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

[mothur.git] / chimeraseqscommand.cpp

diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index 9bd13e3a99578ab1374e2367fc73207e89225f50..63d02f5fd6998e61b65c85012d37d8061f6ff433 100644 (file)
--- a/chimeraseqscommand.cpp
+++ b/chimeraseqscommand.cpp
@@ -26,24 +26,78 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize", "svg", "name", "match","mismatch", "divergence", "minsim", "parents", "iters" };
+                       string Array[] =  {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize", "svg", "name", "match","mismatch", "divergence", "minsim", "parents", "iters","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("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("template");
+                               //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["template"] = inputDir + it->second;         }
+                               }
+                               
+                               it = parameters.find("conservation");
+                               //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["conservation"] = inputDir + it->second;             }
+                               }
+                               
+                               it = parameters.find("quantile");
+                               //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["quantile"] = 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 open") { abort = true; }
                        else if (fastafile == "not found") { fastafile = ""; mothurOut("fasta is a required parameter for the chimera.seqs command."); mothurOutEndLine(); 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  
+                       }
+
                        templatefile = validParameter.validFile(parameters, "template", true);
                        if (templatefile == "not open") { abort = true; }
                        else if (templatefile == "not found") { templatefile = "";  }   
@@ -63,6 +117,12 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                        maskfile = validParameter.validFile(parameters, "mask", false);
                        if (maskfile == "not found") { maskfile = "";  }        
                        else if (maskfile != "default")  { 
+                               if (inputDir != "") {
+                                       string path = hasPath(maskfile);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       maskfile = inputDir + maskfile;         }
+                               }
+
                                ifstream in;
                                int     ableToOpen = openInputFile(maskfile, in);
                                if (ableToOpen == 1) { abort = true; }
@@ -192,10 +252,10 @@ int ChimeraSeqsCommand::execute(){
                
                if (abort == true) { return 0; }
                
-               if (method == "bellerophon")                    {               chimera = new Bellerophon(fastafile);                                           }
-               else if (method == "pintail")                   {               chimera = new Pintail(fastafile, templatefile);                         }
+               if (method == "bellerophon")                    {               chimera = new Bellerophon(fastafile, outputDir);                        }
+               else if (method == "pintail")                   {               chimera = new Pintail(fastafile, templatefile, outputDir);      }
                else if (method == "ccode")                             {               chimera = new Ccode(fastafile, templatefile);                           }
-               else if (method == "chimeracheck")              {               chimera = new ChimeraCheckRDP(fastafile, templatefile);         }
+               else if (method == "chimeracheck")              {               chimera = new ChimeraCheckRDP(fastafile, templatefile, outputDir);      }
                else if (method == "chimeraslayer")             {               chimera = new ChimeraSlayer(fastafile, templatefile);           }
                else { mothurOut("Not a valid method."); mothurOutEndLine(); return 0;          }
                
@@ -231,8 +291,8 @@ int ChimeraSeqsCommand::execute(){
                
                //there was a problem
                if (error == 1) {  return 0;  }
-               
-               string outputFileName = getRootName(fastafile) + method + maskfile + ".chimeras";
+
+               string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + method + maskfile + ".chimeras";
                ofstream out;
                openOutputFile(outputFileName, out);