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 0822582b2d16b4575f584fbefdd2fffefb39cf55..8e8c7b67715ae9fb262fe4a41f7c9ef121dc2bff 100644 (file)
--- a/phylodiversitycommand.cpp
+++ b/phylodiversitycommand.cpp
@@ -52,7 +52,7 @@ string PhyloDiversityCommand::getHelpString(){
                helpString += "The phylo.diversity command should be in the following format: phylo.diversity(groups=yourGroups, rarefy=yourRarefy, iters=yourIters).\n";
                helpString += "Example phylo.diversity(groups=A-B-C, rarefy=T, iters=500).\n";
                helpString += "The phylo.diversity command output two files: .phylo.diversity and if rarefy=T, .rarefaction.\n";
-               helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -84,6 +84,7 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();;
@@ -136,6 +137,10 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
                        }
                        
                        m->runParse = true;
+                       m->Groups.clear();
+                       m->namesOfGroups.clear();
+                       m->Treenames.clear();
+                       m->names.clear();
                        
                        //check for required parameters
                        treefile = validParameter.validFile(parameters, "tree", true);
@@ -149,13 +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; }
@@ -210,9 +210,18 @@ int PhyloDiversityCommand::execute(){
                
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
-               //read in group map info.
-               tmap = new TreeMap(groupfile);
-               tmap->readMap();
+               m->setTreeFile(treefile);
+               
+               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(); }
                
@@ -266,7 +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