X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rabundvector.cpp;fp=rabundvector.cpp;h=fd7f3acecf930dbb39c822748c34c7420da19826;hb=20a2d0350a737a434c89f303662d64a8eeea7b05;hp=0000000000000000000000000000000000000000;hpb=bbb5879a7e566935c23d63d42bb945072424b939;p=mothur.git

diff --git a/rabundvector.cpp b/rabundvector.cpp
new file mode 100644
index 0000000..fd7f3ac
--- /dev/null
+++ b/rabundvector.cpp
@@ -0,0 +1,289 @@
+/*
+ *  rabundvector.cpp
+ *  
+ *
+ *  Created by Pat Schloss on 8/8/08.
+ *  Copyright 2008 Patrick D. Schloss. All rights reserved.
+ *
+ */
+using namespace std;
+ 
+#include "datavector.hpp"
+#include "utilities.hpp"
+#include <exception>
+#include "rabundvector.hpp"
+#include "sabundvector.hpp"
+#include "ordervector.hpp"
+
+
+/***********************************************************************/
+
+RAbundVector::RAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0) {};
+
+/***********************************************************************/
+
+RAbundVector::RAbundVector(int n) : DataVector(), data(n,0) , maxRank(0), numBins(0), numSeqs(0) {};
+
+/***********************************************************************/
+
+//RAbundVector::RAbundVector(const RAbundVector& rav) : DataVector(rav), data(rav.data), (rav.label),  (rav.maxRank), (rav.numBins), (rav.numSeqs){};
+
+
+/***********************************************************************/
+
+RAbundVector::RAbundVector(string id, vector<int> rav) : DataVector(id), data(rav) {
+	try {
+		numBins = 0;
+		maxRank = 0;
+		numSeqs = 0;
+		
+		for(int i=0;i<data.size();i++){
+			if(data[i] != 0)		{	numBins = i+1;		}
+			if(data[i] > maxRank)	{	maxRank = data[i];	}
+			numSeqs += data[i];
+		}
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function RAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the RAbundVector class function RAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+
+
+/***********************************************************************/
+
+
+RAbundVector::RAbundVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
+	try {
+		int hold;
+		f >> label >> hold;
+	
+		data.assign(hold, 0);
+		int 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 RAbundVector class Function RAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the RAbundVector class function RAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+
+/***********************************************************************/
+
+RAbundVector::~RAbundVector() {
+
+}
+
+/***********************************************************************/
+
+void RAbundVector::set(int binNumber, int newBinSize){
+	try {
+		int oldBinSize = data[binNumber];
+		data[binNumber] = newBinSize;
+	
+		if(oldBinSize == 0)			{	numBins++;				}
+		if(newBinSize == 0)			{	numBins--;				}
+		if(newBinSize > maxRank)	{	maxRank = newBinSize;	}
+	
+		numSeqs += (newBinSize - oldBinSize);
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the RAbundVector class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+
+/***********************************************************************/
+
+int RAbundVector::get(int index){
+	return data[index];
+	
+}
+
+/***********************************************************************/
+
+void RAbundVector::push_back(int binSize){
+	try {
+		data.push_back(binSize);
+		numBins++;
+	
+		if(binSize > maxRank){
+			maxRank = binSize;
+		}
+	
+		numSeqs += binSize;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector 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 RAbundVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+
+/***********************************************************************/
+
+void RAbundVector::pop_back(){
+
+	return data.pop_back();
+}
+
+/***********************************************************************/
+
+void RAbundVector::resize(int size){
+	
+	data.resize(size);
+}
+
+/***********************************************************************/
+
+int RAbundVector::size(){
+	return data.size();
+}
+
+/***********************************************************************/
+
+vector<int>::reverse_iterator RAbundVector::rbegin(){
+	return data.rbegin();				
+}
+
+/***********************************************************************/
+
+vector<int>::reverse_iterator RAbundVector::rend(){
+	return data.rend();					
+}
+
+/***********************************************************************/
+void RAbundVector::print(string prefix, ostream& output){
+	try {	
+		output << prefix << '\t' << numBins << '\t';
+	
+		vector<int> hold = data;
+		sort(hold.rbegin(), hold.rend());
+	
+		for(int i=0;i<numBins;i++){		output << hold[i] << '\t';		}
+		output << endl;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the RAbundVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+
+/***********************************************************************/
+void RAbundVector::print(ostream& output){
+	try {
+		output << label << '\t' << numBins << '\t';
+	
+		vector<int> hold = data;
+		sort(hold.rbegin(), hold.rend());
+		
+		for(int i=0;i<numBins;i++){		output << hold[i] << '\t';		}
+		output << endl;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the RAbundVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+
+/***********************************************************************/
+int RAbundVector::getNumBins(){
+	return numBins;
+}
+
+/***********************************************************************/
+
+int RAbundVector::getNumSeqs(){
+	return numSeqs;
+}
+
+/***********************************************************************/
+
+int RAbundVector::getMaxRank(){
+	return maxRank;
+}
+
+/***********************************************************************/
+
+RAbundVector RAbundVector::getRAbundVector(){
+	return *this;			
+}
+
+/***********************************************************************/
+
+SAbundVector RAbundVector::getSAbundVector() {
+	try {
+		SAbundVector sav(maxRank+1);
+		
+		for(int i=0;i<data.size();i++){
+			int abund = data[i];
+			sav.set(abund, sav.get(abund) + 1);
+		}
+		sav.set(0, 0);
+		sav.setLabel(label);
+		return sav;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the RAbundVector class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+
+/***********************************************************************/
+
+OrderVector RAbundVector::getOrderVector(map<string,int>* nameMap = NULL) {
+	try {
+		OrderVector ov;
+	
+		for(int i=0;i<data.size();i++){
+			for(int j=0;j<data[i];j++){
+				ov.push_back(i);
+			}
+		}
+		random_shuffle(ov.begin(), ov.end());
+
+		ov.setLabel(label);	
+		return ov;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the RAbundVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+
+/***********************************************************************/