added logfile feature

[mothur.git] / readtree.cpp

diff --git a/readtree.cpp b/readtree.cpp
index 670c6e0a3126ba73370d2520be2b7ac9e1728dd3..5e909e620d237ed063d9a64bd191f707ddea1daa 100644 (file)
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -16,13 +16,9 @@ ReadTree::ReadTree() {
                globaldata->gTree.clear();
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ReadTree class Function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ReadTree", "ReadTree");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the ReadTree class function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 /***********************************************************************/
 int ReadTree::readSpecialChar(istream& f, char c, string name) {
@@ -32,11 +28,11 @@ int ReadTree::readSpecialChar(istream& f, char c, string name) {
                char d = f.get();
        
                if(d == EOF){
-                       cerr << "Error: Input file ends prematurely, expecting a " << name << "\n";
+                       mothurOut("Error: Input file ends prematurely, expecting a " + name + "\n");
                        exit(1);
                }
                if(d != c){
-                       cerr << "Error: Expected " << name << " in input file.  Found " << d << ".\n";
+                       mothurOut("Error: Expected " + name + " in input file.  Found " + toString(d) + ".\n");
                        exit(1);
                }
                if(d == ')' && f.peek() == '\n'){
@@ -45,13 +41,9 @@ int ReadTree::readSpecialChar(istream& f, char c, string name) {
                return d;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ReadTree class Function readSpecialChar. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ReadTree", "readSpecialChar");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the ReadTree class function readSpecialChar. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 /**************************************************************************************************/
 
@@ -62,19 +54,15 @@ int ReadTree::readNodeChar(istream& f) {
                char d = f.get();
 
                if(d == EOF){
-                       cerr << "Error: Input file ends prematurely, expecting a left parenthesis\n";
+                       mothurOut("Error: Input file ends prematurely, expecting a left parenthesis\n");
                        exit(1);
                }
                return d;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ReadTree class Function readNodeChar. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ReadTree", "readNodeChar");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the ReadTree class function readNodeChar. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 
 /**************************************************************************************************/
@@ -84,20 +72,16 @@ float ReadTree::readBranchLength(istream& f) {
                float b;
        
                if(!(f >> b)){
-                       cerr << "Error: Missing branch length in input tree.\n";
+                       mothurOut("Error: Missing branch length in input tree.\n");
                        exit(1);
                }
                gobble(f);
                return b;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ReadTree class Function readBranchLength. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ReadTree", "readBranchLength");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the ReadTree class function readBranchLength. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 
 /***********************************************************************/
@@ -182,13 +166,9 @@ int ReadNewickTree::read() {
                return readOk;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ReadNewickTree class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ReadNewickTree", "read");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the ReadNewickTree class function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 /**************************************************************************************************/
 //This function read the file through the translation of the sequences names and updates treemap.
@@ -227,13 +207,9 @@ void ReadNewickTree::nexusTranslation() {
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ReadNewickTree class Function nexus. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ReadNewickTree", "nexusTranslation");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the ReadNewickTree class function nexus. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 
 /**************************************************************************************************/
@@ -251,7 +227,7 @@ 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) { cout << "error with lc" << endl; return -1; } //reports an error in reading
+                       if (lc == -1) { mothurOut("error with lc"); mothurOutEndLine(); return -1; } //reports an error in reading
                
                        if(filehandle.peek()==','){                                                     
                                readSpecialChar(filehandle,',',"comma");
@@ -262,7 +238,7 @@ int ReadNewickTree::readTreeString() {
                        }                                                                                               
                        if(rooted != 1){                                                                
                                rc = readNewickInt(filehandle, n, T);
-                               if (rc == -1) { cout << "error with rc" << endl; return -1; } //reports an error in reading
+                               if (rc == -1) { mothurOut("error with rc"); mothurOutEndLine(); return -1; } //reports an error in reading
                                if(filehandle.peek() == ')'){                                   
                                        readSpecialChar(filehandle,')',"right parenthesis");
                                }                                                                                       
@@ -278,14 +254,14 @@ int ReadNewickTree::readTreeString() {
                        n = T->getIndex(name);
 
                        if(n!=0){
-                               cerr << "Internal error: The only taxon is not taxon 0.\n";
+                               mothurOut("Internal error: The only taxon is not taxon 0.\n");
                                //exit(1);
                                readOk = -1; return -1;
                        }
                        lc = rc = -1;
                } 
                
-               while((ch=filehandle.get())!=';'){;}                                            
+               while(((ch=filehandle.get())!=';') && (filehandle.eof() != true)){;}                                            
                if(rooted != 1){                                                                        
                        T->tree[n].setChildren(lc,rc);
                        T->tree[n].setBranchLength(0);
@@ -297,14 +273,9 @@ int ReadNewickTree::readTreeString() {
        
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ReadNewickTree class Function readTreeString. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ReadNewickTree", "readTreeString");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the ReadNewickTree class function readTreeString. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
-
 }
 /**************************************************************************************************/
 
@@ -321,15 +292,22 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                        if (rc == -1) { return -1; }  //reports an error in reading     
                        if(f.peek()==')'){      
                                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){      cerr << "Error: Too many nodes in input tree\n";  readOk = -1; return -1; }
+                               if(n >= numNodes){      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); }                                                
+                       }else{
+                               T->tree[n].setBranchLength(0.0); 
+                       }                                               
                
                        T->tree[n].setChildren(lc,rc);
                        T->tree[lc].setParent(n);
@@ -358,7 +336,7 @@ 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") {
-                               cout << "Name: " << name << " is not in your groupfile, and will be disregarded. \n";  //readOk = -1; return n1;
+                               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";
@@ -392,13 +370,9 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ReadNewickTree class Function readNewickInt. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ReadNewickTree", "readNewickInt");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the ReadNewickTree class function readNewickInt. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 /**************************************************************************************************/
 /**************************************************************************************************/