X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.cpp;h=b3f7729e10a709a202b627148386b7bd66d5ac31;hb=7d38edc137a66a33f67f8cf55cce88331290aaf7;hp=b6b4f522df0b1fc0eeb96d3851d8eda0419a35aa;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index b6b4f52..b3f7729 100644
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -31,8 +31,73 @@
 #include "sharedbraycurtis.h"
 #include "sharedjackknife.h"
 #include "whittaker.h"
+#include "odum.h"
+#include "canberra.h"
+#include "structeuclidean.h"
+#include "structchord.h"
+#include "hellinger.h"
+#include "manhattan.h"
+#include "structpearson.h"
+#include "soergel.h"
+#include "spearman.h"
+#include "structkulczynski.h"
+#include "structchi2.h"
+#include "speciesprofile.h"
+#include "hamming.h"
+#include "gower.h"
+#include "memchi2.h"
+#include "memchord.h"
+#include "memeuclidean.h"
+#include "mempearson.h"
 
-
+//**********************************************************************************************************************
+vector<string> SummarySharedCommand::getValidParameters(){	
+	try {
+		string Array[] =  {"label","calc","groups","all","outputdir","distance","inputdir", "processors"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SummarySharedCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+SummarySharedCommand::SummarySharedCommand(){	
+	try {
+		abort = true;
+		//initialize outputTypes
+		vector<string> tempOutNames;
+		outputTypes["summary"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SummarySharedCommand", "SummarySharedCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> SummarySharedCommand::getRequiredParameters(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SummarySharedCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> SummarySharedCommand::getRequiredFiles(){	
+	try {
+		string Array[] =  {"shared"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SummarySharedCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 
 SummarySharedCommand::SummarySharedCommand(string option)  {
@@ -48,7 +113,7 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
 		
 		else {
 			//valid paramters for this command
-			string Array[] =  {"label","calc","groups","all","outputdir","inputdir"};
+			string Array[] =  {"label","calc","groups","all","outputdir","distance","inputdir", "processors"};
 			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 			
 			OptionParser parser(option);
@@ -66,10 +131,14 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
 				 m->mothurOut("You must read a list and a group, or a shared before you can use the summary.shared command."); m->mothurOutEndLine(); abort = true; 
 			}
 			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["summary"] = tempOutNames;
+			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	
 				outputDir = "";	
-				outputDir += hasPath(globaldata->getSharedFile()); //if user entered a file with a path then preserve it	
+				outputDir += m->hasPath(globaldata->getSharedFile()); //if user entered a file with a path then preserve it	
 			}
 
 			//check for optional parameter and set defaults
@@ -77,7 +146,7 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
 			label = validParameter.validFile(parameters, "label", false);			
 			if (label == "not found") { label = ""; }
 			else { 
-				if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
+				if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 				else { allLines = 1;  }
 			}
 			
@@ -92,17 +161,23 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
 			else { 
 				 if (calc == "default")  {  calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan";  }
 			}
-			splitAtDash(calc, Estimators);
+			m->splitAtDash(calc, Estimators);
 			
 			groups = validParameter.validFile(parameters, "groups", false);			
 			if (groups == "not found") { groups = ""; }
 			else { 
-				splitAtDash(groups, Groups);
+				m->splitAtDash(groups, Groups);
 				globaldata->Groups = Groups;
 			}
 			
 			string temp = validParameter.validFile(parameters, "all", false);				if (temp == "not found") { temp = "false"; }
-			all = isTrue(temp);
+			all = m->isTrue(temp);
+			
+			temp = validParameter.validFile(parameters, "distance", false);					if (temp == "not found") { temp = "false"; }
+			createPhylip = m->isTrue(temp);
+			
+			temp = validParameter.validFile(parameters, "processors", false);	if(temp == "not found"){	temp = "1"; }
+			convert(temp, processors); 
 			
