X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.cpp;h=8cf1f2fd6606f97bed2e10d0301994d769a8aa94;hb=191ae1be0679d5cf4eda950b3b1bf26fb7dd503d;hp=0928d2e6b439b9775e62b5abd8c91b4254216e67;hpb=37519fc35c0eb1523e84227517694c4015847c6d;p=mothur.git

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 0928d2e..8cf1f2f 100644
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -11,56 +11,213 @@
 #include "sharedsobs.h"
 #include "sharednseqs.h"
 
+//**********************************************************************************************************************
+vector<string> RareFactSharedCommand::getValidParameters(){	
+	try {
+		string Array[] =  {"iters","freq","label","calc","groups", "jumble","outputdir","inputdir"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RareFactSharedCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+RareFactSharedCommand::RareFactSharedCommand(){	
+	try {
+		abort = true;
+		//initialize outputTypes
+		vector<string> tempOutNames;
+		outputTypes["sharedrarefaction"] = tempOutNames;
+		outputTypes["sharedr_nseqs"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> RareFactSharedCommand::getRequiredParameters(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RareFactSharedCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> RareFactSharedCommand::getRequiredFiles(){	
+	try {
+		string Array[] =  {"shared"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RareFactSharedCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 
-RareFactSharedCommand::RareFactSharedCommand(){
+RareFactSharedCommand::RareFactSharedCommand(string option)  {
 	try {
 		globaldata = GlobalData::getInstance();
-		string fileNameRoot;
-		fileNameRoot = getRootName(globaldata->inputFileName);
-		format = globaldata->getFormat();
-		validCalculator = new ValidCalculators();
+		
+		abort = false;
+		allLines = 1;
+		labels.clear();
+		Estimators.clear();
+		Groups.clear();
 				
-		int i;
-		for (i=0; i<globaldata->Estimators.size(); i++) {
-			if (validCalculator->isValidCalculator("sharedrarefaction", globaldata->Estimators[i]) == true) { 
-				if (globaldata->Estimators[i] == "sharedobserved") { 
-					rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
-				}else if (globaldata->Estimators[i] == "sharednseqs") { 
-					rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", "")));
-				}
+		//allow user to run help
+		if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+		
+		else {
+			//valid paramters for this command
+			string Array[] =  {"iters","freq","label","calc","groups", "jumble","outputdir","inputdir"};
+			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;  }
+			}
+			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["sharedrarefaction"] = tempOutNames;
+			outputTypes["sharedr_nseqs"] = tempOutNames;
+			
+			//make sure the user has already run the read.otu command
+			if (globaldata->getSharedFile() == "") {
+				if (globaldata->getListFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the collect.shared command."); m->mothurOutEndLine(); abort = true; }
+				else if (globaldata->getGroupFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the collect.shared command."); m->mothurOutEndLine(); abort = true; }
+			}
+			
+			//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 += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it	
+			}
 
+			
+			//check for optional parameter and set defaults
+			// ...at some point should added some additional type checking...
+			label = validParameter.validFile(parameters, "label", false);			
+			if (label == "not found") { label = ""; }
+			else { 
+				if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
+				else { allLines = 1;  }
+			}
+			
+			//if the user has not specified any labels use the ones from read.otu
+			if(label == "") {  
+				allLines = globaldata->allLines; 
+				labels = globaldata->labels; 
 			}
+				
+			calc = validParameter.validFile(parameters, "calc", false);			
+			if (calc == "not found") { calc = "sharedobserved";  }
+			else { 
+				 if (calc == "default")  {  calc = "sharedobserved";  }
+			}
+			m->splitAtDash(calc, Estimators);
+			
+			groups = validParameter.validFile(parameters, "groups", false);			
+			if (groups == "not found") { groups = ""; }
+			else { 
+				m->splitAtDash(groups, Groups);
+			}
+			globaldata->Groups = Groups;
+			
+			string temp;
+			temp = validParameter.validFile(parameters, "freq", false);			if (temp == "not found") { temp = "100"; }
+			convert(temp, freq); 
+			
+			temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }
+			convert(temp, nIters); 
+			
+			temp = validParameter.validFile(parameters, "jumble", false);			if (temp == "not found") { temp = "T"; }
+			if (m->isTrue(temp)) { jumble = true; }
+			else { jumble = false; }
+			globaldata->jumble = jumble;
+			
+			if (abort == false) {
+			
+				string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(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", "")));
+							outputNames.push_back(fileNameRoot+"shared.rarefaction"); outputTypes["sharedrarefaction"].push_back(fileNameRoot+"shared.rarefaction");
+						}else if (Estimators[i] == "sharednseqs") { 
+							rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", "")));
+							outputNames.push_back(fileNameRoot+"shared.r_nseqs"); outputTypes["sharedr_nseqs"].push_back(fileNameRoot+"shared.r_nseqs");
+						}
+					}
+				}
+			}
+				
 		}
-		
-		//reset calc for next command
-		globaldata->setCalc("");
 
