fixed bug with dist.shared subsampling. added mode parameter to dist.shared so...

[mothur.git] / countseqscommand.cpp

diff --git a/countseqscommand.cpp b/countseqscommand.cpp
index 8164e2714db5fc4c1f2c1d59f9593475717386b5..e83c6035731aa5509655dcd25a7a45995c1a0004 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"; }
@@ -146,9 +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();