fixed bug in summary.shared for groups

diff --git a/fullmatrix.cpp b/fullmatrix.cpp
index 64d7b6af2dbe39279164fbe299c86a617af278e7..6ea2318d740003f8cf46ec7e63815c175e1893ca 100644 (file)
--- a/fullmatrix.cpp
+++ b/fullmatrix.cpp
@@ -56,14 +56,9 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
                if (square == true) { readSquareMatrix(filehandle); }
                else { readLTMatrix(filehandle); }
                
-               
-               
-       printMatrix(cout);
                //sort sequences so they are gathered in groups for processing
                sortGroups(0, numSeqs-1);
-               cout << "after sort" << endl;
-       printMatrix(cout);
-               
+                       
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function FullMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -204,8 +199,6 @@ void FullMatrix::sortGroups(int low, int high){
                                
                                i++; 
                                j--;
-cout << "swapping rows " << i << " " << j << endl;
-printMatrix(cout); cout << endl;
                        }
                } while(i <= j);
 

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 040de2067faf9d0dd9d1de74b2b4f6fe2f6a0086..18470d0df300f3b37249b9e4fc7fb05a8211518f 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -105,6 +105,9 @@ int SummarySharedCommand::execute(){
                        order = SharedList->getSharedOrderVector();
                }
                
+               //set users groups
+               setGroups();
+               
                //output estimator names as column headers
                outputFileHandle << "label" <<'\t' << "comparison" << '\t'; 
                for(int i=0;i<sumCalculators.size();i++){
@@ -112,9 +115,6 @@ int SummarySharedCommand::execute(){
                }
                outputFileHandle << endl;
                
-               //set users groups
-               setGroups();
-
                while(order != NULL){
                
                        if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){                       
@@ -176,10 +176,10 @@ void SummarySharedCommand::getSharedVectors(){
 try {
                lookup.clear();
                //create and initialize vector of sharedvectors, one for each group
-               for (int i = 0; i < globaldata->gGroupmap->getNumGroups(); i++) { 
+               for (int i = 0; i < globaldata->Groups.size(); i++) { 
                        SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
                        temp->setLabel(order->getLabel());
-                       temp->setGroup(globaldata->gGroupmap->namesOfGroups[i]);
+                       temp->setGroup(globaldata->Groups[i]);
                        lookup.push_back(temp);
                }
                
@@ -199,14 +199,6 @@ try {
                                }
                        }
                }
-               
-               //get rid of vectors from groups you don't want to analyze
-               for (int r = 0; r < lookup.size(); r++) { 
-                       if (inUsersGroups(lookup[r]->getGroup(), globaldata->Groups) != true) {
-                               lookup.erase(lookup.begin()+r);
-                       }
-               }
-               
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";