X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=otuhierarchycommand.cpp;h=dc026decc9db9916513fcbd1d41fe23298173717;hb=bd27c2b0612942815b7417c79f7ee41f669a2a34;hp=2c71cd56aa8a6341def135ec0a7ddcb092993885;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git

diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp
index 2c71cd5..dc026de 100644
--- a/otuhierarchycommand.cpp
+++ b/otuhierarchycommand.cpp
@@ -9,18 +9,82 @@
 
 #include "otuhierarchycommand.h"
 
+//**********************************************************************************************************************
+vector<string> OtuHierarchyCommand::setParameters(){	
+	try {
+		CommandParameter poutput("output", "Multiple", "name-number", "name", "", "", "","",false,false); parameters.push_back(poutput);
+		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","otuheirarchy",false,true,true); parameters.push_back(plist);
+		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+		
+		vector<string> myArray;
+		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "OtuHierarchyCommand", "setParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+string OtuHierarchyCommand::getHelpString(){	
+	try {
+		string helpString = "";
+		helpString += "The otu.hierarchy command is used to see how otus relate at two distances. \n";
+		helpString += "The otu.hierarchy command parameters are list, label and output.  list and label parameters are required. \n";
+		helpString += "The output parameter allows you to output the names of the sequence in the OTUs or the OTU numbers. Options are name and number, default is name. \n";
+		helpString += "The otu.hierarchy command should be in the following format: \n";
+		helpString += "otu.hierarchy(list=yourListFile, label=yourLabels).\n";
+		helpString += "Example otu.hierarchy(list=amazon.fn.list, label=0.01-0.03).\n";
+		helpString += "The otu.hierarchy command outputs a .otu.hierarchy file which is described on the wiki.\n";
+		helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n";
+		return helpString;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "OtuHierarchyCommand", "getHelpString");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+string OtuHierarchyCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "otuheirarchy") {  pattern = "[filename],[distance1],[tag],[distance2],otu.hierarchy"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "OtuHierarchyCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
+OtuHierarchyCommand::OtuHierarchyCommand(){	
+	try {
+		abort = true; calledHelp = true; 
+		setParameters();
+		vector<string> tempOutNames;
+		outputTypes["otuheirarchy"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 OtuHierarchyCommand::OtuHierarchyCommand(string option) {
 	try {
-		abort = false;
+		abort = false; calledHelp = false;   
 		
 		//allow user to run help
-		if(option == "help") {  help(); abort = true; }
+		if(option == "help") {  help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
-			//valid paramters for this command
-			string Array[] =  {"list","label","output","outputdir","inputdir"};
-			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			vector<string> myArray = setParameters();
 			
 			OptionParser parser(option);
 			map<string,string> parameters = parser.getParameters();
@@ -33,6 +97,10 @@ 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 = "";		}
@@ -48,8 +116,15 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) {
 			}
 
 			listFile = validParameter.validFile(parameters, "list", true);
-			if (listFile == "not found") { m->mothurOut("list is a required parameter for the otu.hierarchy command."); m->mothurOutEndLine(); abort = true; }
-			else if (listFile == "not open") { abort = true; }	
+			if (listFile == "not found") { 
+				listFile = m->getListFile(); 
+				if (listFile != "") {  m->mothurOut("Using " + listFile + " as input file for the list parameter."); m->mothurOutEndLine(); }
+				else { 
+					m->mothurOut("No valid current list file. You must provide a list file."); m->mothurOutEndLine(); 
+					abort = true;
+				}
+			}else if (listFile == "not open") { abort = true; }	
+			else { m->setListFile(listFile); }
 			
 			//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"){	
@@ -79,38 +154,15 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) {
 }
 //**********************************************************************************************************************
 
-void OtuHierarchyCommand::help(){
-	try {
-		m->mothurOut("The otu.hierarchy command is used to see how otus relate at two distances. \n");
-		m->mothurOut("The otu.hierarchy command parameters are list, label and output.  list and label parameters are required. \n");
-		m->mothurOut("The output parameter allows you to output the names of the sequence in the OTUs or the OTU numbers. Options are name and number, default is name. \n");
-		m->mothurOut("The otu.hierarchy command should be in the following format: \n");
-		m->mothurOut("otu.hierarchy(list=yourListFile, label=yourLabels).\n");
-		m->mothurOut("Example otu.hierarchy(list=amazon.fn.list, label=0.01-0.03).\n");
-		m->mothurOut("The otu.hierarchy command outputs a .otu.hierarchy file which is described on the wiki.\n");
-		m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n");
-	}
-	catch(exception& e) {
-		m->errorOut(e, "OtuHierarchyCommand", "help");
-		exit(1);
-	}
-}
-
-//**********************************************************************************************************************
-
-OtuHierarchyCommand::~OtuHierarchyCommand(){}
-
-//**********************************************************************************************************************
-
 int OtuHierarchyCommand::execute(){
 	try {
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		//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 +194,18 @@ int OtuHierarchyCommand::execute(){
 		}
 		
 		ofstream out;
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy";
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listFile));
+        variables["[distance1]"] = lists[0].getLabel();
+        variables["[tag]"] = "-"; 
+        variables["[distance2]"] = lists[1].getLabel();
+		string outputFileName = getOutputFileName("otuheirarchy",variables);
 		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(); m->mothurRemove(outputFileName); return 0; }
 			
 			string names = lists[1].get(i);
 			
@@ -181,11 +238,11 @@ int OtuHierarchyCommand::execute(){
 		
 		out.close();
 		
-		if (m->control_pressed) { remove(outputFileName.c_str()); return 0; }
+		if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0; }
 		
 		m->mothurOutEndLine();
-		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
-		m->mothurOut(outputFileName); m->mothurOutEndLine();	
+		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+		m->mothurOut(outputFileName); m->mothurOutEndLine();	outputNames.push_back(outputFileName); outputTypes["otuheirarchy"].push_back(outputFileName); 
 		m->mothurOutEndLine();
 		
 		return 0;