X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=listvector.cpp;fp=listvector.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=9369a12280b35cd41a6a6e3548258f27ebb36b5c;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/listvector.cpp b/listvector.cpp
deleted file mode 100644
index 9369a12..0000000
--- a/listvector.cpp
+++ /dev/null
@@ -1,268 +0,0 @@
-/*
- *  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);
-	}
-}
-
-/***********************************************************************/