+++ /dev/null
-/*
- * collect.cpp
- * Dotur
- *
- * Created by Sarah Westcott on 11/18/08.
- * Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "collect.h"
-
-/***********************************************************************/
-
-int Collect::getCurve(float percentFreq = 0.01){
- try {
- RAbundVector* lookup = new RAbundVector(order->getNumBins());
- SAbundVector* rank = new SAbundVector(order->getMaxRank()+1);
-
- CollectorsCurveData* ccd = new CollectorsCurveData();
-
- for(int i=0;i<displays.size();i++){
- ccd->registerDisplay(displays[i]); //adds a display[i] to cdd
- displays[i]->init(label); //sets displays label
- }
-
- //convert freq percentage to number
- int increment = 1;
- if (percentFreq < 1.0) { increment = numSeqs * percentFreq; }
- else { increment = percentFreq; }
-
- for(int i=0;i<numSeqs;i++){
-
- if (m->control_pressed) { delete lookup; delete rank; delete ccd; return 1; }
-
- 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); //increment rank(abundance)
-
- if((i == 0) || (i+1) % increment == 0){
- ccd->updateRankData(rank);
- }
- }
-
- if(numSeqs % increment != 0){
- ccd->updateRankData(rank);
- }
-
- for(int i=0;i<displays.size();i++){
- displays[i]->reset();
- }
-
- delete lookup;
- delete rank;
- delete ccd;
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "Collect", "getCurve");
- exit(1);
- }
-}
-
-/***********************************************************************/
-int Collect::getSharedCurve(float percentFreq = 0.01){
-try {
- vector<SharedRAbundVector*> lookup;
- vector<SharedRAbundVector*> subset;
-
- //create and initialize vector of sharedvectors, one for each group
- vector<string> mGroups = m->getGroups();
- for (int i = 0; i < mGroups.size(); i++) {
- SharedRAbundVector* temp = new SharedRAbundVector(sharedorder->getNumBins());
- temp->setLabel(sharedorder->getLabel());
- temp->setGroup(mGroups[i]);
- lookup.push_back(temp);
- }
-
- SharedCollectorsCurveData* ccd = new SharedCollectorsCurveData();
-
- //initialize labels for output
- //makes 'uniqueAB uniqueAC uniqueBC' if your groups are A, B, C
- getGroupComb();
-
- for(int i=0;i<displays.size();i++){
- ccd->registerDisplay(displays[i]); //adds a display[i] to cdd
- bool hasLciHci = displays[i]->hasLciHci();
- groupLabel = "";
- for (int s = 0; s < groupComb.size(); s++) {
- if (hasLciHci) { groupLabel = groupLabel + label + groupComb[s] + "\t" + label + groupComb[s] + "lci\t" + label + groupComb[s] + "hci\t"; }
- else{ groupLabel = groupLabel + label + groupComb[s] + "\t"; }
- }
-
- string groupLabelAll = groupLabel + label + "all\t";
- if ((displays[i]->isCalcMultiple() == true) && (displays[i]->getAll() == true)) { displays[i]->init(groupLabelAll); }
- else { displays[i]->init(groupLabel); }
- }
-
- //convert freq percentage to number
- int increment = 1;
- if (percentFreq < 1.0) { increment = numSeqs * percentFreq; }
- else { increment = percentFreq; }
-
- //sample all the members
- for(int i=0;i<numSeqs;i++){
-
- if (m->control_pressed) { for (int j = 0; j < lookup.size(); j++) { delete lookup[j]; } delete ccd; return 1; }
-
- //get first sample
- individual chosen = sharedorder->get(i);
- int abundance;
-
- //set info for sharedvector in chosens group
- for (int j = 0; j < lookup.size(); j++) {
- if (chosen.group == lookup[j]->getGroup()) {
- abundance = lookup[j]->getAbundance(chosen.bin);
- lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
- break;
- }
- }
-
- //calculate at 0 and the given increment
- if((i == 0) || (i+1) % increment == 0){
-
- //how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
-
- int n = 1;
- bool pair = true;
- for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
- for (int l = n; l < lookup.size(); l++) {
- subset.clear(); //clear out old pair of sharedrabunds
- //add new pair of sharedrabund vectors
- subset.push_back(lookup[k]); subset.push_back(lookup[l]);
-
- //load subset with rest of lookup for those calcs that need everyone to calc for a pair
- for (int w = 0; w < lookup.size(); w++) {
- if ((w != k) && (w != l)) { subset.push_back(lookup[w]); }
- }
-
- ccd->updateSharedData(subset, i+1, m->getNumGroups(), pair);
- }
- n++;
- }
-
- //if this is a calculator that can do multiples then do them
- pair = false;
- ccd->updateSharedData(lookup, i+1, m->getNumGroups(), pair);
-
- }
- totalNumSeq = i+1;
- }
-
- //calculate last label if you haven't already
- if(numSeqs % increment != 0){
- //how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
- int n = 1;
- bool pair = true;
- for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
- for (int l = n; l < lookup.size(); l++) {
- subset.clear(); //clear out old pair of sharedrabunds
- //add new pair of sharedrabund vectors
- subset.push_back(lookup[k]); subset.push_back(lookup[l]);
-
- //load subset with rest of lookup for those calcs that need everyone to calc for a pair
- for (int w = 0; w < lookup.size(); w++) {
- if ((w != k) && (w != l)) { subset.push_back(lookup[w]); }
- }
-
- ccd->updateSharedData(subset, totalNumSeq, m->getNumGroups(), pair);
- }
- n++;
- }
- //if this is a calculator that can do multiples then do them
- pair = false;
- ccd->updateSharedData(lookup, totalNumSeq, m->getNumGroups(), pair);
- }
-
- //resets output files
- for(int i=0;i<displays.size();i++){
- displays[i]->reset();
- }
-
- //memory cleanup
- delete ccd;
- for (int i = 0; i < lookup.size(); i++) {
- delete lookup[i];
- }
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "Collect", "getSharedCurve");
- exit(1);
- }
-}
-
-/**************************************************************************************/
-
-void Collect::getGroupComb() {
- string group;
-
- numGroupComb = 0;
-
- int n = 1;
- vector<string> mGroups = m->getGroups();
- for (int i = 0; i < (m->getNumGroups() - 1); i++) {
- for (int l = n; l < m->getNumGroups(); l++) {
- group = mGroups[i] + mGroups[l];
- groupComb.push_back(group);
- numGroupComb++;
- }
- n++;
- }
-
-}
-
-/**************************************************************************************/
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