changing command name classify.shared to classifyrf.shared

[mothur.git] / collect.cpp

diff --git a/collect.cpp b/collect.cpp
index 78fd05c0c9470117b9750096cbdf8a8a5a6a15f3..9a89020efe91f8bdd2733a3de553611e86ee6da3 100644 (file)
--- a/collect.cpp
+++ b/collect.cpp
@@ -74,10 +74,11 @@ 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);
                 }
        
@@ -142,14 +143,14 @@ try {
                                                                                                        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;
@@ -171,13 +172,13 @@ 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
@@ -208,9 +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++;
                }