 			if (abort == false) {
 			
@@ -153,14 +228,46 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
 							sumCalculators.push_back(new BrayCurtis());
 						}else if (Estimators[i] == "whittaker") { 
 							sumCalculators.push_back(new Whittaker());
+						}else if (Estimators[i] == "odum") { 
+							sumCalculators.push_back(new Odum());
+						}else if (Estimators[i] == "canberra") { 
+							sumCalculators.push_back(new Canberra());
+						}else if (Estimators[i] == "structeuclidean") { 
+							sumCalculators.push_back(new StructEuclidean());
+						}else if (Estimators[i] == "structchord") { 
+							sumCalculators.push_back(new StructChord());
+						}else if (Estimators[i] == "hellinger") { 
+							sumCalculators.push_back(new Hellinger());
+						}else if (Estimators[i] == "manhattan") { 
+							sumCalculators.push_back(new Manhattan());
+						}else if (Estimators[i] == "structpearson") { 
+							sumCalculators.push_back(new StructPearson());
+						}else if (Estimators[i] == "soergel") { 
+							sumCalculators.push_back(new Soergel());
+						}else if (Estimators[i] == "spearman") { 
+							sumCalculators.push_back(new Spearman());
+						}else if (Estimators[i] == "structkulczynski") { 
+							sumCalculators.push_back(new StructKulczynski());
+						}else if (Estimators[i] == "speciesprofile") { 
+							sumCalculators.push_back(new SpeciesProfile());
+						}else if (Estimators[i] == "hamming") { 
+							sumCalculators.push_back(new Hamming());
+						}else if (Estimators[i] == "structchi2") { 
+							sumCalculators.push_back(new StructChi2());
+						}else if (Estimators[i] == "gower") { 
+							sumCalculators.push_back(new Gower());
+						}else if (Estimators[i] == "memchi2") { 
+							sumCalculators.push_back(new MemChi2());
+						}else if (Estimators[i] == "memchord") { 
+							sumCalculators.push_back(new MemChord());
+						}else if (Estimators[i] == "memeuclidean") { 
+							sumCalculators.push_back(new MemEuclidean());
+						}else if (Estimators[i] == "mempearson") { 
+							sumCalculators.push_back(new MemPearson());
 						}
 					}
 				}
 				
-				outputFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "shared.summary";
-				openOutputFile(outputFileName, outputFileHandle);
-				outputNames.push_back(outputFileName);
-				
 				mult = false;
 			}
 		}
@@ -176,13 +283,14 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
 void SummarySharedCommand::help(){
 	try {
 		m->mothurOut("The summary.shared command can only be executed after a successful read.otu command.\n");
-		m->mothurOut("The summary.shared command parameters are label, calc and all.  No parameters are required.\n");
+		m->mothurOut("The summary.shared command parameters are label, calc, distance and all.  No parameters are required.\n");
 		m->mothurOut("The summary.shared command should be in the following format: \n");
 		m->mothurOut("summary.shared(label=yourLabel, calc=yourEstimators, groups=yourGroups).\n");
 		m->mothurOut("Example summary.shared(label=unique-.01-.03, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n");
 		validCalculator->printCalc("sharedsummary", cout);
 		m->mothurOut("The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan\n");
 		m->mothurOut("The default value for groups is all the groups in your groupfile.\n");
+		m->mothurOut("The distance parameter allows you to indicate you would like a distance file created for each calculator for each label, default=f.\n");
 		m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
 		m->mothurOut("The all parameter is used to specify if you want the estimate of all your groups together.  This estimate can only be made for sharedsobs and sharedchao calculators. The default is false.\n");
 		m->mothurOut("If you use sharedchao and run into memory issues, set all to false. \n");
@@ -211,6 +319,9 @@ int SummarySharedCommand::execute(){
 	
 		if (abort == true) { return 0; }
 		
+		ofstream outputFileHandle, outAll;
+		string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "shared.summary";
+		
 		//if the users entered no valid calculators don't execute command
 		if (sumCalculators.size() == 0) { return 0; }
 		//check if any calcs can do multiples
@@ -229,18 +340,24 @@ int SummarySharedCommand::execute(){
 		input = globaldata->ginput;
 		lookup = input->getSharedRAbundVectors();
 		string lastLabel = lookup[0]->getLabel();
-		
+	
+		/******************************************************/
+		//output headings for files
+		/******************************************************/
 		//output estimator names as column headers
+		m->openOutputFile(outputFileName, outputFileHandle);
 		outputFileHandle << "label" <<'\t' << "comparison" << '\t'; 
 		for(int i=0;i<sumCalculators.size();i++){
 			outputFileHandle << '\t' << sumCalculators[i]->getName();
+			if (sumCalculators[i]->getCols() == 3) {   outputFileHandle << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";  }
 		}
 		outputFileHandle << endl;
+		outputFileHandle.close();
 		
