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

[mothur.git] / sharedsabundvector.cpp

diff --git a/sharedsabundvector.cpp b/sharedsabundvector.cpp
deleted file mode 100644 (file)
index efd14bc..0000000
--- a/sharedsabundvector.cpp
+++ /dev/null
@@ -1,275 +0,0 @@
-/*
- *  sharedSharedSAbundVector.cpp
- *  Dotur
- *
- *  Created by Sarah Westcott on 12/10/08.
- *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "sharedsabundvector.h"
-#include "sabundvector.hpp"
-
-
-/***********************************************************************/
-
-SharedSAbundVector::SharedSAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){  }
-
-/***********************************************************************/
-
-SharedSAbundVector::SharedSAbundVector(int size) :     DataVector(), maxRank(0), numBins(0), numSeqs(0) {
-               individual newGuy;
-               //initialize data
-               for (int i=0; i< size; i++) {
-                       newGuy.bin = i;
-                       newGuy.abundance = 0;
-                       data.push_back(newGuy);
-               }
-}
-
-/***********************************************************************/
-
-void SharedSAbundVector::set(int bin, int abundance, string groupName){
-       try {
-
-               int initSize = data[bin].abundance;
-               data[bin].abundance = abundance;
-               data[bin].group = groupName;
-       
-               if(bin != 0){
-                       numBins += (abundance - initSize);
-               }
-       
-               numSeqs += bin * (abundance - initSize);
-       
-               if(bin > maxRank)       {       maxRank = bin;          }
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SharedSAbundVector", "set");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-
-individual SharedSAbundVector::get(int index){
-       return data[index];
-}
-/***********************************************************************/
-
-int SharedSAbundVector::getAbundance(int index){
-       return data[index].abundance;
-}
-
-/***********************************************************************/
-
-void SharedSAbundVector::push_back(int abundance, int bin, string groupName){
-       try {
-               individual newGuy;
-               newGuy.abundance = abundance;
-               newGuy.bin = bin;
-               newGuy.group = groupName;
-               
-               data.push_back(newGuy);
-       
-               maxRank++;      
-       
-               numBins += abundance;
-       
-               numSeqs += (maxRank * abundance);
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SharedSAbundVector", "push_back");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-
-void SharedSAbundVector::resize(int size){
-       data.resize(size);
-}
-
-/***********************************************************************/
-
-int SharedSAbundVector::size(){
-       return data.size();             
-}
-
-/***********************************************************************/
-void SharedSAbundVector::print(ostream& output){
-       try {
-               output << label << '\t' << maxRank << '\t';
-       
-               for(int i=1;i<=maxRank;i++){
-                       output << data[i].abundance << '\t';
-               }
-               output << endl;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SharedSAbundVector", "print");
-               exit(1);
-       }
-}
-/***********************************************************************/
-string SharedSAbundVector::getGroup(){
-       return group;
-}
-
-/***********************************************************************/
-
-void SharedSAbundVector::setGroup(string groupName){
-       group = groupName;
-}
-
-/**********************************************************************/
-int SharedSAbundVector::getNumBins(){
-       return numBins;
-}
-
-/***********************************************************************/
-
-int SharedSAbundVector::getNumSeqs(){
-       return numSeqs;
-}
-
-/***********************************************************************/
-
-int SharedSAbundVector::getMaxRank(){
-       return maxRank;
-}
-/***********************************************************************/
-RAbundVector SharedSAbundVector::getRAbundVector(){
-       try {
-               RAbundVector rav;
-       
-               for(int i=1;i<data.size();i++){         
-                       for(int j=0;j<data[i].abundance;j++){
-                               rav.push_back(i);
-                       }
-               }
-               sort(rav.rbegin(), rav.rend());
-       
-               rav.setLabel(label);
-               return rav;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SharedSAbundVector", "getRAbundVector");
-               exit(1);
-       }
-}
-/***********************************************************************/
-SAbundVector SharedSAbundVector::getSAbundVector(){
-       try {
-               RAbundVector rav;
-               SAbundVector sav;
-               
-               rav = getRAbundVector();
-               sav = rav.getSAbundVector();
-               return sav;
-       
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SharedSAbundVector", "getSAbundVector");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-
-bool compareMembers (individual member, individual member2){
-
-  if(member.abundance < member2.abundance){
-    return true;   }   
-  else{
-       return false; 
-  }
-}
-
-/***********************************************************************/
-SharedRAbundVector SharedSAbundVector::getSharedRAbundVector(){
-       try {
-               SharedRAbundVector rav;
-               
-               for(int i=1;i<data.size();i++){         
-                       for(int j=0;j<data[i].abundance;j++){
-                               rav.push_back(i, data[i].group);
-                       }
-               }
-               sort(rav.rbegin(), rav.rend(), compareMembers);
-       
-               rav.setLabel(label);
-               rav.setGroup(group);
-               
-               return rav;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SharedSAbundVector", "getSharedRAbundVector");
-               exit(1);
-       }
-}
-
-
-/***********************************************************************/
-
-SharedSAbundVector SharedSAbundVector::getSharedSAbundVector(){
-       return *this;                   
-}
-
-/***********************************************************************/
-SharedOrderVector SharedSAbundVector::getSharedOrderVector() {
-       try {
-               SharedRAbundVector rav;
-               SharedOrderVector ov;
-               
-               rav = this->getSharedRAbundVector();
-               ov = rav.getSharedOrderVector();
-               
-               ov.updateStats();
-               
-               return ov;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SharedSAbundVector", "getSharedOrderVector");
-               exit(1);
-       }
-}
-/***********************************************************************/
-
-void SharedSAbundVector::clear(){
-       numBins = 0;
-       maxRank = 0;
-       numSeqs = 0;
-       data.clear();
-}
-
-/***********************************************************************/
-OrderVector SharedSAbundVector::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].abundance;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, "SharedSAbundVector", "getOrderVector");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-