added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index a7d42b331bc3044de372c030175da4663f9e3a9c..7a8fbc8cdfe6236601dbc0b369f6ef415a5c7c48 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -57,6 +57,27 @@ string FilterSeqsCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string FilterSeqsCommand::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 =  "filter.fasta"; }
+            else if (type == "filter") {  outputFileName =  "filter"; }
+            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, "FilterSeqsCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 FilterSeqsCommand::FilterSeqsCommand(){        
        try {
                abort = true; calledHelp = true; 
@@ -278,8 +299,8 @@ int FilterSeqsCommand::execute() {
                
                //prevent giantic file name
                string filterFile;
-               if (fastafileNames.size() > 3) { filterFile = outputDir + "merge.filter"; }
-               else {  filterFile = outputDir + filterFileName + ".filter";  }
+               if (fastafileNames.size() > 3) { filterFile = outputDir + "merge." + getOutputFileNameTag("filter"); }
+               else {  filterFile = outputDir + filterFileName + "." + getOutputFileNameTag("filter");  }
                
                m->openOutputFile(filterFile, outFilter);
                outFilter << filter << endl;
@@ -342,7 +363,7 @@ int FilterSeqsCommand::filterSequences() {
                        
                                for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
                                
-                               string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + "filter.fasta";
+                               string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + getOutputFileNameTag("fasta");
 #ifdef USE_MPI 
                                int pid, numSeqsPerProcessor, num; 
                                int tag = 2001;