working on libshuff

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index b1ac4e87b986cee6380c997c6c40590b089067f7..a0ccdcb690eda34efb4fe9964b375b47b0e71d2f 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
@@ -83,6 +39,11 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        helpRequest = optionText;
                }
                
+               if (commandName == "libshuff") {
+                       iters = "10000";
+                       cutoff = "1.0";
+               }
+               
                string key, value;              
                //reads in parameters and values
                if((optionText != "") && (commandName != "help")){
@@ -110,7 +71,10 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                if (key == "fileroot" )         { fileroot = value;             }
                                if (key == "abund" )        { abund = value;        }
                                if (key == "random" )           { randomtree = value;   }
-                               if (key == "calc")                      { calc = value;         }
+                               if (key == "calc")                      { calc = value;                 }
+                               if (key == "step")                      { step = value;                 }
+                               if (key == "form")                      { form = value;                 }
+                               
 
                                
                                if (key == "line") {//stores lines to be used in a set
@@ -160,22 +124,24 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        if (key == "abund" )        { abund = value;        }
                        if (key == "random" )           { randomtree = value;   }
                        if (key == "calc")                      { calc = value;         }
-
+                       if (key == "step")                      { step = value;                 }
+                       if (key == "form")                      { form = value;                 }
 
                        if (key == "line") {//stores lines to be used in a vector
                                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;
@@ -261,6 +227,8 @@ string GlobalData::getFreq()                        {       return freq;            }
 string GlobalData::getAbund()           {   return abund;       }
 string GlobalData::getRandomTree()             {       return randomtree;      }
 string GlobalData::getGroups()                 {       return groups;          }
+string GlobalData::getStep()                   {       return step;            }
+string GlobalData::getForm()                   {       return form;            }
 void GlobalData::setListFile(string file)      {       listfile = file;        inputFileName = file;}
 void GlobalData::setRabundFile(string file)    {       rabundfile = file;      inputFileName = file;}
 void GlobalData::setSabundFile(string file)    {       sabundfile = file;      inputFileName = file;}
@@ -309,6 +277,8 @@ void GlobalData::clear() {
        method                  =       "furthest";
        fileroot                =       "";
        abund           =   "10";
+       step                    =       "0.01";
+       form                    =       "integral";
 }
 
 //*******************************************************/
@@ -318,15 +288,15 @@ 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.
        freq                    =       "100";
        method                  =       "furthest";
        calc                    =       "";
-       abund = "10";
+       abund                   =   "10";
+       step                    =       "0.01";
+       form                    =       "integral";
 }
 /*******************************************************/