fixed bug in unifrac commands with unrooted trees

[mothur.git] / readtree.cpp

diff --git a/readtree.cpp b/readtree.cpp
index e98524b45e9ec513fe171c5a342ab381a68fcacc..8158a577f478b71139ce5c6f91eeb9dedc4b0d62 100644 (file)
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -129,7 +129,7 @@ int ReadNewickTree::read() {
                        }
                //if you are a nexus file
                }else if ((c = filehandle.peek()) == '#') {
-                       nexusTranslation();  //reads file through the translation and updates treemap
+                       holder = nexusTranslation();  //reads file through the translation and updates treemap
                        while((c = filehandle.peek()) != EOF) { 
                                // get past comments
                                while ((c = filehandle.peek()) != EOF) {        
@@ -175,11 +175,11 @@ int ReadNewickTree::read() {
 }
 /**************************************************************************************************/
 //This function read the file through the translation of the sequences names and updates treemap.
-void ReadNewickTree::nexusTranslation() {
+string ReadNewickTree::nexusTranslation() {
        try {
                
                holder = "";
-               int numSeqs = globaldata->gTreemap->getNumSeqs(); //must save this some when we clear old names we can still know how many sequences there were
+               //int numSeqs = globaldata->gTreemap->getNumSeqs(); //must save this some when we clear old names we can still know how many sequences there were
                int comment = 0;
                
                // get past comments
@@ -191,23 +191,39 @@ void ReadNewickTree::nexusTranslation() {
                                comment = 0;
                        }
                        filehandle >> holder; 
-                       if(holder == "tree" && comment != 1){return;}
+                       if(holder == "tree" && comment != 1){return holder;}
                }
                
                //update treemap
                globaldata->gTreemap->namesOfSeqs.clear();
-               for(int i=0;i<numSeqs;i++){
-                       string number, name;
-                       filehandle >> number;
-                       filehandle >> name;
-                       name.erase(name.end()-1);  //erase the comma
+               
+               char c;
+               string number, name;
+               while ((c = filehandle.peek()) != EOF) {        
+                       
+                       filehandle >> number; 
+                       
+                       if ((number == "tree") || (number == ";") ) {  name = number; break;  }
+                       
+                       filehandle >> name; 
+                       
+                       char lastChar;
+                       if (name.length() != 0) { lastChar = name[name.length()-1]; }
+                       
+                       if ((name == "tree") || (name == ";") ) {  break;  }
+                       
+                       if (lastChar == ',') {  name.erase(name.end()-1); } //erase the comma
+                               
                        //insert new one with new name
-                       globaldata->gTreemap->treemap[toString(number)].groupname = globaldata->gTreemap->treemap[name].groupname;
-                       globaldata->gTreemap->treemap[toString(number)].vectorIndex = globaldata->gTreemap->treemap[name].vectorIndex;
+                       string group = globaldata->gTreemap->getGroup(name);
+                       globaldata->gTreemap->treemap[toString(number)].groupname = group;
+                       globaldata->gTreemap->treemap[toString(number)].vectorIndex = globaldata->gTreemap->getIndex(name);
                        //erase old one.  so treemap[sarah].groupnumber is now treemap[1].groupnumber. if number is 1 and name is sarah.
                        globaldata->gTreemap->treemap.erase(name);
                        globaldata->gTreemap->namesOfSeqs.push_back(number);
                }
+               
+               return name;
        }
        catch(exception& e) {
                m->errorOut(e, "ReadNewickTree", "nexusTranslation");