fixed valid parameters to include shared parameter for read.shared command.

[mothur.git] / readtree.cpp

diff --git a/readtree.cpp b/readtree.cpp
index a253741688c00ddc138d1353ac757456c03643da..c33617fca57a483da46f179e384497661e205878 100644 (file)
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -32,12 +32,12 @@ 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";
-                       exit(1);
+                       cerr << "Error: Input file ends prematurely, expecting a " << name << "\n";  return -1;
+                       //exit(1);
                }
                if(d != c){
-                       cerr << "Error: Expected " << name << " in input file.  Found " << d << ".\n";
-                       exit(1);
+                       cerr << "Error: Expected " << name << " in input file.  Found " << d << ".\n";  return -1;
+                       //exit(1);
                }
                if(d == ')' && f.peek() == '\n'){
                        gobble(f);
@@ -62,8 +62,8 @@ int ReadTree::readNodeChar(istream& f) {
                char d = f.get();
 
                if(d == EOF){
-                       cerr << "Error: Input file ends prematurely, expecting a left parenthesis\n";
-                       exit(1);
+                       cerr << "Error: Input file ends prematurely, expecting a left parenthesis\n";  return -1;
+                       //exit(1);
                }
                return d;
        }
@@ -84,8 +84,8 @@ float ReadTree::readBranchLength(istream& f) {
                float b;
        
                if(!(f >> b)){
-                       cerr << "Error: Missing branch length in input tree.\n";
-                       exit(1);
+                       cerr << "Error: Missing branch length in input tree.\n";  return -1;
+                       //exit(1);
                }
                gobble(f);
                return b;
@@ -111,9 +111,9 @@ float ReadTree::readBranchLength(istream& f) {
 /***********************************************************************/
 //This class reads a file in Newick form and stores it in a tree.
 
-void ReadNewickTree::read() {
+int ReadNewickTree::read() {
        try {
-               int c;
+               int c, error;
                int comment = 0;
                
                //if you are not a nexus file 
@@ -124,7 +124,7 @@ void ReadNewickTree::read() {
                                numNodes = T->getNumNodes();
                                numLeaves = T->getNumLeaves();
                                
-                               readTreeString(); 
+                               error = readTreeString(); 
                                
                                //save trees for later commands
                                globaldata->gTree.push_back(T); 
@@ -158,12 +158,13 @@ void ReadNewickTree::read() {
                                numLeaves = T->getNumLeaves();
                                
                                //read tree info
-                               readTreeString(); 
+                               error = readTreeString(); 
                                 
                                //save trees for later commands
                                globaldata->gTree.push_back(T); 
                        }
                }
+               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";
@@ -221,11 +222,11 @@ void ReadNewickTree::nexusTranslation() {
 }
 
 /**************************************************************************************************/
-void ReadNewickTree::readTreeString() {
+int ReadNewickTree::readTreeString() {
        try {
                
                int n = 0;
-               int lc, rc; 
+               int lc, rc, error; 
                
                int rooted = 0;
        
@@ -235,9 +236,11 @@ void 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) { return -1; } //reports an error in reading
                
                        if(filehandle.peek()==','){                                                     
-                               readSpecialChar(filehandle,',',"comma");
+                               error = readSpecialChar(filehandle,',',"comma");
+                               if (error == -1) { readOk = -1; return -1; }
                        }
                        // ';' means end of tree.                                                                                               
                        else if((ch=filehandle.peek())==';' || ch=='['){                
@@ -245,8 +248,10 @@ void ReadNewickTree::readTreeString() {
                        }                                                                                               
                        if(rooted != 1){                                                                
                                rc = readNewickInt(filehandle, n, T);
+                               if (rc == -1) { return -1; } //reports an error in reading
                                if(filehandle.peek() == ')'){                                   
-                                       readSpecialChar(filehandle,')',"right parenthesis");
+                                       error = readSpecialChar(filehandle,')',"right parenthesis");
+                                       if (error == -1) { readOk = -1; return -1; }
                                }                                                                                       
                        }                                                                                               
                }
@@ -261,7 +266,8 @@ void ReadNewickTree::readTreeString() {
 
                        if(n!=0){
                                cerr << "Internal error: The only taxon is not taxon 0.\n";
-                               exit(1);
+                               //exit(1);
+                               readOk = -1; return -1;
                        }
                        lc = rc = -1;
                } 
@@ -274,6 +280,7 @@ void ReadNewickTree::readTreeString() {
                        if(lc!=-1){             T->tree[lc].setParent(n);               }
                        if(rc!=-1){             T->tree[rc].setParent(n);               }
                }
+               return 0;
        
        }
        catch(exception& e) {
@@ -290,21 +297,31 @@ void ReadNewickTree::readTreeString() {
 
 int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
        try {
+               int error;
+               
                int c = readNodeChar(f);
+               if (c == -1) { readOk = -1; return -1; }
     
                if(c == '('){
                        int lc = readNewickInt(f, n, T);
-                       readSpecialChar(f,',',"comma");
+                       if (lc == -1) { return -1; } //reports an error in reading
+                       error = readSpecialChar(f,',',"comma");
+                       if (error == -1) { readOk = -1; return -1; }
 
-                       int rc = readNewickInt(f, n, T);                
+                       int rc = readNewickInt(f, n, T);
+                       if (rc == -1) { return -1; }  //reports an error in reading     
                        if(f.peek()==')'){      
-                               readSpecialChar(f,')',"right parenthesis");                                     
+                               error = readSpecialChar(f,')',"right parenthesis");     
+                               if (error == -1) { readOk = -1; return -1; }                            
                        }                       
                
                        if(f.peek() == ':'){                                                                          
-                               readSpecialChar(f,':',"colon");                                                 
-                               if(n >= numNodes){      cerr << "Error: Too many nodes in input tree\n";  exit(1); }
-                               T->tree[n].setBranchLength(readBranchLength(f));
+                               error = readSpecialChar(f,':',"colon"); 
+                               if (error == -1) { readOk = -1; return -1; }                                            
+                               if(n >= numNodes){      cerr << "Error: Too many nodes in input tree\n";  readOk = -1; return -1; }
+                               error = readBranchLength(f);
+                               if (error == -1) { readOk = -1; return -1; }
+                               T->tree[n].setBranchLength(error);
                        }else{T->tree[n].setBranchLength(0.0); }                                                
                
                        T->tree[n].setChildren(lc,rc);
@@ -334,7 +351,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                        
                        //adds sequence names that are not in group file to the "xxx" group
                        if(n1 == -1) {
-                               cerr << "Name: " << name << " not found in your groupfile.. \n"; exit(1);
+                               cerr << "Name: " << name << " not found in your groupfile. \n"; readOk = -1; return n1;
                                
                                //globaldata->gTreemap->namesOfSeqs.push_back(name);
                                //globaldata->gTreemap->treemap[name].groupname = "xxx";
@@ -360,8 +377,10 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                        T->tree[n1].setChildren(-1,-1);
                
                        if(blen == 1){  
-                               f.get();                
-                               T->tree[n1].setBranchLength(readBranchLength(f));
+                               f.get();
+                               error = readBranchLength(f);    
+                               if (error == -1) { readOk = -1; return -1; }    
+                               T->tree[n1].setBranchLength(error);
                        }else{
                                T->tree[n1].setBranchLength(0.0);
                        }