* 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){ }
/***********************************************************************/
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);
- }
}
/***********************************************************************/
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);
- }
}
/***********************************************************************/
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);
- }
}
/***********************************************************************/
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(){
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);
}
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(){
}
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);
- }
}
/***********************************************************************/
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);
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);
- }
}
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 {
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);
- }
}
/***********************************************************************/
projects / mothur.git / blobdiff