fixed parsimony for groups

[mothur.git] / readtree.cpp

diff --git a/readtree.cpp b/readtree.cpp
index 77277e71a889171e8b248de4d7ad19c0a78babb3..81a7729ffb474294502407eec1c44620bfff3378 100644 (file)
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -27,9 +27,10 @@ ReadTree::ReadTree() {
 /***********************************************************************/
 int ReadTree::readSpecialChar(istream& f, char c, string name) {
     try {
-               char d;
        
-               while(isspace(d=f.get()))               {;}
+               gobble(f);
+               char d = f.get();
+       
                if(d == EOF){
                        cerr << "Error: Input file ends prematurely, expecting a " << name << "\n";
                        exit(1);
@@ -39,10 +40,8 @@ int ReadTree::readSpecialChar(istream& f, char c, string name) {
                        exit(1);
                }
                if(d == ')' && f.peek() == '\n'){
-                       while(isspace(d=f.get()))               {;}
-                       f.putback(d);
+                       gobble(f);
                }       
-       
                return d;
        }
        catch(exception& e) {
@@ -58,8 +57,10 @@ int ReadTree::readSpecialChar(istream& f, char c, string name) {
 
 int ReadTree::readNodeChar(istream& f) {
        try {
-               char d;
-               while(isspace(d=f.get()))               {;}
+//             while(isspace(d=f.get()))               {;}
+               gobble(f);
+               char d = f.get();
+
                if(d == EOF){
                        cerr << "Error: Input file ends prematurely, expecting a left parenthesis\n";
                        exit(1);
@@ -86,7 +87,7 @@ float ReadTree::readBranchLength(istream& f) {
                        cerr << "Error: Missing branch length in input tree.\n";
                        exit(1);
                }
-    
+               gobble(f);
                return b;
        }
        catch(exception& e) {
@@ -126,6 +127,7 @@ void ReadNewickTree::read() {
                                readTreeString();  
                                //save trees for later commands
                                globaldata->gTree.push_back(T); 
+                               gobble(filehandle);
                        }
                //if you are a nexus file
                }else if ((c = filehandle.peek()) == '#') {
@@ -230,6 +232,7 @@ void ReadNewickTree::readTreeString() {
                
                if(ch == '('){
                        n = numLeaves;  //number of leaves / sequences, we want node 1 to start where the leaves left off
+
                        lc = readNewickInt(filehandle, n, T);
                
                        if(filehandle.peek()==','){                                                     
@@ -253,8 +256,8 @@ void ReadNewickTree::readTreeString() {
                        filehandle.get(name, MAX_LINE,'\n');
                        SKIPLINE(filehandle, ch);
                
-               
                        n = T->getIndex(name);
+
                        if(n!=0){
                                cerr << "Internal error: The only taxon is not taxon 0.\n";
                                exit(1);
@@ -263,7 +266,7 @@ void ReadNewickTree::readTreeString() {
                } 
                
                while((ch=filehandle.get())!=';'){;}                                            
-                       if(rooted != 1){                                                                        
+               if(rooted != 1){                                                                        
                        T->tree[n].setChildren(lc,rc);
                        T->tree[n].setBranchLength(0);
                        T->tree[n].setParent(-1);
@@ -291,7 +294,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                if(c == '('){
                        int lc = readNewickInt(f, n, T);
                        readSpecialChar(f,',',"comma");
-               
+
                        int rc = readNewickInt(f, n, T);                
                        if(f.peek()==')'){      
                                readSpecialChar(f,')',"right parenthesis");                                     
@@ -328,9 +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);