made read.tree not require a groupfile, if one is not given all seqs are assumed...

[mothur.git] / readtreecommand.cpp

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index fdfdb050f22c4ccc281646d1d56c8a5aa6b33806..89efc9abcf0057f68189ddad6975b5e1464fca09 100644 (file)
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -76,8 +76,20 @@ ReadTreeCommand::ReadTreeCommand(string option)  {
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }  
-                       else if (groupfile == "not found") { groupfile = ""; m->mothurOut("group is a required parameter for the read.tree command."); m->mothurOutEndLine(); abort = true;     }
-                       else {  
+                       else if (groupfile == "not found") { 
+                               groupfile = ""; 
+                               
+                               m->mothurOut("You have not provided a group file. I am assumming all sequence are from the same group."); m->mothurOutEndLine();        
+                               
+                               if (treefile != "") {  Tree* tree = new Tree(treefile); delete tree;  } //extracts names from tree to make faked out groupmap
+                               
+                               globaldata->setGroupFile(groupfile); 
+                               //read in group map info.
+                               treeMap = new TreeMap();
+                               for (int i = 0; i < globaldata->Treenames.size(); i++) { treeMap->addSeq(globaldata->Treenames[i], "Group1"); }
+                               globaldata->gTreemap = treeMap;
+                                       
+                       }else {  
                                globaldata->setGroupFile(groupfile); 
                                //read in group map info.
                                treeMap = new TreeMap(groupfile);
@@ -227,7 +239,7 @@ int ReadTreeCommand::readNamesFile() {
                                vector<string> dupNames;
                                m->splitAtComma(second, dupNames);
                                
-                               for (int i = 0; i < dupNames.size(); i++) {     nameMap[dupNames[i]] = dupNames[i];  }
+                               for (int i = 0; i < dupNames.size(); i++) {     nameMap[dupNames[i]] = dupNames[i];  if ((groupfile == "") && (i != 0)) { globaldata->gTreemap->addSeq(dupNames[i], "Group1"); }  }
                        }else {  m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); globaldata->names.clear(); namefile = ""; return 1; }                 
                }
                in.close();