X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=venncommand.cpp;h=0bed752e08ccb5a7672a5b5e1744569700cf73ab;hp=bb3762cc54f741d1e7c0a1fd7bdf9bc6c35f38db;hb=0470f6d037aacb3563c3f7010708120a4a67d4e6;hpb=bede5752eaeedb5a7e339439b6ba2f6670bca2b9

diff --git a/venncommand.cpp b/venncommand.cpp
index bb3762c..0bed752 100644
--- a/venncommand.cpp
+++ b/venncommand.cpp
@@ -19,51 +19,128 @@
 
 //**********************************************************************************************************************
 
-VennCommand::VennCommand(){
+VennCommand::VennCommand(string option){
 	try {
 		globaldata = GlobalData::getInstance();
-		format = globaldata->getFormat();
-		validCalculator = new ValidCalculators();
-		
-		int i;
-		
-		if (format == "list") {
-			for (i=0; i<globaldata->Estimators.size(); i++) {
-				if (validCalculator->isValidCalculator("vennsingle", globaldata->Estimators[i]) == true) { 
-					if (globaldata->Estimators[i] == "sobs") { 
-						vennCalculators.push_back(new Sobs());
-					}else if (globaldata->Estimators[i] == "chao") { 
-						vennCalculators.push_back(new Chao1());
-					}else if (globaldata->Estimators[i] == "ace") {
-						convert(globaldata->getAbund(), abund);
-						if(abund < 5)
-							abund = 10;
-						vennCalculators.push_back(new Ace(abund));
-					//}else if (globaldata->Estimators[i] == "jack") { 	
-						//vennCalculators.push_back(new Jackknife());
-					}
+		abort = false;
+		allLines = 1;
+		lines.clear();
+		labels.clear();
+		
+		//allow user to run help
+		if(option == "help") { help(); abort = true; }
+		
+		else {
+			//valid paramters for this command
+			string AlignArray[] =  {"groups","line","label","calc", "abund"};
+			vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+			
+			parser = new OptionParser();
+			parser->parse(option, parameters);  delete parser;
+			
+			ValidParameters* validParameter = new ValidParameters();
+		
+			//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;  }
+			}
+			
+			//make sure the user has already run the read.otu command
+			if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
+				 cout << "You must read a list, or a list and a group, or a shared before you can use the venn 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;
+			}
+			
+			groups = validParameter->validFile(parameters, "groups", false);			
+			if (groups == "not found") { groups = ""; }
+			else { 
+				splitAtDash(groups, Groups);
+				globaldata->Groups = Groups;
+			}
+			
+			format = globaldata->getFormat();
+			calc = validParameter->validFile(parameters, "calc", false);			
+			if (calc == "not found") { 
+				if(format == "list") { calc = "sobs"; }
+				else { calc = "sharedsobs"; }
+			}
+			else { 
+				 if (calc == "default")  {  
+					if(format == "list") { calc = "sobs"; }
+					else { calc = "sharedsobs"; }
 				}
 			}
-		}else {
-			for (i=0; i<globaldata->Estimators.size(); i++) {
-				if (validCalculator->isValidCalculator("vennshared", globaldata->Estimators[i]) == true) { 
-					if (globaldata->Estimators[i] == "sharedsobs") { 
-						vennCalculators.push_back(new SharedSobsCS());
-					}else if (globaldata->Estimators[i] == "sharedchao") { 
-						vennCalculators.push_back(new SharedChao1());
-					}else if (globaldata->Estimators[i] == "sharedace") { 
-						vennCalculators.push_back(new SharedAce());
+			splitAtDash(calc, Estimators);
+			
+			string temp;
+			temp = validParameter->validFile(parameters, "abund", false);		if (temp == "not found") { temp = "10"; }
+			convert(temp, abund); 
+
+			delete validParameter;
+			
+			if (abort == false) {
+				validCalculator = new ValidCalculators();
+		
+				int i;
+				
+				if (format == "list") {
+					for (i=0; i<Estimators.size(); i++) {
+						if (validCalculator->isValidCalculator("vennsingle", Estimators[i]) == true) { 
+							if (Estimators[i] == "sobs") { 
+								vennCalculators.push_back(new Sobs());
+							}else if (Estimators[i] == "chao") { 
+								vennCalculators.push_back(new Chao1());
+							}else if (Estimators[i] == "ace") {
+								if(abund < 5)
+									abund = 10;
+								vennCalculators.push_back(new Ace(abund));
+							}
+						}
+					}
+				}else {
+					for (i=0; i<Estimators.size(); i++) {
+						if (validCalculator->isValidCalculator("vennshared", Estimators[i]) == true) { 
+							if (Estimators[i] == "sharedsobs") { 
+								vennCalculators.push_back(new SharedSobsCS());
+							}else if (Estimators[i] == "sharedchao") { 
+								vennCalculators.push_back(new SharedChao1());
+							}else if (Estimators[i] == "sharedace") { 
+								vennCalculators.push_back(new SharedAce());
+							}
+						}
 					}
 				}
+				
+				venn = new Venn();
 			}
 		}
-		
-		venn = new Venn();
-		
-		//reset calc for next command
-		globaldata->setCalc("");
 
