added set.dir command and modified commands to redirect input and output, removed...

[mothur.git] / deconvolutecommand.cpp

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index a936c820b56f88609e621894565359892384224a..00c40845484e9ba4eba4e62f7c645135f703e9d2 100644 (file)
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -19,24 +19,54 @@ DeconvoluteCommand::DeconvoluteCommand(string option) {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta", "name"};
+                       string Array[] =  {"fasta", "name","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
                        
                        ValidParameters validParameter;
+                       map<string, string>::iterator it;
                
                        //check to make sure all parameters are valid for command
-                       for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+                       for (it = parameters.begin(); it != parameters.end(); it++) { 
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //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("fasta");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
+                               }
+                               
+                               it = parameters.find("name");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["name"] = inputDir + it->second;             }
+                               }
+                       }
+
+                       
                        //check for required parameters
                        inFastaName = validParameter.validFile(parameters, "fasta", true);
                        if (inFastaName == "not open") { abort = true; }
                        else if (inFastaName == "not found") { inFastaName = ""; mothurOut("fasta is a required parameter for the unique.seqs command."); mothurOutEndLine(); 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 = ""; 
+                               outputDir += hasPath(inFastaName); //if user entered a file with a path then preserve it        
+                       }
+                       
                        oldNameMapFName = validParameter.validFile(parameters, "name", true);
                        if (oldNameMapFName == "not open") { abort = true; }
                        else if (oldNameMapFName == "not found"){       oldNameMapFName = "";   }
@@ -72,8 +102,8 @@ int DeconvoluteCommand::execute() {
                if (abort == true) { return 0; }
 
                //prepare filenames and open files
-               string outNameFile = (getRootName(inFastaName) + "names");
-               string outFastaFile = (getRootName(inFastaName) + "unique" + getExtension(inFastaName));
+               string outNameFile = outputDir + getRootName(getSimpleName(inFastaName)) + "names";
+               string outFastaFile = outputDir + getRootName(getSimpleName(inFastaName)) + "unique" + getExtension(inFastaName);
                
                FastaMap fastamap;