ReadTree::ReadTree() {
try {
globaldata = GlobalData::getInstance();
+ m = MothurOut::getInstance();
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";
+ m->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"; return -1;
- //exit(1);
+ m->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"; return -1;
- //exit(1);
+ m->mothurOut("Error: Expected " + name + " in input file. Found " + toString(d) + ".\n");
+ exit(1);
}
if(d == ')' && f.peek() == '\n'){
gobble(f);
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";
+ m->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"; return -1;
- //exit(1);
+ m->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";
+ m->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"; return -1;
- //exit(1);
+ m->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";
+ m->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
/***********************************************************************/
int ReadNewickTree::read() {
try {
+ 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();
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";
+ m->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";
+ m->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);
- }
}
/**************************************************************************************************/
try {
int n = 0;
- int lc, rc, error;
+ int lc, rc;
int rooted = 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) { 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()==','){
- error = readSpecialChar(filehandle,',',"comma");
- if (error == -1) { readOk = -1; return -1; }
+ readSpecialChar(filehandle,',',"comma");
}
// ';' means end of tree.
else if((ch=filehandle.peek())==';' || ch=='['){
}
if(rooted != 1){
rc = readNewickInt(filehandle, n, T);
- if (rc == -1) { 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() == ')'){
- error = readSpecialChar(filehandle,')',"right parenthesis");
- if (error == -1) { readOk = -1; return -1; }
+ readSpecialChar(filehandle,')',"right parenthesis");
}
}
}
n = T->getIndex(name);
if(n!=0){
- cerr << "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;
}
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);
}
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";
+ m->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);
- }
-
}
/**************************************************************************************************/
int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
try {
- int error;
+
+ if (m->control_pressed) { return -1; }
int c = readNodeChar(f);
- if (c == -1) { readOk = -1; return -1; }
-
+ string k;
+k = c;
+ cout << "at beginning = " << k <<endl;
if(c == '('){
- int lc = readNewickInt(f, n, T);
- if (lc == -1) { return -1; } //reports an error in reading
- error = readSpecialChar(f,',',"comma");
- if (error == -1) { readOk = -1; return -1; }
+
+ //to account for multifurcating trees generated by fasttree, we are forcing them to be bifurcating
+ //read all children
+ vector<int> childrenNodes;
+ while(f.peek() != ')'){
+ int child = readNewickInt(f, n, T);
+ if (child == -1) { return -1; } //reports an error in reading
+
+ childrenNodes.push_back(child);
+
+ //after a child you either have , or ), check for both
+ if(f.peek()==')'){ break; }
+ else if (f.peek()==',') { readSpecialChar(f,',',"comma"); }
+ else { string k;
+ k = f.peek();
+ cout << "in here k = " << k << '\t' << f.tellg() <<endl;
+ }
+ }
+ cout << childrenNodes.size() << endl;
+ if (childrenNodes.size() < 2) { m->mothurOut("Error in tree, please correct."); m->mothurOutEndLine(); return -1; }
+
+ //then force into 2 node structure
+ for (int i = 1; i < childrenNodes.size(); i++) {
+
+ int lc, rc;
+ if (i == 1) { lc = childrenNodes[i-1]; rc = childrenNodes[i]; }
+ else { lc = n; rc = childrenNodes[i]; }
+ cout << i << '\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;
+ n++;
+ }
+
+ //to account for extra ++ in looping
+ n--;
+ //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
+ //int rc = readNewickInt(f, n, T);
+ //if (rc == -1) { return -1; } //reports an error in reading
+
if(f.peek()==')'){
- error = readSpecialChar(f,')',"right parenthesis");
- if (error == -1) { readOk = -1; return -1; }
+ 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() == ':'){
- 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); }
+ 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);
+ }
+
+ //to account for multifurcating trees generated by fasttree, we are forcing them to be bifurcating
+ /*while(f.peek() == ','){
+ string k;
+ k = f.peek();
+ cout << "in here k = " << k << '\t' << f.tellg() <<endl;
+ //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");
+
+ rc = readNewickInt(f, n, T);
- T->tree[n].setChildren(lc,rc);
- T->tree[lc].setParent(n);
- T->tree[rc].setParent(n);
+ 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){ 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;
+ }
+ }*/
+ //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);
string name = "";
name += d;
d=f.get();
}
-
+ cout << name << endl;
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. \n"; readOk = -1; return n1;
+ if(group == "not found") {
+ 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";
- //globaldata->gTreemap->treemap[name].vectorIndex = (globaldata->gTreemap->namesOfSeqs.size() - 1);
+ globaldata->gTreemap->namesOfSeqs.push_back(name);
+ globaldata->gTreemap->treemap[name].groupname = "xxx";
- //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"]++;
- //}
+ 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;
+ group = "xxx";
}
- T->tree[n1].setGroup(group);
+ vector<string> tempGroup; tempGroup.push_back(group);
+
+ T->tree[n1].setGroup(tempGroup);
T->tree[n1].setChildren(-1,-1);
if(blen == 1){
f.get();
- error = readBranchLength(f);
- if (error == -1) { readOk = -1; return -1; }
- T->tree[n1].setBranchLength(error);
+ 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";
+ m->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