From: westcott <westcott>
Date: Mon, 18 May 2009 18:24:13 +0000 (+0000)
Subject: added boneh, efron, and solow calculators
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=37a2c0b7dc68bfa53c8f38a713259929c4c46a9f

added boneh, efron, and solow calculators
---

diff --git a/boneh.cpp b/boneh.cpp
new file mode 100644
index 0000000..7b52683
--- /dev/null
+++ b/boneh.cpp
@@ -0,0 +1,87 @@
+/*
+ *  boneh.cpp
+ *  Mothur
+ *
+ *  Created by Thomas Ryabin on 5/13/09.
+ *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+#include "boneh.h"
+#include <math.h>
+
+/***********************************************************************/
+double Boneh::getV(double f1, double n, double rs) {
+
+	//cout << "f1 = " << f1 << "\nn = " << n << "\nrs = " << rs << "\n\n";
+	
+	double accuracy = .0001;
+	double v = 100000.0;
+	double step = v/2;
+	double ls = v * (1 - pow((1 - f1/(n*v)), n));
+	
+	//cout << "ls = " << ls << "\n";
+	
+	while(abs(ls - rs) > accuracy) {
+		if(ls > rs)
+			v -= step;
+		else
+			v += step;
+		
+		ls = v* (1 - pow((1 - f1/(n*v)), n));
+		step /= 2;
+		
+	//	cout << "ls = " << ls << "\n";
+	}
+	
+	return v;
+}
+	
+/***********************************************************************/	
+EstOutput Boneh::getValues(SAbundVector* rank){
+
+	try {
+		data.resize(1,0);
+		
+		bool valid = false;
+		double sum = 0;
+		double n = (double)rank->size() - 1;
+		double f1 = (double)rank->get(1);
+		
+		for(int i = 1; i < rank->size(); i++)
+			sum += (double)rank->get(i) * exp(-i);
+		
+		if(rank->get(1) > sum)
+			valid = true;
+		
+		sum = 0;
+		if(valid) {
+			for(int j = 1; j < rank->size(); j++)
+				sum += rank->get(j) * pow((1 - (double)j / n), n);
+			
+			double v = getV(f1, n, sum);
+			
+		//	cout << "v = " << v << "\n";
+			
+			sum = 0;
+			for(int j = 1; j < rank->size(); j++)
+				sum += pow(1 - (double)rank->get(j) / n, n) * (1 - pow(1 - (double)rank->get(j) / n, m)) + v * pow(1 - f1/(n*v), n) * (1 - pow(1 - f1/(n*v), m));
+				
+		}
+
+		data[0] = sum;
+		
+		return data;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the Coverage class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the Coverage class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+};
+
+
+/***********************************************************************/
diff --git a/boneh.h b/boneh.h
new file mode 100644
index 0000000..919200c
--- /dev/null
+++ b/boneh.h
@@ -0,0 +1,34 @@
+#ifndef BONEH_H
+#define BONEH_H
+
+/*
+ *  boneh.h
+ *  Mothur
+ *
+ *  Created by Thomas Ryabin on 5/13/09.
+ *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+#include "calculator.h"
+
+/* This class implements the boneh calculator on single group. 
+ It is a child of the calculator class. */
+
+/***********************************************************************/
+
+class Boneh : public Calculator  {
+	
+public: 
+	Boneh(int size) : m(size), Calculator("boneh", 1, false) {};
+	EstOutput getValues(SAbundVector*);	
+	EstOutput getValues(vector<SharedRAbundVector*>) {return data;};
+private:
+	double getV(double, double, double);
+	int m;
+};
+
+
+/***********************************************************************/
+
+#endif
diff --git a/collectcommand.cpp b/collectcommand.cpp
index 233b7be..e429dff 100644
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -23,7 +23,9 @@
 #include "bergerparker.h"
 #include "bstick.h"
 #include "goodscoverage.h"
-
+#include "efron.h"
+#include "boneh.h"
+#include "solow.h"
 
 #include "coverage.h"
 
