#include "subsample.h"
//**********************************************************************************************************************
-Tree* SubSample::getSample(Tree* T, TreeMap* tmap, TreeMap* newTmap, int size, map<string, string> originalNameMap) {
+Tree* SubSample::getSample(Tree* T, CountTable* ct, CountTable* newCt, int size) {
try {
Tree* newTree = NULL;
- map<string, vector<string> > newGroups;
- vector<string> subsampledSeqs = getSample(tmap, size, newGroups);
+ //remove seqs not in sample from counttable
+ vector<string> Groups = ct->getNamesOfGroups();
+ newCt->copy(ct);
+ newCt->addGroup("doNotIncludeMe");
- //remove seqs not in sample from treemap
- for (map<string, vector<string> >::iterator it = newGroups.begin(); it != newGroups.end(); it++) {
- for (int i = 0; i < (it->second).size(); i++) {
- newTmap->addSeq((it->second)[i], it->first);
- }
- }
-
- newTree = new Tree(newTmap);
- newTree->getCopy(T, originalNameMap);
-
- return newTree;
- }
- catch(exception& e) {
- m->errorOut(e, "SubSample", "getSample-Tree");
- exit(1);
- }
-}
-/**********************************************************************************************************************
-Tree* SubSample::getSample(Tree* T, TreeMap* tmap, map<string, string> whole, int size) {
- try {
- Tree* newTree = NULL;
-
- vector<string> subsampledSeqs = getSample(tmap, size);
- map<string, string> sampledNameMap = deconvolute(whole, subsampledSeqs);
+ map<string, int> doNotIncludeTotals;
+ vector<string> namesSeqs = ct->getNamesOfSeqs();
+ for (int i = 0; i < namesSeqs.size(); i++) { doNotIncludeTotals[namesSeqs[i]] = 0; }
+
+ for (int i = 0; i < Groups.size(); i++) {
+ if (m->inUsersGroups(Groups[i], m->getGroups())) {
+ if (m->control_pressed) { break; }
- //remove seqs not in sample from treemap
- for (int i = 0; i < tmap->namesOfSeqs.size(); i++) {
- //is that name in the subsample?
- int count = 0;
- for (int j = 0; j < subsampledSeqs.size(); j++) {
- if (tmap->namesOfSeqs[i] == subsampledSeqs[j]) { break; } //found it
- count++;
+ int thisSize = ct->getGroupCount(Groups[i]);
+
+ if (thisSize >= size) {
+
+ vector<string> names = ct->getNamesOfSeqs(Groups[i]);
+ vector<int> random;
+ for (int j = 0; j < names.size(); j++) {
+ int num = ct->getGroupCount(names[j], Groups[i]);
+ for (int k = 0; k < num; k++) { random.push_back(j); }
+ }
+ random_shuffle(random.begin(), random.end());
+
+ vector<int> sampleRandoms; sampleRandoms.resize(names.size(), 0);
+ for (int j = 0; j < size; j++) { sampleRandoms[random[j]]++; }
+ for (int j = 0; j < sampleRandoms.size(); j++) {
+ newCt->setAbund(names[j], Groups[i], sampleRandoms[j]);
+ }
+ sampleRandoms.clear(); sampleRandoms.resize(names.size(), 0);
+ for (int j = size; j < thisSize; j++) { sampleRandoms[random[j]]++; }
+ for (int j = 0; j < sampleRandoms.size(); j++) { doNotIncludeTotals[names[j]] += sampleRandoms[j]; }
+ }else { m->mothurOut("[ERROR]: You have selected a size that is larger than "+Groups[i]+" number of sequences.\n"); m->control_pressed = true; }
}
- if (m->control_pressed) { return newTree; }
-
- //if you didnt find it, remove it
- if (count == subsampledSeqs.size()) {
- tmap->removeSeq(tmap->namesOfSeqs[i]);
- i--; //need this because removeSeq removes name from namesOfSeqs
- }
}
- //create new tree
- int numUniques = sampledNameMap.size();
- if (sampledNameMap.size() == 0) { numUniques = subsampledSeqs.size(); }
+ for (map<string, int>::iterator it = doNotIncludeTotals.begin(); it != doNotIncludeTotals.end(); it++) {
+ newCt->setAbund(it->first, "doNotIncludeMe", it->second);
+ }
- newTree = new Tree(numUniques, tmap); //numNodes, treemap
