X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotypecommand.cpp;h=2018170648761a91b5b9026fada7079b0b4e73e1;hb=3e2465c16d187247ce3befd29811c2d5dfc15ee8;hp=d04c9604170cf0d5c0f440132d25747b9193ba4c;hpb=a688f253166590ee0b256f02e02f47c9cae44fd1;p=mothur.git

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index d04c960..2018170 100644
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -13,6 +13,56 @@
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
 
+//**********************************************************************************************************************
+vector<string> PhylotypeCommand::getValidParameters(){	
+	try {
+		string Array[] =  {"taxonomy","cutoff","label","name","outputdir","inputdir"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PhylotypeCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+PhylotypeCommand::PhylotypeCommand(){	
+	try {
+		abort = true;
+		//initialize outputTypes
+		vector<string> tempOutNames;
+		outputTypes["list"] = tempOutNames;
+		outputTypes["sabund"] = tempOutNames;
+		outputTypes["rabund"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> PhylotypeCommand::getRequiredParameters(){	
+	try {
+		string Array[] =  {"taxonomy"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PhylotypeCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> PhylotypeCommand::getRequiredFiles(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PhylotypeCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
 /**********************************************************************************************************************/
 PhylotypeCommand::PhylotypeCommand(string option)  {
 	try {
@@ -38,6 +88,12 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
 			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["list"] = tempOutNames;
+			outputTypes["sabund"] = tempOutNames;
+			outputTypes["rabund"] = 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 = "";		}
@@ -46,7 +102,7 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
 				it = parameters.find("taxonomy");
 				//user has given a template file
 				if(it != parameters.end()){ 
-					path = hasPath(it->second);
+					path = m->hasPath(it->second);
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["taxonomy"] = inputDir + it->second;		}
 				}
@@ -54,7 +110,7 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
 				it = parameters.find("name");
 				//user has given a template file
 				if(it != parameters.end()){ 
-					path = hasPath(it->second);
+					path = m->hasPath(it->second);
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["name"] = inputDir + it->second;		}
 				}
@@ -75,7 +131,7 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
 			//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(taxonomyFileName); //if user entered a file with a path then preserve it	
+				outputDir += m->hasPath(taxonomyFileName); //if user entered a file with a path then preserve it	
 			}
 			
 			string temp = validParameter.validFile(parameters, "cutoff", false);
@@ -85,7 +141,7 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
 			label = validParameter.validFile(parameters, "label", false);			
 			if (label == "not found") { label = ""; allLines = 1; }
 			else { 
-				if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
+				if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 				else { allLines = 1;  }
 			}
 			
@@ -127,8 +183,6 @@ int PhylotypeCommand::execute(){
 	
 		if (abort == true) { return 0; }
 		
-		vector<string> outputNames;
-		
 		//reads in taxonomy file and makes all the taxonomies the same length 
 		//by appending the last taxon to a given taxonomy as many times as needed to 
 		//make it as long as the longest taxonomy in the file 
@@ -152,21 +206,21 @@ int PhylotypeCommand::execute(){
 		
 		if (m->control_pressed) { delete tree; return 0; }
 		
-		string fileroot = outputDir + getRootName(getSimpleName(taxonomyFileName));
+		string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName));
 		
 		ofstream outList;
 		string outputListFile = fileroot + "tx.list";
-		openOutputFile(outputListFile, outList);
+		m->openOutputFile(outputListFile, outList);
 		ofstream outSabund;
 		string outputSabundFile = fileroot + "tx.sabund";
-		openOutputFile(outputSabundFile, outSabund);
+		m->openOutputFile(outputSabundFile, outSabund);
 		ofstream outRabund;
 		string outputRabundFile = fileroot + "tx.rabund";
-		openOutputFile(outputRabundFile, outRabund);
+		m->openOutputFile(outputRabundFile, outRabund);
 		
-		outputNames.push_back(outputListFile);
-		outputNames.push_back(outputSabundFile);
-		outputNames.push_back(outputRabundFile);
+		outputNames.push_back(outputListFile); outputTypes["list"].push_back(outputListFile);
+		outputNames.push_back(outputSabundFile); outputTypes["sabund"].push_back(outputSabundFile);
+		outputNames.push_back(outputRabundFile); outputTypes["rabund"].push_back(outputRabundFile);
 		
 		int count = 1;		
 		//start at leaves of tree and work towards root, processing the labels the user wants
@@ -270,13 +324,13 @@ int PhylotypeCommand::readNamesFile() {
 	try {
 				
 		ifstream in;
-		openInputFile(namefile, in);
+		m->openInputFile(namefile, in);
 		
 		string first, second;
 		map<string, string>::iterator itNames;
 		
 		while(!in.eof()) {
-			in >> first >> second; gobble(in);
+			in >> first >> second; m->gobble(in);
 			
 			itNames = namemap.find(first);
 			if (itNames == namemap.end()) {