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

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 75466f95b242ae08a71a88a40efec3a8fd230c86..a68fbfcba365207d7847c7eeaff12d9e4a4914e2 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -75,6 +75,29 @@ string AlignCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string AlignCommand::getOutputFileNameTag(string type, string inputName=""){   
+       try {
+        string tag = "";
+               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") {  tag = "align"; }
+            else if (type == "alignreport") {  tag = "align.report"; }
+            else if (type == "accnos") {  tag = "flip.accnos"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return tag;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "AlignCommand", "getOutputFileName");
+               exit(1);
+       }
+}
+
 //**********************************************************************************************************************
 AlignCommand::AlignCommand(){  
        try {
@@ -305,9 +328,9 @@ int AlignCommand::execute(){
                        m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
                        
                        if (outputDir == "") {  outputDir += m->hasPath(candidateFileNames[s]); }
-                       string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align";
-                       string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align.report";
-                       string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "flip.accnos";
+                       string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("fasta");  
+                       string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("alignreport");
+                       string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("accnos");
                        bool hasAccnos = true;
                        
                        int numFastaSeqs = 0;