- newTree->getSubTree(T, subsampledSeqs, sampledNameMap);
+ newTree = new Tree(newCt);
+ newTree->getCopy(T, true);
return newTree;
}
m->errorOut(e, "SubSample", "getSample-Tree");
exit(1);
}
-}*/
+}
//**********************************************************************************************************************
//assumes whole maps dupName -> uniqueName
map<string, string> SubSample::deconvolute(map<string, string> whole, vector<string>& wanted) {
}
}
//**********************************************************************************************************************
-vector<string> SubSample::getSample(TreeMap* tMap, int size, map<string, vector<string> >& sample) {
- try {
- vector<string> temp2;
- sample["doNotIncludeMe"] = temp2;
-
- vector<string> namesInSample;
-
- vector<string> Groups = tMap->getNamesOfGroups();
- for (int i = 0; i < Groups.size(); i++) {
-
- if (m->inUsersGroups(Groups[i], m->getGroups())) {
- if (m->control_pressed) { break; }
-
- vector<string> thisGroup; thisGroup.push_back(Groups[i]);
- vector<string> thisGroupsSeqs = tMap->getNamesSeqs(thisGroup);
- int thisSize = thisGroupsSeqs.size();
- vector<string> temp;
- sample[Groups[i]] = temp;
-
- if (thisSize >= size) {
-
- random_shuffle(thisGroupsSeqs.begin(), thisGroupsSeqs.end());
-
- for (int j = 0; j < size; j++) { sample[Groups[i]].push_back(thisGroupsSeqs[j]); namesInSample.push_back(thisGroupsSeqs[j]); }
- for (int j = size; j < thisSize; j++) { sample["doNotIncludeMe"].push_back(thisGroupsSeqs[j]); }
-
- }else { m->mothurOut("[ERROR]: You have selected a size that is larger than "+Groups[i]+" number of sequences.\n"); m->control_pressed = true; }
- }
- }
-
- return namesInSample;
- }
- catch(exception& e) {
- m->errorOut(e, "SubSample", "getSample-TreeMap");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-vector<string> SubSample::getSample(TreeMap* tMap, int size) {
- try {
- vector<string> sample;
-
- vector<string> Groups = tMap->getNamesOfGroups();
- for (int i = 0; i < Groups.size(); i++) {
-
- if (m->inUsersGroups(Groups[i], m->getGroups())) {
- if (m->control_pressed) { break; }
-
- vector<string> thisGroup; thisGroup.push_back(Groups[i]);
- vector<string> thisGroupsSeqs = tMap->getNamesSeqs(thisGroup);
- int thisSize = thisGroupsSeqs.size();
-
- if (thisSize >= size) {
-
- random_shuffle(thisGroupsSeqs.begin(), thisGroupsSeqs.end());
-
- for (int j = 0; j < size; j++) { sample.push_back(thisGroupsSeqs[j]); }
- }else { m->mothurOut("[ERROR]: You have selected a size that is larger than "+Groups[i]+" number of sequences.\n"); m->control_pressed = true; }
- }
- }
-
- return sample;
- }
- catch(exception& e) {
- m->errorOut(e, "SubSample", "getSample-TreeMap");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> SubSample::getSample(TreeMap* tMap, vector<string> Groups) {
- try {
- vector<string> sample;
-
- //vector<string> Groups = tMap->getNamesOfGroups();
- for (int i = 0; i < Groups.size(); i++) {
-
- if (m->control_pressed) { break; }
-
- vector<string> thisGroup; thisGroup.push_back(Groups[i]);
- vector<string> thisGroupsSeqs = tMap->getNamesSeqs(thisGroup);
- int thisSize = thisGroupsSeqs.size();
-
- for (int j = 0; j < thisSize; j++) { sample.push_back(thisGroupsSeqs[j]); }
- }
-
- return sample;
- }
- catch(exception& e) {
- m->errorOut(e, "SubSample", "getSample-TreeMap");
- exit(1);
- }
-}
-//**********************************************************************************************************************
vector<string> SubSample::getSample(vector<SharedRAbundVector*>& thislookup, int size) {
try {
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