ReadTree::ReadTree() {
try {
globaldata = GlobalData::getInstance();
+ m = MothurOut::getInstance();
globaldata->gTree.clear();
}
catch(exception& e) {
- errorOut(e, "ReadTree", "ReadTree");
+ m->errorOut(e, "ReadTree", "ReadTree");
exit(1);
}
}
int ReadTree::readSpecialChar(istream& f, char c, string name) {
try {
- gobble(f);
+ m->gobble(f);
char d = f.get();
if(d == EOF){
- mothurOut("Error: Input file ends prematurely, expecting a " + name + "\n");
+ m->mothurOut("Error: Input file ends prematurely, expecting a " + name + "\n");
exit(1);
}
if(d != c){
- mothurOut("Error: Expected " + name + " in input file. Found " + toString(d) + ".\n");
+ m->mothurOut("Error: Expected " + name + " in input file. Found " + toString(d) + ".\n");
exit(1);
}
if(d == ')' && f.peek() == '\n'){
- gobble(f);
+ m->gobble(f);
}
return d;
}
catch(exception& e) {
- errorOut(e, "ReadTree", "readSpecialChar");
+ m->errorOut(e, "ReadTree", "readSpecialChar");
exit(1);
}
}
int ReadTree::readNodeChar(istream& f) {
try {
// while(isspace(d=f.get())) {;}
- gobble(f);
+ m->gobble(f);
char d = f.get();
if(d == EOF){
- mothurOut("Error: Input file ends prematurely, expecting a left parenthesis\n");
+ m->mothurOut("Error: Input file ends prematurely, expecting a left parenthesis\n");
exit(1);
}
return d;
}
catch(exception& e) {
- errorOut(e, "ReadTree", "readNodeChar");
+ m->errorOut(e, "ReadTree", "readNodeChar");
exit(1);
}
}
float b;
if(!(f >> b)){
- mothurOut("Error: Missing branch length in input tree.\n");
+ m->mothurOut("Error: Missing branch length in input tree.\n");
exit(1);
}
- gobble(f);
+ m->gobble(f);
return b;
}
catch(exception& e) {
- errorOut(e, "ReadTree", "readBranchLength");
+ m->errorOut(e, "ReadTree", "readBranchLength");
exit(1);
}
}
//save trees for later commands
globaldata->gTree.push_back(T);
- gobble(filehandle);
+ m->gobble(filehandle);
}
//if you are a nexus file
}else if ((c = filehandle.peek()) == '#') {
if (error != 0) { readOk = error; }
filehandle.close();
+
return readOk;
}
catch(exception& e) {
- errorOut(e, "ReadNewickTree", "read");
+ m->errorOut(e, "ReadNewickTree", "read");
exit(1);
}
}
}
}
catch(exception& e) {
- errorOut(e, "ReadNewickTree", "nexusTranslation");
+ m->errorOut(e, "ReadNewickTree", "nexusTranslation");
exit(1);
}
}
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 (lc == -1) { m->mothurOut("error with lc"); m->mothurOutEndLine(); return -1; } //reports an error in reading
+
if(filehandle.peek()==','){
readSpecialChar(filehandle,',',"comma");
}
// ';' means end of tree.
else if((ch=filehandle.peek())==';' || ch=='['){
rooted = 1;
- }
+ }
+
if(rooted != 1){
rc = readNewickInt(filehandle, n, T);
- if (rc == -1) { mothurOut("error with rc"); mothurOutEndLine(); 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() == ')'){
readSpecialChar(filehandle,')',"right parenthesis");
}
- }
+ }
}
//note: treeclimber had the code below added - not sure why?
else{
n = T->getIndex(name);
if(n!=0){
- mothurOut("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())!=';') && (filehandle.eof() != true)){;}
+ while(((ch=filehandle.get())!=';') && (filehandle.eof() != true)){;}
+
if(rooted != 1){
T->tree[n].setChildren(lc,rc);
T->tree[n].setBranchLength(0);
if(lc!=-1){ T->tree[lc].setParent(n); }
if(rc!=-1){ T->tree[rc].setParent(n); }
}
+
+ //T->printTree(); cout << endl;
return 0;
}
catch(exception& e) {
- errorOut(e, "ReadNewickTree", "readTreeString");
+ m->errorOut(e, "ReadNewickTree", "readTreeString");
exit(1);
}
}
int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
try {
+
+ if (m->control_pressed) { return -1; }
+
int c = readNodeChar(f);
-
- 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);
- if (rc == -1) { return -1; } //reports an error in reading
+ if(c == '('){
+
+ //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
+ //cout << "child = " << child << endl;
+ 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 {;}
+ }
+ //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-1; 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--;
+
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(); }
+ while((c!=',') && (c != -1) && (c!= ':') && (c!=';')&& (c!=')')){ c=filehandle.get(); }
filehandle.putback(c);
-
}
if(f.peek() == ':'){
readSpecialChar(f,':',"colon");
- if(n >= numNodes){ mothurOut("Error: Too many nodes in input tree\n"); readOk = -1; return -1; }
+ 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);
}
-
- T->tree[n].setChildren(lc,rc);
- T->tree[lc].setParent(n);
- T->tree[rc].setParent(n);
-
+
+ //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; }
//adds sequence names that are not in group file to the "xxx" group
if(group == "not found") {
- mothurOut("Name: " + name + " is not in your groupfile, and will be disregarded. \n"); //readOk = -1; return n1;
+ 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";
}
while((c=f.get())!=0 && (c != ':' && c != ',' && c!=')') ) {;}
+
f.putback(c);
return n1;
}
}
catch(exception& e) {
- errorOut(e, "ReadNewickTree", "readNewickInt");
+ m->errorOut(e, "ReadNewickTree", "readNewickInt");
exit(1);
}
}
projects / mothur.git / blobdiff