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

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 473d4d11d78bed00e56a02472afeb4980e19e87e..0d9e797a00c226ba2e2eea219d041fa1143d03fa 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -25,19 +25,45 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option){
                else {
                        
                        //valid paramters for this command
-                       string AlignArray[] =  {"template","fasta","name","search","ksize","method","processors","taxonomy","match","mismatch","gapopen","gapextend","numwanted","cutoff","probs","iters"};
+                       string AlignArray[] =  {"template","fasta","name","search","ksize","method","processors","taxonomy","match","mismatch","gapopen","gapextend","numwanted","cutoff","probs","iters", "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;  }
                        }
                        
+                       //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("template");
+                               //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["template"] = inputDir + it->second;         }
+                               }
+                               
+                               it = parameters.find("taxonomy");
+                               //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["taxonomy"] = inputDir + it->second;         }
+                               }
+                       }
+
                        //check for required parameters
                        templateFileName = validParameter.validFile(parameters, "template", true);
                        if (templateFileName == "not found") { 
@@ -54,6 +80,12 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option){
                                
                                //go through files and make sure they are good, if not, then disregard them
                                for (int i = 0; i < fastaFileNames.size(); i++) {
+                                       if (inputDir != "") {
+                                               string path = hasPath(fastaFileNames[i]);
+                                               //if the user has not given a path then, add inputdir. else leave path alone.
+                                               if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
+                                       }
+                                       
                                        int ableToOpen;
                                        ifstream in;
                                        ableToOpen = openInputFile(fastaFileNames[i], in);
@@ -88,6 +120,12 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option){
                                
                                //go through files and make sure they are good, if not, then disregard them
                                for (int i = 0; i < namefileNames.size(); i++) {
+                                       if (inputDir != "") {
+                                               string path = hasPath(namefileNames[i]);
+                                               //if the user has not given a path then, add inputdir. else leave path alone.
+                                               if (path == "") {       namefileNames[i] = inputDir + namefileNames[i];         }
+                                       }
+
                                        int ableToOpen;
                                        ifstream in;
                                        ableToOpen = openInputFile(namefileNames[i], in);
@@ -227,9 +265,11 @@ int ClassifySeqsCommand::execute(){
                        }
                
                        mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); mothurOutEndLine();
-                       string newTaxonomyFile = getRootName(fastaFileNames[s]) + getRootName(taxonomyFileName) + "taxonomy";
-                       string tempTaxonomyFile = getRootName(fastaFileNames[s]) + "taxonomy.temp";
-                       string taxSummary = getRootName(fastaFileNames[s]) + getRootName(taxonomyFileName) + "tax.summary";
+                       
+                       if (outputDir == "") { outputDir += hasPath(fastaFileNames[s]); }
+                       string newTaxonomyFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + getRootName(getSimpleName(taxonomyFileName)) + "taxonomy";
+                       string tempTaxonomyFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "taxonomy.temp";
+                       string taxSummary = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + getRootName(getSimpleName(taxonomyFileName)) + "tax.summary";
                        
                        int start = time(NULL);
                        int numFastaSeqs = 0;