--- /dev/null
+/*
+ * sharedrabundfloatvector.cpp
+ * Mothur
+ *
+ * Created by westcott on 8/18/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "sharedrabundfloatvector.h"
+#include "sharedutilities.h"
+
+/***********************************************************************/
+
+SharedRAbundFloatVector::SharedRAbundFloatVector() : DataVector(), maxRank(0.0), numBins(0), numSeqs(0.0) {}
+/***********************************************************************/
+
+SharedRAbundFloatVector::~SharedRAbundFloatVector() {}
+
+/***********************************************************************/
+SharedRAbundFloatVector::SharedRAbundFloatVector(int n) : DataVector(), maxRank(0.0), numBins(n), numSeqs(0.0) {
+
+ individualFloat newGuy;
+ //initialize data
+ for (int i=0; i< n; i++) {
+ newGuy.bin = i;
+ newGuy.abundance = 0.0;
+ data.push_back(newGuy);
+ }
+}
+/***********************************************************************/
+//reads a shared file
+SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), maxRank(0.0), numBins(0), numSeqs(0.0) {
+ try {
+
+ m->clearAllGroups();
+ vector<string> allGroups;
+
+ int num, count;
+ float inputData;
+ count = 0;
+ string holdLabel, nextLabel, groupN;
+ individualFloat 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
+ SharedRAbundFloatVector* temp = new SharedRAbundFloatVector();
+ 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() != true) { f >> nextLabel; }
+
+ //read the rest of the groups info in
+ while ((nextLabel == holdLabel) && (f.eof() != true)) {
+ f >> groupN >> num;
+
+ if (num != 1000) { break; }
+ count++;
+
+ allGroups.push_back(groupN);
+
+ //add new vector to lookup
+ temp = new SharedRAbundFloatVector();
+ 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, "SharedRAbundFloatVector", "SharedRAbundFloatVector");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void SharedRAbundFloatVector::set(int binNumber, float newBinSize, string groupname){
+ try {
+ float oldBinSize = data[binNumber].abundance;
+ data[binNumber].abundance = newBinSize;
+ data[binNumber].group = groupname;
+
+ if(newBinSize > maxRank) { newBinSize = newBinSize; }
+
+ numSeqs += (newBinSize - oldBinSize);
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedRAbundFloatVector", "set");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+void SharedRAbundFloatVector::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();
+}
+/***********************************************************************/
+float SharedRAbundFloatVector::getAbundance(int index){
+ return data[index].abundance;
+}
+/***********************************************************************/
+individualFloat SharedRAbundFloatVector::get(int index){
+ return data[index];
+}
+/***********************************************************************/
+void SharedRAbundFloatVector::push_back(float binSize, string groupName){
+ try {
+ individualFloat 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, "SharedRAbundFloatVector", "push_back");
+ exit(1);
+ }
+}
+/***********************************************************************/
+void SharedRAbundFloatVector::insert(float binSize, int otu, string groupName){
+ try {
+ individualFloat 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, "SharedRAbundFloatVector", "insert");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+void SharedRAbundFloatVector::push_front(float binSize, int otu, string groupName){
+ try {
+ individualFloat 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, "SharedRAbundFloatVector", "push_front");
+ exit(1);
+ }
+}
+/**********************************************************************/
+void SharedRAbundFloatVector::pop_back(){
+ numSeqs -= data[data.size()-1].abundance;
+ numBins--;
+ data.pop_back();
+}
+/***********************************************************************/
+void SharedRAbundFloatVector::resize(int size){
+ data.resize(size);
+}
+/**********************************************************************/
+int SharedRAbundFloatVector::size(){
+ return data.size();
+}
+/***********************************************************************/
+void SharedRAbundFloatVector::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 SharedRAbundFloatVector::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, "SharedRAbundFloatVector", "print");
+ exit(1);
+ }
+}
+/***********************************************************************/
+string SharedRAbundFloatVector::getGroup(){
