committing so I can work on the other machine

[mothur.git] / readtree.cpp

diff --git a/readtree.cpp b/readtree.cpp
index cdaa38701e0593817d5af7b415e308429fe2e6a1..1df49b5502f405bf29b31ee585fb5d6a264f9cda 100644 (file)
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -13,10 +13,11 @@
 ReadTree::ReadTree() {
        try {
                globaldata = GlobalData::getInstance();
+               m = MothurOut::getInstance();
                globaldata->gTree.clear();
        }
        catch(exception& e) {
-               errorOut(e, "ReadTree", "ReadTree");
+               m->errorOut(e, "ReadTree", "ReadTree");
                exit(1);
        }
 }
@@ -28,11 +29,11 @@ int ReadTree::readSpecialChar(istream& f, char c, string name) {
                char d = f.get();
        
                if(d == EOF){
-                       mothurOut("Error: Input file ends prematurely, expecting a " + name + "\n");
+                       m->mothurOut("Error: Input file ends prematurely, expecting a " + name + "\n");
                        exit(1);
                }
                if(d != c){
-                       mothurOut("Error: Expected " + name + " in input file.  Found " + toString(d) + ".\n");
+                       m->mothurOut("Error: Expected " + name + " in input file.  Found " + toString(d) + ".\n");
                        exit(1);
                }
                if(d == ')' && f.peek() == '\n'){
@@ -41,7 +42,7 @@ int ReadTree::readSpecialChar(istream& f, char c, string name) {
                return d;
        }
        catch(exception& e) {
-               errorOut(e, "ReadTree", "readSpecialChar");
+               m->errorOut(e, "ReadTree", "readSpecialChar");
                exit(1);
        }
 }
@@ -54,13 +55,13 @@ int ReadTree::readNodeChar(istream& f) {
                char d = f.get();
 
                if(d == EOF){
-                       mothurOut("Error: Input file ends prematurely, expecting a left parenthesis\n");
+                       m->mothurOut("Error: Input file ends prematurely, expecting a left parenthesis\n");
                        exit(1);
                }
                return d;
        }
        catch(exception& e) {
-               errorOut(e, "ReadTree", "readNodeChar");
+               m->errorOut(e, "ReadTree", "readNodeChar");
                exit(1);
        }
 }
@@ -72,14 +73,14 @@ float ReadTree::readBranchLength(istream& f) {
                float b;
        
                if(!(f >> b)){
-                       mothurOut("Error: Missing branch length in input tree.\n");
+                       m->mothurOut("Error: Missing branch length in input tree.\n");
                        exit(1);
                }
                gobble(f);
                return b;
        }
        catch(exception& e) {
-               errorOut(e, "ReadTree", "readBranchLength");
+               m->errorOut(e, "ReadTree", "readBranchLength");
                exit(1);
        }
 }
@@ -167,7 +168,7 @@ int ReadNewickTree::read() {
                return readOk;
        }
        catch(exception& e) {
-               errorOut(e, "ReadNewickTree", "read");
+               m->errorOut(e, "ReadNewickTree", "read");
                exit(1);
        }
 }
@@ -208,7 +209,7 @@ void ReadNewickTree::nexusTranslation() {
                }
        }
        catch(exception& e) {
-               errorOut(e, "ReadNewickTree", "nexusTranslation");
+               m->errorOut(e, "ReadNewickTree", "nexusTranslation");
                exit(1);
        }
 }
@@ -228,8 +229,8 @@ int ReadNewickTree::readTreeString() {
                        n = numLeaves;  //number of leaves / sequences, we want node 1 to start where the leaves left off
 
                        lc = readNewickInt(filehandle, n, T);
-                       if (lc == -1) { mothurOut("error with lc"); mothurOutEndLine(); return -1; } //reports an error in reading
-               
+                       if (lc == -1) { m->mothurOut("error with lc"); m->mothurOutEndLine(); return -1; } //reports an error in reading
+       
                        if(filehandle.peek()==','){                                                     
                                readSpecialChar(filehandle,',',"comma");
                        }
@@ -239,7 +240,7 @@ int ReadNewickTree::readTreeString() {
                        }                                                                                               
                        if(rooted != 1){                                                                
                                rc = readNewickInt(filehandle, n, T);
-                               if (rc == -1) { mothurOut("error with rc"); mothurOutEndLine(); return -1; } //reports an error in reading
+                               if (rc == -1) { m->mothurOut("error with rc"); m->mothurOutEndLine(); return -1; } //reports an error in reading
                                if(filehandle.peek() == ')'){                                   
                                        readSpecialChar(filehandle,')',"right parenthesis");
                                }                                                                                       
@@ -255,7 +256,7 @@ int ReadNewickTree::readTreeString() {
                        n = T->getIndex(name);
 
