X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readotucommand.cpp;h=f39e8df2c382f02451848ca41ec6edb23e07aa49;hb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;hp=efd7073fae39fd493ef28f22d81d6bfdcf795859;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git

diff --git a/readotucommand.cpp b/readotucommand.cpp
index efd7073..f39e8df 100644
--- a/readotucommand.cpp
+++ b/readotucommand.cpp
@@ -9,17 +9,33 @@
 
 #include "readotucommand.h"
 
+
+//**********************************************************************************************************************
+ReadOtuCommand::ReadOtuCommand(){	
+	try {
+		abort = true; calledHelp = true; 
+		setParameters();
+		vector<string> tempOutNames;
+		outputTypes["rabund"] = tempOutNames;
+		outputTypes["shared"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 ReadOtuCommand::ReadOtuCommand(string option)  {
 	try {
-		globaldata = GlobalData::getInstance();
-		abort = false;
+		abort = false; calledHelp = false;   
 		allLines = 1;
 		
 		//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","order","shared","relabund","label","group","sabund", "rabund","groups","ordergroup","outputdir","inputdir"};
 			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
@@ -34,7 +50,12 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
 			for (it = parameters.begin(); it != parameters.end(); it++) { 
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
-	
+			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["rabund"] = tempOutNames;
+			outputTypes["shared"] = tempOutNames;
+			
 			globaldata->newRead();
 			
 			//if the user changes the input directory command factory will send this info to us in the output parameter 
@@ -193,6 +214,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
 				//gets whichever one of the above is set
 				filename = globaldata->inputFileName;
 			}
+			 */
 		}
 
 	}
@@ -201,43 +223,15 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
 		exit(1);
 	}
 }
-//**********************************************************************************************************************
-
-void ReadOtuCommand::help(){
-	try {
-		m->mothurOut("The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, \n");
-		m->mothurOut("collect.shared, rarefaction.shared, summary.shared heatmap.bin, heatmap.sim or venn command.   Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command \n");
-		m->mothurOut("or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, relabund, group, order, ordergroup, label and groups.\n");
-		m->mothurOut("The read.otu command can be used in two ways.  The first is to read a list, rabund or sabund and run the collect.single, rarefaction.single or summary.single.\n");
-		m->mothurOut("For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels).\n");
-		m->mothurOut("The list, rabund or sabund parameter is required, but you may only use one of them.\n");
-		m->mothurOut("The label parameter is used to read specific labels in your input.\n");
-		m->mothurOut("The second way to use the read.otu command is to read a list and a group, or a shared so you can use the collect.shared, rarefaction.shared or summary.shared commands.\n");
-		m->mothurOut("In this case the read.otu command should be in the following format: read.otu(list=yourListFile, group=yourGroupFile) or read.otu(shared=yourSharedFile).  \n");
-		m->mothurOut("The list parameter and group paramaters or the shared paremeter is required. When using the command the second way with a list and group file read.otu command parses the .list file\n");
-		m->mothurOut("and separates it into groups.  It outputs a .shared file containing the OTU information for each group. The read.otu command also outputs a .rabund file for each group. \n");
-		m->mothurOut("You can use the groups parameter to choose only specific groups to be used in the .shared and .rabund files. \n");
-		m->mothurOut("You can use the ordergroup parameter to provide a file containing a list of group names in the order you would like them to appear in your shared file. \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, "ReadOtuCommand", "help");
-		exit(1);
-	}
-}
-
-
-
-//**********************************************************************************************************************
-ReadOtuCommand::~ReadOtuCommand(){}
-//**********************************************************************************************************************
+///**********************************************************************************************************************
 
 int ReadOtuCommand::execute(){
 	try {
 	
-		if (abort == true) {	return 0;	}
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
+		m->mothurOut(getHelpString()); m->mothurOutEndLine();
 	
+		/*
 		if (globaldata->getFormat() == "shared") {
 			
 			shared = new SharedCommand(outputDir);
@@ -255,8 +249,24 @@ int ReadOtuCommand::execute(){
 				//m->mothurOutEndLine();
 			}
 			
+			outputTypes = shared->getOutputFiles();
+			
+			//set rabund file as new current rabundfile
+			string current = "";
+			itTypes = outputTypes.find("rabund");
+			if (itTypes != outputTypes.end()) {
+				if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
+			}
+			
+			itTypes = outputTypes.find("shared");
+			if (itTypes != outputTypes.end()) {
+				if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
+			}			
+			
 			delete shared;
 		}
+		*/
+				
 		return 0;
 	}
 	catch(exception& e) {