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

[mothur.git] / phylotypecommand.cpp

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index 8ba0a091ee7b77ff8f1abe37ae30117b64cec597..2dbd53a5dad36477279961d76d547fff3d8e83d3 100644 (file)
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -24,19 +24,34 @@ PhylotypeCommand::PhylotypeCommand(string option){
                else {
                        
                        //valid paramters for this command
-                       string AlignArray[] =  {"taxonomy","cutoff","label"};
+                       string AlignArray[] =  {"taxonomy","cutoff","label","outputdir","inputdir"};
                        vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/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("taxonomy");
+                               //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["taxonomy"] = inputDir + it->second;         }
+                               }
+                       }
+
                        taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
                        if (taxonomyFileName == "not found") { 
                                mothurOut("taxonomy is a required parameter for the phylotype command."); 
@@ -44,6 +59,12 @@ PhylotypeCommand::PhylotypeCommand(string option){
                                abort = true; 
                        }else if (taxonomyFileName == "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(taxonomyFileName); //if user entered a file with a path then preserve it   
+                       }
+                       
                        string temp = validParameter.validFile(parameters, "cutoff", false);
                        if (temp == "not found") { temp = "-1"; }
                        convert(temp, cutoff); 
@@ -112,14 +133,16 @@ int PhylotypeCommand::execute(){
                bool done = false;
                if (tree->get(leaves[0]).parent == -1) {  mothurOut("Empty Tree"); mothurOutEndLine();  done = true;    }
                
+               string fileroot = outputDir + getRootName(getSimpleName(taxonomyFileName));
+               
                ofstream outList;
-               string outputListFile = getRootName(taxonomyFileName) + "tx.list";
+               string outputListFile = fileroot + "tx.list";
                openOutputFile(outputListFile, outList);
                ofstream outSabund;
-               string outputSabundFile = getRootName(taxonomyFileName) + "tx.sabund";
+               string outputSabundFile = fileroot + "tx.sabund";
                openOutputFile(outputSabundFile, outSabund);
                ofstream outRabund;
-               string outputRabundFile = getRootName(taxonomyFileName) + "tx.rabund";
+               string outputRabundFile = fileroot + "tx.rabund";
                openOutputFile(outputRabundFile, outRabund);
                
                int count = 1;