X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=splitabundcommand.cpp;h=8131fa9195f6b8d939b27891605dd862d618964b;hb=72e0be6b9c80009d4dbee24e8d690ad9514dc6fb;hp=810b83915dadb9ed8863340dcfb27ac34e286dd8;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index 810b839..8131fa9 100644
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -48,7 +48,7 @@ string SplitAbundCommand::getHelpString(){
 		helpString += "If you want .abund and .rare files for all groups, set groups=all.  \n";
 		helpString += "The split.abund command should be used in the following format: split.abund(fasta=yourFasta, list=yourListFile, group=yourGroupFile, label=yourLabels, cutoff=yourCutoff).\n";
 		helpString += "Example: split.abund(fasta=abrecovery.fasta, list=abrecovery.fn.list, group=abrecovery.groups, label=0.03, cutoff=2).\n";
-		helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n";
+		helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -82,11 +82,9 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
 			
 		//allow user to run help
 		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[] =  {"name","group","list","label","accnos","groups","fasta","cutoff","outputdir","inputdir"}; //
-			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			vector<string> myArray = setParameters();
 			
 			OptionParser parser(option);
 			map<string, string> parameters = parser.getParameters();
@@ -154,12 +152,12 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
 			listfile = validParameter.validFile(parameters, "list", true);
 			if (listfile == "not open") { abort = true; }
 			else if (listfile == "not found") { listfile = ""; }
-			else{ inputFile = listfile; }	
+			else{ inputFile = listfile; m->setListFile(listfile); }	
 			
 			namefile = validParameter.validFile(parameters, "name", true);
 			if (namefile == "not open") { abort = true; }
 			else if (namefile == "not found") { namefile = ""; }	
-			else{ inputFile = namefile; }	
+			else{ inputFile = namefile; m->setNameFile(namefile); }	
 		
 			fastafile = validParameter.validFile(parameters, "fasta", true);
 			if (fastafile == "not open") { abort = true; }
@@ -167,7 +165,7 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
 				fastafile = m->getFastaFile(); 
 				if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}	
+			}else { m->setFastaFile(fastafile); }	
 			
 			groupfile = validParameter.validFile(parameters, "group", true);
 			if (groupfile == "not open") {  groupfile = ""; abort = true; }	
@@ -177,13 +175,13 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
 				
 				int error = groupMap->readMap();
 				if (error == 1) { abort = true; }
-	
+				m->setGroupFile(groupfile);
 			}
 			
 			groups = validParameter.validFile(parameters, "groups", false);		
 			if (groups == "not found") { groups = ""; }
 			else if (groups == "all") { 
-				if (groupfile != "") {  Groups = groupMap->namesOfGroups;  } 
+				if (groupfile != "") {  Groups = groupMap->getNamesOfGroups();  } 
 				else {  m->mothurOut("You cannot select groups without a valid groupfile, I will disregard your groups selection. "); m->mothurOutEndLine(); groups = "";   }
 			}else { 
 				m->splitAtDash(groups, Groups);
@@ -215,10 +213,9 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
 			accnos = m->isTrue(temp); 
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);				if (temp == "not found") { temp = "0"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 
 			if (cutoff == 0) {  m->mothurOut("You must provide a cutoff to qualify what is abundant for the split.abund command. "); m->mothurOutEndLine(); abort = true;  }
-
 		}
 
 	}
@@ -252,11 +249,11 @@ int SplitAbundCommand::execute(){
 			if (namefile != "") {  readNamesFile();		}
 			else				{ createNameMap(list);	}
 			
-			if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
+			if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } return 0; }
 			
 			while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 			
-				if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
+				if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } return 0; }
 				
 				if(allLines == 1 || labels.count(list->getLabel()) == 1){
 						
@@ -290,7 +287,7 @@ int SplitAbundCommand::execute(){
 				list = input->getListVector(); //get new list vector to process
 			}
 			
-			if (m->control_pressed) { delete input;  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
+			if (m->control_pressed) { delete input;  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } return 0; }
 			
 			//output error messages about any remaining user labels
 			set<string>::iterator it;
@@ -306,7 +303,7 @@ int SplitAbundCommand::execute(){
 
 			}
 			
-			if (m->control_pressed) { delete input;  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
+			if (m->control_pressed) { delete input;  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } return 0; }
 			
 			//run last label if you need to
 			if (needToRun == true)  {
@@ -321,7 +318,7 @@ int SplitAbundCommand::execute(){
 			
 			delete input;
 			
-			if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); }	return 0;	}
+			if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); }	return 0;	}
 									
 		}else { //you are using the namefile to determine abundance
 			if (outputDir == "") { outputDir = m->hasPath(namefile); }