Merge remote-tracking branch 'mothur/master'

[mothur.git] / phylodiversitycommand.cpp

diff --git a/phylodiversitycommand.cpp b/phylodiversitycommand.cpp
index 69c7b304623e44878cdafb8925fbffd9f45cd718..abf9591f4060482a158df9b008e0f357d6c6b069 100644 (file)
--- a/phylodiversitycommand.cpp
+++ b/phylodiversitycommand.cpp
@@ -144,7 +144,7 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
                        
                        //check for required parameters
                        treefile = validParameter.validFile(parameters, "tree", true);
-                       if (treefile == "not open") { abort = true; }
+                       if (treefile == "not open") { treefile = ""; abort = true; }
                        else if (treefile == "not found") {                             
                                //if there is a current design file, use it
                                treefile = m->getTreeFile(); 
@@ -159,7 +159,7 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
                        else { m->setGroupFile(groupfile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
-                       if (namefile == "not open") { abort = true; }
+                       if (namefile == "not open") { namefile = ""; abort = true; }
                        else if (namefile == "not found") { namefile = ""; }
                        else { m->setNameFile(namefile); }
                        
@@ -197,6 +197,11 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
                        }
                        
                        if ((!collect) && (!rarefy) && (!summary)) { m->mothurOut("No outputs selected. You must set either collect, rarefy or summary to true, summary=T by default."); m->mothurOutEndLine(); abort=true; }
+                       
+                       if (namefile == "") {
+                               vector<string> files; files.push_back(treefile);
+                               parser.getNameFile(files);
+                       }
                }
                
        }
@@ -348,7 +353,7 @@ int PhyloDiversityCommand::execute(){
                                if (numSampledList.count(diversity[mGroups[j]].size()-1) == 0) {  numSampledList.insert(diversity[mGroups[j]].size()-1); }
                        }
                        
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                                if(processors == 1){
                                        driver(trees[i], diversity, sumDiversity, iters, increment, randomLeaf, numSampledList, outCollect, outSum, true);      
                                }else{
@@ -398,7 +403,7 @@ int PhyloDiversityCommand::execute(){
 //**********************************************************************************************************************
 int PhyloDiversityCommand::createProcesses(vector<int>& procIters, Tree* t, map< string, vector<float> >& div, map<string, vector<float> >& sumDiv, int numIters, int increment, vector<int>& randomLeaf, set<int>& numSampledList, ofstream& outCollect, ofstream& outSum){
        try {
-               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                int process = 1;
                
                vector<int> processIDS;