moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / sabundvector.cpp

diff --git a/sabundvector.cpp b/sabundvector.cpp
deleted file mode 100644 (file)
index 1bceec2..0000000
--- a/sabundvector.cpp
+++ /dev/null
@@ -1,254 +0,0 @@
-/*
- *  sabund.cpp
- *  
- *
- *  Created by Pat Schloss on 8/8/08.
- *  Copyright 2008 Patrick D. Schloss. All rights resesaved.
- *
- */
-
-#include "sabundvector.hpp"
-#include "calculator.h"
-
-/***********************************************************************/
-
-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(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) {
-               m->errorOut(e, "SAbundVector", "SAbundVector");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-
-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) {
-       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) {
-               m->errorOut(e, "SAbundVector", "SAbundVector");
-               exit(1);
-       }
-}
-
-
-/***********************************************************************/
-
-void SAbundVector::set(int sabund, int abundance){
-       try {
-
-               int initSize = data[sabund];
-               data[sabund] = abundance;
-       
-               if(sabund != 0){
-                       numBins += (abundance - initSize);
-               }
-       
-               numSeqs += sabund * (abundance - initSize);
-       
-               if(sabund > maxRank)    {       maxRank = sabund;               }
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SAbundVector", "set");
-               exit(1);
-       }
-}
-
-
-/***********************************************************************/
-
-int SAbundVector::get(int index){
-       return data[index];
-}
-
-/***********************************************************************/
-
-void SAbundVector::push_back(int abundance){
-       try {
-               data.push_back(abundance);
-       
-               maxRank++;      
-       
-               numBins += abundance;
-       
-               numSeqs += (maxRank * abundance);
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SAbundVector", "push_back");
-               exit(1);
-       }
-}
-/***********************************************************************/
-
-void SAbundVector::quicksort(){
-       sort(data.rbegin(), data.rend());
-}
-
-/***********************************************************************/
-
-int SAbundVector::sum(){
-       VecCalc vecCalc;
-       return vecCalc.sumElements(data);
-}
-
-/***********************************************************************/
-
-void SAbundVector::resize(int size){
-       data.resize(size);
-}
-
-/***********************************************************************/
-
-int SAbundVector::size(){
-       return data.size();             
-}
-
-/***********************************************************************/
-void SAbundVector::print(string prefix, ostream& output){
-       
-       output << prefix << '\t' << maxRank << '\t';
-       
-       for(int i=1;i<=maxRank;i++){
-               output << data[i] << '\t';
-       }
-       output << endl;
-}
-/***********************************************************************/
-void SAbundVector::clear(){
-       numBins = 0;
-       maxRank = 0;
-       numSeqs = 0;
-       data.clear();   
-}
-/***********************************************************************/
-void SAbundVector::print(ostream& output){
-       try {
-               output << label << '\t' << maxRank << '\t';
-       
-               for(int i=1;i<=maxRank;i++){
-                       output << data[i] << '\t';
-               }
-               output << endl;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SAbundVector", "print");
-               exit(1);
-       }
-}
-
-/**********************************************************************/
-int SAbundVector::getNumBins(){
-//     if(needToUpdate == 1){  updateStats();  }
-       return numBins;
-}
-
-/***********************************************************************/
-
-int SAbundVector::getNumSeqs(){
-//     if(needToUpdate == 1){  updateStats();  }
-       return numSeqs;
-}
-
-/***********************************************************************/
-
-int SAbundVector::getMaxRank(){
-//     if(needToUpdate == 1){  updateStats();  }
-       return maxRank;
-}
-/***********************************************************************/
-RAbundVector SAbundVector::getRAbundVector(){
-       try {
-               RAbundVector rav;
-       
-               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) {
-               m->errorOut(e, "SAbundVector", "getRAbundVector");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-
-SAbundVector SAbundVector::getSAbundVector(){
-       return *this;                   
-}
-
-/***********************************************************************/
-
-OrderVector SAbundVector::getOrderVector(map<string,int>* hold = NULL){
-       try {
-               OrderVector ov;
-       
-               int binIndex = 0;
-       
-               for(int i=1;i<data.size();i++){
-                       for(int j=0;j<data[i];j++){
-                               for(int k=0;k<i;k++){
-                                       ov.push_back(binIndex);
-                               }
-                               binIndex++;
-                       }
-               }
-       
-               random_shuffle(ov.begin(), ov.end());
-
-               ov.setLabel(label);
-               ov.getNumBins();
-               return ov;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SAbundVector", "getOrderVector");
-               exit(1);
-       }
-}
-
-/***********************************************************************/