*
*/
-
-using namespace std;
-
#include "sharedrabundvector.h"
-#include "datavector.hpp"
-#include "utilities.hpp"
-#include <exception>
-#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) {};
+SharedRAbundVector::~SharedRAbundVector() {
+ //for (int i = 0; i < lookup.size(); i++) { delete lookup[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, hold;
- individual newGuy;
+ m->clearAllGroups();
+ vector<string> allGroups;
- f >> label >> hold;
+ int num, inputData, count;
+ count = 0;
+ string holdLabel, nextLabel, groupN;
+ individual newguy;
- //initialize data
- for (i=0; i<hold; i++) {
- newGuy = new individual;
- newGuy.abundance = 0;
- newGuy.bin = i;
- data.push_back(newGuy);
- }
- int inputData;
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; } lookup.clear();
+
+ //are we at the beginning of the file??
+ if (m->saveNextLabel == "") {
+ f >> label;
- for(int i=0;i<hold;i++){
+ //is this a shared file that has headers
+ if (label == "label") {
+ //gets "group"
+ f >> label; m->gobble(f);
+
+ //gets "numOtus"
+ f >> label; m->gobble(f);
+
+ //eat rest of line
+ label = m->getline(f); m->gobble(f);
+
+ //parse labels to save
+ istringstream iStringStream(label);
+ m->binLabelsInFile.clear();
+ while(!iStringStream.eof()){
+ if (m->control_pressed) { break; }
+ string temp;
+ iStringStream >> temp; m->gobble(iStringStream);
+
+ m->binLabelsInFile.push_back(temp);
+ }
+
+ f >> label >> groupN >> num;
+ }else {
+ //read in first row since you know there is at least 1 group.
+ f >> groupN >> num;
+
+ //make binlabels because we don't have any
+ string snumBins = toString(num);
+ m->binLabelsInFile.clear();
+ for (int i = 0; i < num; i++) {
+ //if there is a bin label use it otherwise make one
+ string binLabel = "Otu";
+ string sbinNumber = toString(i+1);
+ if (sbinNumber.length() < snumBins.length()) {
+ int diff = snumBins.length() - sbinNumber.length();
+ for (int h = 0; h < diff; h++) { binLabel += "0"; }
+ }
+ binLabel += sbinNumber;
+ m->binLabelsInFile.push_back(binLabel);
+ }
+ }
+ }else {
+ label = m->saveNextLabel;
+
+ //read in first row since you know there is at least 1 group.
+ f >> groupN >> num;
+ }
+
+ //reset labels, currentLabels may have gotten changed as otus were eliminated because of group choices or sampling
+ m->currentBinLabels = m->binLabelsInFile;
+
+ holdLabel = label;
+
+ //add new vector to lookup
+ SharedRAbundVector* temp = new SharedRAbundVector();
+ lookup.push_back(temp);
+ lookup[0]->setLabel(label);
+ lookup[0]->setGroup(groupN);
+
+ allGroups.push_back(groupN);
+
+ //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);
+
+ 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++;
+
+ allGroups.push_back(groupN);
+
+ //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; }
}
+ m->saveNextLabel = nextLabel;
+ m->setAllGroups(allGroups);
}
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";
+ m->errorOut(e, "SharedRAbundVector", "SharedRAbundVector");
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";
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-SharedRAbundVector::~SharedRAbundVector() {
-
}
/***********************************************************************/
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::setData(vector <individual> newData){
+ data = newData;
+}
/***********************************************************************/
return data[index].abundance;
}
+/***********************************************************************/
+
+int SharedRAbundVector::numNZ(){
+ int sum = 0;
+ for(int i = 1; i < numBins; i++)
+ if(data[i].abundance > 0)
+ sum++;
+ return sum;
+}
+/***********************************************************************/
+void SharedRAbundVector::sortD(){
+ struct individual indObj;
+ sort(data.begin()+1, data.end(), indObj);
+}
/***********************************************************************/
individual SharedRAbundVector::get(int index){
return data[index];
}
+/***********************************************************************/
+
+vector <individual> SharedRAbundVector::getData(){
+ return data;
+}
+/***********************************************************************/
+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, int otu, string groupName){
+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";
+ m->errorOut(e, "SharedRAbundVector", "push_back");
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";
+}
+
+/***********************************************************************/
+
+void SharedRAbundVector::insert(int binSize, int otu, string groupName){
+ try {
+ individual newGuy;
+ newGuy.abundance = binSize;
+ newGuy.group = groupName;
+ newGuy.bin = otu;
+
+ data.insert(data.begin()+otu, newGuy);
+ numBins++;
+
+ if(binSize > maxRank){
+ maxRank = binSize;
+ }
+
+ numSeqs += binSize;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedRAbundVector", "insert");
exit(1);
}
}
/***********************************************************************/
-void SharedRAbundVector::pop_back(){
+void SharedRAbundVector::push_front(int binSize, int otu, string groupName){
+ try {
+ individual newGuy;
+ newGuy.abundance = binSize;
+ newGuy.group = groupName;
+ newGuy.bin = otu;
+
+ data.insert(data.begin(), newGuy);
+ numBins++;
+
+ if(binSize > maxRank){
