sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / sharedsabundvector.cpp

diff --git a/sharedsabundvector.cpp b/sharedsabundvector.cpp
index 7babf1c1f519dc28aa45fab6ec7c378f217499db..efd14bcc249207ac4181fc552b8a918d57144083 100644 (file)
--- a/sharedsabundvector.cpp
+++ b/sharedsabundvector.cpp
@@ -9,14 +9,11 @@
 
 #include "sharedsabundvector.h"
 #include "sabundvector.hpp"
-#include "utilities.hpp"
-
-using namespace std;
 
 
 /***********************************************************************/
 
-SharedSAbundVector::SharedSAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){};
+SharedSAbundVector::SharedSAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){  }
 
 /***********************************************************************/
 
@@ -28,7 +25,7 @@ SharedSAbundVector::SharedSAbundVector(int size) :    DataVector(), maxRank(0), num
                        newGuy.abundance = 0;
                        data.push_back(newGuy);
                }
-};
+}
 
 /***********************************************************************/
 
@@ -48,13 +45,9 @@ void SharedSAbundVector::set(int bin, int abundance, string groupName){
                if(bin > maxRank)       {       maxRank = bin;          }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedSAbundVector", "set");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedSAbundVector class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/
@@ -86,13 +79,9 @@ void SharedSAbundVector::push_back(int abundance, int bin, string groupName){
                numSeqs += (maxRank * abundance);
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedSAbundVector", "push_back");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedSAbundVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 
 /***********************************************************************/
@@ -118,13 +107,9 @@ void SharedSAbundVector::print(ostream& output){
                output << endl;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedSAbundVector", "print");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedSAbundVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 /***********************************************************************/
 string SharedSAbundVector::getGroup(){
@@ -158,7 +143,7 @@ RAbundVector SharedSAbundVector::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].abundance;j++){
                                rav.push_back(i);
                        }
@@ -169,13 +154,9 @@ RAbundVector SharedSAbundVector::getRAbundVector(){
                return rav;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedSAbundVector", "getRAbundVector");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedSAbundVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 /***********************************************************************/
 SAbundVector SharedSAbundVector::getSAbundVector(){
@@ -189,13 +170,9 @@ SAbundVector SharedSAbundVector::getSAbundVector(){
        
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedSAbundVector", "getSAbundVector");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedSAbundVector class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 
 /***********************************************************************/
@@ -214,11 +191,9 @@ SharedRAbundVector SharedSAbundVector::getSharedRAbundVector(){
        try {
                SharedRAbundVector rav;
                
-               int binNumber = 0;
-               for(int i=1;i<=data.size();i++){                
+               for(int i=1;i<data.size();i++){         
                        for(int j=0;j<data[i].abundance;j++){
-                               rav.push_back(i, binNumber, data[i].group);
-                               binNumber++;
+                               rav.push_back(i, data[i].group);
                        }
                }
                sort(rav.rbegin(), rav.rend(), compareMembers);
@@ -229,13 +204,9 @@ SharedRAbundVector SharedSAbundVector::getSharedRAbundVector(){
                return rav;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function getSharedVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedSAbundVector", "getSharedRAbundVector");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedSAbundVector class function getSharedVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 
 
@@ -254,17 +225,24 @@ SharedOrderVector SharedSAbundVector::getSharedOrderVector() {
                rav = this->getSharedRAbundVector();
                ov = rav.getSharedOrderVector();
                
+               ov.updateStats();
+               
                return ov;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedSAbundVector", "getSharedOrderVector");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedSAbundVector class function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
+/***********************************************************************/
+
+void SharedSAbundVector::clear(){
+       numBins = 0;
+       maxRank = 0;
+       numSeqs = 0;
+       data.clear();
+}
+
 /***********************************************************************/
 OrderVector SharedSAbundVector::getOrderVector(map<string,int>* hold = NULL){
        try {
@@ -288,13 +266,9 @@ OrderVector SharedSAbundVector::getOrderVector(map<string,int>* hold = NULL){
                return ov;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedSAbundVector", "getOrderVector");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedSAbundVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 
 /***********************************************************************/