X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getgroupscommand.cpp;h=84b168a4c75164b339b7ed2b6f350d13021da5e4;hb=9bc68cbe7fd7c5cf00b66d73d60624de80fb7933;hp=1832f96aed8122020b5ddf0ad5881275e3cc6481;hpb=5694c92fbf646fe01abc87bde2af59e14a9a56b6;p=mothur.git

diff --git a/getgroupscommand.cpp b/getgroupscommand.cpp
index 1832f96..84b168a 100644
--- a/getgroupscommand.cpp
+++ b/getgroupscommand.cpp
@@ -27,8 +27,7 @@ vector<string> GetGroupsCommand::getValidParameters(){
 //**********************************************************************************************************************
 GetGroupsCommand::GetGroupsCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["fasta"] = tempOutNames;
 		outputTypes["taxonomy"] = tempOutNames;
@@ -67,10 +66,10 @@ vector<string> GetGroupsCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 GetGroupsCommand::GetGroupsCommand(string option)  {
 	try {
-		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 {
 			//valid paramters for this command
@@ -207,8 +206,8 @@ void GetGroupsCommand::help(){
 		m->mothurOut("You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n");
 		m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like.  You can separate group names with dashes.\n");
 		m->mothurOut("The get.groups command should be in the following format: get.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n");
-		m->mothurOut("Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n");
-		m->mothurOut("or get.seqs(groups=pasture, fasta=amazon.fasta, amazon.groups).\n");
+		m->mothurOut("Example get.groups(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n");
+		m->mothurOut("or get.groups(groups=pasture, fasta=amazon.fasta, group=amazon.groups).\n");
 		m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 	}
 	catch(exception& e) {
@@ -222,7 +221,7 @@ void GetGroupsCommand::help(){
 int GetGroupsCommand::execute(){
 	try {
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		groupMap = new GroupMap(groupfile);
 		groupMap->readMap();
@@ -251,14 +250,43 @@ int GetGroupsCommand::execute(){
 		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
 		
 		m->mothurOut("Selected " + toString(names.size()) + " sequences. From the groups: "); m->mothurOutEndLine();
-		for (int i = 0; i < Groups.size(); i++) {	m->mothurOut(Groups[i]); m->mothurOutEndLine();	}
+		for (int i = 0; i < Groups.size(); i++) {	m->mothurOut(Groups[i]); m->mothurOut(" contains " + toString(groupMap->getNumSeqs(Groups[i])) + " sequences."); m->mothurOutEndLine();	}
 		m->mothurOutEndLine();
 		
+		
+		
 		if (outputNames.size() != 0) {
 			m->mothurOutEndLine();
 			m->mothurOut("Output File names: "); m->mothurOutEndLine();
 			for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}
 			m->mothurOutEndLine();
+			
+			//set fasta file as new current fastafile
+			string current = "";
+			itTypes = outputTypes.find("fasta");
+			if (itTypes != outputTypes.end()) {
+				if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+			}
+			
+			itTypes = outputTypes.find("name");
+			if (itTypes != outputTypes.end()) {
+				if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+			}
+			
+			itTypes = outputTypes.find("group");
+			if (itTypes != outputTypes.end()) {
+				if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+			}
+			
+			itTypes = outputTypes.find("list");
+			if (itTypes != outputTypes.end()) {
+				if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
+			}
+			
+			itTypes = outputTypes.find("taxonomy");
+			if (itTypes != outputTypes.end()) {
+				if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
+			}
 		}
 		
 		return 0;