added countable class to read and store count file. added count parameter to make...

[mothur.git] / binsequencecommand.cpp

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index 4977cad1f769690e300013e89c936eefb4228e84..7569a4be3113144a96048f5a4d624d271c15b9f4 100644 (file)
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -50,6 +50,26 @@ string BinSeqCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string BinSeqCommand::getOutputFileNameTag(string type, string inputName=""){  
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "fasta") {  outputFileName =  "fasta"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "BinSeqCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 BinSeqCommand::BinSeqCommand(){        
        try {
                abort = true; calledHelp = true; 
@@ -167,7 +187,7 @@ BinSeqCommand::BinSeqCommand(string option) {
                        }
                        
                        namesfile = validParameter.validFile(parameters, "name", true);
-                       if (namesfile == "not open") { abort = true; }  
+                       if (namesfile == "not open") { namesfile = ""; abort = true; }  
                        else if (namesfile == "not found") { namesfile = ""; }
                        else {  m->setNameFile(namesfile); }
 
@@ -176,6 +196,11 @@ BinSeqCommand::BinSeqCommand(string option) {
                        else if (groupfile == "not found") { groupfile = ""; }
                        else { m->setGroupFile(groupfile); }
                        
+                       if (namesfile == ""){
+                               vector<string> files; files.push_back(fastafile); 
+                               parser.getNameFile(files);
+                       }
+                       
                }
        }
        catch(exception& e) {
@@ -339,8 +364,8 @@ int BinSeqCommand::process(ListVector* list) {
        try {
                                string binnames, name, sequence;
                                
-                               string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + ".fasta";
-                               m->openOutputFile(outputFileName, out);
+        string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + getOutputFileNameTag("fasta");
+        m->openOutputFile(outputFileName, out);
                                
                                //save to output list of output file names
                                outputNames.push_back(outputFileName);  outputTypes["fasta"].push_back(outputFileName);