
                                }
-                               if (key == "groups") {//stores lines to be used in a vector
+                               if (key == "groups") {//stores groups to be used in a vector
                                        Groups.clear();
                                        groups = value;
                                        splitAtDash(value, Groups);
@@ -178,7 +178,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
                        if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
                        if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
-                       if (key == "treefile" )         { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }  
+                       if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }  
                        if (key == "name" )             { namefile = value;             }
                        if (key == "order" )    { orderfile = value;    }
                        if (key == "group" )    { groupfile = value;    }
@@ -190,6 +190,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        if (key == "method" )           { method = value;               }
                        if (key == "fileroot" )         { fileroot = value;             }
                        if (key == "randomtree" )       { randomtree = value;   }
+                       if (key == "groups" )           { groups = value;       }
+
                        
                        if (key == "single") {//stores estimators in a vector
                                singleEstimators.clear(); //clears out old values
@@ -236,6 +238,12 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                splitAtDash(value, labels);
                                allLines = 0;
                        }
+                       if (key == "groups") {//stores groups to be used in a vector
+                                       Groups.clear();
+                                       groups = value;
+                                       splitAtDash(value, Groups);
+                       }
+
                }
                
                //set format for shared
@@ -345,6 +353,7 @@ void GlobalData::clear() {
        iters                   =       "1000"; 
        line                    =   "";
        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.
        freq                    =       "100";