From 28b6634fd8f44d28b957b9ace79703c0ac79741c Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Mon, 9 Mar 2009 16:54:55 +0000
Subject: [PATCH] fixed bug in summary.shared for groups

---
 fullmatrix.cpp           |  9 +--------
 summarysharedcommand.cpp | 18 +++++-------------
 2 files changed, 6 insertions(+), 21 deletions(-)

diff --git a/fullmatrix.cpp b/fullmatrix.cpp
index 64d7b6a..6ea2318 100644
--- 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 040de20..18470d0 100644
--- 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";
-- 
2.39.2