changing command name classify.shared to classifyrf.shared

[mothur.git] / collect.cpp

diff --git a/collect.cpp b/collect.cpp
index ec5366b627d8e8f776ffd00c0bb63f98a748f4bc..9a89020efe91f8bdd2733a3de553611e86ee6da3 100644 (file)
--- a/collect.cpp
+++ b/collect.cpp
@@ -70,19 +70,18 @@ int Collect::getCurve(float percentFreq = 0.01){
 /***********************************************************************/
 int Collect::getSharedCurve(float percentFreq = 0.01){
 try {
-                               globaldata = GlobalData::getInstance();
                 vector<SharedRAbundVector*> lookup; 
                                vector<SharedRAbundVector*> subset;
 
                 //create and initialize vector of sharedvectors, one for each group
-                for (int i = 0; i < globaldata->Groups.size(); i++) { 
+                               vector<string> mGroups = m->getGroups();
+                for (int i = 0; i < mGroups.size(); i++) { 
                         SharedRAbundVector* temp = new SharedRAbundVector(sharedorder->getNumBins());
                         temp->setLabel(sharedorder->getLabel());
-                        temp->setGroup(globaldata->Groups[i]);
-                        temp->setGroupIndex(globaldata->gGroupmap->groupIndex[globaldata->Groups[i]]);
-                        lookup.push_back(temp);
+                        temp->setGroup(mGroups[i]);
+                                               lookup.push_back(temp);
                 }
-
+       
                 SharedCollectorsCurveData* ccd = new SharedCollectorsCurveData();
         
                 //initialize labels for output
@@ -116,7 +115,7 @@ try {
                         //get first sample
                         individual chosen = sharedorder->get(i);
                         int abundance; 
-                                        
+                                                    
                         //set info for sharedvector in chosens group
                         for (int j = 0; j < lookup.size(); j++) { 
                                                        if (chosen.group == lookup[j]->getGroup()) {
@@ -143,14 +142,16 @@ try {
                                                                                                for (int w = 0; w < lookup.size(); w++) {
                                                                                                        if ((w != k) && (w != l)) { subset.push_back(lookup[w]); }
                                                                                                }
-                                                                                       
-                                                ccd->updateSharedData(subset, i+1, globaldata->Groups.size(), pair);
+                                               
+                                                ccd->updateSharedData(subset, i+1, m->getNumGroups(), pair);
                                         }
                                         n++;
                                 }
+                                                       
                                                                //if this is a calculator that can do multiples then do them
                                                                pair = false;
-                                                               ccd->updateSharedData(lookup, i+1, globaldata->Groups.size(), pair); 
+                                                               ccd->updateSharedData(lookup, i+1, m->getNumGroups(), pair); 
+                                                       
                         }
                         totalNumSeq = i+1;
                 }
@@ -171,15 +172,15 @@ try {
                                                                                        if ((w != k) && (w != l)) { subset.push_back(lookup[w]); }
                                                                                }
                                                                        
-                                                                               ccd->updateSharedData(subset, totalNumSeq, globaldata->Groups.size(), pair);
+                                                                               ccd->updateSharedData(subset, totalNumSeq, m->getNumGroups(), pair);
                                 }
                                 n++;
                         }
                                                //if this is a calculator that can do multiples then do them
                                                pair = false;
-                                               ccd->updateSharedData(lookup, totalNumSeq, globaldata->Groups.size(), pair); 
+                                               ccd->updateSharedData(lookup, totalNumSeq, m->getNumGroups(), pair); 
                 }
-                
+        
                 //resets output files
                 for(int i=0;i<displays.size();i++){
                         displays[i]->reset();
@@ -208,9 +209,10 @@ void Collect::getGroupComb() {
        numGroupComb = 0;
                 
        int n = 1;
-       for (int i = 0; i < (globaldata->Groups.size() - 1); i++) {
-               for (int l = n; l < globaldata->Groups.size(); l++) {
-                       group = globaldata->Groups[i] + globaldata->Groups[l];
+       vector<string> mGroups = m->getGroups();
+       for (int i = 0; i < (m->getNumGroups() - 1); i++) {
+               for (int l = n; l < m->getNumGroups(); l++) {
+                       group = mGroups[i] + mGroups[l];
                        groupComb.push_back(group);        
                        numGroupComb++;
                }