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

[mothur.git] / binsequencecommand.cpp

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index ad90ff45202213fcb88cb222004628a82930ba80..6618eb6e5aa60109cf908786f4b50f7a06b02293 100644 (file)
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -22,19 +22,27 @@ BinSeqCommand::BinSeqCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string AlignArray[] =  {"fasta","label","name", "group"};
+                       string AlignArray[] =  {"fasta","label","name", "group","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 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(globaldata->getListFile()); //if user entered a file with a path then preserve it  
+                       }
+
+                       
                        //make sure the user has already run the read.otu command
                        if (globaldata->getListFile() == "") { 
                                mothurOut("You must read a listfile before running the bin.seqs command."); 
@@ -42,6 +50,36 @@ BinSeqCommand::BinSeqCommand(string option){
                                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;             }
+                               }
+                               
+                               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;            }
+                               }
+                       }
+
                        
                        //check for required parameters
                        fastafile = validParameter.validFile(parameters, "fasta", true);
@@ -77,7 +115,9 @@ BinSeqCommand::BinSeqCommand(string option){
                                fasta = new FastaMap();
                                if (groupfile != "") {
                                        groupMap = new GroupMap(groupfile);
-                                       groupMap->readMap();
+                                       
+                                       int error = groupMap->readMap();
+                                       if (error == 1) { delete groupMap; abort = true; }
                                }
                        }
        
@@ -258,7 +298,8 @@ void BinSeqCommand::readNamesFile() {
 int BinSeqCommand::process(ListVector* list) {
        try {
                                string binnames, name, sequence;
-                               string outputFileName = getRootName(globaldata->getListFile()) + list->getLabel() + ".fasta";
+                               
+                               string outputFileName = outputDir + getRootName(getSimpleName(globaldata->getListFile())) + list->getLabel() + ".fasta";
                                openOutputFile(outputFileName, out);
 
                                mothurOut(list->getLabel()); mothurOutEndLine();