X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylodiversitycommand.cpp;h=abb12435b0a414cf3bcea5f69505ba263fe733de;hb=b1d143351bcd1b3b4a06ec525c386f161579ee32;hp=48d8555e1285ce854b0a45efbfdb75057bad5a1f;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git

diff --git a/phylodiversitycommand.cpp b/phylodiversitycommand.cpp
index 48d8555..abb1243 100644
--- a/phylodiversitycommand.cpp
+++ b/phylodiversitycommand.cpp
@@ -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);
@@ -145,21 +150,18 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
 				treefile = m->getTreeFile(); 
 				if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }								
-			}	
+			}else { m->setTreeFile(treefile); }	
 			
 			//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 = ""; }
+			else { m->setGroupFile(groupfile); }
 			
 			namefile = validParameter.validFile(parameters, "name", true);
 			if (namefile == "not open") { abort = true; }
 			else if (namefile == "not found") { namefile = ""; }
+			else { m->setNameFile(namefile); }
 			
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = m->hasPath(treefile);	}
 			
@@ -210,9 +212,18 @@ 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 +277,7 @@ 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