+++ /dev/null
-/*
- * sharedSharedOrderVector.cpp
- * Dotur
- *
- * Created by Sarah Westcott on 12/9/08.
- * Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "sharedordervector.h"
-#include "sharedutilities.h"
-
-/***********************************************************************/
-
-SharedOrderVector::SharedOrderVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0) {}
-
-/***********************************************************************/
-
-SharedOrderVector::SharedOrderVector(string id, vector<individual> ov) :
- DataVector(id), data(ov)
-{
- updateStats();
-}
-
-/***********************************************************************/
-//This function is used to read a .shared file for the collect.shared, rarefaction.shared and summary.shared commands
-//if you don't use a list and groupfile.
-
-SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() { //reads in a shared file
- try {
- maxRank = 0; numBins = 0; numSeqs = 0;
-
- groupmap = new GroupMap();
-
- int num, inputData, count;
- count = 0; numSeqs = 0;
- string holdLabel, nextLabel, groupN;
- individual newguy;
-
- //read in first row since you know there is at least 1 group.
- //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;
- }
- }else { label = m->saveNextLabel; }
-
- //reset labels, currentLabels may have gotten changed as otus were eliminated because of group choices or sampling
- m->currentBinLabels = m->binLabelsInFile;
-
- //read in first row since you know there is at least 1 group.
- f >> groupN >> num;
-
- holdLabel = label;
-
-
- vector<string> allGroups;
- //save group in groupmap
- allGroups.push_back(groupN);
- groupmap->groupIndex[groupN] = 0;
-
-
- for(int i=0;i<num;i++){
- f >> inputData;
-
- for (int j = 0; j < inputData; j++) {
- push_back(i, i, groupN);
- numSeqs++;
- }
- }
-
- 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++;
-
-
- //save group in groupmap
- allGroups.push_back(groupN);
- groupmap->groupIndex[groupN] = count;
-
-
- for(int i=0;i<num;i++){
- f >> inputData;
-
- for (int j = 0; j < inputData; j++) {
- push_back(i, i, groupN);
- numSeqs++;
- }
- }
-
- m->gobble(f);
-
- if (f.eof() != true) { f >> nextLabel; }
-
- }
-
- m->saveNextLabel = nextLabel;
-
- groupmap->setNamesOfGroups(allGroups);
- m->setAllGroups(allGroups);
-
- updateStats();
-
- }
- catch(exception& e) {
- m->errorOut(e, "SharedOrderVector", "SharedOrderVector");
- exit(1);
- }
-}
-/***********************************************************************/
-
-int SharedOrderVector::getNumBins(){
- return numBins;
-}
-
-/***********************************************************************/
-
-int SharedOrderVector::getNumSeqs(){
- return numSeqs;
-}
-
-/***********************************************************************/
-
-int SharedOrderVector::getMaxRank(){
- return maxRank;
-}
-
-
-/***********************************************************************/
-
-
-
-void SharedOrderVector::set(int index, int binNumber, int abund, string groupName){
-
- data[index].group = groupName;
- data[index].bin = binNumber;
- data[index].abundance = abund;
- //if (abund > maxRank) { maxRank = abund; }
- updateStats();
-}
-
-/***********************************************************************/
-
-individual SharedOrderVector::get(int index){
- return data[index];
-}
-
-
-/***********************************************************************/
-//commented updateStats out to improve speed, but whoever calls this must remember to update when they are done with all the pushbacks they are doing
-void SharedOrderVector::push_back(int binNumber, int abund, string groupName){
- individual newGuy;
- newGuy.group = groupName;
- newGuy.abundance = abund;
- newGuy.bin = binNumber;
- data.push_back(newGuy);
- //numSeqs++;
- //numBins++;
- //if (abund > maxRank) { maxRank = abund; }
-
- //updateStats();
-}
-
-/***********************************************************************/
-
-void SharedOrderVector::print(ostream& output){
- try {
- output << label << '\t' << numSeqs << '\t';
-
- for(int i=0;i<data.size();i++){
- output << data[i].bin << '\t';
- }
- output << endl;
- }
- catch(exception& e) {
- m->errorOut(e, "SharedOrderVector", "print");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-void SharedOrderVector::clear(){
