dist.seqs can now use n processors, and only outputs the phylip formatted distance...

[mothur.git] / sharedsabundvector.cpp

diff --git a/sharedsabundvector.cpp b/sharedsabundvector.cpp
index b2624840e568d5d90715db1d662bc0ee5d8e7567..51058cf585fb511655a97d9b1a15d108dab99df5 100644 (file)
--- a/sharedsabundvector.cpp
+++ b/sharedsabundvector.cpp
@@ -3,22 +3,17 @@
  *  Dotur
  *
  *  Created by Sarah Westcott on 12/10/08.
- *  Copyright 2008 __MyCompanyName__. All rights reserved.
+ *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
 #include "sharedsabundvector.h"
 #include "sabundvector.hpp"
-#include "datavector.hpp"
-#include "utilities.hpp"
-#include <exception>
-
-using namespace std;
 
 
 /***********************************************************************/
 
-SharedSAbundVector::SharedSAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){};
+SharedSAbundVector::SharedSAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){}
 
 /***********************************************************************/
 
@@ -30,58 +25,6 @@ SharedSAbundVector::SharedSAbundVector(int size) :   DataVector(), maxRank(0), num
                        newGuy.abundance = 0;
                        data.push_back(newGuy);
                }
-       //      for(int i=0;i<data.size();i++){
-       //              if(data[i].abundance != 0){     maxRank = i;    }
-       //              numSeqs += i*data[i].abundance;
-       //              numBins += data[i].abundance;
-       //      }
-
-};
-
-/***********************************************************************
-
-SharedSAbundVector::SharedSAbundVector(string id, vector<int> sav) : DataVector(id), data(sav) {
-       try {
-               
-               for(int i=0;i<sav.size();i++){
-                       if(data[i] != 0){       maxRank = i;    }
-                       numSeqs += i*data[i];
-                       numBins += data[i];
-               }
-       }
-       catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function SharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedSAbundVector class function SharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-}
-
-/***********************************************************************
-
-SharedSAbundVector::SharedSAbundVector(ifstream& f): DataVector(), maxRank(0), numBins(0), numSeqs(0) {
-       try {
-               int hold;
-               f >> label >> hold;
-       
-               data.assign(hold+1, 0);
-               int inputData;
-       
-               for(int i=1;i<=hold;i++){
-                       f >> inputData;
-                       set(i, inputData);
-               }
-       }
-       catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function SharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedSAbundVector class function SharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
 }
 
 /***********************************************************************/
@@ -308,6 +251,8 @@ SharedOrderVector SharedSAbundVector::getSharedOrderVector() {
                rav = this->getSharedRAbundVector();
                ov = rav.getSharedOrderVector();
                
+               ov.updateStats();
+               
                return ov;
        }
        catch(exception& e) {