removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / sharedrabundfloatvector.cpp

diff --git a/sharedrabundfloatvector.cpp b/sharedrabundfloatvector.cpp
index d65cc204cc97bd43941928bad593b515522625e6..6c2dea195fdea527678277633ad08f9fbe4fc795 100644 (file)
--- a/sharedrabundfloatvector.cpp
+++ b/sharedrabundfloatvector.cpp
@@ -12,14 +12,14 @@
 
 /***********************************************************************/
 
-SharedRAbundFloatVector::SharedRAbundFloatVector() : DataVector(), maxRank(0.0), numBins(0), numSeqs(0.0) {globaldata = GlobalData::getInstance();}
+SharedRAbundFloatVector::SharedRAbundFloatVector() : DataVector(), maxRank(0.0), numBins(0), numSeqs(0.0) {}
 /***********************************************************************/
 
 SharedRAbundFloatVector::~SharedRAbundFloatVector() {}
 
 /***********************************************************************/
 SharedRAbundFloatVector::SharedRAbundFloatVector(int n) : DataVector(), maxRank(0.0), numBins(n), numSeqs(0.0) {
-               globaldata = GlobalData::getInstance();
+               
                individualFloat newGuy;
                //initialize data
                for (int i=0; i< n; i++) {
@@ -32,9 +32,8 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(int n) : DataVector(), maxRank(
 //reads a shared file
 SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), maxRank(0.0), numBins(0), numSeqs(0.0) {
        try {
-               globaldata = GlobalData::getInstance();
                
-               if (globaldata->gGroupmap == NULL) {  groupmap = new GroupMap(); }
+               m->namesOfGroups.clear();
                
                int num, count;
                float inputData;
@@ -45,8 +44,8 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
                for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
                lookup.clear();
                
-               if (globaldata->saveNextLabel == "") {  f >> label;  }
-               else { label = globaldata->saveNextLabel; }
+               if (m->saveNextLabel == "") {  f >> label;  }
+               else { label = m->saveNextLabel; }
                
                //read in first row since you know there is at least 1 group.
                f >> groupN >> num;
@@ -59,11 +58,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
                lookup[0]->setLabel(label);
                lookup[0]->setGroup(groupN);
                
-               if (globaldata->gGroupmap == NULL) { 
-                       //save group in groupmap
-                       groupmap->namesOfGroups.push_back(groupN);
-                       groupmap->groupIndex[groupN] = 0;
-               }
+               m->namesOfGroups.push_back(groupN);
                
                //fill vector.  data = first sharedrabund in file
                for(int i=0;i<num;i++){
@@ -84,11 +79,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
                        f >> groupN >> num;
                        count++;
                        
-                       if (globaldata->gGroupmap == NULL) { 
-                               //save group in groupmap
-                               groupmap->namesOfGroups.push_back(groupN);
-                               groupmap->groupIndex[groupN] = count;
-                       }
+                       m->namesOfGroups.push_back(groupN);
                        
                        //add new vector to lookup
                        temp = new SharedRAbundFloatVector();
@@ -107,10 +98,8 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
                        if (f.eof() != true) { f >> nextLabel; }
                }
                
-               globaldata->saveNextLabel = nextLabel;
+               m->saveNextLabel = nextLabel;
        
-               if (globaldata->gGroupmap == NULL) { globaldata->gGroupmap = groupmap;  }
-               
        }
        catch(exception& e) {
                m->errorOut(e, "SharedRAbundFloatVector", "SharedRAbundFloatVector");
@@ -287,12 +276,12 @@ vector<SharedRAbundFloatVector*> SharedRAbundFloatVector::getSharedRAbundFloatVe
                SharedUtil* util;
                util = new SharedUtil();
                
-               util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
+               util->setGroups(m->Groups, m->namesOfGroups);
                
                bool remove = false;
                for (int i = 0; i < lookup.size(); i++) {
                        //if this sharedrabund is not from a group the user wants then delete it.
-                       if (util->isValidGroup(lookup[i]->getGroup(), globaldata->Groups) == false) { 
+                       if (util->isValidGroup(lookup[i]->getGroup(), m->Groups) == false) { 
                                delete lookup[i]; lookup[i] = NULL;
                                lookup.erase(lookup.begin()+i); 
                                i--;