pat's ../ bug fix

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 784155745fa9c0141d6b2db0ba80133b39e3a85f..7782d1eac5354261c6727e240a33ae2d89984224 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -52,16 +52,20 @@ AlignCommand::AlignCommand(string option){
                        for (it = parameters.begin(); it != parameters.end(); it++) { 
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
-                       
+
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
                        
+
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
+                       
                        if (inputDir == "not found"){   inputDir = "";          }
                        else {
                                string path;
+
                                it = parameters.find("template");
+
                                //user has given a template file
                                if(it != parameters.end()){ 
                                        path = hasPath(it->second);
@@ -69,9 +73,10 @@ AlignCommand::AlignCommand(string option){
                                        if (path == "") {       parameters["template"] = inputDir + it->second;         }
                                }
                        }
-                       
+
                        //check for required parameters
                        templateFileName = validParameter.validFile(parameters, "template", true);
+                       
                        if (templateFileName == "not found") { 
                                mothurOut("template is a required parameter for the align.seqs command."); 
                                mothurOutEndLine();
@@ -106,7 +111,6 @@ AlignCommand::AlignCommand(string option){
                                //make sure there is at least one valid file left
                                if (candidateFileNames.size() == 0) { mothurOut("no valid files."); mothurOutEndLine(); abort = true; }
                        }
-                               
                        
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...