X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=otuhierarchycommand.cpp;h=14138de30355151035a7ddca66f5bd928e534bc5;hb=3b137af694d322b7162e97275c070c41b42597a3;hp=05d6443725be6028411573b6ee280220cb52ff0c;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp
index 05d6443..14138de 100644
--- a/otuhierarchycommand.cpp
+++ b/otuhierarchycommand.cpp
@@ -9,6 +9,54 @@
 
 #include "otuhierarchycommand.h"
 
+//**********************************************************************************************************************
+vector<string> OtuHierarchyCommand::getValidParameters(){	
+	try {
+		string Array[] =  {"list","label","output","outputdir","inputdir"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "OtuHierarchyCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+OtuHierarchyCommand::OtuHierarchyCommand(){	
+	try {
+		abort = true;
+		//initialize outputTypes
+		vector<string> tempOutNames;
+		outputTypes["otuheirarchy"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> OtuHierarchyCommand::getRequiredParameters(){	
+	try {
+		string Array[] =  {"list","label"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "OtuHierarchyCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> OtuHierarchyCommand::getRequiredFiles(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "OtuHierarchyCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 OtuHierarchyCommand::OtuHierarchyCommand(string option) {
 	try {
@@ -33,6 +81,10 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) {
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
 			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["otuheirarchy"] = 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 = "";		}
@@ -41,7 +93,7 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) {
 				it = parameters.find("list");
 				//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["list"] = inputDir + it->second;		}
 				}
@@ -54,7 +106,7 @@ OtuHierarchyCommand::OtuHierarchyCommand(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(listFile); //if user entered a file with a path then preserve it	
+				outputDir += m->hasPath(listFile); //if user entered a file with a path then preserve it	
 			}
 			
 			//check for optional parameter and set defaults
@@ -62,7 +114,7 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) {
 			label = validParameter.validFile(parameters, "label", false);			
 			if (label == "not found") { m->mothurOut("label is a required parameter for the otu.hierarchy command."); m->mothurOutEndLine(); abort = true; }
 			else { 
-				splitAtDash(label, labels);
+				m->splitAtDash(label, labels);
 				if (labels.size() != 2) { m->mothurOut("You must provide 2 labels."); m->mothurOutEndLine(); abort = true; }
 			}	
 			
@@ -110,7 +162,7 @@ int OtuHierarchyCommand::execute(){
 		//get listvectors that correspond to labels requested, (or use smart distancing to get closest listvector)
 		vector<ListVector> lists = getListVectors();
 		
-		if (m->control_pressed) { return 0; }
+		if (m->control_pressed) { outputTypes.clear(); return 0; }
 		
 		//determine which is little and which is big, putting little first
 		if (lists.size() == 2) {
@@ -142,13 +194,13 @@ int OtuHierarchyCommand::execute(){
 		}
 		
 		ofstream out;
-		string outputFileName = outputDir + getRootName(getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy";
-		openOutputFile(outputFileName, out);
+		string outputFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy";
+		m->openOutputFile(outputFileName, out);
 		
 		//go through each bin in "big" otu and output the bins in "little" otu which created it
 		for (int i = 0; i < lists[1].getNumBins(); i++) {
 		
-			if (m->control_pressed) { out.close(); remove(outputFileName.c_str()); return 0; }
+			if (m->control_pressed) { outputTypes.clear(); out.close(); remove(outputFileName.c_str()); return 0; }
 			
 			string names = lists[1].get(i);
 			
@@ -181,11 +233,11 @@ int OtuHierarchyCommand::execute(){
 		
 		out.close();
 		
-		if (m->control_pressed) { remove(outputFileName.c_str()); return 0; }
+		if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0; }
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
-		m->mothurOut(outputFileName); m->mothurOutEndLine();	
+		m->mothurOut(outputFileName); m->mothurOutEndLine();	outputNames.push_back(outputFileName); outputTypes["otuheirarchy"].push_back(outputFileName); 
 		m->mothurOutEndLine();
 		
 		return 0;
@@ -211,7 +263,7 @@ vector<ListVector> OtuHierarchyCommand::getListVectors() {
 
 		//open file
 		ifstream in;
-		openInputFile(listFile, in);
+		m->openInputFile(listFile, in);
 		
 		//get first list vector in file
 		ListVector* list = NULL;
@@ -220,7 +272,7 @@ vector<ListVector> OtuHierarchyCommand::getListVectors() {
 			pos = in.tellg();
 			lastPos = pos;
 			list = new ListVector(in);  
-			gobble(in);
+			m->gobble(in);
 			lastLabel = list->getLabel();
 		}
 		
@@ -240,7 +292,7 @@ vector<ListVector> OtuHierarchyCommand::getListVectors() {
 			}
 		
 			//you have a label the user want that is smaller than this label and the last label has not already been processed 
-			if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+			if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 				string saveLabel = list->getLabel();
 				int savePos = in.tellg();
 				
@@ -271,7 +323,7 @@ vector<ListVector> OtuHierarchyCommand::getListVectors() {
 			if (!in.eof())	{	
 				pos = in.tellg();
 				list = new ListVector(in);  
-				gobble(in);
+				m->gobble(in);
 			}else { list = NULL; }
 		}