#include "readtree.h"
/***********************************************************************/
-//Parent Class
-// The following functions are used by all reading formats.
-/***********************************************************************/
-ReadTree::ReadTree() {
+ReadTree::ReadTree() {
try {
- globaldata = GlobalData::getInstance();
- T = new Tree();
- numNodes = T->getNumNodes();
- numLeaves = T->getNumLeaves();
+ globaldata = GlobalData::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";
/***********************************************************************/
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);
+ 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'){
- while(isspace(d=f.get())) {;}
- f.putback(d);
+ gobble(f);
}
-
return d;
}
catch(exception& e) {
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);
+ cerr << "Error: Input file ends prematurely, expecting a left parenthesis\n"; return -1;
+ //exit(1);
}
return d;
}
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;
}
catch(exception& e) {
/***********************************************************************/
//This class reads a file in Newick form and stores it in a tree.
-void ReadNewickTree::read() {
+int ReadNewickTree::read() {
+ try {
+ int c, error;
+ int comment = 0;
+
+ //if you are not a nexus file
+ if ((c = filehandle.peek()) != '#') {
+ while((c = filehandle.peek()) != EOF) {
+ //make new tree
+ T = new Tree();
+ numNodes = T->getNumNodes();
+ numLeaves = T->getNumLeaves();
+
+ 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()) == '#') {
+ nexusTranslation(); //reads file through the translation and updates treemap
+ while((c = filehandle.peek()) != EOF) {
+ // get past comments
+ while ((c = filehandle.peek()) != EOF) {
+ if(holder == "[" || holder == "[!"){
+ comment = 1;
+ }
+ if(holder == "]"){
+ comment = 0;
+ }
+ if((holder == "tree" || holder == "end;") && comment != 1){ holder = ""; comment = 0; break;}
+ filehandle >> holder;
+ }
+
+ //pass over the "tree rep.6878900 = "
+ while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF) ) {;}
+
+ if (c == EOF ) { break; }
+ filehandle.putback(c); //put back first ( of tree.
+
+ //make new tree
+ T = new Tree();
+ numNodes = T->getNumNodes();
+ numLeaves = T->getNumLeaves();
+
+ //read tree info
+ 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";
+ 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.
+void ReadNewickTree::nexusTranslation() {
+ try {
+
+ holder = "";
+ int numSeqs = globaldata->gTreemap->getNumSeqs(); //must save this some when we clear old names we can still know how many sequences there were
+ int comment = 0;
+
+ // get past comments
+ while(holder != "translate" && holder != "Translate"){
+ if(holder == "[" || holder == "[!"){
+ comment = 1;
+ }
+ if(holder == "]"){
+ comment = 0;
+ }
+ filehandle >> holder;
+ if(holder == "tree" && comment != 1){return;}
+ }
+
+ //update treemap
+ globaldata->gTreemap->namesOfSeqs.clear();
+ for(int i=0;i<numSeqs;i++){
+ string number, name;
+ filehandle >> number;
+ filehandle >> name;
+ name.erase(name.end()-1); //erase the comma
+ //insert new one with new name
+ globaldata->gTreemap->treemap[toString(number)].groupname = globaldata->gTreemap->treemap[name].groupname;
+ globaldata->gTreemap->treemap[toString(number)].vectorIndex = globaldata->gTreemap->treemap[name].vectorIndex;
+ //erase old one. so treemap[sarah].groupnumber is now treemap[1].groupnumber. if number is 1 and name is sarah.
+ globaldata->gTreemap->treemap.erase(name);
+ globaldata->gTreemap->namesOfSeqs.push_back(number);
+ }
+ }
+ 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";
+ 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);
+ }
+}
+
+/**************************************************************************************************/
+int ReadNewickTree::readTreeString() {
try {
+
int n = 0;
- int lc, rc;
+ int lc, rc, error;
int rooted = 0;
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");
+ error = readSpecialChar(filehandle,',',"comma");
+ if (error == -1) { readOk = -1; return -1; }
}
// ';' 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(filehandle.peek() == ')'){
- readSpecialChar(filehandle,')',"right parenthesis");
+ error = readSpecialChar(filehandle,')',"right parenthesis");
+ if (error == -1) { readOk = -1; return -1; }
}
}
}
//note: treeclimber had the code below added - not sure why?
- else{
+ else{
filehandle.putback(ch);
char name[MAX_LINE];
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); }
}
-
- //save tree for later commands
- globaldata->gTree = T;
+ return 0;
+
}
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";
+ cout << "Standard Error: " << e.what() << " has occurred in the ReadNewickTree class Function readTreeString. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
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";
+ 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;
+
int c = readNodeChar(f);
+ if (c == -1) { readOk = -1; return -1; }
if(c == '('){
int lc = readNewickInt(f, n, T);
- readSpecialChar(f,',',"comma");
-
- int rc = 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; }
+
+ 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);
//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();
- 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);
}
}
/**************************************************************************************************/
/**************************************************************************************************/
-
\ No newline at end of file
+
projects / mothur.git / blobdiff