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

[mothur.git] / mgclustercommand.cpp

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index 81e80ccaf6ee82a0bbed8cd5a757a4502fd5449d..07c51479f35ff00db1694dcef2bc135df32976da 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -20,24 +20,54 @@ MGClusterCommand::MGClusterCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"blast", "method", "name", "cutoff", "precision", "length", "min", "penalty", "hcluster","merge"};
+                       string Array[] =  {"blast", "method", "name", "cutoff", "precision", "length", "min", "penalty", "hcluster","merge","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("blast");
+                               //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["blast"] = 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
                        blastfile = validParameter.validFile(parameters, "blast", true);
                        if (blastfile == "not open") { abort = true; }  
                        else if (blastfile == "not found") { blastfile = ""; }
                        
+                       //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(blastfile); //if user entered a file with a path then preserve it  
+                       }
+                       
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }   
                        else if (namefile == "not found") { namefile = ""; }
@@ -120,7 +150,7 @@ int MGClusterCommand::execute(){
                        nameMap->readMap();
                }else{ nameMap= new NameAssignment(); }
                
-               string fileroot = getRootName(blastfile);
+               string fileroot = outputDir + getRootName(getSimpleName(blastfile));
                string tag = "";
                time_t start;
                float previousDist = 0.00000;
@@ -210,7 +240,6 @@ int MGClusterCommand::execute(){
                        delete cluster;
                        
                }else { //use hcluster to cluster
-                       tag = "fn";
                        //get distmatrix and overlap
                        overlapFile = read->getOverlapFile();
                        distFile = read->getDistFile();