finishing the container classes, combining read.otu and read.list commands. some...

[mothur.git] / sharedrabundvector.cpp

diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp
index 6bdeed0753e767de6616930a6cdc560c6e0f2610..ba8f94d2e03b85589c62238748bc1b4fa8e01676 100644 (file)
--- a/sharedrabundvector.cpp
+++ b/sharedrabundvector.cpp
@@ -224,7 +224,6 @@ void SharedRAbundVector::setGroup(string groupName){
        group = groupName;
 }
 
-
 /***********************************************************************/
 int SharedRAbundVector::getNumBins(){
        return numBins;
@@ -247,7 +246,54 @@ int SharedRAbundVector::getMaxRank(){
 SharedRAbundVector SharedRAbundVector::getSharedRAbundVector(){
        return *this;                   
 }
+/***********************************************************************/
+
+RAbundVector SharedRAbundVector::getRAbundVector() {
+       try {
+               RAbundVector rav(data.size());
+               
+               for (int i = 0; i < data.size(); i++) {
+                       rav.set(i, data[i].abundance);
+               }
+       
+               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(){
+       try {
+               SharedSAbundVector sav(maxRank+1);
+               
+               for(int i=0;i<data.size();i++){
+                       int abund = data[i].abundance;
+                       sav.set(abund, sav.getAbundance(abund) + 1, group);
+               }
+               
+               sav.set(0, 0, group);
+               sav.setLabel(label);
+               sav.setGroup(group);
+               
+               return sav;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getSharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the SharedRAbundVector class function getSharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+}
 /***********************************************************************/
 
 SAbundVector SharedRAbundVector::getSAbundVector() {