@@ -71,6 +73,15 @@ CollectCommand::CollectCommand(){
 					cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
 				}else if (globaldata->Estimators[i] == "goodscoverage") { 
 					cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
+				}else if (globaldata->Estimators[i] == "efron") {
+					convert(globaldata->getSize(), size); 
+					cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron")));
+				}else if (globaldata->Estimators[i] == "boneh") {
+					convert(globaldata->getSize(), size); 
+					cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh")));
+				}else if (globaldata->Estimators[i] == "solow") {
+					convert(globaldata->getSize(), size); 
+					cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow")));
 				}
 			}
 		}
diff --git a/collectcommand.h b/collectcommand.h
index 016f37e..8057f9f 100644
--- a/collectcommand.h
+++ b/collectcommand.h
@@ -49,7 +49,7 @@ private:
 	Collect* cCurve;
 	ValidCalculators* validCalculator;
 	vector<Display*> cDisplays;
-	int freq, abund;
+	int freq, abund, size;
 
 };
 
diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 0ac767d..582628d 100644
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -30,7 +30,7 @@
 #include "sharedmorisitahorn.h"
 #include "sharedbraycurtis.h"
 #include "sharedjackknife.h"
-#include "sharedwhittaker.h"
+#include "whittaker.h"
 
 
 
diff --git a/efron.cpp b/efron.cpp
new file mode 100644
index 0000000..e843641
--- /dev/null
+++ b/efron.cpp
@@ -0,0 +1,44 @@
+/*
+ *  efron.cpp
+ *  Mothur
+ *
+ *  Created by Thomas Ryabin on 5/13/09.
+ *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+#include "efron.h"
+#include <math.h>
+
+/***********************************************************************/
+EstOutput Efron::getValues(SAbundVector* rank){
+
+	try {
+		data.resize(1,0);
+		
+		if(m > rank->size()-1) {
+			cout << "Error in the 'efron' calculator. 'size' must be less than the length of the smalled sabund vector.\n";
+			data[0] = 0;
+			return data;
+		}
+		
+		double sum = 0;
+		for(int i = 1; i < rank->size(); i++)
+			sum += pow(-1, (double)(i+1)) * pow(((double)m / (double)(rank->size()-1)), i) * (double)(rank->get(i));
+
+		data[0] = sum;
+		
+		return data;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the Coverage class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the Coverage class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+};
+
+
+/***********************************************************************/
diff --git a/efron.h b/efron.h
new file mode 100644
index 0000000..652159d
--- /dev/null
+++ b/efron.h
@@ -0,0 +1,33 @@
+#ifndef EFRON_H
+#define EFRON_H
+
+/*
+ *  efron.h
+ *  Mothur
+ *
+ *  Created by Thomas Ryabin on 5/13/09.
+ *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+#include "calculator.h"
+
+/* This class implements the efron calculator on single group. 
+ It is a child of the calculator class. */
+
+/***********************************************************************/
+
+class Efron : public Calculator  {
+	
+public: 
+	Efron(int size) : m(size), Calculator("efron", 1, false) {};
+	EstOutput getValues(SAbundVector*);	
+	EstOutput getValues(vector<SharedRAbundVector*>) {return data;};
+private:
+	int m;
+};
+
+
+/***********************************************************************/
+
+#endif
diff --git a/errorchecking.cpp b/errorchecking.cpp
index dfe9607..b460987 100644
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -118,6 +118,8 @@ bool ErrorCheck::checkInput(string input) {
 				if (parameter == "scale" )			{ scale = value;	}
 				if (parameter == "ends" )			{ ends = value; }
 				if (parameter == "processors" )		{ processors = value;	}
+				if (parameter == "size" )			{ size = value; }
+
 				if (parameter == "template")		{ templatefile = value;	}
 				if (parameter == "search")			{ search = value;		}
 				if (parameter == "ksize")			{ ksize = value;		}
@@ -167,6 +169,7 @@ bool ErrorCheck::checkInput(string input) {
 				if (parameter == "scale" )			{ scale = value;	}
 				if (parameter == "ends" )			{ ends = value; }
 				if (parameter == "processors" )		{ processors = value;	}
+				if (parameter == "size" )			{ size = value; }
 				if (parameter == "template")		{ templatefile = value;	}
 				if (parameter == "search")			{ search = value;		}
 				if (parameter == "ksize")			{ ksize = value;		}
diff --git a/errorchecking.h b/errorchecking.h
index d6388f7..5057ab0 100644
--- a/errorchecking.h
+++ b/errorchecking.h
@@ -35,7 +35,7 @@ class ErrorCheck {
 		void clear();
 		void refresh();
 		string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, nexusfile, clustalfile, treefile, sharedfile, cutoff, format; 
-		string precision, method, fileroot, label, line, iters, jumble, freq, single, rarefaction, shared, summary, randomtree, abund, sorted, trump, soft, filter, scale, ends, processors;
+		string precision, method, fileroot, label, line, iters, jumble, freq, single, rarefaction, shared, summary, randomtree, abund, sorted, trump, soft, filter, scale, ends, processors, size;
 		string templatefile, search, ksize, align, match, mismatch, gapopen, gapextend;
 		string commandName, optionText;
 		bool errorFree;
diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 6170d00..f4cc6d8 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -14,7 +14,7 @@ void FilterSeqsCommand::doTrump() {
 	trump = globaldata->getTrump();
 	for(int i = 0; i < db->size(); i++) {
 		Sequence cur = db->get(i);
-		string curAligned = cur.getUnaligned();
+		string curAligned = cur.getAligned();
 		for(int j = 0; j < curAligned.length(); j++) {
 			string curChar = curAligned.substr(j, 1);
 			if(curChar.compare(trump) == 0) 
@@ -37,7 +37,7 @@ void FilterSeqsCommand::doSoft() {
 	