 		//create file and put column headers for multiple groups file
+		string outAllFileName = ((m->getRootName(globaldata->inputFileName)) + "sharedmultiple.summary");
 		if (mult == true) {
-			outAllFileName = ((getRootName(globaldata->inputFileName)) + "sharedmultiple.summary");
-			openOutputFile(outAllFileName, outAll);
+			m->openOutputFile(outAllFileName, outAll);
 			outputNames.push_back(outAllFileName);
 			
 			outAll << "label" <<'\t' << "comparison" << '\t'; 
@@ -250,6 +367,7 @@ int SummarySharedCommand::execute(){
 				}
 			}
 			outAll << endl;
+			outAll.close();
 		}
 		
 		if (lookup.size() < 2) { 
@@ -257,40 +375,71 @@ int SummarySharedCommand::execute(){
 			for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
 			
 			//close files and clean up
-			outputFileHandle.close();  remove(outputFileName.c_str());
-			if (mult == true) {  outAll.close();  remove(outAllFileName.c_str());  }
+			remove(outputFileName.c_str());
+			if (mult == true) { remove(outAllFileName.c_str());  }
 			return 0;
 		//if you only have 2 groups you don't need a .sharedmultiple file
 		}else if ((lookup.size() == 2) && (mult == true)) { 
 			mult = false;
-			outAll.close();  
 			remove(outAllFileName.c_str());
 			outputNames.pop_back();
 		}
-					
+		
+		if (m->control_pressed) {
+			if (mult) {  remove(outAllFileName.c_str());  }
+			remove(outputFileName.c_str()); 
+			delete input; globaldata->ginput = NULL;
+			for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+			for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
+			globaldata->Groups.clear(); 
+			return 0;
+		}
+		/******************************************************/
+		
+		
+		/******************************************************/
+		//comparison breakup to be used by different processes later
+		numGroups = globaldata->Groups.size();
+		lines.resize(processors);
+		for (int i = 0; i < processors; i++) {
+			lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
+			lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
+		}		
+		/******************************************************/
+		
 		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 		set<string> processedLabels;
 		set<string> userLabels = labels;
 			
 		//as long as you are not at the end of the file or done wih the lines you want
 		while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+			if (m->control_pressed) {
+				if (mult) {  remove(outAllFileName.c_str());  }
+				remove(outputFileName.c_str()); 
+				delete input; globaldata->ginput = NULL;
+				for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+				for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
+				globaldata->Groups.clear(); 
+				return 0;
+			}
+
 		
 			if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){			
 				m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-				process(lookup);
+				process(lookup, outputFileName, outAllFileName);
 				
 				processedLabels.insert(lookup[0]->getLabel());
 				userLabels.erase(lookup[0]->getLabel());
 			}
 			
-			if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+			if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 					string saveLabel = lookup[0]->getLabel();
 					
 					for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
 					lookup = input->getSharedRAbundVectors(lastLabel);
 
 					m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-					process(lookup);
+					process(lookup, outputFileName, outAllFileName);
 					
 					processedLabels.insert(lookup[0]->getLabel());
 					userLabels.erase(lookup[0]->getLabel());
@@ -307,6 +456,15 @@ int SummarySharedCommand::execute(){
 			lookup = input->getSharedRAbundVectors();
 		}
 		
+		if (m->control_pressed) {
+			if (mult) { remove(outAllFileName.c_str());  }
+			remove(outputFileName.c_str()); 
+			delete input; globaldata->ginput = NULL;
+			for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
+			globaldata->Groups.clear(); 
+			return 0;
+		}
+
 		//output error messages about any remaining user labels
 		set<string>::iterator it;
 		bool needToRun = false;
@@ -326,25 +484,28 @@ int SummarySharedCommand::execute(){
 				lookup = input->getSharedRAbundVectors(lastLabel);
 
 				m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-				process(lookup);
+				process(lookup, outputFileName, outAllFileName);
 				for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
 		}
 		
