X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=countseqscommand.cpp;h=e83c6035731aa5509655dcd25a7a45995c1a0004;hb=f816b683e586575bfe3479760a8afd5ab08e8573;hp=a9bffc6eca25d3ad78ce7b01d96e196ba6308bfb;hpb=220dc345e493cddc569521111ce32ac4d965ab7f;p=mothur.git

diff --git a/countseqscommand.cpp b/countseqscommand.cpp
index a9bffc6..e83c603 100644
--- a/countseqscommand.cpp
+++ b/countseqscommand.cpp
@@ -147,9 +147,9 @@ int CountSeqsCommand::execute(){
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		ofstream out;
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + ".seq.count";
+		string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + "seq.count";
 		m->openOutputFile(outputFileName, out); outputTypes["summary"].push_back(outputFileName);
-		out << "Representative Sequence\t total\t";
+		out << "Representative_Sequence\ttotal\t";
 		
 		GroupMap* groupMap;
 		if (groupfile != "") { 
@@ -157,7 +157,8 @@ int CountSeqsCommand::execute(){
 			
 			//make sure groups are valid. takes care of user setting groupNames that are invalid or setting groups=all
 			SharedUtil* util = new SharedUtil();
-			util->setGroups(Groups, groupMap->namesOfGroups);
+			vector<string> nameGroups = groupMap->getNamesOfGroups();
+			util->setGroups(Groups, nameGroups);
 			delete util;
 			
 			//sort groupNames so that the group title match the counts below, this is needed because the map object automatically sorts
@@ -173,7 +174,8 @@ int CountSeqsCommand::execute(){
 		//open input file
 		ifstream in;
 		m->openInputFile(namefile, in);
-		
+        
+		int total = 0;
 		while (!in.eof()) {
 			if (m->control_pressed) { break; }
 			
@@ -216,14 +218,16 @@ int CountSeqsCommand::execute(){
 				out << firstCol << '\t' << names.size() << endl;
 			}
 			
-			
+			total += names.size();
 		}
 		in.close();
 		
 		if (groupfile != "") { delete groupMap; }
 		
-		if (m->control_pressed) { remove(outputFileName.c_str()); return 0; }
+		if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
 		
+        m->mothurOutEndLine();
+		m->mothurOut("Total number of sequences: " + toString(total)); m->mothurOutEndLine();
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 		m->mothurOut(outputFileName); m->mothurOutEndLine();