X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=listvector.cpp;fp=listvector.cpp;h=3af7cfe93f2d2b6dba45ab7b9ae5cd8c17184255;hb=20a2d0350a737a434c89f303662d64a8eeea7b05;hp=0000000000000000000000000000000000000000;hpb=bbb5879a7e566935c23d63d42bb945072424b939;p=mothur.git

diff --git a/listvector.cpp b/listvector.cpp
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index 0000000..3af7cfe
--- /dev/null
+++ b/listvector.cpp
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+/*
+ *  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);
+	}
+}
+
+/***********************************************************************/