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 b1ac4e87b986cee6380c997c6c40590b089067f7..17b4908515179211b792a6d06801d2dc878a7bca 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -16,66 +16,22 @@ GlobalData* GlobalData::getInstance() {
 }
 /*******************************************************/
 
-/******************************************************/
-
-ListVector* GlobalData::getListVector()                {       return gListVector;             }
-/*******************************************************/
-
-/******************************************************/
-void GlobalData::setListVector(ListVector* lv){
-       try {
-               if(gListVector != NULL){        delete gListVector;     }
-               gListVector = new ListVector(*lv);
-       }
-       catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function setListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the GlobalData class function setListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-}
-/*******************************************************/
-
-/******************************************************/
-
-SparseMatrix* GlobalData::getSparseMatrix()    {       return gSparseMatrix;   }
-/*******************************************************/
-
-/******************************************************/
-void GlobalData::setSparseMatrix(SparseMatrix* sm){
-       try{
-               if(gSparseMatrix != NULL){      delete gSparseMatrix;   }
-               gSparseMatrix = new SparseMatrix(*sm);
-       }
-       catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function setSparseMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the GlobalData class function setSparseMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-}
-/*******************************************************/
-
 /******************************************************/
 //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
                reset();
                
                //clears out data from previous read
-               if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree") || (commandName == "read.shared")) { 
+               if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree")) { 
                        clear();
                        gGroupmap = NULL;
                        gTree.clear();
                        labels.clear(); lines.clear(); groups.clear();
+                       allLines = 1;
                }
                
                //saves help request
@@ -166,16 +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;
@@ -318,8 +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.