deleted read.shared command and added its functionality to read.otu.

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index eeb1f4d5c51d36d5f38942f6c0b328a7386eb20b..3ddd02e5c24dc03cd8ff7549b6b03a32982562e9 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -16,50 +16,6 @@ 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){
@@ -71,12 +27,11 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                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();
-                       
                }
                
                //saves help request
@@ -109,9 +64,10 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                if (key == "freq" )                     { freq = value;                 }
                                if (key == "method" )           { method = value;               }
                                if (key == "fileroot" )         { fileroot = value;             }
+                               if (key == "abund" )        { abund = value;        }
                                if (key == "random" )           { randomtree = value;   }
-                               if (key == "groups" )           { groups = value;       }
                                if (key == "calc")                      { calc = value;         }
+
                                
                                if (key == "line") {//stores lines to be used in a set
                                        lines.clear();
@@ -127,11 +83,13 @@ 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);
                                }
+
                        }
                        
                        //saves the last parameter
@@ -155,8 +113,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        if (key == "freq" )                     { freq = value;                 }
                        if (key == "method" )           { method = value;               }
                        if (key == "fileroot" )         { fileroot = value;             }
+                       if (key == "abund" )        { abund = value;        }
                        if (key == "random" )           { randomtree = value;   }
-                       if (key == "groups" )           { groups = value;       }
                        if (key == "calc")                      { calc = value;         }
 
 
@@ -183,6 +141,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                
                //set format for shared
                if ((listfile != "") && (groupfile != "")) { format = "shared"; }
+               if ((phylipfile != "") && (groupfile != "")) { format = "matrix"; }
                                
                //input defaults for calculators
                if (commandName == "collect.single") {
@@ -255,7 +214,9 @@ string GlobalData::getFileRoot()            {       return fileroot;        }
 string GlobalData::getIters()                  {       return iters;           }
 string GlobalData::getJumble()                 {       return jumble;          }
 string GlobalData::getFreq()                   {       return freq;            }
+string GlobalData::getAbund()           {   return abund;       }
 string GlobalData::getRandomTree()             {       return randomtree;      }
+string GlobalData::getGroups()                 {       return groups;          }
 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;}
@@ -264,7 +225,8 @@ void GlobalData::setColumnFile(string file) {       columnfile = file;    inputFileNam
 void GlobalData::setNameFile(string file)              {       namefile = file;                }
 void GlobalData::setFormat(string Format)              {       format = Format;                }
 void GlobalData::setRandomTree(string Random)  {       randomtree = Random;    }
-void GlobalData::setCalc(string Calc)                  {       calc = Calc;    }
+void GlobalData::setGroups(string g)                   {       groups = g;                             }
+void GlobalData::setCalc(string Calc)                  {       calc = Calc;                    }
 
 /*******************************************************/
 
@@ -302,9 +264,10 @@ void GlobalData::clear() {
        freq                    =       "100";
        method                  =       "furthest";
        fileroot                =       "";
-       calc                    =       "";
+       abund           =   "10";
 }
-/*******************************************************/
+
+//*******************************************************/
 
 /******************************************************/
 void GlobalData::reset() {
@@ -319,6 +282,7 @@ void GlobalData::reset() {
        freq                    =       "100";
        method                  =       "furthest";
        calc                    =       "";
+       abund = "10";
 }
 /*******************************************************/
 
@@ -330,6 +294,3 @@ GlobalData::~GlobalData() {
        if(gorder != NULL)                      {       delete gorder;          }
 }
 /*******************************************************/
-
-/******************************************************/
-