added the Calculators Thomas made in the fall. Added parameter and command error...

[mothur.git] / sharedrabundvector.cpp

diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp
index b35b06d05813f3819cefc2919f5fbb18b4b8c2af..846f9cdb705c7a801097feaeca59272d4001d361 100644 (file)
--- a/sharedrabundvector.cpp
+++ b/sharedrabundvector.cpp
@@ -14,6 +14,7 @@ using namespace std;
 #include "utilities.hpp"
 #include "sabundvector.hpp"
 #include "ordervector.hpp"
+#include <algorithm>
 
 
 /***********************************************************************/
@@ -119,6 +120,11 @@ void SharedRAbundVector::set(int binNumber, int newBinSize, string groupname){
                exit(1);
        }
 }
+/***********************************************************************/
+
+void SharedRAbundVector::setData(vector <individual> newData){
+       data = newData;
+}
 
 /***********************************************************************/
 
@@ -126,14 +132,32 @@ int SharedRAbundVector::getAbundance(int index){
        return data[index].abundance;
        
 }
+/***********************************************************************/
+
+int SharedRAbundVector::numNZ(){
+       int sum = 0;
+       for(int i = 1; i < numBins; i++)
+               if(data[i].abundance > 0)
+                       sum++;
+       return sum;
+}
+/***********************************************************************/
 
+void SharedRAbundVector::sortD(){
+       struct individual indObj;
+       sort(data.begin()+1, data.end(), indObj);
+}
 /***********************************************************************/
 
 individual SharedRAbundVector::get(int index){
        return data[index];
        
 }
+/***********************************************************************/
 
+vector <individual> SharedRAbundVector::getData(){
+       return data;
+}
 /***********************************************************************/
 
 void SharedRAbundVector::push_back(int binSize, int otu, string groupName){
@@ -241,7 +265,6 @@ int SharedRAbundVector::getNumSeqs(){
 int SharedRAbundVector::getMaxRank(){
        return maxRank;
 }
-
 /***********************************************************************/
 
 SharedRAbundVector SharedRAbundVector::getSharedRAbundVector(){
@@ -268,7 +291,25 @@ RAbundVector SharedRAbundVector::getRAbundVector() {
                exit(1);
        }
 }
+/***********************************************************************/
 
+RAbundVector SharedRAbundVector::getRAbundVector2() {
+       try {
+               RAbundVector rav;
+               for(int i = 0; i < numBins; i++)
+                       if(data[i].abundance != 0)
+                               rav.push_back(data[i].abundance-1);
+               return rav;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the SharedRAbundVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+}
 /***********************************************************************/
 
 SharedSAbundVector SharedRAbundVector::getSharedSAbundVector(){