                        if(n!=0){
-                               mothurOut("Internal error: The only taxon is not taxon 0.\n");
+                               m->mothurOut("Internal error: The only taxon is not taxon 0.\n");
                                //exit(1);
                                readOk = -1; return -1;
                        }
@@ -274,7 +275,7 @@ int ReadNewickTree::readTreeString() {
        
        }
        catch(exception& e) {
-               errorOut(e, "ReadNewickTree", "readTreeString");
+               m->errorOut(e, "ReadNewickTree", "readTreeString");
                exit(1);
        }
 }
@@ -282,15 +283,20 @@ int ReadNewickTree::readTreeString() {
 
 int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
        try {
+               
+               if (m->control_pressed) { return -1; } 
+               
                int c = readNodeChar(f);
     
                if(c == '('){
                        int lc = readNewickInt(f, n, T);
                        if (lc == -1) { return -1; } //reports an error in reading
+                       
                        readSpecialChar(f,',',"comma");
 
                        int rc = readNewickInt(f, n, T);
                        if (rc == -1) { return -1; }  //reports an error in reading     
+                       
                        if(f.peek()==')'){      
                                readSpecialChar(f,')',"right parenthesis");     
                                //to pass over labels in trees
@@ -303,17 +309,60 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                        if(f.peek() == ':'){                                                                          
                                readSpecialChar(f,':',"colon"); 
                                                                                
-                               if(n >= numNodes){      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{
                                T->tree[n].setBranchLength(0.0); 
                        }                                               
-               
+                       
+                       //to account for multifurcating trees generated by fasttree, we are forcing them to be bifurcating
+                       while(f.peek() == ','){
+                               
+                               //force this node to be left child and read new rc
+                               T->tree[n].setChildren(lc,rc);
+                               T->tree[lc].setParent(n);
+                               T->tree[rc].setParent(n);
+                               
+                               T->printTree(); cout << endl;
+                               lc = n;
+                               n++;
+                               
+                               readSpecialChar(f,',',"comma");
+
+                               int rc = readNewickInt(f, n, T);
+               cout << n << '\t' << lc << '\t' << rc << endl;
+                               if (rc == -1) { return -1; }  //reports an error in reading     
+                               
+                               if(f.peek()==')'){      
+                               string k;
+                               k = f.peek();
+               cout << "in here " << k << endl;
+                                       readSpecialChar(f,')',"right parenthesis");     
+                                       //to pass over labels in trees
+                                       c=filehandle.get();
+                                       while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ c=filehandle.get(); }
+                                       filehandle.putback(c);
+                                       
+                                       if(f.peek() == ':'){                                                                          
+                                       readSpecialChar(f,':',"colon"); 
+                                       
+                                       if(n >= numNodes){      m->mothurOut("Error: Too many nodes in input tree\n");  readOk = -1; return -1; }
+                                       
+                                       T->tree[n].setBranchLength(readBranchLength(f));
+                                       }else{
+                                               T->tree[n].setBranchLength(0.0); 
+                                       }                                               
+
+                                       break;
+                               }                       
+                       }
+       cout << n << '\t' << lc << '\t' << rc << endl;          
                        T->tree[n].setChildren(lc,rc);
                        T->tree[lc].setParent(n);
                        T->tree[rc].setParent(n);
-               
+                       T->printTree();  cout << endl;
+                       
                        return n++;
                }else{
                        f.putback(c);
@@ -323,7 +372,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                                name += d;
                                d=f.get();
                        }
-               
+               cout << name << endl;
                        int blen = 0;
                        if(d == ':')    {               blen = 1;       }               
                
@@ -337,7 +386,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                        
                        //adds sequence names that are not in group file to the "xxx" group
                        if(group == "not found") {
-                               mothurOut("Name: " + name + " is not in your groupfile, and will be disregarded. \n");  //readOk = -1; return n1;
+                               m->mothurOut("Name: " + name + " is not in your groupfile, and will be disregarded. \n");  //readOk = -1; return n1;
                                
                                globaldata->gTreemap->namesOfSeqs.push_back(name);
                                globaldata->gTreemap->treemap[name].groupname = "xxx";
@@ -373,7 +422,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                }
        }
        catch(exception& e) {
-               errorOut(e, "ReadNewickTree", "readNewickInt");
+               m->errorOut(e, "ReadNewickTree", "readNewickInt");
                exit(1);
        }
 }