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) {
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'){
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);
- }
}
/**************************************************************************************************/
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);
- }
}
/**************************************************************************************************/
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);
- }
}
-
/***********************************************************************/
/***********************************************************************/
-
//Child Classes Below
/***********************************************************************/
/***********************************************************************/
//This class reads a file in Newick form and stores it in a tree.
-void ReadNewickTree::read() {
+int ReadNewickTree::read() {
try {
- int c;
+ holder = "";
+ int c, error;
int comment = 0;
//if you are not a nexus file
if ((c = filehandle.peek()) != '#') {
while((c = filehandle.peek()) != EOF) {
+ while ((c = filehandle.peek()) != EOF) {
+ // get past comments
+ if(c == '[') {
+ comment = 1;
+ }
+ if(c == ']'){
+ comment = 0;
+ }
+ if((c == '(') && (comment != 1)){ break; }
+ filehandle.get();
+ }
+
//make new tree
T = new Tree();
numNodes = T->getNumNodes();
numLeaves = T->getNumLeaves();
- readTreeString();
+ error = readTreeString();
//save trees for later commands
globaldata->gTree.push_back(T);
numLeaves = T->getNumLeaves();
//read tree info
- readTreeString();
+ error = readTreeString();
//save trees for later commands
globaldata->gTree.push_back(T);
}
}
+
+ if (error != 0) { readOk = error; }
+
+ filehandle.close();
+ 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.
}
}
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);
- }
}
/**************************************************************************************************/
-void ReadNewickTree::readTreeString() {
+int ReadNewickTree::readTreeString() {
try {
int n = 0;
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(filehandle.peek()==','){
readSpecialChar(filehandle,',',"comma");
}
if(rooted != 1){
rc = readNewickInt(filehandle, n, T);
+ if (rc == -1) { mothurOut("error with rc"); mothurOutEndLine(); return -1; } //reports an error in reading
if(filehandle.peek() == ')'){
readSpecialChar(filehandle,')',"right parenthesis");
}
n = T->getIndex(name);
if(n!=0){
- cerr << "Internal error: The only taxon is not taxon 0.\n";
- exit(1);
+ 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);
T->tree[n].setParent(-1);
if(lc!=-1){ T->tree[lc].setParent(n); }
if(rc!=-1){ T->tree[rc].setParent(n); }
- cout << "new loop "<< endl;
}
+ return 0;
}
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);
- }
-
}
/**************************************************************************************************/
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");
+ //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"; exit(1); }
+ readSpecialChar(f,':',"colon");
+
+ 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);
}
int blen = 0;
- if(d == ':') { blen = 1; }
+ if(d == ':') { blen = 1; }
f.putback(d);
int n1 = T->getIndex(name);
//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";
+ if(group == "not found") {
+ 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";
- globaldata->gTreemap->treemap[name].vectorIndex = (globaldata->gTreemap->namesOfSeqs.size() - 1);
map<string, int>::iterator it;
it = globaldata->gTreemap->seqsPerGroup.find("xxx");
globaldata->gTreemap->seqsPerGroup["xxx"]++;
}
- //find index in tree of name
- n1 = T->getIndex(name);
group = "xxx";
- numLeaves++;
- numNodes = 2*numLeaves - 1;
- T->resetTree();
}
T->tree[n1].setGroup(group);
- T->printTree();
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);
}
}
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);
- }
}
/**************************************************************************************************/
/**************************************************************************************************/
projects / mothur.git / blobdiff