updated errorchecking so it checks if the parameter is valid for the command.

[mothur.git] / readtree.cpp

diff --git a/readtree.cpp b/readtree.cpp
index 77277e71a889171e8b248de4d7ad19c0a78babb3..029164452c49d2247bd97262369a649cfbd3d190 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) {
@@ -110,9 +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 
@@ -123,9 +124,11 @@ void ReadNewickTree::read() {
                                numNodes = T->getNumNodes();
                                numLeaves = T->getNumLeaves();
                                
-                               readTreeString();  
+                               error = readTreeString(); 
+                               
                                //save trees for later commands
                                globaldata->gTree.push_back(T); 
+                               gobble(filehandle);
                        }
                //if you are a nexus file
                }else if ((c = filehandle.peek()) == '#') {
@@ -155,12 +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";
@@ -218,7 +222,7 @@ void ReadNewickTree::nexusTranslation() {
 }
 
 /**************************************************************************************************/
-void ReadNewickTree::readTreeString() {
+int ReadNewickTree::readTreeString() {
        try {
                
                int n = 0;
@@ -230,7 +234,9 @@ 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 (lc == -1) { return -1; } //reports an error in reading
                
                        if(filehandle.peek()==','){                                                     
                                readSpecialChar(filehandle,',',"comma");
@@ -241,6 +247,7 @@ 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");
                                }                                                                                       
@@ -253,23 +260,25 @@ 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);
+                               //exit(1);
+                               readOk = -1; return -1;
                        }
                        lc = rc = -1;
                } 
                
                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);
                        if(lc!=-1){             T->tree[lc].setParent(n);               }
                        if(rc!=-1){             T->tree[rc].setParent(n);               }
                }
+               return 0;
        
        }
        catch(exception& e) {
@@ -290,16 +299,20 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
     
                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);                
+
+                       int rc = readNewickInt(f, n, T);
+                       if (rc == -1) { return -1; }  //reports an error in reading     
                        if(f.peek()==')'){      
-                               readSpecialChar(f,')',"right parenthesis");                                     
+                               readSpecialChar(f,')',"right parenthesis");     
                        }                       
                
                        if(f.peek() == ':'){                                                                          
-                               readSpecialChar(f,':',"colon");                                                 
-                               if(n >= numNodes){      cerr << "Error: Too many nodes in input tree\n";  exit(1); }
+                               readSpecialChar(f,':',"colon"); 
+                                                                               
+                               if(n >= numNodes){      cerr << "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); }                                                
                
@@ -328,14 +341,35 @@ 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. \n"; readOk = -1; return n1;
+                               
+                               //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";
+                               //numLeaves++;
+                               //numNodes = 2*numLeaves - 1;
+                       }
                        
-                       else T->tree[n1].setGroup(group);
-               
+                       T->tree[n1].setGroup(group);
                        T->tree[n1].setChildren(-1,-1);
                
                        if(blen == 1){  
-                               f.get();                
+                               f.get();
                                T->tree[n1].setBranchLength(readBranchLength(f));
                        }else{
                                T->tree[n1].setBranchLength(0.0);