fixed unweighted command

[mothur.git] / readtree.cpp

diff --git a/readtree.cpp b/readtree.cpp
index 1dd77f9152b241321f6658d0e0efc025c01a1a71..308115d844bdf8aa24adf05de9841a60c1708fd8 100644 (file)
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -25,7 +25,7 @@ ReadTree::ReadTree() {
 int ReadTree::readSpecialChar(istream& f, char c, string name) {
     try {
        
-               gobble(f);
+               m->gobble(f);
                char d = f.get();
        
                if(d == EOF){
@@ -37,7 +37,7 @@ int ReadTree::readSpecialChar(istream& f, char c, string name) {
                        exit(1);
                }
                if(d == ')' && f.peek() == '\n'){
-                       gobble(f);
+                       m->gobble(f);
                }       
                return d;
        }
@@ -51,7 +51,7 @@ int ReadTree::readSpecialChar(istream& f, char c, string name) {
 int ReadTree::readNodeChar(istream& f) {
        try {
 //             while(isspace(d=f.get()))               {;}
-               gobble(f);
+               m->gobble(f);
                char d = f.get();
 
                if(d == EOF){
@@ -76,7 +76,7 @@ float ReadTree::readBranchLength(istream& f) {
                        m->mothurOut("Error: Missing branch length in input tree.\n");
                        exit(1);
                }
-               gobble(f);
+               m->gobble(f);
                return b;
        }
        catch(exception& e) {
@@ -125,10 +125,13 @@ int ReadNewickTree::read() {
                                
                                //save trees for later commands
                                globaldata->gTree.push_back(T); 
-                               gobble(filehandle);
+                               m->gobble(filehandle);
                        }
                //if you are a nexus file
                }else if ((c = filehandle.peek()) == '#') {
+                       //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
@@ -175,11 +178,11 @@ 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->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
@@ -191,23 +194,47 @@ 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();
+               
+               /*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
+                       */      
+               
+               string number, name;
                for(int i=0;i<numSeqs;i++){
-                       string number, name;
+                       
                        filehandle >> number;
                        filehandle >> name;
                        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");
@@ -341,7 +368,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                        if(f.peek() == ':'){                                                                          
                                readSpecialChar(f,':',"colon"); 
                                                                                
-                               if(n >= numNodes){      m->mothurOut("Error: Too many nodes in input tree\n");  readOk = -1; return -1; }
+                               if(n >= numNodes){ m->mothurOut("Error: Too many nodes in input tree\n");  readOk = -1; return -1; }
                                
                                T->tree[n].setBranchLength(readBranchLength(f));
                        }else{