 	for(int i = 0; i < db->size(); i++) {
 		Sequence cur = db->get(i);
-		string curAligned = cur.getUnaligned();
+		string curAligned = cur.getAligned();
 		
 		for(int j = 0; j < curAligned.length(); j++) {
 			string curChar = curAligned.substr(j, 1);
@@ -112,7 +112,7 @@ int FilterSeqsCommand::execute() {
 		db = readSeqs->getDB();
 		
 		//for(int i = 0; i < db->size(); i++) {
-//			cout << db->get(i).getLength() << "\n" << db->get(i).getName() << ": " << db->get(i).getUnaligned() << "\n\n";
+//			cout << db->get(i).getLength() << "\n" << db->get(i).getName() << ": " << db->get(i).getAligned() << "\n\n";
 //		}
 
 		for(int i = 0; i < db->get(0).getLength(); i++) 
@@ -140,7 +140,7 @@ int FilterSeqsCommand::execute() {
 		SequenceDB newDB;
 		for(int i = 0; i < db->size(); i++) {
 			Sequence curSeq = db->get(i);
-			string curAligned = curSeq.getUnaligned();
+			string curAligned = curSeq.getAligned();
 			string curName = curSeq.getName();
 			string newAligned = "";
 			for(int j = 0; j < curAligned.length(); j++) 
diff --git a/globaldata.cpp b/globaldata.cpp
index b4239f3..88c5a13 100644
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -85,6 +85,11 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 				if (key == "scale")			{ scale = value;		}
 				if (key == "ends" )			{ ends = value;			}
 				if (key == "processors" )	{ processors = value;	}
+				if (key == "size" )         { size = value;         }
+				
+
+				
+
 				if (key == "template")		{ templatefile = value;	}
 				if (key == "search")		{ search = value;		}
 				if (key == "ksize")			{ ksize = value;		}
@@ -155,6 +160,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			if (key == "scale")			{ scale = value;		}
 			if (key == "ends" )			{ ends = value;			}
 			if (key == "processors" )	{ processors = value;	}
+			if (key == "size" )         { size = value;         }
+
 			if (key == "template")		{ templatefile = value;	}
 			if (key == "search")		{ search = value;		}
 			if (key == "ksize")			{ ksize = value;		}
@@ -196,7 +203,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 		//input defaults for calculators
 		if (commandName == "collect.single") {
 
-			if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
+			if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson-efron-boneh-solow"; }
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
@@ -212,7 +219,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			splitAtDash(calc, Estimators); 
 		}
 		if (commandName == "summary.single") {
-			if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
+			if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson-efron-boneh-solow"; }
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
@@ -300,6 +307,13 @@ string GlobalData::getFilter()			{   return filter;		}
 string GlobalData::getScale()			{	return scale;		}
 string GlobalData::getEnds()			{   return ends;		}
 string GlobalData::getProcessors()		{	return processors;	}
+string GlobalData::getSize()            {   return size;        }
+
+void GlobalData::setListFile(string file)	{	listfile = file;	inputFileName = file;}
+void GlobalData::setRabundFile(string file)	{	rabundfile = file;	inputFileName = file;}
+void GlobalData::setSabundFile(string file)	{	sabundfile = file;	inputFileName = file;}
+void GlobalData::setPhylipFile(string file)	{	phylipfile = file;    inputFileName = file;}
+void GlobalData::setColumnFile(string file)	{	columnfile = file;    inputFileName = file;}
 string GlobalData::getTemplateFile()	{	return templatefile;}
 string GlobalData::getSearch()			{	return search;		}
 string GlobalData::getKSize()			{	return ksize;		}
@@ -309,12 +323,7 @@ string GlobalData::getMismatch()		{	return mismatch;	}
 string GlobalData::getGapopen()			{	return gapopen;		}
 string GlobalData::getGapextend()		{	return gapextend;	}
 
