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

[mothur.git] / preclustercommand.cpp

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index 89e6cbfb9e2560e4860cae8dd6a0ee4632a687da..d638bd2240a46ab20a7b5253e15be5a056a41aa4 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -22,28 +22,56 @@ PreClusterCommand::PreClusterCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta", "name", "diffs"};
+                       string Array[] =  {"fasta", "name", "diffs", "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 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;
+                               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
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not found") { mothurOut("fasta is a required parameter for the pre.cluster command."); mothurOutEndLine(); abort = true; }
                        else if (fastafile == "not open") { 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(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...
                        namefile = validParameter.validFile(parameters, "name", true);
-
                        if (namefile == "not found") { namefile =  "";  }
                        else if (namefile == "not open") { abort = true; }      
 //                     else {  readNameFile();  }
@@ -132,9 +160,11 @@ int PreClusterCommand::execute(){
                        }//end if active i
                        if(i % 100 == 0)        { cout << i << '\t' << numSeqs - count << '\t' << count << endl;        }
                }
-       
-               string newFastaFile = getRootName(fastafile) + "precluster" + getExtension(fastafile);
-               string newNamesFile = getRootName(fastafile) + "precluster.names";
+               
+               string fileroot = outputDir + getRootName(getSimpleName(fastafile));
+               
+               string newFastaFile = fileroot + "precluster" + getExtension(fastafile);
+               string newNamesFile = fileroot + "precluster.names";
                
                
                mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); mothurOutEndLine();