X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=subsamplecommand.cpp;h=95a0442d6c970bd74a383c1e13765af305eeac57;hb=ae9c5b48da9047548f86fc84897926d9f5102312;hp=a055e81a1a1f6228ee069ad38760868c7cbaf082;hpb=5cc45e630ccee2c3503e1bfe7e9b3524898cef8a;p=mothur.git

diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index a055e81..95a0442 100644
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -88,6 +88,7 @@ SubSampleCommand::SubSampleCommand(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 {
 			vector<string> myArray = setParameters();
@@ -181,32 +182,38 @@ SubSampleCommand::SubSampleCommand(string option) {
 			//check for required parameters
 			listfile = validParameter.validFile(parameters, "list", true);
 			if (listfile == "not open") { listfile = ""; abort = true; }
-			else if (listfile == "not found") { listfile = ""; }	
+			else if (listfile == "not found") { listfile = ""; }
+			else { m->setListFile(listfile); }
 			
 			sabundfile = validParameter.validFile(parameters, "sabund", true);
 			if (sabundfile == "not open") { sabundfile = ""; abort = true; }	
 			else if (sabundfile == "not found") { sabundfile = ""; }
+			else { m->setSabundFile(sabundfile); }
 			
 			rabundfile = validParameter.validFile(parameters, "rabund", true);
 			if (rabundfile == "not open") { rabundfile = ""; abort = true; }	
 			else if (rabundfile == "not found") { rabundfile = ""; }
+			else { m->setRabundFile(rabundfile); }
 			
 			fastafile = validParameter.validFile(parameters, "fasta", true);
 			if (fastafile == "not open") { fastafile = ""; abort = true; }	
 			else if (fastafile == "not found") { fastafile = ""; }
+			else { m->setFastaFile(fastafile); }
 			
 			sharedfile = validParameter.validFile(parameters, "shared", true);
 			if (sharedfile == "not open") { sharedfile = ""; abort = true; }	
 			else if (sharedfile == "not found") { sharedfile = ""; }
+			else { m->setSharedFile(sharedfile); }
 			
 			namefile = validParameter.validFile(parameters, "name", 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") { groupfile = ""; abort = true; }	
 			else if (groupfile == "not found") { groupfile = ""; }
-			
+			else { m->setGroupFile(groupfile); }
 			
 			//check for optional parameter and set defaults
 			// ...at some point should added some additional type checking...
@@ -701,6 +708,7 @@ int SubSampleCommand::getSubSampleShared() {
 				
 				m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 				
+				if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 				processShared(lookup, out);
 				
 				processedLabels.insert(lookup[0]->getLabel());
@@ -715,6 +723,7 @@ int SubSampleCommand::getSubSampleShared() {
 				lookup = input->getSharedRAbundVectors(lastLabel);
 				m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 				
+				if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 				processShared(lookup, out);
 				
 				processedLabels.insert(lookup[0]->getLabel());
@@ -755,6 +764,7 @@ int SubSampleCommand::getSubSampleShared() {
 			
 			m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 			
+			if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 			processShared(lookup, out);
 			
 			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
@@ -1146,7 +1156,7 @@ int SubSampleCommand::processList(ListVector*& list, ofstream& out, set<string>&
 					individual += binnames[j];
 				}
 			}
-			if (subset.count(individual) != 0) {  newNames += individual;  }
+			if (subset.count(individual) != 0) {  newNames += individual + ",";  }
 			
 			
 			//if there are names in this bin add to new list