-void GlobalData::setListFile(string file)		{	listfile = file;	inputFileName = file;}
 void GlobalData::setGroupFile(string file)		{	groupfile = file;	}
-void GlobalData::setRabundFile(string file)		{	rabundfile = file;	inputFileName = file;}
-void GlobalData::setSabundFile(string file)		{	sabundfile = file;	inputFileName = file;}
-void GlobalData::setPhylipFile(string file)		{	phylipfile = file;    inputFileName = file;}
-void GlobalData::setColumnFile(string file)		{	columnfile = file;    inputFileName = file;}
 void GlobalData::setSharedFile(string file)		{	sharedfile = file;	inputFileName = file; fileroot = file;}
 void GlobalData::setNameFile(string file)		{	namefile = file;		}
 void GlobalData::setFormat(string Format)		{	format = Format;		}
@@ -377,6 +386,7 @@ void GlobalData::clear() {
 	scale			=	"log10";
 	ends			=   "T";  //yes
 	processors		=	"1";
+	size            =   "1000";
 	search			=	"suffix";
 	ksize			=	"7";
 	align			=	"blast";
@@ -384,8 +394,6 @@ void GlobalData::clear() {
 	mismatch		=	"-1.0";
 	gapopen			=	"-5.0";
 	gapextend		=	"-2.0";
-	
-
 }
 
 //*******************************************************/
@@ -407,6 +415,7 @@ void GlobalData::reset() {
 	form			=	"integral";
 	ends			=   "T";
 	processors		=	"1";
+	size            =   "1000";
 	search			=	"suffix";
 	ksize			=	"7";
 	align			=	"blast";
diff --git a/globaldata.hpp b/globaldata.hpp
index cb9aff6..d427aba 100644
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -77,6 +77,7 @@ public:
 	string getSorted();
 	string getEnds();
 	string getProcessors();
+	string getSize();
 	string getTemplateFile();
 	string getSearch();
 	string getKSize();
@@ -123,7 +124,7 @@ public:
 private:
 
 	string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, nexusfile, clustalfile, treefile, sharedfile, line, label, randomtree, groups;
-	string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, trump, soft, filter, scale, ends, processors, templatefile, search, ksize, align, match;
+	string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, trump, soft, filter, scale, ends, processors, templatefile, search, ksize, align, match, size;
 	string mismatch, gapopen, gapextend;
 
 
diff --git a/solow.cpp b/solow.cpp
new file mode 100644
index 0000000..3a15fdf
--- /dev/null
+++ b/solow.cpp
@@ -0,0 +1,39 @@
+/*
+ *  solow.cpp
+ *  Mothur
+ *
+ *  Created by Thomas Ryabin on 5/13/09.
+ *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+#include "solow.h"
+#include <math.h>
+
+	
+/***********************************************************************/	
+EstOutput Solow::getValues(SAbundVector* rank){
+
+	try {
+		data.resize(1,0);
+		
+		double n = (double)rank->size() - 1;
+		double f1 = (double)rank->get(1);
+		double f2 = (double)rank->get(2);
+
+		data[0] = f1*f1/2/f2 * (1 - pow(1 - 2*f2/n/f1, m));
+		
+		return data;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the Coverage class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the Coverage class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+};
+
+
+/***********************************************************************/
diff --git a/solow.h b/solow.h
new file mode 100644
index 0000000..6d58df2
--- /dev/null
+++ b/solow.h
@@ -0,0 +1,33 @@
+#ifndef SOLOW_H
+#define SOLOW_H
+
+/*
+ *  solow.h
+ *  Mothur
+ *
+ *  Created by Thomas Ryabin on 5/13/09.
+ *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+#include "calculator.h"
+
+/* This class implements the solow calculator on single group. 
+ It is a child of the calculator class. */
+
+/***********************************************************************/
+
+class Solow : public Calculator  {
+	
+public: 
+	Solow(int size) : m(size), Calculator("solow", 1, false) {};
+	EstOutput getValues(SAbundVector*);	
+	EstOutput getValues(vector<SharedRAbundVector*>) {return data;};
+private:
+	int m;
+};
+
+
+/***********************************************************************/
+
+#endif
diff --git a/summarycommand.cpp b/summarycommand.cpp
index bd8deb1..d0124d8 100644
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -24,6 +24,9 @@
 #include "bstick.h"
 #include "goodscoverage.h"
 #include "coverage.h"
+#include "efron.h"
+#include "boneh.h"
+#include "solow.h"
 
