changed blastdb.cpp to no include sequence names in blast input filenames. modified...

[mothur.git] / phylodiversitycommand.cpp

diff --git a/phylodiversitycommand.cpp b/phylodiversitycommand.cpp
index bf502abe715baadd43112377c374ba218414d3d8..8e8c7b67715ae9fb262fe4a41f7c9ef121dc2bff 100644 (file)
--- a/phylodiversitycommand.cpp
+++ b/phylodiversitycommand.cpp
@@ -154,13 +154,8 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
                        
                        //check for required parameters
                        groupfile = validParameter.validFile(parameters, "group", true);
-                       if (groupfile == "not open") { abort = true; }
-                       else if (groupfile == "not found") { 
-                               //if there is a current design file, use it
-                               groupfile = m->getGroupFile(); 
-                               if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
-                               else {  m->mothurOut("You have no current group file and the group parameter is required."); m->mothurOutEndLine(); abort = true; }                                                             
-                       }
+                       if (groupfile == "not open") { groupfile = ""; abort = true; }
+                       else if (groupfile == "not found") { groupfile = ""; }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
@@ -217,9 +212,16 @@ int PhyloDiversityCommand::execute(){
                
                m->setTreeFile(treefile);
                
-               //read in group map info.
-               tmap = new TreeMap(groupfile);
-               tmap->readMap();
+               if (groupfile != "") {
+                       //read in group map info.
+                       tmap = new TreeMap(groupfile);
+                       tmap->readMap();
+               }else{ //fake out by putting everyone in one group
+                       Tree* tree = new Tree(treefile); delete tree;  //extracts names from tree to make faked out groupmap
+                       tmap = new TreeMap();
+                       
+                       for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); }
+               }
                
                if (namefile != "") { readNamesFile(); }
                
@@ -273,7 +275,7 @@ int PhyloDiversityCommand::execute(){
                }
                
                SharedUtil* util = new SharedUtil();
-               util->setGroups(m->Groups, tmap->namesOfGroups, "treegroup");   //sets the groups the user wants to analyze
+               util->setGroups(m->Groups, tmap->namesOfGroups, "phylo.diversity");     //sets the groups the user wants to analyze
                delete util;
                
                //incase the user had some mismatches between the tree and group files we don't want group xxx to be analyzed