-
+				
 		//reset groups parameter
 		globaldata->Groups.clear();  
 		
-		//close files
-		outputFileHandle.close();
-		if (mult == true) {  outAll.close();  }
-		
 		for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
-		
 		delete input;  globaldata->ginput = NULL;
 		
+		if (m->control_pressed) {
+			remove(outAllFileName.c_str());  
+			remove(outputFileName.c_str()); 
+			return 0;
+		}
+		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
-		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}
+		m->mothurOut(outputFileName); m->mothurOutEndLine();	
+		if (mult) { m->mothurOut(outAllFileName); m->mothurOutEndLine();	outputTypes["summary"].push_back(outAllFileName); }
+		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	} outputTypes["summary"].push_back(outputFileName);
 		m->mothurOutEndLine();
 
 		return 0;
@@ -356,65 +517,248 @@ int SummarySharedCommand::execute(){
 }
 
 /***********************************************************/
-void SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup) {
+int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string sumFileName, string sumAllFileName) {
 	try {
-				//loop through calculators and add to file all for all calcs that can do mutiple groups
-				if (mult == true) {
-					//output label
-					outAll << thisLookup[0]->getLabel() << '\t';
+			vector< vector<seqDist> > calcDists;  //vector containing vectors that contains the summary results for each group compare
+			calcDists.resize(sumCalculators.size()); //one for each calc, this will be used to make .dist files
+				
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				if(processors == 1){
+					driver(thisLookup, 0, numGroups, sumFileName+".temp", sumAllFileName+".temp", calcDists);
+					m->appendFiles((sumFileName + ".temp"), sumFileName);
+					remove((sumFileName + ".temp").c_str());
+					if (mult) {
+						m->appendFiles((sumAllFileName + ".temp"), sumAllFileName);
+						remove((sumAllFileName + ".temp").c_str());
+					}
+				}else{
+					int process = 1;
+					vector<int> processIDS;
+		
+					//loop through and create all the processes you want
+					while (process != processors) {
+						int pid = fork();
+						
+						if (pid > 0) {
+							processIDS.push_back(pid); 
+							process++;
+						}else if (pid == 0){
+							driver(thisLookup, lines[process].start, lines[process].end, sumFileName + toString(getpid()) + ".temp", sumAllFileName + toString(getpid()) + ".temp", calcDists);   
+							
+							//only do this if you want a distance file
+							if (createPhylip) {
+								string tempdistFileName = m->getRootName(m->getSimpleName(sumFileName)) + toString(getpid()) + ".dist";
+								ofstream outtemp;
+								m->openOutputFile(tempdistFileName, outtemp);
+								
+								for (int i = 0; i < calcDists.size(); i++) {
+									outtemp << calcDists[i].size() << endl;
+									
+									for (int j = 0; j < calcDists[i].size(); j++) {
+										outtemp << calcDists[i][j].seq1 << '\t' << calcDists[i][j].seq2 << '\t' << calcDists[i][j].dist << endl;
+									}
+								}
+								outtemp.close();
+							}
+							
+							exit(0);
+						}else { 
+							m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
+							for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+							exit(0);
+						}
+					}
 					
-					//output groups names
-					string outNames = "";
-					for (int j = 0; j < thisLookup.size(); j++) {
-						outNames += thisLookup[j]->getGroup() +  "-";
+					//parent do your part
+					driver(thisLookup, lines[0].start, lines[0].end, sumFileName + toString(getpid()) + ".temp", sumAllFileName + toString(getpid()) + ".temp", calcDists);   
+					m->appendFiles((sumFileName + toString(getpid()) + ".temp"), sumFileName);
+					remove((sumFileName + toString(getpid()) + ".temp").c_str());
+					if (mult) { m->appendFiles((sumAllFileName + toString(getpid()) + ".temp"), sumAllFileName); }
+						
+					//force parent to wait until all the processes are done
+					for (int i = 0; i < processIDS.size(); i++) {
+						int temp = processIDS[i];
+						wait(&temp);
 					}
-					outNames = outNames.substr(0, outNames.length()-1); //rip off extra '-';
-					outAll << outNames << '\t';
 					
