X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getgroupscommand.cpp;h=432894b06fe9d5ffa6982fdaaa49474a44c403e0;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=e533bc47defa9467b345a0a58cc8b80b59710275;hpb=3094cb29c613d9687e861e1d0cf9104b7141d24e;p=mothur.git

diff --git a/getgroupscommand.cpp b/getgroupscommand.cpp
index e533bc4..432894b 100644
--- a/getgroupscommand.cpp
+++ b/getgroupscommand.cpp
@@ -16,12 +16,12 @@
 //**********************************************************************************************************************
 vector<string> GetGroupsCommand::setParameters(){	
 	try {
-		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
-		CommandParameter pshared("shared", "InputTypes", "", "", "none", "FNGLT-sharedGroup", "none",false,false); parameters.push_back(pshared);
-		CommandParameter pname("name", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pname);
-		CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT-sharedGroup", "none",false,false); parameters.push_back(pgroup);
-		CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
-		CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
+		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(pfasta);
+		CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none",false,false); parameters.push_back(pshared);
+		CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+		CommandParameter pgroup("group", "InputTypes", "", "", "none", "sharedGroup", "FNGLT",false,false); parameters.push_back(pgroup);
+		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(plist);
+		CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(ptaxonomy);
 		CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
 		CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
 		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
@@ -180,23 +180,19 @@ GetGroupsCommand::GetGroupsCommand(string option)  {
 			else { m->setAccnosFile(accnosfile); }
 			
 			fastafile = validParameter.validFile(parameters, "fasta", true);
-			if (fastafile == "not open") { abort = true; }
+			if (fastafile == "not open") { fastafile = ""; abort = true; }
 			else if (fastafile == "not found") {  fastafile = "";  }
 			else { m->setFastaFile(fastafile); }
 			
 			namefile = validParameter.validFile(parameters, "name", true);
-			if (namefile == "not open") { abort = true; }
+			if (namefile == "not open") { namefile = ""; abort = true; }
 			else if (namefile == "not found") {  namefile = "";  }	
 			else { m->setNameFile(namefile); }
 			
 			groupfile = validParameter.validFile(parameters, "group", true);
-			if (groupfile == "not open") { abort = true; }
-			else if (groupfile == "not found") {  
-				//if there is a current group file, use it
-				groupfile = m->getGroupFile(); 
-				if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
-				else { 	m->mothurOut("You have no current groupfile and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}else { m->setGroupFile(groupfile); }	
+			if (groupfile == "not open") { groupfile = ""; abort = true; }
+			else if (groupfile == "not found") {  groupfile = "";			}
+			else { m->setGroupFile(groupfile); }	
 			
 			listfile = validParameter.validFile(parameters, "list", true);
 			if (listfile == "not open") { abort = true; }
@@ -204,7 +200,7 @@ GetGroupsCommand::GetGroupsCommand(string option)  {
 			else { m->setListFile(listfile); }
 			
 			taxfile = validParameter.validFile(parameters, "taxonomy", true);
-			if (taxfile == "not open") { abort = true; }
+			if (taxfile == "not open") { taxfile = ""; abort = true; }
 			else if (taxfile == "not found") {  taxfile = "";  }
 			else { m->setTaxonomyFile(taxfile); }
 			
@@ -257,6 +253,10 @@ GetGroupsCommand::GetGroupsCommand(string option)  {
 			if ((fastafile == "") && (namefile == "") && (groupfile == "")  && (sharedfile == "") && (listfile == "") && (taxfile == ""))  { m->mothurOut("You must provide at least one of the following: fasta, name, taxonomy, group, shared or list."); m->mothurOutEndLine(); abort = true; }
 			if ((groupfile == "") && ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != "")))  { m->mothurOut("If using a fasta, name, taxonomy, group or list, then you must provide a group file."); m->mothurOutEndLine(); abort = true; }
 
+			if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
+				vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
+				parser.getNameFile(files);
+			}
 		}
 		
 	}