X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=countseqscommand.cpp;h=e83c6035731aa5509655dcd25a7a45995c1a0004;hb=2c97dd48b8e27ee0a6a86c7a082f4c504c3357c6;hp=8164e2714db5fc4c1f2c1d59f9593475717386b5;hpb=fe0f86cb70ff3ce31df98ed49e404c7e12e21b3d;p=mothur.git

diff --git a/countseqscommand.cpp b/countseqscommand.cpp
index 8164e27..e83c603 100644
--- a/countseqscommand.cpp
+++ b/countseqscommand.cpp
@@ -33,7 +33,7 @@ vector<string> CountSeqsCommand::setParameters(){
 string CountSeqsCommand::getHelpString(){	
 	try {
 		string helpString = "";
-		helpString += "The count.seqs command reads a name file and outputs a .count.summary file.  You may also provide a group file to get the counts broken down by group.\n";
+		helpString += "The count.seqs command reads a name file and outputs a .seq.count file.  You may also provide a group file to get the counts broken down by group.\n";
 		helpString += "The groups parameter allows you to indicate which groups you want to include in the counts, by default all groups in your groupfile are used.\n";
 		helpString += "When you use the groups parameter and a sequence does not represent any sequences from the groups you specify it is not included in the .count.summary file.\n";
 		helpString += "The count.seqs command should be in the following format: count.seqs(name=yourNameFile).\n";
@@ -117,11 +117,12 @@ CountSeqsCommand::CountSeqsCommand(string option)  {
 				namefile = m->getNameFile(); 
 				if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current namefile and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}
+			}else { m->setNameFile(namefile); }
 			
 			groupfile = validParameter.validFile(parameters, "group", true);
 			if (groupfile == "not open") { abort = true; }
 			else if (groupfile == "not found") {  groupfile = "";  }	
+			else { m->setGroupFile(groupfile); }
 			
 			groups = validParameter.validFile(parameters, "groups", false);			
 			if (groups == "not found") { groups = "all"; }
@@ -146,9 +147,9 @@ int CountSeqsCommand::execute(){
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		ofstream out;
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + "count.summary";
+		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 != "") { 
@@ -156,7 +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
@@ -172,7 +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; }
 			
@@ -215,14 +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();