-					for(int i=0;i<sumCalculators.size();i++){
-						if (sumCalculators[i]->getMultiple() == true) { 
-							sumCalculators[i]->getValues(thisLookup);
-							outAll << '\t';
-							sumCalculators[i]->print(outAll);
+					for (int i = 0; i < processIDS.size(); i++) {
+						m->appendFiles((sumFileName + toString(processIDS[i]) + ".temp"), sumFileName);
+						remove((sumFileName + toString(processIDS[i]) + ".temp").c_str());
+						if (mult) {	remove((sumAllFileName + toString(processIDS[i]) + ".temp").c_str());	}
+						
+						if (createPhylip) {
+							string tempdistFileName = m->getRootName(m->getSimpleName(sumFileName)) + toString(processIDS[i]) +  ".dist";
+							ifstream intemp;
+							m->openInputFile(tempdistFileName, intemp);
+							
+							for (int i = 0; i < calcDists.size(); i++) {
+								int size = 0;
+								intemp >> size; m->gobble(intemp);
+									
+								for (int j = 0; j < size; j++) {
+									int seq1 = 0;
+									int seq2 = 0;
+									float dist = 1.0;
+									
+									intemp >> seq1 >> seq2 >> dist;   m->gobble(intemp);
+									
+									seqDist tempDist(seq1, seq2, dist);
+									calcDists[i].push_back(tempDist);
+								}
+							}
+							intemp.close();
+							remove(tempdistFileName.c_str());
 						}
 					}
-					outAll << endl;
+
 				}
-	
-				int n = 1; 
-				vector<SharedRAbundVector*> subset;
-				for (int k = 0; k < (thisLookup.size() - 1); k++) { // pass cdd each set of groups to commpare
-					for (int l = n; l < thisLookup.size(); l++) {
-						
-						outputFileHandle << thisLookup[0]->getLabel() << '\t';
-						
-						subset.clear(); //clear out old pair of sharedrabunds
-						//add new pair of sharedrabunds
-						subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]); 
+			#else
+				driver(thisLookup, 0, numGroups, (sumFileName + ".temp"), (sumAllFileName + ".temp"), calcDists);
+				m->appendFiles((sumFileName + ".temp"), sumFileName);
+				remove((sumFileName + ".temp").c_str());
+				if (mult) {
+					m->appendFiles((sumAllFileName + ".temp"), sumAllFileName);
+					remove((sumAllFileName + ".temp").c_str());
+				}
+			#endif
+			
+			if (createPhylip) {
+				for (int i = 0; i < calcDists.size(); i++) {
+					if (m->control_pressed) { break; }
+				
+					string distFileName = outputDir + m->getRootName(m->getSimpleName(sumFileName)) + sumCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".dist";
+					outputNames.push_back(distFileName);
+					ofstream outDist;
+					m->openOutputFile(distFileName, outDist);
+					outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
+					
+					//initialize matrix
+					vector< vector<float> > matrix; //square matrix to represent the distance
+					matrix.resize(thisLookup.size());
+					for (int k = 0; k < thisLookup.size(); k++) {  matrix[k].resize(thisLookup.size(), 0.0); }
+					
+					
+					for (int j = 0; j < calcDists[i].size(); j++) {
+						int row = calcDists[i][j].seq1;
+						int column = calcDists[i][j].seq2;
+						float dist = calcDists[i][j].dist;
 						
