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

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index c115c54ce1bcb39786ec7c54fcd4ba11df3115ab..e8f68e7f34c52258e480bd8e6f369a200734df1f 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -36,37 +36,68 @@ TreeGroupCommand::TreeGroupCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"label","calc","groups", "phylip", "column", "name", "precision","cutoff"};
+                       string Array[] =  {"label","calc","groups", "phylip", "column", "name", "precision","cutoff","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;           }
+                               }
+                               
+                               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;             }
+                               }
+                       }
+                       
+                       format = globaldata->getFormat();
+                       
                        //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";  globaldata->setPhylipFile(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"; globaldata->setColumnFile(columnfile);       }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }   
                        else if (namefile == "not found") { namefile = ""; }
                        else {  globaldata->setNameFile(namefile);      }
                        
-                       format = globaldata->getFormat();
-                       
                        //error checking on files                       
                        if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == "")))  { mothurOut("You must run the read.otu command or provide a distance file before running the tree.shared command."); mothurOutEndLine(); abort = true; }
                        else if ((phylipfile != "") && (columnfile != "")) { mothurOut("When running the tree.shared command with a distance file you may not use both the column and the phylip parameters."); mothurOutEndLine(); abort = true; }
@@ -111,6 +142,12 @@ TreeGroupCommand::TreeGroupCommand(string option){
                        temp = validParameter.validFile(parameters, "cutoff", false);                   if (temp == "not found") { temp = "10"; }
                        convert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0));
+                       
+                       //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->inputFileName); //if user entered a file with a path then preserve it  
+                       }
 
                                
                        if (abort == false) {
@@ -262,7 +299,7 @@ int TreeGroupCommand::execute(){
                        makeSimsDist();
 
                        //create a new filename
-                       outputFile = getRootName(globaldata->inputFileName) + "tre";    
+                       outputFile = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "tre"; 
                                
                        createTree();
                        mothurOut("Tree complete. "); mothurOutEndLine();
@@ -519,7 +556,7 @@ void TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                                        for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
                
                                        //create a new filename
-                                       outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";                         
+                                       outputFile = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";                              
                                                                                                
                                        for (int k = 0; k < thisLookup.size(); k++) { 
                                                for (int l = k; l < thisLookup.size(); l++) {