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

[mothur.git] / sharedordervector.cpp

diff --git a/sharedordervector.cpp b/sharedordervector.cpp
index fc81febade9a6287dbedb24ef6504adf9f2445c2..575ae18ea050e90c416efa480181773799a25af5 100644 (file)
--- a/sharedordervector.cpp
+++ b/sharedordervector.cpp
@@ -3,7 +3,7 @@
  *  Dotur
  *
  *  Created by Sarah Westcott on 12/9/08.
- *  Copyright 2008 __MyCompanyName__. All rights reserved.
+ *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
@@ -11,7 +11,6 @@ using namespace std;
 
 
 #include "sharedordervector.h"
-#include "datavector.hpp"
 #include "utilities.hpp"
 #include <exception>
 
@@ -29,6 +28,8 @@ SharedOrderVector::SharedOrderVector(string id, vector<individual>  ov) :
 
 /***********************************************************************
 
+//does not work since we don't have a shared order file format yet.
+
 SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {
        try {
                int hold;
@@ -42,7 +43,7 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {
        
                for(int i=0;i<hold;i++){
                        f >> inputData;
-                       set(i, inputData);
+                       set(i, inputData, inputData, group);
                }
        
                updateStats();
@@ -221,6 +222,49 @@ SAbundVector SharedOrderVector::getSAbundVector(){
        RAbundVector rav(this->getRAbundVector());
        return rav.getSAbundVector();
 
+}
+/***********************************************************************/
+SharedRAbundVector SharedOrderVector::getSharedRAbundVector(string group) {
+       try {
+               SharedRAbundVector sharedRav(data.size());
+               
+               sharedRav.setLabel(label);
+               sharedRav.setGroup(group);
+               
+               for (int i = 0; i < data.size(); i++) {
+                       if (data[i].group == group) {
+                               sharedRav.set(data[i].abundance, sharedRav.getAbundance(data[i].abundance) + 1, data[i].group);
+                       }
+               }
+               return sharedRav;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the SharedOrderVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       
+}
+/***********************************************************************/
+SharedSAbundVector SharedOrderVector::getSharedSAbundVector(string group) {
+       try {
+               
+               SharedRAbundVector sharedRav(this->getSharedRAbundVector(group));
+               return sharedRav.getSharedSAbundVector();
+                               
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the SharedOrderVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       
 }
 
 /***********************************************************************/