X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=rarefactsharedcommand.cpp;fp=rarefactsharedcommand.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=64bdbb4ceebd18f5abeff63b26fbb4d4ac3dc924;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
deleted file mode 100644
index 64bdbb4..0000000
--- a/rarefactsharedcommand.cpp
+++ /dev/null
@@ -1,341 +0,0 @@
-/*
- *  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);
-	}
-}
-
-
-//**********************************************************************************************************************