added set.current and get.current commands and modified existing commands to update...

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 77e99c0b0f4d512ce1c9409207e50fdde18d32c6..a820542e42f4d7a7b9956b194f790555e634536a 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -79,7 +79,6 @@ AlignCommand::AlignCommand(){
 AlignCommand::AlignCommand(string option)  {
        try {
                abort = false; calledHelp = false;   
-               currentFiles = CurrentFile::getInstance();
        
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true;}
@@ -139,9 +138,6 @@ AlignCommand::AlignCommand(string option)  {
                        
                        candidateFileName = validParameter.validFile(parameters, "candidate", false);
                        if (candidateFileName == "not found") { 
-                               //check currentFiles for a fasta file
-                               if (currentFiles->getFastaFile() != "") {  candidateFileName = currentFiles->getFastaFile(); m->mothurOut("Using " + candidateFileName + " as candidate file."); m->mothurOutEndLine();
-                               }else { m->mothurOut("candidate is a required parameter for the align.seqs command."); m->mothurOutEndLine(); abort = true;  }
                        }else { 
                                m->splitAtDash(candidateFileName, candidateFileNames);
                                
@@ -471,10 +467,9 @@ int AlignCommand::execute(){
                string currentFasta = "";
                itTypes = outputTypes.find("fasta");
                if (itTypes != outputTypes.end()) {
-                       if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; }
+                       if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
                }
-               currentFiles->setFastaFile(currentFasta);
-               cout << "current fasta = " << currentFiles->getFastaFile() << endl;
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }