X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.cpp;h=324f02852189c175ec7383d44a4e498fa4ccc7d5;hb=8f7164a88df624fd0a8d1eddbb3d744463cc9ecb;hp=fdc967856043fc8e191c9b3167fb83634f82ec0a;hpb=753dc84cf289b1d5dc0ca5b0c043640927aa951a;p=mothur.git

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index fdc9678..324f028 100644
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -13,13 +13,12 @@
 
 //**********************************************************************************************************************
 
-RareFactSharedCommand::RareFactSharedCommand(string option){
+RareFactSharedCommand::RareFactSharedCommand(string option)  {
 	try {
 		globaldata = GlobalData::getInstance();
 		
 		abort = false;
 		allLines = 1;
-		lines.clear();
 		labels.clear();
 		Estimators.clear();
 		Groups.clear();
@@ -29,7 +28,7 @@ RareFactSharedCommand::RareFactSharedCommand(string option){
 		
 		else {
 			//valid paramters for this command
-			string Array[] =  {"iters","line","label","calc","groups"};
+			string Array[] =  {"iters","freq","label","calc","groups", "jumble","outputdir","inputdir"};
 			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 			
 			OptionParser parser(option);
@@ -44,20 +43,19 @@ RareFactSharedCommand::RareFactSharedCommand(string option){
 			
 			//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; }
+				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 += 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...
-			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 { 
@@ -65,13 +63,10 @@ RareFactSharedCommand::RareFactSharedCommand(string option){
 				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 == "")) {  
+			//if the user has not specified any labels use the ones from read.otu
+			if(label == "") {  
 				allLines = globaldata->allLines; 
 				labels = globaldata->labels; 
-				lines = globaldata->lines;
 			}
 				
 			calc = validParameter.validFile(parameters, "calc", false);			
@@ -89,12 +84,20 @@ RareFactSharedCommand::RareFactSharedCommand(string option){
 			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 (isTrue(temp)) { jumble = true; }
+			else { jumble = false; }
+			globaldata->jumble = jumble;
+			
 			if (abort == false) {
 			
-				string fileNameRoot = getRootName(globaldata->inputFileName);
+				string fileNameRoot = outputDir + getRootName(getSimpleName(globaldata->inputFileName));
 //				format = globaldata->getFormat();
 
 				
@@ -104,8 +107,10 @@ RareFactSharedCommand::RareFactSharedCommand(string option){
 					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");
 						}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");
 						}
 					}
 				}
@@ -115,49 +120,42 @@ RareFactSharedCommand::RareFactSharedCommand(string option){
 
 	}
 	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";
-		exit(1);
-	}	
-			
 }
 
 //**********************************************************************************************************************
 
 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";
+		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);
-		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";
+		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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "RareFactSharedCommand", "help");
 		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 input;
-	delete rCurve;
-	delete read;
-	delete validCalculator;
+	if (abort == false) {
+		delete input;   globaldata->ginput = NULL;
+		delete read;
+		delete validCalculator;
+	}
 }
 
 //**********************************************************************************************************************
@@ -167,8 +165,6 @@ int RareFactSharedCommand::execute(){
 	
 		if (abort == true) { return 0; }
 		
-		int count = 1;
-		
 		//if the users entered no valid calculators don't execute command
 		if (rDisplays.size() == 0) { return 0; }
 
@@ -177,10 +173,19 @@ int RareFactSharedCommand::execute(){
 			
 		input = globaldata->ginput;
 		lookup = input->getSharedRAbundVectors();
-		vector<SharedRAbundVector*> lastLookup = lookup;
+		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;
 		}
@@ -188,80 +193,113 @@ int RareFactSharedCommand::execute(){
 		//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))) {
+		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 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
-				
+			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;
 			
-				cout << lookup[0]->getLabel() << '\t' << count << endl;
 				processedLabels.insert(lookup[0]->getLabel());
 				userLabels.erase(lookup[0]->getLabel());
-				userLines.erase(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);
+			if ((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(lastLookup[0]->getLabel());
-					userLabels.erase(lastLookup[0]->getLabel());
+					processedLabels.insert(lookup[0]->getLabel());
+					userLabels.erase(lookup[0]->getLabel());
+					
+					//restore real lastlabel to save below
+					lookup[0]->setLabel(saveLabel);
 			}
 				
-			//prevent memory leak
-			if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  } }
-			lastLookup = lookup;
+			
+			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++) {  
-			cout << "Your file does not include the label "<< *it; 
-			if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
-				cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+			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 {
-				cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+				m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 			}
 		}
 		
-		//run last line if you need to
+		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)  {
-			cout << lastLookup[0]->getLabel() << '\t' << count << endl;
-			rCurve = new Rarefact(lastLookup, rDisplays);
+			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 < lastLookup.size(); i++) {  delete lastLookup[i];  }
-
 		for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}	
 		
 		//reset groups parameter
 		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);
-	}	
 }