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

[mothur.git] / heatmapsimcommand.cpp

diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp
index 3287e62fd297b440e46971e3c57093799369ff08..cef790633454b7d8136556d6441a684f0e45e3de 100644 (file)
--- a/heatmapsimcommand.cpp
+++ b/heatmapsimcommand.cpp
@@ -36,31 +36,64 @@ HeatMapSimCommand::HeatMapSimCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string AlignArray[] =  {"groups","label", "calc","phylip","column","name"};
+                       string AlignArray[] =  {"groups","label", "calc","phylip","column","name","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;  }
                        }
                        
                        format = "";
+                       //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 = "";         }
                        
+                       //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;             }
+                               }
+                       }
+
                        //required parameters
                        phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not open") { abort = true; }
                        else if (phylipfile == "not found") { phylipfile = ""; }        
-                       else {  format = "phylip";      }
+                       else {  format = "phylip";      if (outputDir == "") { outputDir += hasPath(phylipfile); }  }
                        
                        columnfile = validParameter.validFile(parameters, "column", true);
                        if (columnfile == "not open") { abort = true; } 
                        else if (columnfile == "not found") { columnfile = ""; }
-                       else {  format = "column";      }
+                       else {  format = "column";      if (outputDir == "") { outputDir += hasPath(columnfile); } }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }   
@@ -80,6 +113,8 @@ HeatMapSimCommand::HeatMapSimCommand(string option){
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
                        if (format == "shared") {
+                               if (outputDir == "") { outputDir += hasPath(globaldata->getSharedFile()); }
+                               
                                label = validParameter.validFile(parameters, "label", false);                   
                                if (label == "not found") { label = ""; }
                                else { 
@@ -190,7 +225,7 @@ int HeatMapSimCommand::execute(){
        
                if (abort == true)  { return 0; }
                
-               heatmap = new HeatMapSim();
+               heatmap = new HeatMapSim(outputDir);
                
                if (format == "shared") {
                        runCommandShared();