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

[mothur.git] / readotucommand.cpp

diff --git a/readotucommand.cpp b/readotucommand.cpp
index b58dc607ec20891dd760360d74402ffa90bc9ea0..e55e9805af42cf37728fad27cc4f8b60f36fc882 100644 (file)
--- a/readotucommand.cpp
+++ b/readotucommand.cpp
@@ -21,21 +21,81 @@ ReadOtuCommand::ReadOtuCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"list","order","shared", "label","group","sabund", "rabund","groups"};
+                       string Array[] =  {"list","order","shared", "label","group","sabund", "rabund","groups","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;  }
                        }
                        
                        globaldata->newRead();
                        
+                       //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("order");
+                               //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["order"] = inputDir + it->second;            }
+                               }
+                               
+                               it = parameters.find("shared");
+                               //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["shared"] = 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;            }
+                               }
+                               
+                               it = parameters.find("sabund");
+                               //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["sabund"] = inputDir + it->second;           }
+                               }
+                               
+                               it = parameters.find("rabund");
+                               //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["rabund"] = 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
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
@@ -63,7 +123,10 @@ ReadOtuCommand::ReadOtuCommand(string option){
                        else {  
                                globaldata->setGroupFile(groupfile); 
                                groupMap = new GroupMap(groupfile);
-                               groupMap->readMap();
+                               
+                               int error = groupMap->readMap();
+                               if (error == 1) { abort = true; }
+                               
                                globaldata->gGroupmap = groupMap;
                        }
                        
@@ -154,9 +217,8 @@ int ReadOtuCommand::execute(){
                
                if (globaldata->getFormat() == "shared") {
                        
-                       shared = new SharedCommand();
+                       shared = new SharedCommand(outputDir);
                        int okay = shared->execute();
-                       delete shared;
                        
                        //problem with shared
                        if (okay == 1) {
@@ -169,8 +231,8 @@ int ReadOtuCommand::execute(){
                                globaldata->setFormat("sharedfile");
                                globaldata->setListFile("");
                                globaldata->setGroupFile("");
-                               globaldata->setSharedFile(getRootName(filename) + "shared");
                        }
+                       delete shared;
                }
                return 0;
        }