+++ /dev/null
-/*
- * list.cpp
- *
- *
- * Created by Pat Schloss on 8/8/08.
- * Copyright 2008 Patrick D. Schloss. All rights reserved.
- *
- */
-
-
-#include "sabundvector.hpp"
-#include "rabundvector.hpp"
-#include "ordervector.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 = m->getNumNames(data[i]);
- numBins = i+1;
- if(binSize > maxRank) { maxRank = binSize; }
- numSeqs += binSize;
- }
- }
- }
- catch(exception& e) {
- m->errorOut(e, "ListVector", "ListVector");
- 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);
- }
- m->gobble(f);
- }
- catch(exception& e) {
- m->errorOut(e, "ListVector", "ListVector");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-void ListVector::set(int binNumber, string seqNames){
- try {
- int nNames_old = m->getNumNames(data[binNumber]);
- data[binNumber] = seqNames;
- int nNames_new = m->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) {
- m->errorOut(e, "ListVector", "set");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-string ListVector::get(int index){
- return data[index];
-}
-
-/***********************************************************************/
-
-void ListVector::push_back(string seqNames){
- try {
- data.push_back(seqNames);
- int nNames = m->getNumNames(seqNames);
-
- numBins++;
-
- if(nNames > maxRank) { maxRank = nNames; }
-
- numSeqs += nNames;
- }
- catch(exception& e) {
- m->errorOut(e, "ListVector", "push_back");
- 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) {
- m->errorOut(e, "ListVector", "print");
- exit(1);
- }
-}
-
-
-/***********************************************************************/
-
-RAbundVector ListVector::getRAbundVector(){
- try {
- RAbundVector rav;
-
- for(int i=0;i<data.size();i++){
- int binSize = m->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) {
- m->errorOut(e, "ListVector", "getRAbundVector");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-SAbundVector ListVector::getSAbundVector(){
- try {
- SAbundVector sav(maxRank+1);
-
- for(int i=0;i<data.size();i++){
- int binSize = m->getNumNames(data[i]);
- sav.set(binSize, sav.get(binSize) + 1);
- }
- sav.set(0, 0);
- sav.setLabel(label);
-
- return sav;
- }
- catch(exception& e) {
- m->errorOut(e, "ListVector", "getSAbundVector");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-OrderVector ListVector::getOrderVector(map<string,int>* orderMap = NULL){
-
- try {
- if(orderMap == NULL){
- OrderVector ov;
-
- for(int i=0;i<data.size();i++){
- int binSize = m->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){
- m->mothurOut(seqName + " not found, check *.names file\n");
- exit(1);
- }
-
- ov.set((*orderMap)[seqName], i);
- seqName = "";
- }
- }
-
- if(orderMap->count(seqName) == 0){
- m->mothurOut(seqName + " not found, check *.names file\n");
- exit(1);
- }
- ov.set((*orderMap)[seqName], i);
- }
-
- ov.setLabel(label);
- ov.getNumBins();
-
- return ov;
- }
- }
- catch(exception& e) {
- m->errorOut(e, "ListVector", "getOrderVector");
- exit(1);
- }
-}
-
-/***********************************************************************/
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