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

[mothur.git] / distancecommand.cpp

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 0422532c4b11bb8e64573a6bbc734f42a8b542b2..5364cbfee12cb3bc1813d0112beccb96126528cf 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -26,19 +26,34 @@ DistanceCommand::DistanceCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta", "phylip", "calc", "countends", "cutoff", "processors"};
+                       string Array[] =  {"fasta", "phylip", "calc", "countends", "cutoff", "processors", "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 it2;
                
                        //check to make sure all parameters are valid for command
-                       for (map<string, string>::iterator it2 = parameters.begin(); it2 != parameters.end(); it2++) { 
+                       for (it2 = parameters.begin(); it2 != parameters.end(); it2++) { 
                                if (validParameter.isValidParameter(it2->first, myArray, it2->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;
+                               it2 = parameters.find("fasta");
+                               //user has given a template file
+                               if(it2 != parameters.end()){ 
+                                       path = hasPath(it2->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["fasta"] = inputDir + it2->second;           }
+                               }
+                       }
+
                        //check for required parameters
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not found") { mothurOut("fasta is a required parameter for the dist.seqs command."); mothurOutEndLine(); abort = true; }
@@ -49,6 +64,12 @@ DistanceCommand::DistanceCommand(string option){
                                alignDB = SequenceDB(inFASTA); 
                                inFASTA.close();
                        }
+                       
+                       //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(fastafile); //if user entered a file with a path then preserve it  
+                       }
 
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
@@ -146,21 +167,15 @@ int DistanceCommand::execute(){
                
                //doses the user want the phylip formatted file as well
                if (isTrue(phylip) == true) {
-                       outputFile = getRootName(fastafile) + "phylip.dist";
+                       outputFile = outputDir + getRootName(getSimpleName(fastafile)) + "phylip.dist";
                        remove(outputFile.c_str());
                        
                        //output numSeqs to phylip formatted dist file
                }else { //user wants column format
-                       outputFile = getRootName(fastafile) + "dist";
+                       outputFile = outputDir + getRootName(getSimpleName(fastafile)) + "dist";
                        remove(outputFile.c_str());
                }
                                
-               //#     if defined (_WIN32)
-               //figure out how to implement the fork and wait commands in windows
-               //      driver(distCalculator, seqDB, 0, numSeqs, distFile, phylipFile, cutoff);
-               //#     endif
-               
-                               
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                //if you don't need to fork anything
                if(processors == 1){