X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readdistcommand.cpp;h=8bf6996333b246814a28009d309ab8f3b6bf8718;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=0445eec63328e2cf7a646f1cc662bb36fdd3bb98;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git

diff --git a/readdistcommand.cpp b/readdistcommand.cpp
index 0445eec..8bf6996 100644
--- a/readdistcommand.cpp
+++ b/readdistcommand.cpp
@@ -12,16 +12,17 @@
 #include "readcolumn.h"
 #include "readmatrix.hpp"
 
+//**********************************************************************************************************************
 ReadDistCommand::ReadDistCommand(string option) {
 	try {
-		globaldata = GlobalData::getInstance();
-		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
+			/*//valid paramters for this command
 			string Array[] =  {"phylip", "column", "name", "cutoff", "precision", "group","outputdir","inputdir","sim"};
 			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 			
@@ -120,7 +121,7 @@ ReadDistCommand::ReadDistCommand(string option) {
 			//get user cutoff and precision or use defaults
 			string temp;
 			temp = validParameter.validFile(parameters, "precision", false);		if (temp == "not found") { temp = "100"; }
-			convert(temp, precision); 
+			m->mothurConvert(temp, precision); 
 			
 			temp = validParameter.validFile(parameters, "sim", false);				if (temp == "not found") { temp = "F"; }
 			sim = m->isTrue(temp); 
@@ -157,7 +158,7 @@ ReadDistCommand::ReadDistCommand(string option) {
 					}
 				}
 			}
-
+*/
 		}
 
 	}
@@ -166,50 +167,16 @@ ReadDistCommand::ReadDistCommand(string option) {
 		exit(1);
 	}
 }
-//**********************************************************************************************************************
-
-void ReadDistCommand::help(){
-	try {
-		m->mothurOut("The read.dist command parameter options are phylip or column, group, name, sim, cutoff and precision\n");
-		m->mothurOut("The read.dist command can be used in two ways.  The first is to read a phylip or column and run the cluster command\n");
-		m->mothurOut("For this use the read.dist command should be in the following format: \n");
-		m->mothurOut("read.dist(phylip=yourDistFile, name=yourNameFile, cutoff=yourCutoff, precision=yourPrecision) \n");
-		m->mothurOut("The phylip or column parameter is required, but only one may be used.  If you use a column file the name filename is required. \n");
-		m->mothurOut("The sim parameter is used to indicate that your distance file contains similarity values instead of distance values. The default is false, if sim=true then mothur will convert the similarity values to distances. \n");
-		m->mothurOut("If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n");
-		m->mothurOut("The second way to use the read.dist command is to read a phylip or column and a group, so you can use the libshuff command.\n");
-		m->mothurOut("For this use the read.dist command should be in the following format: \n");
-		m->mothurOut("read.dist(phylip=yourPhylipfile, group=yourGroupFile). The cutoff and precision parameters are not valid with this use.  \n");
-		m->mothurOut("Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourPhylipfile).\n\n");
-	}
-	catch(exception& e) {
-		m->errorOut(e, "ReadDistCommand", "help");
-		exit(1);
-	}
-}
-
-//**********************************************************************************************************************
-
-ReadDistCommand::~ReadDistCommand(){
-	if (abort == false) {
-		if (format != "matrix") { 
-			delete read; 
-			delete nameMap; 
-		}
-	}
-}
-
 //**********************************************************************************************************************
 int ReadDistCommand::execute(){
 	try {
 		
-		if (abort == true) {	return 0;	}
-
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
+		m->mothurOut(getHelpString()); m->mothurOutEndLine();
+/*
 		time_t start = time(NULL);
 		size_t numDists = 0;
 		
-		vector<string> outputNames;
-		
 		if (format == "matrix") {
 			ifstream in;
 			m->openInputFile(distFileName, in);
@@ -230,7 +197,7 @@ int ReadDistCommand::execute(){
 				m->openOutputFile(newGroupFile, outGroups);
 				
 				for (int i = 0; i < matrix->getNumSeqs(); i++) {
-					if (m->control_pressed) { delete groupMap; delete matrix; outGroups.close(); remove(newGroupFile.c_str()); return 0; }
+					if (m->control_pressed) { delete groupMap; delete matrix; outGroups.close(); m->mothurRemove(newGroupFile); return 0; }
 					
 					Names temp = matrix->getRowInfo(i);
 					outGroups << temp.seqName << '\t' << temp.groupName << endl;
@@ -247,7 +214,7 @@ int ReadDistCommand::execute(){
 				groupMap = new GroupMap(groupfile);
 				groupMap->readMap();
 				
-				if (m->control_pressed) { delete groupMap; delete matrix; remove(newGroupFile.c_str()); return 0; }
+				if (m->control_pressed) { delete groupMap; delete matrix; m->mothurRemove(newGroupFile); return 0; }
 	
 				globaldata->gGroupmap = groupMap;
 			}
@@ -280,6 +247,7 @@ int ReadDistCommand::execute(){
 		}
 		
 		m->mothurOut("It took " + toString(time(NULL) - start) + " secs to read "); m->mothurOutEndLine();
+ */
 		return 0;
 		
 	}