X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=getrabundcommand.cpp;h=c978bb19439db11e9fada887112ab708d7551fd2;hb=786d5631d9cd5baa6ed6ef16f8b4b384cbc7470f;hp=b0f7a92638663095cf860ed6b8ff34a9ada9402c;hpb=0024441c1ff9a98467ba53cc7420a37c98f32e86;p=mothur.git

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index b0f7a92..c978bb1 100644
--- a/getrabundcommand.cpp
+++ b/getrabundcommand.cpp
@@ -11,12 +11,66 @@
 
 //**********************************************************************************************************************
 
-GetRAbundCommand::GetRAbundCommand(){
+GetRAbundCommand::GetRAbundCommand(string option){
 	try {
 		globaldata = GlobalData::getInstance();
-		filename = getRootName(globaldata->inputFileName) + "rabund";
+		abort = false;
+		allLines = 1;
+		lines.clear();
+		labels.clear();
 		
-		openOutputFile(filename, out);
+		//allow user to run help
+		if(option == "help") { help(); abort = true; }
+		
+		else {
+			//valid paramters for this command
+			string Array[] =  {"line","label"};
+			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;  }
+			}
+			
+			//make sure the user has already run the read.otu command
+			if (globaldata->getListFile() == "") { cout << "You must read a listfile before you can use the get.rabund 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;
+			}
+				
+			if (abort == false) {
+				filename = getRootName(globaldata->inputFileName) + "rabund";
+				openOutputFile(filename, out);
+			}
+		}
+
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the GetRAbundCommand class Function GetRAbundCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -28,6 +82,28 @@ GetRAbundCommand::GetRAbundCommand(){
 	}	
 			
 }
+//**********************************************************************************************************************
+
+void GetRAbundCommand::help(){
+	try {
+		cout << "The get.rabund command can only be executed after a successful read.otu of a listfile." << "\n";
+		cout << "The get.rabund command parameters are line and label.  No parameters are required, and you may not use line and label at the same time." << "\n";
+		cout << "The line and label allow you to select what distance levels you would like included in your .rabund file, and are separated by dashes." << "\n";
+		cout << "The get.rabund command should be in the following format: get.rabund(line=yourLines, label=yourLabels)." << "\n";
+		cout << "Example get.rabund(line=1-3-5)." << "\n";
+		cout << "The default value for line and label are all lines in your inputfile." << "\n";
+		cout << "The get.rabund command outputs a .rabund file containing the lines you selected." << "\n";
+		cout << "Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines)." << "\n" << "\n";
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the GetRAbundCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the GetRAbundCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+}
 
 //**********************************************************************************************************************
 
@@ -38,6 +114,9 @@ GetRAbundCommand::~GetRAbundCommand(){
 
 int GetRAbundCommand::execute(){
 	try {
+	
+		if (abort == true) { return 0; }
+		
 		int count = 1;
 		
 		//read first line
@@ -50,13 +129,13 @@ int GetRAbundCommand::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;
 
 		
-		while((list != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+		while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 			
-			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(list->getLabel()) == 1){
+			if(allLines == 1 || lines.count(count) == 1 || labels.count(list->getLabel()) == 1){
 					cout << list->getLabel() << '\t' << count << endl;
 					rabund = new RAbundVector();
 					*rabund = (list->getRAbundVector());