-						//sort groups to be alphanumeric
-						if (thisLookup[k]->getGroup() > thisLookup[l]->getGroup()) {
-							outputFileHandle << (thisLookup[l]->getGroup() +'\t' + thisLookup[k]->getGroup()) << '\t'; //print out groups
-						}else{
-							outputFileHandle << (thisLookup[k]->getGroup() +'\t' + thisLookup[l]->getGroup()) << '\t'; //print out groups
+						matrix[row][column] = dist;
+						matrix[column][row] = dist;
+					}
+					
+					//output to file
+					outDist << thisLookup.size() << endl;
+					for (int r=0; r<thisLookup.size(); r++) { 
+						//output name
+						string name = thisLookup[r]->getGroup();
+						if (name.length() < 10) { //pad with spaces to make compatible
+							while (name.length() < 10) {  name += " ";  }
 						}
-						
-						for(int i=0;i<sumCalculators.size();i++) {
+						outDist << name << '\t';
+					
+						//output distances
+						for (int l = 0; l < r; l++) {	outDist  << matrix[r][l] << '\t';  }
+						outDist << endl;
+					}
+					
+					outDist.close();
+				}
+			}
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SummarySharedCommand", "process");
+		exit(1);
+	}
+}
+/**************************************************************************************************/
+int SummarySharedCommand::driver(vector<SharedRAbundVector*> thisLookup, int start, int end, string sumFile, string sumAllFile, vector< vector<seqDist> >& calcDists) { 
+	try {
+		
+		//loop through calculators and add to file all for all calcs that can do mutiple groups
+		if (mult == true) {
+			ofstream outAll;
+			m->openOutputFile(sumAllFile, outAll);
+			
+			//output label
+			outAll << thisLookup[0]->getLabel() << '\t';
+			
+			//output groups names
+			string outNames = "";
+			for (int j = 0; j < thisLookup.size(); j++) {
+				outNames += thisLookup[j]->getGroup() +  "-";
+			}
+			outNames = outNames.substr(0, outNames.length()-1); //rip off extra '-';
+			outAll << outNames << '\t';
+			
+			for(int i=0;i<sumCalculators.size();i++){
+				if (sumCalculators[i]->getMultiple() == true) { 
+					sumCalculators[i]->getValues(thisLookup);
+					
+					if (m->control_pressed) { outAll.close(); return 1; }
+					
+					outAll << '\t';
+					sumCalculators[i]->print(outAll);
+				}
+			}
+			outAll << endl;
+			outAll.close();
+		}
+		
+		ofstream outputFileHandle;
+		m->openOutputFile(sumFile, outputFileHandle);
+		
+		vector<SharedRAbundVector*> subset;
+		for (int k = start; k < end; k++) { // pass cdd each set of groups to compare
 
-							sumCalculators[i]->getValues(subset); //saves the calculator outputs
-							outputFileHandle << '\t';
-							sumCalculators[i]->print(outputFileHandle);
+			for (int l = 0; l < k; l++) {
+				
+				outputFileHandle << thisLookup[0]->getLabel() << '\t';
+				
+				subset.clear(); //clear out old pair of sharedrabunds
+				//add new pair of sharedrabunds
+				subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]); 
+				
+				//sort groups to be alphanumeric
+				if (thisLookup[k]->getGroup() > thisLookup[l]->getGroup()) {
+					outputFileHandle << (thisLookup[l]->getGroup() +'\t' + thisLookup[k]->getGroup()) << '\t'; //print out groups
+				}else{
+					outputFileHandle << (thisLookup[k]->getGroup() +'\t' + thisLookup[l]->getGroup()) << '\t'; //print out groups
+				}
+				
+				for(int i=0;i<sumCalculators.size();i++) {
+					
+					//if this calc needs all groups to calculate the pair load all groups
+					if (sumCalculators[i]->getNeedsAll()) { 
+						//load subset with rest of lookup for those calcs that need everyone to calc for a pair
+						for (int w = 0; w < thisLookup.size(); w++) {
+							if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); }
 						}
-						outputFileHandle << endl;
 					}
-					n++;
+					
+					vector<double> tempdata = sumCalculators[i]->getValues(subset); //saves the calculator outputs
+					
+					if (m->control_pressed) { outputFileHandle.close(); return 1; }
+					
+					outputFileHandle << '\t';
+					sumCalculators[i]->print(outputFileHandle);
+					
+					seqDist temp(l, k, tempdata[0]);
+					calcDists[i].push_back(temp);
 				}
-
+				outputFileHandle << endl;
+			}
+		}
+		
+		outputFileHandle.close();
+		
+		return 0;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "SummarySharedCommand", "process");
+		m->errorOut(e, "SummarySharedCommand", "driver");
 		exit(1);
 	}
 }
+/**************************************************************************************************/
+
 
-/***********************************************************/