+++ /dev/null
-/*
- * sharedvector.cpp
- * Dotur
- *
- * Created by Sarah Westcott on 12/5/08.
- * Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "sharedrabundvector.h"
-#include "sabundvector.hpp"
-#include "ordervector.hpp"
-#include "sharedutilities.h"
-
-
-/***********************************************************************/
-SharedRAbundVector::SharedRAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0) {}
-/***********************************************************************/
-
-SharedRAbundVector::~SharedRAbundVector() {
- //for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
-
-}
-
-/***********************************************************************/
-
-SharedRAbundVector::SharedRAbundVector(int n) : DataVector(), maxRank(0), numBins(n), numSeqs(0) {
- individual newGuy;
- //initialize data
- for (int i=0; i< n; i++) {
- newGuy.bin = i;
- newGuy.abundance = 0;
- data.push_back(newGuy);
- }
-}
-
-/***********************************************************************
-
-SharedRAbundVector::SharedRAbundVector(string id, vector<individual> rav) : DataVector(id), data(rav) {
- try {
- numBins = 0;
- maxRank = 0;
- numSeqs = 0;
-
- for(int i=0;i<data.size();i++){
- if(data[i].abundance != 0) { numBins = i+1; }
- if(data[i].abundance > maxRank) { maxRank = data[i].abundance; }
- numSeqs += data[i].abundance;
- }
- }
- catch(exception& e) {
- m->errorOut(e, "SharedRAbundVector", "SharedRAbundVector");
- exit(1);
- }
-}
-
-
-***********************************************************************/
-//reads a shared file
-SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
- try {
- m->clearAllGroups();
- vector<string> allGroups;
-
- 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();
-
- //are we at the beginning of the file??
- if (m->saveNextLabel == "") {
- f >> label;
-
- //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;
-
- 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) {
- m->errorOut(e, "SharedRAbundVector", "SharedRAbundVector");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-void SharedRAbundVector::set(int binNumber, int newBinSize, string groupname){
- try {
- int oldBinSize = data[binNumber].abundance;
- data[binNumber].abundance = newBinSize;
- data[binNumber].group = groupname;
-
- if(newBinSize > maxRank) { maxRank = newBinSize; }
-
- numSeqs += (newBinSize - oldBinSize);
- }
- catch(exception& e) {
- m->errorOut(e, "SharedRAbundVector", "set");
- exit(1);
- }
-}
-/***********************************************************************/
-
-void SharedRAbundVector::setData(vector <individual> newData){
- data = newData;
-}
-
-/***********************************************************************/
-
-int SharedRAbundVector::getAbundance(int index){
- 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, string groupName){
- try {
- individual newGuy;
- newGuy.abundance = binSize;
- newGuy.group = groupName;
- newGuy.bin = data.size();
-
- data.push_back(newGuy);
- numBins++;
-
- if(binSize > maxRank){
- maxRank = binSize;
- }
-
- numSeqs += binSize;
- }
- catch(exception& e) {
- m->errorOut(e, "SharedRAbundVector", "push_back");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-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::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();
-}
-
-/***********************************************************************/
-
-
-vector<individual>::reverse_iterator SharedRAbundVector::rbegin(){
- return data.rbegin();
-}
-
-/***********************************************************************/
-
-vector<individual>::reverse_iterator SharedRAbundVector::rend(){
- return data.rend();
-}
-
-/***********************************************************************/
-void SharedRAbundVector::resize(int size){
-
- data.resize(size);
-}
-
-/***********************************************************************/
-
-int SharedRAbundVector::size(){
- return data.size();
-}
-
-
-/***********************************************************************/
-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<data.size();i++){ output << data[i].abundance << '\t'; }
- output << endl;
- }
- catch(exception& e) {
- m->errorOut(e, "SharedRAbundVector", "print");
- exit(1);
- }
-}
-/***********************************************************************/
-string SharedRAbundVector::getGroup(){
- return group;
-}
-
-/***********************************************************************/
-
-void SharedRAbundVector::setGroup(string groupName){
- group = groupName;
-}
-/***********************************************************************/
-int SharedRAbundVector::getGroupIndex() { return index; }
-/***********************************************************************/
-void SharedRAbundVector::setGroupIndex(int vIndex) { index = vIndex; }
-/***********************************************************************/
-int SharedRAbundVector::getNumBins(){
- return numBins;
-}
-
-/***********************************************************************/
-
-int SharedRAbundVector::getNumSeqs(){
- return numSeqs;
-}
-
-/***********************************************************************/
-
-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() {
- try {
- SAbundVector sav(maxRank+1);
-
- for(int i=0;i<data.size();i++){
- int abund = data[i].abundance;
- sav.set(abund, sav.get(abund) + 1);
- }
- sav.set(0, 0);
- sav.setLabel(label);
- return sav;
- }
- catch(exception& e) {
- m->errorOut(e, "SharedRAbundVector", "getSAbundVector");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-SharedOrderVector SharedRAbundVector::getSharedOrderVector() {
- try {
- SharedOrderVector ov;
-
- for(int i=0;i<data.size();i++){
- for(int j=0;j<data[i].abundance;j++){
- ov.push_back(data[i].bin, data[i].abundance, data[i].group);
- }
- }
- random_shuffle(ov.begin(), ov.end());
-
- ov.setLabel(label);
- ov.updateStats();
-
- return ov;
- }
- catch(exception& e) {
- m->errorOut(e, "SharedRAbundVector", "getSharedOrderVector");
- exit(1);
- }
-}
-/***********************************************************************/
-
-OrderVector SharedRAbundVector::getOrderVector(map<string,int>* nameMap = NULL) {
- try {
- OrderVector ov;
- 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) {
- m->errorOut(e, "SharedRAbundVector", "getOrderVector");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
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