X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readotucommand.cpp;h=bb866ed9364557765a38ad78cf1bb047ea502fc9;hb=28d65de5f06f5b033109a3b8bbb6d3c4060914d3;hp=7c3e1995ecf9315839b5f26ab9f7768d59e6ca08;hpb=cd37904452dc95b183ff313ff05720c562902487;p=mothur.git

diff --git a/readotucommand.cpp b/readotucommand.cpp
index 7c3e199..bb866ed 100644
--- a/readotucommand.cpp
+++ b/readotucommand.cpp
@@ -64,6 +64,7 @@ ReadOtuCommand::ReadOtuCommand(string option){
 				globaldata->setGroupFile(groupfile); 
 				groupMap = new GroupMap(groupfile);
 				groupMap->readMap();
+				globaldata->gGroupmap = groupMap;
 			}
 
 			//you are doing a list and group shared
@@ -71,7 +72,7 @@ ReadOtuCommand::ReadOtuCommand(string option){
 			
 			//you have not given a file
 			if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "")) {
-				cout << "You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. " << endl; abort = true; 
+				mothurOut("You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. "); mothurOutEndLine(); abort = true; 
 			}
 		
 			//check for optional parameter and set defaults
@@ -95,7 +96,7 @@ ReadOtuCommand::ReadOtuCommand(string option){
 			globaldata->allLines = allLines;
 			
 			//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 ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
 			
 			orderfile = validParameter.validFile(parameters, "order", true);
 			if (orderfile == "not open") { abort = true; }	
@@ -106,18 +107,13 @@ ReadOtuCommand::ReadOtuCommand(string option){
 			if (abort == false) {
 				//gets whichever one of the above is set
 				filename = globaldata->inputFileName;
-				read = new ReadOTUFile(filename);
 			}
 
 		}
 
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function ReadOtuCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ReadOtuCommand class function ReadOtuCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
 		exit(1);
 	}
 }
@@ -125,29 +121,25 @@ ReadOtuCommand::ReadOtuCommand(string option){
 
 void ReadOtuCommand::help(){
 	try {
-		cout << "The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, " << "\n";
-		cout << "collect.shared, rarefaction.shared or summary.shared command.   Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command " << "\n";
-		cout << "or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order, line and label." << "\n";
-		cout << "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";
-		cout << "For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels)." << "\n";
-		cout << "The list, rabund or sabund parameter is required, but you may only use one of them." << "\n";
-		cout << "The line and label parameters are optional but you may not use both the line and label parameters at the same time." << "\n";
-		cout << "The label and line parameters are used to read specific lines in your input." << "\n";
-		cout << "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";
-		cout << "In this case the read.otu command should be in the following format: read.otu(list=yourListFile, group=yourGroupFile, line=yourLines) or read.otu(shared=yourSharedFile).  " << "\n";
-		cout << "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";
-		cout << "and separates it into groups.  It outputs a .shared file containing the OTU information for each group. The read.otu command also outputs a .list file for each group. " << "\n";
-		cout << "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";
+		mothurOut("The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, \n");
+		mothurOut("collect.shared, rarefaction.shared or summary.shared command.   Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command \n");
+		mothurOut("or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order, line and label.\n");
+		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");
+		mothurOut("For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels).\n");
+		mothurOut("The list, rabund or sabund parameter is required, but you may only use one of them.\n");
+		mothurOut("The line and label parameters are optional but you may not use both the line and label parameters at the same time.\n");
+		mothurOut("The label and line parameters are used to read specific lines in your input.\n");
+		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");
+		mothurOut("In this case the read.otu command should be in the following format: read.otu(list=yourListFile, group=yourGroupFile, line=yourLines) or read.otu(shared=yourSharedFile).  \n");
+		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");
+		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 .list file for each group. \n");
+		mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
 
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "ReadOtuCommand", "help");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ReadOtuCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 
@@ -155,8 +147,7 @@ void ReadOtuCommand::help(){
 //**********************************************************************************************************************
 
 ReadOtuCommand::~ReadOtuCommand(){
-	if (abort == false) {  delete read;  }
-}
+	}
 
 //**********************************************************************************************************************
 
@@ -165,18 +156,12 @@ int ReadOtuCommand::execute(){
 	
 		if (abort == true) {	return 0;	}
 		
-		read->read(&*globaldata); 
 		if (globaldata->getFormat() == "shared") {
-			groupMap->readMap();
 			
-			//if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap;  }
-			globaldata->gGroupmap = groupMap;		
 			shared = new SharedCommand();
 			shared->execute();
-
-			parselist = new ParseListCommand();
-			parselist->execute();
-			
+			delete shared;
+				
 			//change format to shared  to speed up commands
 			globaldata->setFormat("sharedfile");
 			globaldata->setListFile("");
@@ -186,11 +171,7 @@ int ReadOtuCommand::execute(){
 		return 0;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ReadOtuCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "ReadOtuCommand", "execute");
 		exit(1);
 	}
 }