more calculator edits and added coverage and whittaker

[mothur.git] / sharedlistvector.cpp

diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp
index 2bceace2565f404a08b85e5af59cf18e295bd41a..b5624508ac792aa82d367ed04ed1fbaf571d4cd6 100644 (file)
--- a/sharedlistvector.cpp
+++ b/sharedlistvector.cpp
@@ -10,16 +10,17 @@
 
 using namespace std;
 
-#include <map>
-#include <exception>
+
 #include "sabundvector.hpp"
 #include "rabundvector.hpp"
 #include "ordervector.hpp"
-#include "datavector.hpp"
-#include "utilities.hpp"
 #include "sharedlistvector.h"
 #include "sharedordervector.h"
+#include "sharedutilities.h"
+
+/***********************************************************************/
 
+SharedListVector::SharedListVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){};
 
 /***********************************************************************/
 
@@ -29,21 +30,22 @@ SharedListVector::SharedListVector(int n):  DataVector(), data(n, "") , maxRank(0
 SharedListVector::SharedListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
        try {
                globaldata = GlobalData::getInstance();
-               
+
                //set up groupmap for later.
                groupmap = new GroupMap(globaldata->getGroupFile());
                groupmap->readMap();
 
                int hold;
+               string inputData;
                f >> label >> hold;
        
                data.assign(hold, "");
-               string inputData = "";
        
                for(int i=0;i<hold;i++){
                        f >> inputData;
                        set(i, inputData);
                }
+       
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function SharedListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -283,6 +285,28 @@ SharedRAbundVector SharedListVector::getSharedRAbundVector(string groupName) {
                exit(1);
        }
 }
+/***********************************************************************/
+vector<SharedRAbundVector*> SharedListVector::getSharedRAbundVector() {
+       try {
+               SharedUtil* util;
+               util = new SharedUtil();
+               vector<SharedRAbundVector*> lookup;
+               
+               util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
+               util->getSharedVectors(globaldata->Groups, lookup, this->getSharedOrderVector());
+               
+               return lookup;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the SharedListVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       
+}
 
 /***********************************************************************/
 SharedSAbundVector SharedListVector::getSharedSAbundVector(string groupName) {