X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.cpp;h=fdc967856043fc8e191c9b3167fb83634f82ec0a;hb=753dc84cf289b1d5dc0ca5b0c043640927aa951a;hp=5e36299505246ecbdbae8c64822a59e916f54dcc;hpb=8c548985e92f5be0bde10eddea89a6ae888b73da;p=mothur.git

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 5e36299..fdc9678 100644
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -9,21 +9,110 @@
 
 #include "rarefactsharedcommand.h"
 #include "sharedsobs.h"
+#include "sharednseqs.h"
 
 //**********************************************************************************************************************
 
-RareFactSharedCommand::RareFactSharedCommand(){
+RareFactSharedCommand::RareFactSharedCommand(string option){
 	try {
 		globaldata = GlobalData::getInstance();
-		string fileNameRoot;
-		fileNameRoot = getRootName(globaldata->inputFileName);
+		
+		abort = false;
+		allLines = 1;
+		lines.clear();
+		labels.clear();
+		Estimators.clear();
+		Groups.clear();
+				
+		//allow user to run help
+		if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+		
+		else {
+			//valid paramters for this command
+			string Array[] =  {"iters","line","label","calc","groups"};
+			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			
+			OptionParser parser(option);
+			map<string,string> parameters = parser.getParameters();
+			
+			ValidParameters validParameter;
+			
+			//check to make sure all parameters are valid for command
+			for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+			}
+			
+			//make sure the user has already run the read.otu command
+			if (globaldata->getSharedFile() == "") {
+				if (globaldata->getListFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared command." << endl; abort = true; }
+				else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared command." << endl; abort = true; }
+			}
+
+			
+			//check for optional parameter and set defaults
+			// ...at some point should added some additional type checking...
+			line = validParameter.validFile(parameters, "line", false);				
+			if (line == "not found") { line = "";  }
+			else { 
+				if(line != "all") {  splitAtDash(line, lines);  allLines = 0;  }
+				else { allLines = 1;  }
+			}
+			
+			label = validParameter.validFile(parameters, "label", false);			
+			if (label == "not found") { label = ""; }
+			else { 
+				if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
+				else { allLines = 1;  }
+			}
+			
+			//make sure user did not use both the line and label parameters
+			if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
+			//if the user has not specified any line or labels use the ones from read.otu
+			else if((line == "") && (label == "")) {  
+				allLines = globaldata->allLines; 
+				labels = globaldata->labels; 
+				lines = globaldata->lines;
+			}
 				
-		int i;
-		for (i=0; i<globaldata->sharedRareEstimators.size(); i++) {
-			if (globaldata->sharedRareEstimators[i] == "sharedobserved") { 
-				rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
+			calc = validParameter.validFile(parameters, "calc", false);			
+			if (calc == "not found") { calc = "sharedobserved";  }
+			else { 
+				 if (calc == "default")  {  calc = "sharedobserved";  }
 			}
+			splitAtDash(calc, Estimators);
+			
+			groups = validParameter.validFile(parameters, "groups", false);			
+			if (groups == "not found") { groups = ""; }
+			else { 
+				splitAtDash(groups, Groups);
+			}
+			globaldata->Groups = Groups;
+			
+			string temp;
+			temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }
+			convert(temp, nIters); 
+			
+			if (abort == false) {
+			
+				string fileNameRoot = getRootName(globaldata->inputFileName);
+//				format = globaldata->getFormat();
+
+				
+				validCalculator = new ValidCalculators();
+				
+				for (int i=0; i<Estimators.size(); i++) {
+					if (validCalculator->isValidCalculator("sharedrarefaction", Estimators[i]) == true) { 
+						if (Estimators[i] == "sharedobserved") { 
+							rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
+						}else if (Estimators[i] == "sharednseqs") { 
+							rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", "")));
+						}
+					}
+				}
+			}
+				
 		}
+
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -38,50 +127,131 @@ RareFactSharedCommand::RareFactSharedCommand(){
 
 //**********************************************************************************************************************
 