 //**********************************************************************************************************************
 
@@ -70,6 +73,15 @@ SummaryCommand::SummaryCommand(){
 					sumCalculators.push_back(new NSeqs());
 				}else if (globaldata->Estimators[i] == "goodscoverage") { 
 					sumCalculators.push_back(new GoodsCoverage());
+				}else if (globaldata->Estimators[i] == "efron") { 
+					convert(globaldata->getSize(), size);
+					sumCalculators.push_back(new Efron(size));
+				}else if (globaldata->Estimators[i] == "boneh") { 
+					convert(globaldata->getSize(), size);
+					sumCalculators.push_back(new Boneh(size));
+				}else if (globaldata->Estimators[i] == "solow") { 
+					convert(globaldata->getSize(), size);
+					sumCalculators.push_back(new Solow(size));
 				}
 			}
 		}
diff --git a/summarycommand.h b/summarycommand.h
index 8f42f45..135c402 100644
--- a/summarycommand.h
+++ b/summarycommand.h
@@ -46,6 +46,6 @@ private:
 	SAbundVector* sabund;
 	string outputFileName;
 	ofstream outputFileHandle;
-	int abund;
+	int abund, size;
 };
 #endif
diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 486e6c4..46055c0 100644
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -30,7 +30,7 @@
 #include "sharedmorisitahorn.h"
 #include "sharedbraycurtis.h"
 #include "sharedjackknife.h"
-#include "sharedwhittaker.h"
+#include "whittaker.h"
 
 
 //**********************************************************************************************************************
diff --git a/validcalculator.cpp b/validcalculator.cpp
index 14fa775..7a07fd1 100644
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -201,6 +201,9 @@ void ValidCalculators::initialSingle() {
 		single["goodscoverage"] = "goodscoverage";
 		single["nseqs"]			= "nseqs";
 		single["coverage"]		= "coverage";
+		single["efron"]         = "efron";
+		single["boneh"]         = "boneh";
+		single["solow"]         = "solow";
 		single["default"]	    = "default";
 	}
 	catch(exception& e) {
@@ -294,6 +297,9 @@ void ValidCalculators::initialSummary() {
 		summary["nseqs"]		= "nseqs";
 		summary["goodscoverage"]= "goodscoverage";
 		summary["coverage"]		= "coverage";
+		summary["efron"]        = "efron";
+		summary["boneh"]        = "boneh";
+		summary["solow"]        = "solow";
 		summary["default"]	    = "default";
 	}
 	catch(exception& e) {
diff --git a/validparameter.cpp b/validparameter.cpp
index e79a2db..1a1555d 100644
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -225,7 +225,7 @@ void ValidParameters::initCommandParameters() {
 		string deconvoluteArray[] =  {"fasta"};
 		commandParameters["deconvolute"] = addParameters(deconvoluteArray, sizeof(deconvoluteArray)/sizeof(string));
 		
-		string collectsingleArray[] =  {"freq","line","label","calc","abund"};
+		string collectsingleArray[] =  {"freq","line","label","calc","abund","size"};
 		commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string));
 
 		string collectsharedArray[] =  {"freq","line","label","calc","groups"};
@@ -249,7 +249,7 @@ void ValidParameters::initCommandParameters() {
 		string libshuffArray[] =  {"iters","groups","step","form","cutoff"};
 		commandParameters["libshuff"] = addParameters(libshuffArray, sizeof(libshuffArray)/sizeof(string));
 		
-		string summarysingleArray[] =  {"line","label","calc","abund"};
+		string summarysingleArray[] =  {"line","label","calc","abund","size"};
 		commandParameters["summary.single"] = addParameters(summarysingleArray, sizeof(summarysingleArray)/sizeof(string));
 
 		string summarysharedArray[] =  {"line","label","calc","groups"};
@@ -346,6 +346,9 @@ void ValidParameters::initParameterRanges() {
 		
 		string softArray[] = {">=","0", "<=","100", "between"};
 		parameterRanges["soft"] = addParameters(softArray, rangeSize);
+		
+		string sizeArray[] = {">=","1", "<","NA", "between"};
+		parameterRanges["size"] = addParameters(sizeArray, rangeSize);
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";