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

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index d37ee19eb573bba0ade4c91320c9766f1712be69..6b9cee90c40f8f2848a076596d9ed3c88665ffb0 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -48,19 +48,78 @@ GetOTURepCommand::GetOTURepCommand(string option){
                        help(); abort = true;
                } else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta","list","label","name", "group", "sorted", "phylip","column","large","cutoff","precision"};
+                       string Array[] =  {"fasta","list","label","name", "group", "sorted", "phylip","column","large","cutoff","precision","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;             }
+                               }
+                               
+                               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("phylip");
+                               //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["phylip"] = inputDir + it->second;           }
+                               }
+                               
+                               it = parameters.find("column");
+                               //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["column"] = 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;             }
+                               }
+                               
+                               it = parameters.find("group");
+                               //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["group"] = inputDir + it->second;            }
+                               }
+                       }
+
+                       
+                       //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 = "";         }
+                       
                        //check for required parameters
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not found") { mothurOut("fasta is a required parameter for the get.oturep command."); mothurOutEndLine(); abort = true; }
@@ -104,7 +163,8 @@ GetOTURepCommand::GetOTURepCommand(string option){
                        else {
                                //read in group map info.
                                groupMap = new GroupMap(groupfile);
-                               groupMap->readMap();
+                               int error = groupMap->readMap();
+                               if (error == 1) { delete groupMap; abort = true; }
                        }
                        
                        sorted = validParameter.validFile(parameters, "sorted", false);         if (sorted == "not found"){     sorted = "";    }
@@ -490,12 +550,13 @@ int GetOTURepCommand::process(ListVector* processList) {
                string nameRep, name, sequence;
 
                //create output file
-               string outputFileName = getRootName(listfile) + processList->getLabel() + ".rep.fasta";
+               if (outputDir == "") { outputDir += hasPath(listfile); }
+               string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + processList->getLabel() + ".rep.fasta";
                openOutputFile(outputFileName, out);
                vector<repStruct> reps;
                
                ofstream newNamesOutput;
-               string outputNamesFile = getRootName(listfile) + processList->getLabel() + ".rep.names";
+               string outputNamesFile = outputDir + getRootName(getSimpleName(listfile)) + processList->getLabel() + ".rep.names";
                openOutputFile(outputNamesFile, newNamesOutput);
                
                //for each bin in the list vector