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

[mothur.git] / libshuffcommand.cpp

diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index 74acd841b676acc429df6df4e303210d82ae92ba..cfccdf6514297fe16af59234d94cdfd758b94c43 100644 (file)
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -32,7 +32,7 @@ LibShuffCommand::LibShuffCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"iters","groups","step","form","cutoff"};
+                       string Array[] =  {"iters","groups","step","form","cutoff","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -45,6 +45,12 @@ LibShuffCommand::LibShuffCommand(string option){
                                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 = ""; 
+                               outputDir += hasPath(globaldata->getPhylipFile()); //if user entered a file with a path then preserve it        
+                       }
+                       
                        //make sure the user has already run the read.dist command
                        if ((globaldata->gMatrix == NULL) || (globaldata->gGroupmap == NULL)) {
                                mothurOut("You must read in a matrix and groupfile using the read.dist command, before you use the libshuff command. "); mothurOutEndLine(); abort = true;; 
@@ -186,7 +192,7 @@ void LibShuffCommand::printCoverageFile() {
        try {
 
                ofstream outCov;
-               summaryFile = getRootName(globaldata->getPhylipFile()) + "libshuff.coverage";
+               summaryFile = outputDir + getRootName(getSimpleName(globaldata->getPhylipFile())) + "libshuff.coverage";
                openOutputFile(summaryFile, outCov);
                outCov.setf(ios::fixed, ios::floatfield); outCov.setf(ios::showpoint);
                //cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
@@ -273,7 +279,7 @@ void LibShuffCommand::printSummaryFile() {
        try {
 
                ofstream outSum;
-               summaryFile = getRootName(globaldata->getPhylipFile()) + "libshuff.summary";
+               summaryFile = outputDir + getRootName(getSimpleName(globaldata->getPhylipFile())) + "libshuff.summary";
                openOutputFile(summaryFile, outSum);
 
                outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);