working on current change

[mothur.git] / countseqscommand.cpp

diff --git a/countseqscommand.cpp b/countseqscommand.cpp
index 8164e2714db5fc4c1f2c1d59f9593475717386b5..a9bffc6eca25d3ad78ce7b01d96e196ba6308bfb 100644 (file)
--- 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"; }
@@ -146,7 +147,7 @@ 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";