fixed bug in unifrac commands with nexus translation if files don't match

[mothur.git] / readtree.cpp

diff --git a/readtree.cpp b/readtree.cpp
index 8158a577f478b71139ce5c6f91eeb9dedc4b0d62..e8aeacc4431688ca0dfc8f94bf546c1fea2a91dd 100644 (file)
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -129,7 +129,10 @@ int ReadNewickTree::read() {
                        }
                //if you are a nexus file
                }else if ((c = filehandle.peek()) == '#') {
-                       holder = nexusTranslation();  //reads file through the translation and updates treemap
+                       //get right number of seqs from nexus file.
+                       Tree* temp = new Tree();  delete temp;
+                       
+                       nexusTranslation();  //reads file through the translation and updates treemap
                        while((c = filehandle.peek()) != EOF) { 
                                // get past comments
                                while ((c = filehandle.peek()) != EOF) {        
@@ -179,7 +182,7 @@ 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->Treenames.size(); //must save this some when we clear old names we can still know how many sequences there were
                int comment = 0;
                
                // get past comments
@@ -197,7 +200,7 @@ string ReadNewickTree::nexusTranslation() {
                //update treemap
                globaldata->gTreemap->namesOfSeqs.clear();
                
-               char c;
+               /*char c;
                string number, name;
                while ((c = filehandle.peek()) != EOF) {        
                        
@@ -213,7 +216,15 @@ string ReadNewickTree::nexusTranslation() {
                        if ((name == "tree") || (name == ";") ) {  break;  }
                        
                        if (lastChar == ',') {  name.erase(name.end()-1); } //erase the comma
-                               
+                       */      
+               cout << "numseqs = " << numSeqs << endl;
+               string number, name;
+               for(int i=0;i<numSeqs;i++){
+                       
+                       filehandle >> number;
+                       filehandle >> name;
+                       name.erase(name.end()-1);  //erase the comma
+                       
                        //insert new one with new name
                        string group = globaldata->gTreemap->getGroup(name);
                        globaldata->gTreemap->treemap[toString(number)].groupname = group;