#include "collect.h"
-
/***********************************************************************/
-void Collect::getCurve(int increment = 1){
- 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
- }
- for(int i=0;i<numSeqs;i++){
-
- 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();
- }
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Collect class Function getCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the Collect class function getCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
+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);
+ }
}
/***********************************************************************/
-void Collect::getSharedCurve(int increment = 1){
+int Collect::getSharedCurve(float percentFreq = 0.01){
try {
- globaldata = GlobalData::getInstance();
- vector<SharedRAbundVector*> lookup;
-
- //create and initialize vector of sharedvectors, one for each group
- for (int i = 0; i < globaldata->gGroupmap->getNumGroups(); i++) {
- SharedRAbundVector* temp = new SharedRAbundVector(sharedorder->getNumBins());
- temp->setLabel(sharedorder->getLabel());
- temp->setGroup(globaldata->gGroupmap->namesOfGroups[i]);
- temp->setGroupIndex(globaldata->gGroupmap->groupIndex[globaldata->gGroupmap->namesOfGroups[i]]);
- lookup.push_back(temp);
- }
-
- SharedCollectorsCurveData* ccd = new SharedCollectorsCurveData();
+ 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);
+ }
- //initialize labels for output
- //makes 'uniqueAB uniqueAC uniqueBC' if your groups are A, B, C
- getGroupComb();
- groupLabel = "";
- for (int s = 0; s < groupComb.size(); s++) {
- groupLabel = groupLabel + label + groupComb[s] + "\t";
- }
-
- for(int i=0;i<displays.size();i++){
- ccd->registerDisplay(displays[i]); //adds a display[i] to cdd
- displays[i]->init(groupLabel);
- }
-
- //sample all the members
- for(int i=0;i<numSeqs;i++){
- //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){
- //randomize group order
- if (globaldata->getJumble() == "1") { random_shuffle(lookup.begin(), lookup.end()); }
- //how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
- int n = 1;
- 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++) {
- ccd->updateSharedData(lookup[k], lookup[l], i+1, globaldata->gGroupmap->namesOfGroups.size());
- }
- n++;
- }
- }
- totalNumSeq = i+1;
- }
-
- //calculate last line 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;
- 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++) {
- ccd->updateSharedData(lookup[k], lookup[l], totalNumSeq, globaldata->gGroupmap->namesOfGroups.size());
+ 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];
}
- n++;
- }
- }
-
- //resets output files
- for(int i=0;i<displays.size();i++){
- displays[i]->reset();
- }
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Collect class Function getSharedCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the Collect class function getSharedCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Collect", "getSharedCurve");
+ exit(1);
+ }
}
/**************************************************************************************/
void Collect::getGroupComb() {
- string group;
-
- numGroupComb = 0;
-
- int n = 1;
- for (int i = 0; i < (globaldata->gGroupmap->getNumGroups() - 1); i++) {
- for (int l = n; l < globaldata->gGroupmap->getNumGroups(); l++) {
- group = globaldata->gGroupmap->namesOfGroups[i] + globaldata->gGroupmap->namesOfGroups[l];
- groupComb.push_back(group);
- numGroupComb++;
- }
- n++;
+ 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++;
+ }
}
projects / mothur.git / blobdiff