sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / sabundvector.cpp

diff --git a/sabundvector.cpp b/sabundvector.cpp
index 4a926b26f17a7002217240156fdf9ae8e936b41f..1bceec210779221ce0dfce33886b177e5250efd8 100644 (file)
--- a/sabundvector.cpp
+++ b/sabundvector.cpp
@@ -6,26 +6,22 @@
  *  Copyright 2008 Patrick D. Schloss. All rights resesaved.
  *
  */
-using namespace std;
 
 #include "sabundvector.hpp"
-#include "datavector.hpp"
-#include "utilities.hpp"
-#include <exception>
+#include "calculator.h"
 
 /***********************************************************************/
 
-SAbundVector::SAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){};
+SAbundVector::SAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){}
 
 /***********************************************************************/
 
-SAbundVector::SAbundVector(int size) : DataVector(), data(size, 0), maxRank(0), numBins(0), numSeqs(0) {};
+SAbundVector::SAbundVector(int size) : DataVector(), data(size, 0), maxRank(0), numBins(0), numSeqs(0) {}
 
 /***********************************************************************/
 
 SAbundVector::SAbundVector(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];
@@ -33,15 +29,25 @@ SAbundVector::SAbundVector(string id, vector<int> sav) : DataVector(id), data(sa
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SAbundVector class Function SAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SAbundVector", "SAbundVector");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SAbundVector class function SAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+/***********************************************************************/
+
+SAbundVector::SAbundVector(vector <int> dataVec, int mr, int nb, int ns) {
+       try {
+               data = dataVec;
+               maxRank = mr;
+               numBins = nb;
+               numSeqs = ns;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SAbundVector", "SAbundVector");
                exit(1);
        }
 }
-
 /***********************************************************************/
 
 SAbundVector::SAbundVector(ifstream& f): DataVector(), maxRank(0), numBins(0), numSeqs(0) {
@@ -54,19 +60,18 @@ SAbundVector::SAbundVector(ifstream& f): DataVector(), maxRank(0), numBins(0), n
        
                for(int i=1;i<=hold;i++){
                        f >> inputData;
+
                        set(i, inputData);
                }
+
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SAbundVector class Function SAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SAbundVector class function SAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SAbundVector", "SAbundVector");
                exit(1);
        }
 }
 
+
 /***********************************************************************/
 
 void SAbundVector::set(int sabund, int abundance){
@@ -84,15 +89,12 @@ void SAbundVector::set(int sabund, int abundance){
                if(sabund > maxRank)    {       maxRank = sabund;               }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SAbundVector class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SAbundVector", "set");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SAbundVector class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
+
 /***********************************************************************/
 
 int SAbundVector::get(int index){
@@ -112,13 +114,21 @@ void SAbundVector::push_back(int abundance){
                numSeqs += (maxRank * abundance);
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SAbundVector class Function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SAbundVector", "push_back");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SAbundVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
+}
+/***********************************************************************/
+
+void SAbundVector::quicksort(){
+       sort(data.rbegin(), data.rend());
+}
+
+/***********************************************************************/
+
+int SAbundVector::sum(){
+       VecCalc vecCalc;
+       return vecCalc.sumElements(data);
 }
 
 /***********************************************************************/
@@ -143,7 +153,13 @@ void SAbundVector::print(string prefix, ostream& output){
        }
        output << endl;
 }
-
+/***********************************************************************/
+void SAbundVector::clear(){
+       numBins = 0;
+       maxRank = 0;
+       numSeqs = 0;
+       data.clear();   
+}
 /***********************************************************************/
 void SAbundVector::print(ostream& output){
        try {
@@ -155,13 +171,9 @@ void SAbundVector::print(ostream& output){
                output << endl;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SAbundVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SAbundVector", "print");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SAbundVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 
 /**********************************************************************/
@@ -188,24 +200,20 @@ RAbundVector SAbundVector::getRAbundVector(){
        try {
                RAbundVector rav;
        
-               for(int i=1;i<=data.size();i++){                
+               for(int i=1;i < data.size();i++){
                        for(int j=0;j<data[i];j++){
                                rav.push_back(i);
                        }
                }
                sort(rav.rbegin(), rav.rend());
-       
+
                rav.setLabel(label);
                return rav;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SAbundVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SAbundVector", "getRAbundVector");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SAbundVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 
 /***********************************************************************/
@@ -238,13 +246,9 @@ OrderVector SAbundVector::getOrderVector(map<string,int>* hold = NULL){
                return ov;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SAbundVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SAbundVector", "getOrderVector");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SAbundVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 
 /***********************************************************************/