+ return group;
+}
+/***********************************************************************/
+void SharedRAbundFloatVector::setGroup(string groupName){
+ group = groupName;
+}
+/***********************************************************************/
+int SharedRAbundFloatVector::getGroupIndex() { return index; }
+/***********************************************************************/
+void SharedRAbundFloatVector::setGroupIndex(int vIndex) { index = vIndex; }
+/***********************************************************************/
+int SharedRAbundFloatVector::getNumBins(){ return numBins; }
+/***********************************************************************/
+float SharedRAbundFloatVector::getNumSeqs(){ return numSeqs; }
+/***********************************************************************/
+float SharedRAbundFloatVector::getMaxRank(){ return maxRank; }
+/***********************************************************************/
+SharedRAbundFloatVector SharedRAbundFloatVector::getSharedRAbundFloatVector(){
+ return *this;
+}
+/***********************************************************************
+SharedRAbundVector SharedRAbundFloatVector::getSharedRAbundVector(){
+ try {
+ SharedRAbundVector rav(numBins);
+ rav.setLabel(label);
+ rav.setGroup(group);
+
+ for (int i = 0; i < data.size(); i++) {
+
+ rav.push_back(data[i].abundance);
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedRAbundFloatVector", "getSharedRAbundVector");
+ exit(1);
+ }
+}
+***********************************************************************/
+vector<SharedRAbundFloatVector*> SharedRAbundFloatVector::getSharedRAbundFloatVectors(){
+ 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) {
+ delete lookup[i]; lookup[i] = NULL;
+ lookup.erase(lookup.begin()+i);
+ i--;
+ remove = true;
+ }
+ }
+
+ delete util;
+
+ if (remove) { eliminateZeroOTUS(lookup); }
+
+ return lookup;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedRAbundFloatVector", "getSharedRAbundFloatVectors");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+RAbundVector SharedRAbundFloatVector::getRAbundVector() {
+ try {
+ RAbundVector rav(numBins);
+
+ //this is not functional, not sure how to handle it yet, but I need the stub because it is a pure function
+
+ rav.setLabel(label);
+ return rav;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedRAbundFloatVector", "getRAbundVector");
+ 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 SharedRAbundFloatVector::getSAbundVector() {
+ try {
+ SAbundVector sav(ceil(maxRank)+1);
+
+ //this is not functional, not sure how to handle it yet, but I need the stub because it is a pure function
+
+ sav.set(0, 0);
+ sav.setLabel(label);
+ return sav;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedRAbundFloatVector", "getSAbundVector");
+ exit(1);
+ }
+}
+
+/***********************************************************************
+
+SharedOrderVector SharedRAbundFloatVector::getSharedOrderVector() {
+ try {
+ SharedOrderVector ov;
+
+ for(int i=0;i<data.size();i++){
+ int round = ceil(data[i].abundance);
+ for(int j=0;j<round;j++){
+ ov.push_back(data[i].bin, round, data[i].group);
+ }
+ }
+ random_shuffle(ov.begin(), ov.end());
+
+ ov.setLabel(label);
+ ov.updateStats();
+
+ return ov;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedRAbundFloatVector", "getSharedOrderVector");
+ exit(1);
+ }
+}
+***********************************************************************/
+//this is not functional, not sure how to handle it yet, but I need the stub because it is a pure function
+OrderVector SharedRAbundFloatVector::getOrderVector(map<string,int>* nameMap = NULL) {
+ try {
+ OrderVector ov;
+
+ for(int i=0;i<data.size();i++){
+ int round = ceil(data[i].abundance);
+ for(int j=0;j<round;j++){
+ ov.push_back(i);
+ }
+ }
+ random_shuffle(ov.begin(), ov.end());
+
+ ov.setLabel(label);
+ return ov;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedRAbundFloatVector", "getOrderVector");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SharedRAbundFloatVector::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>& thislookup) {
+ try {
+
+ vector<SharedRAbundFloatVector*> newLookup;
+ for (int i = 0; i < thislookup.size(); i++) {
+ SharedRAbundFloatVector* temp = new SharedRAbundFloatVector();
+ 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, "SharedRAbundFloatVector", "eliminateZeroOTUS");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
projects / mothur.git / blobdiff