X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=collect.cpp;h=9a89020efe91f8bdd2733a3de553611e86ee6da3;hp=8db4a28c5d33661741916e0d7560be470fd97ab2;hb=615301e57c25e241356a9c2380648d117709458d;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6

diff --git a/collect.cpp b/collect.cpp
index 8db4a28..9a89020 100644
--- a/collect.cpp
+++ b/collect.cpp
@@ -74,13 +74,14 @@ try {
 				vector<SharedRAbundVector*> subset;
 
                 //create and initialize vector of sharedvectors, one for each group
-                for (int i = 0; i < m->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(m->Groups[i]);
+                        temp->setGroup(mGroups[i]);
 						lookup.push_back(temp);
                 }
-
+	
                 SharedCollectorsCurveData* ccd = new SharedCollectorsCurveData();
         
                 //initialize labels for output
@@ -114,7 +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()) {
@@ -141,14 +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, m->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, m->Groups.size(), pair); 
+								ccd->updateSharedData(lookup, i+1, m->getNumGroups(), pair); 
+							
                         }
                         totalNumSeq = i+1;
                 }
@@ -169,15 +172,15 @@ try {
 											if ((w != k) && (w != l)) { subset.push_back(lookup[w]); }
 										}
 									
-										ccd->updateSharedData(subset, totalNumSeq, m->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, m->Groups.size(), pair); 
+						ccd->updateSharedData(lookup, totalNumSeq, m->getNumGroups(), pair); 
                 }
-                
+	 
                 //resets output files
                 for(int i=0;i<displays.size();i++){
                         displays[i]->reset();
@@ -206,9 +209,10 @@ void Collect::getGroupComb() {
 	numGroupComb = 0;
                 
 	int n = 1;
-	for (int i = 0; i < (m->Groups.size() - 1); i++) {
-		for (int l = n; l < m->Groups.size(); l++) {
-			group = m->Groups[i] + m->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++;
 		}