+void RareFactSharedCommand::help(){
+	try {
+		cout << "The rarefaction.shared command can only be executed after a successful read.otu command." << "\n";
+		cout << "The rarefaction.shared command parameters are label, line, iters, groups and calc.  No parameters are required, but you may not use " << "\n";
+		cout << "both the line and label parameters at the same time. The rarefaction command should be in the following format: " << "\n";
+		cout << "rarefaction.shared(label=yourLabel, line=yourLines, iters=yourIters, calc=yourEstimators, groups=yourGroups)." << "\n";
+		cout << "Example rarefaction.shared(label=unique-.01-.03, line=0-5-10, iters=10000, groups=B-C, calc=sharedobserved)." << "\n";
+		cout << "The default values for iters is 1000, freq is 100, and calc is sharedobserved which calculates the shared rarefaction curve for the observed richness." << "\n";
+		cout << "The default value for groups is all the groups in your groupfile." << "\n";
+		validCalculator->printCalc("sharedrarefaction", cout);
+		cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
+		cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups." << "\n";
+		cout << "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\n";
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the RareFactSharedCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+}
+
+//**********************************************************************************************************************
+
 RareFactSharedCommand::~RareFactSharedCommand(){
-	delete order;
 	delete input;
 	delete rCurve;
 	delete read;
+	delete validCalculator;
 }
 
 //**********************************************************************************************************************
 
 int RareFactSharedCommand::execute(){
 	try {
+	
+		if (abort == true) { return 0; }
+		
 		int count = 1;
-		read = new ReadPhilFile(globaldata->inputFileName);	
-		read->read(&*globaldata); 
 		
+		//if the users entered no valid calculators don't execute command
+		if (rDisplays.size() == 0) { return 0; }
+
+		read = new ReadOTUFile(globaldata->inputFileName);	
+		read->read(&*globaldata); 
+			
 		input = globaldata->ginput;
-		SharedList = globaldata->gSharedList;
-		order = SharedList->getSharedOrderVector();
-		
-		while(order != NULL){
+		lookup = input->getSharedRAbundVectors();
+		vector<SharedRAbundVector*> lastLookup = lookup;
+
+		if (lookup.size() < 2) { 
+			cout << "I cannot run the command without at least 2 valid groups."; 
+			for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+			return 0;
+		}
 		
-			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
-				//create collectors curve
-				rCurve = new Rarefact(order, rDisplays);
-				convert(globaldata->getFreq(), freq);
-				convert(globaldata->getIters(), nIters);
-				rCurve->getSharedCurve(freq, nIters);
+		//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;
+		set<int> userLines = lines;
+	
+		//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) || (userLines.size() != 0))) {
 			
+			if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
+				
+				rCurve = new Rarefact(lookup, rDisplays);
+				rCurve->getSharedCurve(freq, nIters);
 				delete rCurve;
 			
-				cout << order->getLabel() << '\t' << count << endl;
+				cout << lookup[0]->getLabel() << '\t' << count << endl;
+				processedLabels.insert(lookup[0]->getLabel());
+				userLabels.erase(lookup[0]->getLabel());
+				userLines.erase(count);
 			}
 			
-			SharedList = input->getSharedListVector(); //get new list vector to process
-			if (SharedList != NULL) {
-				order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
-				count++;
+			if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
+					cout << lastLookup[0]->getLabel() << '\t' << count << endl;
+					rCurve = new Rarefact(lastLookup, rDisplays);
+					rCurve->getSharedCurve(freq, nIters);
+					delete rCurve;
+
+					processedLabels.insert(lastLookup[0]->getLabel());
+					userLabels.erase(lastLookup[0]->getLabel());
+			}
+				
+			//prevent memory leak
+			if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  } }
+			lastLookup = lookup;
+			
+			//get next line to process
+			lookup = input->getSharedRAbundVectors();
+			count++;
+		}
+		
+		//output error messages about any remaining user labels
+		set<string>::iterator it;
+		bool needToRun = false;
+		for (it = userLabels.begin(); it != userLabels.end(); it++) {  
+			cout << "Your file does not include the label "<< *it; 
+			if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
+				cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+				needToRun = true;
 			}else {
-				break;
+				cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
 			}
+		}
 		
+		//run last line if you need to
+		if (needToRun == true)  {
+			cout << lastLookup[0]->getLabel() << '\t' << count << endl;
+			rCurve = new Rarefact(lastLookup, rDisplays);
+			rCurve->getSharedCurve(freq, nIters);
+			delete rCurve;
 		}
-	
+		
+		for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  }
+
 		for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}	
+		
+		//reset groups parameter
+		globaldata->Groups.clear();  
+
 		return 0;
 	}
 	catch(exception& e) {