+++ /dev/null
-/*
- * rarefact.cpp
- * Dotur
- *
- * Created by Sarah Westcott on 11/18/08.
- * Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "rarefact.h"
-//#include "ordervector.hpp"
-
-/***********************************************************************/
-
-int Rarefact::getCurve(float percentFreq = 0.01, int nIters = 1000){
- try {
- RarefactionCurveData* rcd = new RarefactionCurveData();
- for(int i=0;i<displays.size();i++){
- rcd->registerDisplay(displays[i]);
- }
-
- //convert freq percentage to number
- int increment = 1;
- if (percentFreq < 1.0) { increment = numSeqs * percentFreq; }
- else { increment = percentFreq; }
-
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- if(processors == 1){
- driver(rcd, increment, nIters);
- }else{
- vector<int> procIters;
-
- int numItersPerProcessor = nIters / processors;
-
- //divide iters between processes
- for (int i = 0; i < processors; i++) {
- if(i == processors - 1){
- numItersPerProcessor = nIters - i * numItersPerProcessor;
- }
- procIters.push_back(numItersPerProcessor);
- }
-
- createProcesses(procIters, rcd, increment);
- }
-
- #else
- driver(rcd, increment, nIters);
- #endif
-
- for(int i=0;i<displays.size();i++){
- displays[i]->close();
- }
-
- delete rcd;
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "Rarefact", "getCurve");
- exit(1);
- }
-}
-/***********************************************************************/
-int Rarefact::driver(RarefactionCurveData* rcd, int increment, int nIters = 1000){
- try {
-
- for(int iter=0;iter<nIters;iter++){
-
- for(int i=0;i<displays.size();i++){
- displays[i]->init(label);
- }
-
- RAbundVector* lookup = new RAbundVector(order->getNumBins());
- SAbundVector* rank = new SAbundVector(order->getMaxRank()+1);
- random_shuffle(order->begin(), order->end());
-
- for(int i=0;i<numSeqs;i++){
-
- if (m->control_pressed) { delete lookup; delete rank; delete rcd; return 0; }
-
- int binNumber = order->get(i);
- int abundance = lookup->get(binNumber);
-
- rank->set(abundance, rank->get(abundance)-1);
- abundance++;
-
- lookup->set(binNumber, abundance);
- rank->set(abundance, rank->get(abundance)+1);
-
- if((i == 0) || (i+1) % increment == 0){
- rcd->updateRankData(rank);
- }
- }
-
- if(numSeqs % increment != 0){
- rcd->updateRankData(rank);
- }
-
- for(int i=0;i<displays.size();i++){
- displays[i]->reset();
- }
-
- delete lookup;
- delete rank;
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "Rarefact", "driver");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
-int Rarefact::createProcesses(vector<int>& procIters, RarefactionCurveData* rcd, int increment) {
- try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- int process = 1;
-
- vector<int> processIDS;
-
- EstOutput results;
-
- //loop through and create all the processes you want
- while (process != processors) {
- int pid = fork();
-
- if (pid > 0) {
- processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
- process++;
- }else if (pid == 0){
- driver(rcd, increment, procIters[process]);
-
- //pass numSeqs to parent
- for(int i=0;i<displays.size();i++){
- string tempFile = toString(getpid()) + toString(i) + ".rarefact.temp";
- displays[i]->outputTempFiles(tempFile);
- }
- exit(0);
- }else {
- m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
- for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
- exit(0);
- }
- }
-
- driver(rcd, increment, procIters[0]);
-
- //force parent to wait until all the processes are done
- for (int i=0;i<(processors-1);i++) {
- int temp = processIDS[i];
- wait(&temp);
- }
-
- //get data created by processes
- for (int i=0;i<(processors-1);i++) {
- for(int j=0;j<displays.size();j++){
- string s = toString(processIDS[i]) + toString(j) + ".rarefact.temp";
- displays[j]->inputTempFiles(s);
- m->mothurRemove(s);
- }
- }
-
- return 0;
-#endif
- }
- catch(exception& e) {
- m->errorOut(e, "Rarefact", "createProcesses");
- exit(1);
- }
-}
-/***********************************************************************/
-
-int Rarefact::getSharedCurve(float percentFreq = 0.01, int nIters = 1000){
-try {
- SharedRarefactionCurveData* rcd = new SharedRarefactionCurveData();
-
- label = lookup[0]->getLabel();
-
- //register the displays
- for(int i=0;i<displays.size();i++){
- rcd->registerDisplay(displays[i]);
- }
-
- //if jumble is false all iters will be the same
- if (m->jumble == false) { nIters = 1; }
-
- //convert freq percentage to number
- int increment = 1;
- if (percentFreq < 1.0) { increment = numSeqs * percentFreq; }
- else { increment = percentFreq; }
-
- for(int iter=0;iter<nIters;iter++){
-
- for(int i=0;i<displays.size();i++){
- displays[i]->init(label);
- }
-
- if (m->jumble == true) {
- //randomize the groups
- random_shuffle(lookup.begin(), lookup.end());
- }
-
- //make merge the size of lookup[0]
- SharedRAbundVector* merge = new SharedRAbundVector(lookup[0]->size());
-
- //make copy of lookup zero
- for(int i = 0; i<lookup[0]->size(); i++) {
- merge->set(i, lookup[0]->getAbundance(i), "merge");
- }
-
- vector<SharedRAbundVector*> subset;
- //send each group one at a time
- for (int k = 0; k < lookup.size(); k++) {
- if (m->control_pressed) { delete merge; delete rcd; return 0; }
-
- subset.clear(); //clears out old pair of sharedrabunds
- //add in new pair of sharedrabunds
- subset.push_back(merge); subset.push_back(lookup[k]);
-
- rcd->updateSharedData(subset, k+1, numGroupComb);
- mergeVectors(merge, lookup[k]);
- }
-
- //resets output files
- for(int i=0;i<displays.size();i++){
- displays[i]->reset();
- }
-
- delete merge;
- }
-
- for(int i=0;i<displays.size();i++){
- displays[i]->close();
- }
-
- delete rcd;
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "Rarefact", "getSharedCurve");
- exit(1);
- }
-}
-
-/**************************************************************************************/
-void Rarefact::mergeVectors(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
- try{
- for (int k = 0; k < shared1->size(); k++) {
- //merge new species into shared1
- shared1->set(k, (shared1->getAbundance(k) + shared2->getAbundance(k)), "combo"); //set to 'combo' since this vector now contains multiple groups
- }
- }
- catch(exception& e) {
- m->errorOut(e, "Rarefact", "mergeVectors");
- exit(1);
- }
-}
-
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