*
*/
-
-using namespace std;
-
#include "sharedrabundvector.h"
#include "sabundvector.hpp"
#include "ordervector.hpp"
+#include "sharedutilities.h"
/***********************************************************************/
-SharedRAbundVector::SharedRAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0) {};
+SharedRAbundVector::SharedRAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0) {globaldata = GlobalData::getInstance();}
+/***********************************************************************/
+
+SharedRAbundVector::~SharedRAbundVector() {
+ //for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+
+}
/***********************************************************************/
SharedRAbundVector::SharedRAbundVector(int n) : DataVector(), maxRank(0), numBins(n), numSeqs(0) {
+ globaldata = GlobalData::getInstance();
individual newGuy;
//initialize data
for (int i=0; i< n; i++) {
newGuy.abundance = 0;
data.push_back(newGuy);
}
-};
+}
/***********************************************************************
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function SharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedRAbundVector class function SharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedRAbundVector", "SharedRAbundVector");
exit(1);
}
}
-/***********************************************************************
-
-
+/***********************************************************************/
+//reads a shared file
SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
try {
- int i, num;
- string holdLabel, group
- individual newGuy;
+ globaldata = GlobalData::getInstance();
- f >> label >> group >> num;
+ if (globaldata->gGroupmap == NULL) { groupmap = new GroupMap(); }
- //initialize data
- for (i=0; i<hold; i++) {
- newGuy = new individual;
- newGuy.abundance = 0;
- newGuy.bin = i;
- data.push_back(newGuy);
+ int num, inputData, count;
+ count = 0;
+ string holdLabel, nextLabel, groupN;
+ individual newguy;
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; } lookup.clear();
+
+ if (globaldata->saveNextLabel == "") { f >> label; }
+ else { label = globaldata->saveNextLabel; }
+
+ //read in first row since you know there is at least 1 group.
+ f >> groupN >> num;
+
+ holdLabel = label;
+
+ //add new vector to lookup
+ SharedRAbundVector* temp = new SharedRAbundVector();
+ lookup.push_back(temp);
+ lookup[0]->setLabel(label);
+ lookup[0]->setGroup(groupN);
+
+ if (globaldata->gGroupmap == NULL) {
+ //save group in groupmap
+ groupmap->namesOfGroups.push_back(groupN);
+ groupmap->groupIndex[groupN] = 0;
}
- int inputData;
-
- for(int i=0;i<hold;i++){
+
+ //fill vector. data = first sharedrabund in file
+ for(int i=0;i<num;i++){
f >> inputData;
- set(i, inputData);
+
+ lookup[0]->push_back(inputData, groupN); //abundance, bin, group
+ push_back(inputData, groupN);
+ //numSeqs += inputData;
+ //numBins++;
+ if (inputData > maxRank) { maxRank = inputData; }
}
+
+ m->gobble(f);
+
+ if (!(f.eof())) { f >> nextLabel; }
+
+ //read the rest of the groups info in
+ while ((nextLabel == holdLabel) && (f.eof() != true)) {
+ f >> groupN >> num;
+ count++;
+
+ if (globaldata->gGroupmap == NULL) {
+ //save group in groupmap
+
+ groupmap->namesOfGroups.push_back(groupN);
+ groupmap->groupIndex[groupN] = count;
+ }
+
+ //add new vector to lookup
+ temp = new SharedRAbundVector();
+ lookup.push_back(temp);
+ lookup[count]->setLabel(label);
+ lookup[count]->setGroup(groupN);
+
+ //fill vector.
+ for(int i=0;i<num;i++){
+ f >> inputData;
+ lookup[count]->push_back(inputData, groupN); //abundance, bin, group
+ }
+
+ m->gobble(f);
+
+ if (f.eof() != true) { f >> nextLabel; }
+ }
+
+ globaldata->saveNextLabel = nextLabel;
+
+ if (globaldata->gGroupmap == NULL) { globaldata->gGroupmap = groupmap; }
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function SharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedRAbundVector class function SharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedRAbundVector", "SharedRAbundVector");
exit(1);
}
}
/***********************************************************************/
-SharedRAbundVector::~SharedRAbundVector() {
-
-}
-
-/***********************************************************************/
-
void SharedRAbundVector::set(int binNumber, int newBinSize, string groupname){
try {
int oldBinSize = data[binNumber].abundance;
numSeqs += (newBinSize - oldBinSize);
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedRAbundVector class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedRAbundVector", "set");
exit(1);
}
}
}
/***********************************************************************/
-void SharedRAbundVector::push_back(int binSize, int otu, string groupName){
+void SharedRAbundVector::clear(){
+ numBins = 0;
+ maxRank = 0;
+ numSeqs = 0;
+ data.clear();
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
+ lookup.clear();
+}
+/***********************************************************************/
+
+void SharedRAbundVector::push_back(int binSize, string groupName){
try {
individual newGuy;
newGuy.abundance = binSize;
newGuy.group = groupName;
- newGuy.bin = otu;
+ newGuy.bin = data.size();
data.push_back(newGuy);
numBins++;
numSeqs += binSize;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedRAbundVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedRAbundVector", "push_back");
exit(1);
}
}
numSeqs += binSize;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function insert. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedRAbundVector class function insert. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedRAbundVector", "insert");
exit(1);
}
}
numSeqs += binSize;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function push_front. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedRAbundVector class function push_front. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedRAbundVector", "push_front");
exit(1);
}
}
/***********************************************************************/
void SharedRAbundVector::pop_back(){
-
+ numSeqs -= data[data.size()-1].abundance;
+ numBins--;
return data.pop_back();
}
try {
output << numBins << '\t';
- for(int i=0;i<numBins;i++){ output << data[i].abundance << '\t'; }
+ for(int i=0;i<data.size();i++){ output << data[i].abundance << '\t'; }
output << endl;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedRAbundVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedRAbundVector", "print");
exit(1);
}
}
return *this;
}
/***********************************************************************/
+vector<SharedRAbundVector*> SharedRAbundVector::getSharedRAbundVectors(){
+ try {
+ SharedUtil* util;
+ util = new SharedUtil();
+
+ util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
+
+ bool remove = false;
+ for (int i = 0; i < lookup.size(); i++) {
+ //if this sharedrabund is not from a group the user wants then delete it.