- numBins = 0;
- maxRank = 0;
- numSeqs = 0;
- data.clear();
-}
-/***********************************************************************/
-
-void SharedOrderVector::resize(int){
- m->mothurOut("resize() did nothing in class SharedOrderVector");
-}
-
-/***********************************************************************/
-
-
-vector<individual>::iterator SharedOrderVector::begin(){
- return data.begin();
-}
-
-/***********************************************************************/
-
-vector<individual>::iterator SharedOrderVector::end(){
- return data.end();
-}
-
-/***********************************************************************/
-
-int SharedOrderVector::size(){
- return data.size();
-}
-
-/***********************************************************************/
-
-RAbundVector SharedOrderVector::getRAbundVector(){
- try {
- RAbundVector rav(data.size());
-
- for(int i=0;i<numSeqs;i++){
- rav.set(data[i].bin, rav.get(data[i].bin) + 1);
- }
- sort(rav.rbegin(), rav.rend());
- for(int i=numSeqs-1;i>=0;i--){
- if(rav.get(i) == 0){ rav.pop_back(); }
- else{
- break;
- }
- }
- rav.setLabel(label);
-
- return rav;
- }
- catch(exception& e) {
- m->errorOut(e, "SharedOrderVector", "getRAbundVector");
- exit(1);
- }
-}
-/***********************************************************************/
-
-OrderVector SharedOrderVector::getOrderVector(map<string,int>* nameMap = NULL) {
- try {
- OrderVector ov;
-
- for (int i = 0; i < data.size(); i++) {
- ov.push_back(data[i].bin);
- }
-
- random_shuffle(ov.begin(), ov.end());
-
- ov.setLabel(label);
- return ov;
- }
- catch(exception& e) {
- m->errorOut(e, "SharedOrderVector", "getOrderVector");
- exit(1);
- }
-}
-
-
-/***********************************************************************/
-
-SAbundVector SharedOrderVector::getSAbundVector(){
-
- RAbundVector rav(this->getRAbundVector());
- return rav.getSAbundVector();
-
-}
-/***********************************************************************/
-SharedRAbundVector SharedOrderVector::getSharedRAbundVector(string group) {
- try {
- SharedRAbundVector sharedRav(data.size());
-
- sharedRav.setLabel(label);
- sharedRav.setGroup(group);
-
- for (int i = 0; i < data.size(); i++) {
- if (data[i].group == group) {
- sharedRav.set(data[i].abundance, sharedRav.getAbundance(data[i].abundance) + 1, data[i].group);
- }
- }
- return sharedRav;
- }
- catch(exception& e) {
- m->errorOut(e, "SharedOrderVector", "getSharedRAbundVector");
- exit(1);
- }
-}
-/***********************************************************************/
-vector<SharedRAbundVector*> SharedOrderVector::getSharedRAbundVector() {
- try {
- SharedUtil* util;
- util = new SharedUtil();
- vector<SharedRAbundVector*> lookup;
-
- vector<string> Groups = m->getGroups();
- vector<string> allGroups = m->getAllGroups();
- util->setGroups(Groups, allGroups);
- util->getSharedVectors(Groups, lookup, this);
- m->setGroups(Groups);
- m->setAllGroups(allGroups);
-
- return lookup;
- }
- catch(exception& e) {
- m->errorOut(e, "SharedOrderVector", "getSharedRAbundVector");
- exit(1);
- }
-}
-/***********************************************************************/
-SharedSAbundVector SharedOrderVector::getSharedSAbundVector(string group) {
- try {
-
- SharedRAbundVector sharedRav(this->getSharedRAbundVector(group));
- return sharedRav.getSharedSAbundVector();
-
- }
- catch(exception& e) {
- m->errorOut(e, "SharedOrderVector", "getSharedSAbundVector");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-SharedOrderVector SharedOrderVector::getSharedOrderVector(){
- random_shuffle(data.begin(), data.end());
- return *this;
-}
-
-/***********************************************************************/
-
-void SharedOrderVector::updateStats(){
- try {
- needToUpdate = 0;
- numSeqs = 0;
- numBins = 0;
- maxRank = 0;
-
- numSeqs = data.size();
-
- vector<int> hold(numSeqs, 0);
- for(int i=0;i<numSeqs;i++){
- hold[data[i].bin] = hold[data[i].bin]+1;
- }
-
- for(int i=0;i<numSeqs;i++){
- if(hold[i] > 0) { numBins++; }
- if(hold[i] > maxRank) { maxRank = hold[i]; }
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "SharedOrderVector", "updateStats");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-
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