X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.cpp;fp=rarefactsharedcommand.cpp;h=64bdbb4ceebd18f5abeff63b26fbb4d4ac3dc924;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
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--- /dev/null
+++ b/rarefactsharedcommand.cpp
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+/*
+ *  rarefactsharedcommand.cpp
+ *  Dotur
+ *
+ *  Created by Sarah Westcott on 1/6/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "rarefactsharedcommand.h"
+#include "sharedsobs.h"
+#include "sharednseqs.h"
+
+//**********************************************************************************************************************
+vector<string> RareFactSharedCommand::setParameters(){	
+	try {
+		CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
+		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+		CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq);
+		CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
+		CommandParameter pcalc("calc", "Multiple", "sharednseqs-sharedobserved", "sharedobserved", "", "", "",true,false); parameters.push_back(pcalc);
+		CommandParameter pjumble("jumble", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pjumble);
+		CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		
+		vector<string> myArray;
+		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RareFactSharedCommand", "setParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+string RareFactSharedCommand::getHelpString(){	
+	try {
+		string helpString = "";
+		ValidCalculators validCalculator;
+		helpString += "The collect.shared command parameters are shared, label, freq, calc and groups.  shared is required if there is no current sharedfile. \n";
+		helpString += "The rarefaction.shared command parameters are shared, label, iters, groups, jumble and calc.  shared is required if there is no current sharedfile. \n";
+		helpString += "The rarefaction command should be in the following format: \n";
+		helpString += "rarefaction.shared(label=yourLabel, iters=yourIters, calc=yourEstimators, jumble=yourJumble, groups=yourGroups).\n";
+		helpString += "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";
+		helpString += "Example rarefaction.shared(label=unique-0.01-0.03,  iters=10000, groups=B-C, jumble=T, calc=sharedobserved).\n";
+		helpString += "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";
+		helpString += "The default value for groups is all the groups in your groupfile, and jumble is true.\n";
+		helpString += validCalculator.printCalc("sharedrarefaction");
+		helpString += "The label parameter is used to analyze specific labels in your input.\n";
+		helpString += "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";
+		helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n";
+		return helpString;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RareFactSharedCommand", "getHelpString");
+		exit(1);
+	}
+}
+
+//**********************************************************************************************************************
+RareFactSharedCommand::RareFactSharedCommand(){	
+	try {
+		abort = true; calledHelp = true; 
+		setParameters();
+		vector<string> tempOutNames;
+		outputTypes["sharedrarefaction"] = tempOutNames;
+		outputTypes["sharedr_nseqs"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+
+RareFactSharedCommand::RareFactSharedCommand(string option)  {
+	try {
+		abort = false; calledHelp = false;   
+		allLines = 1;
+				
+		//allow user to run help
+		if(option == "help") {  help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+		
+		else {
+			vector<string> myArray = setParameters();
+			
+			OptionParser parser(option);
+			map<string,string> parameters = parser.getParameters();
+			map<string,string>::iterator it;
+			
+			ValidParameters validParameter;
+			
+			//check to make sure all parameters are valid for command
+			for (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;
+			
+			//if the user changes the input directory command factory will send this info to us in the output parameter 
+			string inputDir = validParameter.validFile(parameters, "inputdir", false);		
+			if (inputDir == "not found"){	inputDir = "";		}
+			else {
+				string path;
+				it = parameters.find("shared");
+				//user has given a template file
+				if(it != parameters.end()){ 
+					path = m->hasPath(it->second);
+					//if the user has not given a path then, add inputdir. else leave path alone.
+					if (path == "") {	parameters["shared"] = inputDir + it->second;		}
+				}
+			}
+			
+			//get shared file
+			sharedfile = validParameter.validFile(parameters, "shared", true);
+			if (sharedfile == "not open") { sharedfile = ""; abort = true; }	
+			else if (sharedfile == "not found") { 
+				//if there is a current shared file, use it
+				sharedfile = m->getSharedFile(); 
+				if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+				else { 	m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
+			}else { m->setSharedFile(sharedfile); }
+			
+			
+			//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 = m->hasPath(sharedfile);		}
+			
+			
+			//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;  }
+			}
+			
+				
+			calc = validParameter.validFile(parameters, "calc", false);			
+			if (calc == "not found") { calc = "sharedobserved";  }
+			else { 
+				 if (calc == "default")  {  calc = "sharedobserved";  }
+			}
+			m->splitAtDash(calc, Estimators);
+			if (m->inUsersGroups("citation", Estimators)) { 
+				ValidCalculators validCalc; validCalc.printCitations(Estimators); 
+				//remove citation from list of calcs
+				for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
+			}
+			
+			groups = validParameter.validFile(parameters, "groups", false);			
+			if (groups == "not found") { groups = ""; }
+			else { 
+				m->splitAtDash(groups, Groups);
+			}
+			m->setGroups(Groups);
+			
+			string temp;
+			temp = validParameter.validFile(parameters, "freq", false);			if (temp == "not found") { temp = "100"; }
+			m->mothurConvert(temp, freq); 
+			
+			temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }
+			m->mothurConvert(temp, nIters); 
+			
+			temp = validParameter.validFile(parameters, "jumble", false);			if (temp == "not found") { temp = "T"; }
+			if (m->isTrue(temp)) { jumble = true; }
+			else { jumble = false; }
+			m->jumble = jumble;
+				
+		}
+
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+
+int RareFactSharedCommand::execute(){
+	try {
+	
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
+	
+		string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+		
+		ValidCalculators validCalculator;
+			
+		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");
+				}
+			}
+		}
+		
+		//if the users entered no valid calculators don't execute command
+		if (rDisplays.size() == 0) { return 0; }
+			
+		input = new InputData(sharedfile, "sharedfile");
+		lookup = input->getSharedRAbundVectors();
+		string lastLabel = lookup[0]->getLabel();
+		
+		if (m->control_pressed) { 
+			m->clearGroups(); 
+			delete input;
+			for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	}
+			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
+			return 0;
+		}
+
+
+		if (lookup.size() < 2) { 
+			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;
+		}
+		
+		//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) { 
+				m->clearGroups(); 
+				delete input;
+				for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}
+				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	}
+				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);
+				rCurve->getSharedCurve(freq, nIters);
+				delete rCurve;
+			
+				processedLabels.insert(lookup[0]->getLabel());
+				userLabels.erase(lookup[0]->getLabel());
+			}
+			
+			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();
+		}
+		
+		if (m->control_pressed) { 
+			m->clearGroups(); 
+			delete input;
+			for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	}
+			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) { 
+			m->clearGroups(); 
+			delete input; 
+			for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	}
+			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];	}	
+		m->clearGroups(); 
+		delete input;
+		
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } 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) {
+		m->errorOut(e, "RareFactSharedCommand", "execute");
+		exit(1);
+	}
+}
+
+
+//**********************************************************************************************************************