+ if (util->isValidGroup(lookup[i]->getGroup(), globaldata->Groups) == false) {
+ remove = true;
+ delete lookup[i]; lookup[i] = NULL;
+ lookup.erase(lookup.begin()+i);
+ i--;
+ }
+ }
+
+ delete util;
+
+ if (remove) { eliminateZeroOTUS(lookup); }
+
+ return lookup;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedRAbundVector", "getSharedRAbundVectors");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SharedRAbundVector::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
+ try {
+
+ vector<SharedRAbundVector*> newLookup;
+ for (int i = 0; i < thislookup.size(); i++) {
+ SharedRAbundVector* temp = new SharedRAbundVector();
+ temp->setLabel(thislookup[i]->getLabel());
+ temp->setGroup(thislookup[i]->getGroup());
+ newLookup.push_back(temp);
+ }
+
+ //for each bin
+ for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
+ if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
+
+ //look at each sharedRabund and make sure they are not all zero
+ bool allZero = true;
+ for (int j = 0; j < thislookup.size(); j++) {
+ if (thislookup[j]->getAbundance(i) != 0) { allZero = false; break; }
+ }
+
+ //if they are not all zero add this bin
+ if (!allZero) {
+ for (int j = 0; j < thislookup.size(); j++) {
+ newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
+ }
+ }
+ }
+
+ for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; }
+
+ thislookup = newLookup;
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedRAbundVector", "eliminateZeroOTUS");
+ exit(1);
+ }
+ }
+
+/***********************************************************************/
+vector<SharedRAbundFloatVector*> SharedRAbundVector::getSharedRAbundFloatVectors(vector<SharedRAbundVector*> thislookup){
+ try {
+ vector<SharedRAbundFloatVector*> newLookupFloat;
+ for (int i = 0; i < lookup.size(); i++) {
+ SharedRAbundFloatVector* temp = new SharedRAbundFloatVector();
+ temp->setLabel(thislookup[i]->getLabel());
+ temp->setGroup(thislookup[i]->getGroup());
+ newLookupFloat.push_back(temp);
+ }
+
+ for (int i = 0; i < thislookup.size(); i++) {
+
+ for (int j = 0; j < thislookup[i]->getNumBins(); j++) {
+
+ if (m->control_pressed) { return newLookupFloat; }
+
+ int abund = thislookup[i]->getAbundance(j);
+
+ float relabund = abund / (float) thislookup[i]->getNumSeqs();
+
+ newLookupFloat[i]->push_back(relabund, thislookup[i]->getGroup());
+ }
+ }
+
+ return newLookupFloat;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedRAbundVector", "getSharedRAbundVectors");
+ exit(1);
+ }
+}
+/***********************************************************************/
RAbundVector SharedRAbundVector::getRAbundVector() {
try {
- RAbundVector rav(data.size());
+ RAbundVector rav;
for (int i = 0; i < data.size(); i++) {
- rav.set(i, data[i].abundance);
+ if(data[i].abundance != 0) {
+ rav.push_back(data[i].abundance);
+ }
}
-
+
+ rav.setLabel(label);
return rav;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedRAbundVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedRAbundVector", "getRAbundVector");
exit(1);
}
}
return rav;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedRAbundVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedRAbundVector", "getRAbundVector2");
exit(1);
}
}
return sav;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getSharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedRAbundVector class function getSharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedRAbundVector", "getSharedSAbundVector");
exit(1);
}
}
return sav;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedRAbundVector class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedRAbundVector", "getSAbundVector");
exit(1);
}
}
random_shuffle(ov.begin(), ov.end());
ov.setLabel(label);
+ ov.updateStats();
+
return ov;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedRAbundVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedRAbundVector", "getSharedOrderVector");
exit(1);
}
}
OrderVector SharedRAbundVector::getOrderVector(map<string,int>* nameMap = NULL) {
try {
OrderVector ov;
-
- for(int i=0;i<data.size();i++){
+ for(int i=0;i<numBins;i++){
for(int j=0;j<data[i].abundance;j++){
ov.push_back(i);
}
}
random_shuffle(ov.begin(), ov.end());
-
+
ov.setLabel(label);
+
return ov;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedRAbundVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedRAbundVector", "getOrderVector");
exit(1);
}
}
projects / mothur.git / blobdiff