--- /dev/null
+/*
+ * list.cpp
+ *
+ *
+ * Created by Pat Schloss on 8/8/08.
+ * Copyright 2008 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+using namespace std;
+
+#include <map>
+#include <exception>
+#include "sabundvector.hpp"
+#include "rabundvector.hpp"
+#include "ordervector.hpp"
+#include "datavector.hpp"
+#include "utilities.hpp"
+#include "listvector.hpp"
+
+
+/***********************************************************************/
+
+ListVector::ListVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){};
+
+/***********************************************************************/
+
+ListVector::ListVector(int n): DataVector(), data(n, "") , maxRank(0), numBins(0), numSeqs(0){};
+
+/***********************************************************************/
+
+ListVector::ListVector(string id, vector<string> lv) : DataVector(id), data(lv){
+ try {
+ for(int i=0;i<data.size();i++){
+ if(data[i] != ""){
+ int binSize = getNumNames(data[i]);
+ numBins = i+1;
+ if(binSize > maxRank) { maxRank = binSize; }
+ numSeqs += binSize;
+ }
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function ListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ListVector class function ListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/**********************************************************************/
+
+ListVector::ListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
+ try {
+ int hold;
+ f >> label >> hold;
+
+ data.assign(hold, "");
+ string inputData = "";
+
+ for(int i=0;i<hold;i++){
+ f >> inputData;
+ set(i, inputData);
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function ListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ListVector class function ListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void ListVector::set(int binNumber, string seqNames){
+ try {
+ int nNames_old = getNumNames(data[binNumber]);
+ data[binNumber] = seqNames;
+ int nNames_new = getNumNames(seqNames);
+
+ if(nNames_old == 0) { numBins++; }
+ if(nNames_new == 0) { numBins--; }
+ if(nNames_new > maxRank) { maxRank = nNames_new; }
+
+ numSeqs += (nNames_new - nNames_old);
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ListVector class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+string ListVector::get(int index){
+ return data[index];
+}
+
+/***********************************************************************/
+
+void ListVector::push_back(string seqNames){
+ try {
+ data.push_back(seqNames);
+ int nNames = getNumNames(seqNames);
+
+ numBins++;
+
+ if(nNames > maxRank) { maxRank = nNames; }
+
+ numSeqs += nNames;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ListVector 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 ListVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void ListVector::resize(int size){
+ data.resize(size);
+}
+
+/***********************************************************************/
+
+int ListVector::size(){
+ return data.size();
+}
+/***********************************************************************/
+
+void ListVector::clear(){
+ numBins = 0;
+ maxRank = 0;
+ numSeqs = 0;
+ return data.clear();
+
+}
+
+/***********************************************************************/
+
+void ListVector::print(ostream& output){
+ try {
+ output << label << '\t' << numBins << '\t';
+
+ for(int i=0;i<data.size();i++){
+ if(data[i] != ""){
+ output << data[i] << '\t';
+ }
+ }
+ output << endl;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ListVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+
+/***********************************************************************/
+
+RAbundVector ListVector::getRAbundVector(){
+ try {
+ RAbundVector rav;
+
+ for(int i=0;i<data.size();i++){
+ int binSize = getNumNames(data[i]);
+ rav.push_back(binSize);
+ }
+
+ // This was here before to output data in a nice format, but it screws up the name mapping steps
+ // sort(rav.rbegin(), rav.rend());
+ //
+ // for(int i=data.size()-1;i>=0;i--){
+ // if(rav.get(i) == 0){ rav.pop_back(); }
+ // else{
+ // break;
+ // }
+ // }
+ rav.setLabel(label);
+
+ return rav;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ListVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+SAbundVector ListVector::getSAbundVector(){
+ try {
+ SAbundVector sav(maxRank+1);
+
+ for(int i=0;i<data.size();i++){
+ int binSize = getNumNames(data[i]);
+ sav.set(binSize, sav.get(binSize) + 1);
+ }
+ sav.set(0, 0);
+ sav.setLabel(label);
+
+ return sav;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ListVector class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+SharedOrderVector* ListVector::getSharedOrderVector(){
+ globaldata = GlobalData::getInstance();
+ string groupName, names, name;
+ groupmap = globaldata->gGroupmap;
+ SharedOrderVector* order;
+ order = new SharedOrderVector();
+ order->setLabel(label);
+
+ for(int i=0;i<numBins;i++){
+ int binSize = getNumNames(get(i)); //find number of individual in given bin
+ names = get(i);
+ while (names.find_first_of(',') != -1) {
+ name = names.substr(0,names.find_first_of(','));
+ names = names.substr(names.find_first_of(',')+1, names.length());
+ groupName = groupmap->getGroup(name);
+ order->push_back(i, binSize, groupName); //i represents what bin you are in
+ }
+ //get last name
+ groupName = groupmap->getGroup(names);
+ order->push_back(i, binSize, groupName);
+ }
+ random_shuffle(order->begin(), order->end());
+ return order;
+}
+
+/***********************************************************************/
+
+OrderVector ListVector::getOrderVector(map<string,int>* orderMap = NULL){
+
+ try {
+ if(orderMap == NULL){
+ OrderVector ov;
+
+ for(int i=0;i<data.size();i++){
+ int binSize = getNumNames(data[i]);
+ for(int j=0;j<binSize;j++){
+ ov.push_back(i);
+ }
+ }
+ random_shuffle(ov.begin(), ov.end());
+ ov.setLabel(label);
+ ov.getNumBins();
+
+ return ov;
+
+ }
+ else{
+ OrderVector ov(numSeqs);
+
+ for(int i=0;i<data.size();i++){
+ string listOTU = data[i];
+ int length = listOTU.size();
+
+ string seqName="";
+
+ for(int j=0;j<length;j++){
+
+ if(listOTU[j] != ','){
+ seqName += listOTU[j];
+ }
+ else{
+ if(orderMap->count(seqName) == 0){
+ cerr << seqName << " not found, check *.names file\n";
+ exit(1);
+ }
+
+ ov.set((*orderMap)[seqName], i);
+ seqName = "";
+ }
+ }
+
+ if(orderMap->count(seqName) == 0){
+ cerr << seqName << " not found, check *.names file\n";
+ exit(1);
+ }
+ ov.set((*orderMap)[seqName], i);
+ }
+
+ ov.setLabel(label);
+ ov.getNumBins();
+
+ return ov;
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ListVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
projects / mothur.git / blobdiff