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

[mothur.git] / otuhierarchycommand.cpp

diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp
index d0951387dc5e70dbe4e86eee3a8d8a777a4296e8..bc87211e0bde9a4581119a91592683e34262d006 100644 (file)
--- a/otuhierarchycommand.cpp
+++ b/otuhierarchycommand.cpp
@@ -18,23 +18,43 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"list","label"};
+                       string Array[] =  {"list","label","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("list");
+                               //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["list"] = inputDir + it->second;             }
+                               }
+                       }
+
                        listFile = validParameter.validFile(parameters, "list", true);
                        if (listFile == "not found") { mothurOut("list is a required parameter for the otu.hierarchy command."); mothurOutEndLine(); abort = true; }
                        else if (listFile == "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(listFile); //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...
@@ -111,7 +131,7 @@ int OtuHierarchyCommand::execute(){
                }
                
                ofstream out;
-               string outputFileName = getRootName(listFile) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy";
+               string outputFileName = outputDir + getRootName(getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy";
                openOutputFile(outputFileName, out);
                
                //go through each bin in "big" otu and output the bins in "little" otu which created it