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

[mothur.git] / readdistcommand.cpp

diff --git a/readdistcommand.cpp b/readdistcommand.cpp
index 9d38e76b10935e2ea7fe9f485e53eab662fc982e..9cb2046139ba7d275aa31cb1e9024bf9a729cbf2 100644 (file)
--- a/readdistcommand.cpp
+++ b/readdistcommand.cpp
@@ -22,21 +22,63 @@ ReadDistCommand::ReadDistCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"phylip", "column", "name", "cutoff", "precision", "group"};
+                       string Array[] =  {"phylip", "column", "name", "cutoff", "precision", "group","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("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
                        phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not open") { abort = true; }
@@ -92,10 +134,12 @@ ReadDistCommand::ReadDistCommand(string option){
                                else if (format == "phylip") { read = new ReadPhylipMatrix(distFileName); }
                                else if (format == "matrix") { 
                                        groupMap = new GroupMap(groupfile);
-                                       groupMap->readMap();
-       
-                                       if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap;  }
-                                       globaldata->gGroupmap = groupMap;
+                                       int error = groupMap->readMap();
+                                       if (error == 1) { delete groupMap; abort = true; }
+                                       else {
+                                               if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap;  }
+                                               globaldata->gGroupmap = groupMap;
+                                       }
                                }
                
                                if (format != "matrix" ) {
@@ -169,7 +213,9 @@ int ReadDistCommand::execute(){
                        if (matrix->getNumSeqs() < groupMap->getNumSeqs()) {  
                                mothurOut("Your distance file contains " + toString(matrix->getNumSeqs()) + " sequences, and your group file contains " + toString(groupMap->getNumSeqs()) + " sequences.");  mothurOutEndLine();                               
                                //create new group file
-                               string newGroupFile = getRootName(groupfile) + "editted.groups";
+                               if(outputDir == "") { outputDir += hasPath(groupfile); }
+                               
+                               string newGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "editted.groups";
                                ofstream outGroups;
                                openOutputFile(newGroupFile, outGroups);