+ maxRank = binSize;
+ }
+
+ numSeqs += binSize;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedRAbundVector", "push_front");
+ exit(1);
+ }
+}
+/***********************************************************************/
+void SharedRAbundVector::pop_back(){
+ numSeqs -= data[data.size()-1].abundance;
+ numBins--;
return data.pop_back();
}
return data.size();
}
+
/***********************************************************************/
-void SharedRAbundVector::print(ostream& output){
+void SharedRAbundVector::printHeaders(ostream& output){
+ try {
+ string snumBins = toString(numBins);
+ output << "label\tGroup\tnumOtus\t";
+ if (m->sharedHeaderMode == "tax") {
+ for (int i = 0; i < numBins; i++) {
+
+ //if there is a bin label use it otherwise make one
+ string binLabel = "PhyloType";
+ string sbinNumber = toString(i+1);
+ if (sbinNumber.length() < snumBins.length()) {
+ int diff = snumBins.length() - sbinNumber.length();
+ for (int h = 0; h < diff; h++) { binLabel += "0"; }
+ }
+ binLabel += sbinNumber;
+ if (i < m->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; }
+
+ output << binLabel << '\t';
+ }
+ output << endl;
+ }else {
+ for (int i = 0; i < numBins; i++) {
+ //if there is a bin label use it otherwise make one
+ string binLabel = "Otu";
+ string sbinNumber = toString(i+1);
+ if (sbinNumber.length() < snumBins.length()) {
+ int diff = snumBins.length() - sbinNumber.length();
+ for (int h = 0; h < diff; h++) { binLabel += "0"; }
+ }
+ binLabel += sbinNumber;
+ if (i < m->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; }
+
+ output << binLabel << '\t';
+ }
+
+ output << endl;
+ }
+ m->printedHeaders = true;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedRAbundVector", "printHeaders");
+ exit(1);
+ }
+}
+/***********************************************************************/
+void SharedRAbundVector::print(ostream& output) {
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);
}
}
void SharedRAbundVector::setGroup(string groupName){
group = groupName;
}
-
-
+/***********************************************************************/
+int SharedRAbundVector::getGroupIndex() { return index; }
+/***********************************************************************/
+void SharedRAbundVector::setGroupIndex(int vIndex) { index = vIndex; }
/***********************************************************************/
int SharedRAbundVector::getNumBins(){
- return numBins;
+ return numBins;
}
/***********************************************************************/
int SharedRAbundVector::getMaxRank(){
return maxRank;
}
-
/***********************************************************************/
SharedRAbundVector SharedRAbundVector::getSharedRAbundVector(){
return *this;
}
+/***********************************************************************/
+vector<SharedRAbundVector*> SharedRAbundVector::getSharedRAbundVectors(){
+ try {
+ SharedUtil* util;
+ util = new SharedUtil();
+
+ vector<string> Groups = m->getGroups();
+ vector<string> allGroups = m->getAllGroups();
+ util->setGroups(Groups, allGroups);
+ m->setGroups(Groups);
+
+ 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(), m->getGroups()) == 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
+ vector<string> newBinLabels;
+ string snumBins = toString(thislookup[0]->getNumBins());
+ 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());
+ }
+
+ //if there is a bin label use it otherwise make one
+ string binLabel = "Otu";
+ string sbinNumber = toString(i+1);
+ if (sbinNumber.length() < snumBins.length()) {
+ int diff = snumBins.length() - sbinNumber.length();
+ for (int h = 0; h < diff; h++) { binLabel += "0"; }
+ }
+ binLabel += sbinNumber;
+ if (i < m->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; }
+
+ newBinLabels.push_back(binLabel);
+ }
+ }
+
+ for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; }
+
+ thislookup = newLookup;
+ m->currentBinLabels = newBinLabels;
+
+ 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;
+
+ for (int i = 0; i < data.size(); i++) {
+ if(data[i].abundance != 0) {
+ rav.push_back(data[i].abundance);
+ }
+ }
+
+ rav.setLabel(label);
+ return rav;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedRAbundVector", "getRAbundVector");
+ exit(1);
+ }
+}
+/***********************************************************************/
+RAbundVector SharedRAbundVector::getRAbundVector2() {
+ try {
+ RAbundVector rav;
+ for(int i = 0; i < numBins; i++)
+ if(data[i].abundance != 0)
+ rav.push_back(data[i].abundance-1);
+ return rav;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedRAbundVector", "getRAbundVector2");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+SharedSAbundVector SharedRAbundVector::getSharedSAbundVector(){
+ try {
+ SharedSAbundVector sav(maxRank+1);
+
+ for(int i=0;i<data.size();i++){
+ int abund = data[i].abundance;
+ sav.set(abund, sav.getAbundance(abund) + 1, group);
+ }
+
+ sav.set(0, 0, group);
+ sav.setLabel(label);
+ sav.setGroup(group);
+
+ return sav;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedRAbundVector", "getSharedSAbundVector");
+ exit(1);
+ }
+}
/***********************************************************************/
SAbundVector SharedRAbundVector::getSAbundVector() {
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