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

[mothur.git] / unifracweightedcommand.cpp

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index ea79475038dc3abf2cbbc5be8eaaa750e3489bc1..a9f9570e771b7c45c95f96e9a162ddc9ec8dfdb8 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -21,7 +21,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"groups","iters","distance","random"};
+                       string Array[] =  {"groups","iters","distance","random","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -36,7 +36,13 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
                        
                        if (globaldata->gTree.size() == 0) {//no trees were read
                                mothurOut("You must execute the read.tree command, before you may execute the unifrac.weighted command."); mothurOutEndLine(); 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->inputFileName); //if user entered a file with a path then preserve it  
+                       }
+                                                                                                                                       
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
                        groups = validParameter.validFile(parameters, "groups", false);                 
@@ -61,7 +67,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
                        if (abort == false) {
                                T = globaldata->gTree;
                                tmap = globaldata->gTreemap;
-                               sumFile = globaldata->getTreeFile() + ".wsummary";
+                               sumFile = outputDir + getSimpleName(globaldata->getTreeFile()) + ".wsummary";
                                openOutputFile(sumFile, outSum);
                                
                                util = new SharedUtil();
@@ -125,7 +131,7 @@ int UnifracWeightedCommand::execute() {
                        rScores.resize(numComp);  //data[0] = weightedscore AB, data[1] = weightedscore AC...
                        uScores.resize(numComp);  //data[0] = weightedscore AB, data[1] = weightedscore AC...
                        
-                       if (random) {  output = new ColumnFile(globaldata->getTreeFile()  + toString(i+1) + ".weighted", itersString);  } 
+                       if (random) {  output = new ColumnFile(outputDir + getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".weighted", itersString);  } 
 
                        userData = weighted->getValues(T[i]);  //userData[0] = weightedscore
                        
@@ -283,7 +289,7 @@ void UnifracWeightedCommand::createPhylipFile() {
                //for each tree
                for (int i = 0; i < T.size(); i++) { 
                
-                       string phylipFileName = globaldata->getTreeFile()  + toString(i+1) + ".weighted.dist";
+                       string phylipFileName = outputDir + getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".weighted.dist";
                        ofstream out;
                        openOutputFile(phylipFileName, out);