fixed parsimony for groups

diff --git a/parsimony.cpp b/parsimony.cpp
index 6239f75f08a59c9a5f690401e15ef93c19fe8f50..3ef141ed8518eb4ff9a0057152484d2ef85b3968 100644 (file)
--- a/parsimony.cpp
+++ b/parsimony.cpp
@@ -17,47 +17,35 @@ EstOutput Parsimony::getValues(Tree* t) {
                data.resize(1,0);
                        
                int score = 0;
-                       
+                                       
                for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
                        int lc = t->tree[i].getLChild();
                        int rc = t->tree[i].getRChild();
                        
-                       int iSize = 0;
-                       int rcSize = 0;
-                       int lcSize = 0;
-
+                       int iSize = t->tree[i].pGroups.size();
+                       int rcSize = t->tree[rc].pGroups.size();
+                       int lcSize = t->tree[lc].pGroups.size();
+                       
                        //add in all the groups the users wanted
                        for (it = t->tree[i].pGroups.begin(); it != t->tree[i].pGroups.end(); it++) {
-                               if (inUsersGroups(it->first, globaldata->Groups) == true) {  iSize++;  }
+                               if (inUsersGroups(it->first, globaldata->Groups) != true) {  iSize--;  }
                        }
-
-                       //if that leaves no groups give it 1 so it will cause no change to parent
-                       if (iSize == 0) { iSize++; }
-                       
                        //add in all the groups the users wanted
                        for (it = t->tree[rc].pGroups.begin(); it != t->tree[rc].pGroups.end(); it++) {
-
-                               if (inUsersGroups(it->first, globaldata->Groups) == true) {  rcSize++;  }
+                               if (inUsersGroups(it->first, globaldata->Groups) != true) {  rcSize--;  }
                        }
                        
-                       //if that leaves no groups give it 1 so it will cause no change to parent
-                       if (rcSize == 0) { rcSize++; }
-
-                               
                        //add in all the groups the users wanted
                        for (it = t->tree[lc].pGroups.begin(); it != t->tree[lc].pGroups.end(); it++) {
-
-                               if (inUsersGroups(it->first, globaldata->Groups) == true) {  lcSize++;  }
+                               if (inUsersGroups(it->first, globaldata->Groups) != true) {  lcSize--;  }
                        }
                        
-                       //if that leaves no groups give it 1 so it will cause no change to parent
-                       if (lcSize == 0) { lcSize++; }
-
-
+                       //if isize are 0 then that branch is to be ignored
+                       if (iSize == 0) { }
+                       else if ((rcSize == 0) || (lcSize == 0)) { }
                        //if you have more groups than either of your kids then theres been a change.
-                        if(iSize > rcSize || iSize > lcSize){
+                       else if(iSize > rcSize || iSize > lcSize){
                                score++;
-
                        }
                } 
                

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);
                

diff --git a/treemap.h b/treemap.h
index 0dc74eec2fad5ebc157b4fd12e63a7b8b37c967a..941ca9a8f79e4de463f99719d6ffd37fe7733961 100644 (file)
--- a/treemap.h
+++ b/treemap.h
@@ -39,6 +39,7 @@ public:
        map<string, GroupIndex> treemap; //sequence name and <groupname, vector index>
        void print(ostream&);
        
+       
 private:
        ifstream fileHandle;
        string groupFileName;
@@ -47,6 +48,7 @@ private:
        map<string, int>::iterator it2;
        void setNamesOfGroups(string); 
        
+       
 };
 
 #endif