 		
+				
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function VennCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -74,6 +151,35 @@ VennCommand::VennCommand(){
 		exit(1);
 	}	
 }
+
+//**********************************************************************************************************************
+
+void VennCommand::help(){
+	try {
+		cout << "The venn command can only be executed after a successful read.otu command." << "\n";
+		cout << "The venn command parameters are groups, calc, abund, line and label.  No parameters are required, but you may not use line and label at the same time." << "\n";
+		cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your venn diagram, you may only use a maximum of 4 groups." << "\n";
+		cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like a venn diagram created for, and are also separated by dashes." << "\n";
+		cout << "The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels, abund=yourAbund)." << "\n";
+		cout << "Example venn(groups=A-B-C, line=1-3-5, calc=sharedsobs-sharedchao, abund=20)." << "\n";
+		cout << "The default value for groups is all the groups in your groupfile up to 4, and all lines in your inputfile will be used." << "\n";
+		cout << "The default value for calc is sobs if you have only read a list file or if you have selected only one group, and sharedsobs if you have multiple groups." << "\n";
+		cout << "The default available estimators for calc are sobs, chao and ace if you have only read a list file, and sharedsobs, sharedchao and sharedace if you have read a list and group file or a shared file." << "\n";
+		cout << "The only estmiator available four 4 groups is sharedsobs." << "\n";
+		cout << "The venn command outputs a .svg file for each calculator you specify at each distance you choose." << "\n";
+		cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the VennCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+}
+
+
 //**********************************************************************************************************************
 
 VennCommand::~VennCommand(){
@@ -87,10 +193,13 @@ VennCommand::~VennCommand(){
 
 int VennCommand::execute(){
 	try {
+	
+		if (abort == true) { return 0; }
+		
 		int count = 1;
 		SAbundVector* lastSAbund;
 		vector<SharedRAbundVector*> lastLookup;	
-		
+
 		//if the users entered no valid calculators don't execute command
 		if (vennCalculators.size() == 0) { return 0; }
 		
@@ -114,15 +223,15 @@ int VennCommand::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 = globaldata->labels;
-		set<int> userLines = globaldata->lines;
+		set<string> userLabels = labels;
+		set<int> userLines = lines;
 		
 		if (format != "list") {	
 			
 			//as long as you are not at the end of the file or done wih the lines you want
-			while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
-		
-				if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){			
+			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){			
 					cout << lookup[0]->getLabel() << '\t' << count << endl;
 					processedLabels.insert(lookup[0]->getLabel());
 					userLabels.erase(lookup[0]->getLabel());
@@ -186,9 +295,9 @@ int VennCommand::execute(){
 			
 		}else{
 		
-			while((sabund != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+			while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 		
-				if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){			
+				if(allLines == 1 || lines.count(count) == 1 || labels.count(sabund->getLabel()) == 1){			
 	
 					cout << sabund->getLabel() << '\t' << count << endl;
 					venn->getPic(sabund, vennCalculators);
@@ -235,8 +344,6 @@ int VennCommand::execute(){
 			delete lastSAbund;
 		}
 		
-		
-		globaldata->setGroups("");
 		return 0;
 	}
 	catch(exception& e) {