 	}
 	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";
+		m->errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the RareFactSharedCommand class function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+//**********************************************************************************************************************
+
+void RareFactSharedCommand::help(){
+	try {
+		m->mothurOut("The rarefaction.shared command can only be executed after a successful read.otu command.\n");
+		m->mothurOut("The rarefaction.shared command parameters are label, iters, groups, jumble and calc.  No parameters are required.\n");
+		m->mothurOut("The rarefaction command should be in the following format: \n");
+		m->mothurOut("rarefaction.shared(label=yourLabel, iters=yourIters, calc=yourEstimators, jumble=yourJumble, groups=yourGroups).\n");
+		m->mothurOut("The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n");
+		m->mothurOut("Example rarefaction.shared(label=unique-0.01-0.03,  iters=10000, groups=B-C, jumble=T, calc=sharedobserved).\n");
+		m->mothurOut("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");
+		m->mothurOut("The default value for groups is all the groups in your groupfile, and jumble is true.\n");
+		validCalculator->printCalc("sharedrarefaction", cout);
+		m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
+		m->mothurOut("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");
+		m->mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n");
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RareFactSharedCommand", "help");
 		exit(1);
-	}	
-			
+	}
 }
 
 //**********************************************************************************************************************
 
 RareFactSharedCommand::~RareFactSharedCommand(){
-	delete input;
-	delete rCurve;
-	delete read;
+	if (abort == false) {
+		delete input;   globaldata->ginput = NULL;
+		delete read;
+		delete validCalculator;
+	}
 }
 
 //**********************************************************************************************************************
 
 int RareFactSharedCommand::execute(){
 	try {
-		int count = 1;
+	
+		if (abort == true) { return 0; }
 		
 		//if the users entered no valid calculators don't execute command
 		if (rDisplays.size() == 0) { return 0; }
@@ -70,51 +227,133 @@ int RareFactSharedCommand::execute(){
 			
 		input = globaldata->ginput;
 		lookup = input->getSharedRAbundVectors();
+		string lastLabel = lookup[0]->getLabel();
 		
+		if (m->control_pressed) { 
+			globaldata->Groups.clear(); 
+			for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}
+			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}
+			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
+			return 0;
+		}
+
+
 		if (lookup.size() < 2) { 
-			cout << "I cannot run the command without at least 2 valid groups."; 
+			m->mothurOut("I cannot run the command without at least 2 valid groups."); 
 			for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
 			return 0;
 		}
-					
 		
-		while(lookup[0] != NULL){
-		
-			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
-				//create collectors curve
+		//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) { 
+				globaldata->Groups.clear(); 
+				for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}
+				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}
+				for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
+				return 0;
+			}
+			
+			if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
+				m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 				rCurve = new Rarefact(lookup, rDisplays);
-				convert(globaldata->getFreq(), freq);
-				convert(globaldata->getIters(), nIters);
 				rCurve->getSharedCurve(freq, nIters);
-			
 				delete rCurve;
 			
-				cout << lookup[0]->getLabel() << '\t' << count << endl;
+				processedLabels.insert(lookup[0]->getLabel());
+				userLabels.erase(lookup[0]->getLabel());
 			}
 			
-			//prevent memory leak
-			for (int i = 0; i < lookup.size(); i++) {	delete lookup[i];	}
+			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();
+					rCurve = new Rarefact(lookup, rDisplays);
+					rCurve->getSharedCurve(freq, nIters);
+					delete rCurve;
+
+					processedLabels.insert(lookup[0]->getLabel());
+					userLabels.erase(lookup[0]->getLabel());
+					
+					//restore real lastlabel to save below
+					lookup[0]->setLabel(saveLabel);
+			}
 				
+			
+			lastLabel = lookup[0]->getLabel();
+			
 			//get next line to process
+			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
 			lookup = input->getSharedRAbundVectors();
-			count++;
 		}
-	
+		
+		if (m->control_pressed) { 
+				globaldata->Groups.clear(); 
+				for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}
+				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}
+				return 0;
+		}
+		
+		//output error messages about any remaining user labels
+		set<string>::iterator it;
+		bool needToRun = false;
+		for (it = userLabels.begin(); it != userLabels.end(); it++) {  
+			m->mothurOut("Your file does not include the label " + *it); 
+			if (processedLabels.count(lastLabel) != 1) {
+				m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+				needToRun = true;
+			}else {
+				m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+			}
+		}
+		
+		if (m->control_pressed) { 
+				globaldata->Groups.clear(); 
+				for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}
+				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}
+				return 0;
+		}
+		
+		//run last label if you need to
+		if (needToRun == true)  {
+			for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {	delete lookup[i]; }  } 
+			lookup = input->getSharedRAbundVectors(lastLabel);
+
+			m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+			rCurve = new Rarefact(lookup, rDisplays);
+			rCurve->getSharedCurve(freq, nIters);
+			delete rCurve;
+			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
+		}
+		
 		for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}	
 		
 		//reset groups parameter
-		globaldata->Groups.clear();  globaldata->setGroups("");
+		globaldata->Groups.clear();  
+		
+		if (m->control_pressed) { 
+				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].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->mothurOutEndLine();
 
 		return 0;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "RareFactSharedCommand", "execute");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the RareFactSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }