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

[mothur.git] / pcacommand.cpp

diff --git a/pcacommand.cpp b/pcacommand.cpp
index 09324c9d3eaf3dd5a525a44cf233abe7df6e7285..77b16e82d58a427634f6bcd5c58fafdd2fe9a1f5 100644 (file)
--- a/pcacommand.cpp
+++ b/pcacommand.cpp
@@ -21,51 +21,47 @@ PCACommand::PCACommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"phylip"};
+                       string Array[] =  {"phylip","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("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;           }
+                               }
+                       }
+
                        //required parameters
                        phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not open") { abort = true; }
                        else if (phylipfile == "not found") { phylipfile = ""; abort = true; }  
                        else {  filename = phylipfile;  }
                        
-                       //columnfile = validParameter.validFile(parameters, "column", true);
-                       //if (columnfile == "not open") { abort = true; }       
-                       //else if (columnfile == "not found") { columnfile = ""; }
-                       //else {  format = "column";    }
-                       
-                       //namefile = validParameter.validFile(parameters, "name", true);
-                       //if (namefile == "not open") { abort = true; } 
-                       //else if (namefile == "not found") { namefile = ""; }
-                       
+                       //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(phylipfile); //if user entered a file with a path then preserve it 
+                       }
                        
                        //error checking on files       
                        if (phylipfile == "")   { mothurOut("You must provide a distance file before running the pca command."); mothurOutEndLine(); abort = true; }            
-                       //if ((phylipfile == "") && (columnfile == "")) { mothurOut("You must provide a distance file before running the pca command."); mothurOutEndLine(); abort = true; }
-                       //else if ((phylipfile != "") && (columnfile != "")) { mothurOut("You may not use both the column and the phylip parameters."); mothurOutEndLine(); abort = true; }
-                       
-                       //if (columnfile != "") {
-                       //      if (namefile == "") {  mothurOut("You need to provide a namefile if you are going to use the column format."); mothurOutEndLine(); abort = true; }
-                       //}
-                       
-                       //string temp = validParameter.validFile(parameters, "lt", false);                              if (temp == "not found") { temp = "false"; }
-                       //bool lt = isTrue(temp);
-                       
-                       //if (lt)               {  matrix = 2;  }
-                       //else          {  matrix = 1;  }
-
-
                }
 
        }
@@ -101,13 +97,16 @@ int PCACommand::execute(){
                vector<string> names;
                vector<vector<double> > D;
        
-               fbase = filename;
-               if(fbase.find_last_of(".")!=string::npos){
-                       fbase.erase(fbase.find_last_of(".")+1); 
-               }
-               else{
-                       fbase += ".";
-               }
+               //fbase = filename;
+               //if(fbase.find_last_of(".")!=string::npos){
+               //      fbase.erase(fbase.find_last_of(".")+1); 
+               //}
+               //else{
+               //      fbase += ".";
+               //}
+               
+               fbase = outputDir + getRootName(getSimpleName(filename));
+               
                read(filename, names, D);
        
                double offset = 0.0000;