Revert to previous commit

[mothur.git] / sabundvector.cpp

diff --git a/sabundvector.cpp b/sabundvector.cpp
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+++ b/sabundvector.cpp
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+/*
+ *  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);
+       }
+}
+
+/***********************************************************************/