fixed parsimony for groups

[mothur.git] / readtree.cpp

diff --git a/readtree.cpp b/readtree.cpp
index 1910c4a5a1761e4cf73cd95ce8a1df9b97ee4b33..81a7729ffb474294502407eec1c44620bfff3378 100644 (file)
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -331,9 +331,28 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                        //find index in tree of name
                        int n1 = T->getIndex(name);
                        
-                       if(n1 == -1){cerr << "Name: " << name << " not found\n"; exit(1);}
+                       //adds sequence names that are not in group file to the "xxx" group
+                       if(n1 == -1) {
+                               cerr << "Name: " << name << " not found in your groupfile and it will be ignored. \n";
+                               globaldata->gTreemap->namesOfSeqs.push_back(name);
+                               globaldata->gTreemap->treemap[name].groupname = "xxx";
+                               globaldata->gTreemap->treemap[name].vectorIndex = (globaldata->gTreemap->namesOfSeqs.size() - 1);
+                               
+                               map<string, int>::iterator it;
+                               it = globaldata->gTreemap->seqsPerGroup.find("xxx");
+                               if (it == globaldata->gTreemap->seqsPerGroup.end()) { //its a new group
+                                       globaldata->gTreemap->namesOfGroups.push_back("xxx");
+                                       globaldata->gTreemap->seqsPerGroup["xxx"] = 1;
+                               }else {
+                                       globaldata->gTreemap->seqsPerGroup["xxx"]++;
+                               }
+                               
+                               //find index in tree of name
+                               n1 = T->getIndex(name);
+                               group = "xxx";
+                       }
                        
-                       else T->tree[n1].setGroup(group);
+                       T->tree[n1].setGroup(group);
                
                        T->tree[n1].setChildren(-1,-1);