#include "readtree.h"
+/***********************************************************************/
+ReadTree::ReadTree() {
+ try {
+ 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";
+ 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) {
+ try {
+
+ gobble(f);
+ char d = f.get();
+
+ if(d == EOF){
+ 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"; return -1;
+ //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";
+ 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);
+ }
+}
+/**************************************************************************************************/
+
+int ReadTree::readNodeChar(istream& f) {
+ try {
+// 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"; return -1;
+ //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";
+ 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 ReadTree::readBranchLength(istream& f) {
+ try {
+ float b;
+
+ if(!(f >> b)){
+ cerr << "Error: Missing branch length in input tree.\n"; return -1;
+ //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";
+ 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.
+
+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, error;
+
+ int rooted = 0;
+
+ int ch = filehandle.peek();
+
+ 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()==','){
+ error = readSpecialChar(filehandle,',',"comma");
+ if (error == -1) { readOk = -1; return -1; }
+ }
+ // ';' means end of tree.
+ else if((ch=filehandle.peek())==';' || ch=='['){
+ rooted = 1;
+ }
+ if(rooted != 1){
+ rc = readNewickInt(filehandle, n, T);
+ if (rc == -1) { return -1; } //reports an error in reading
+ if(filehandle.peek() == ')'){
+ error = readSpecialChar(filehandle,')',"right parenthesis");
+ if (error == -1) { readOk = -1; return -1; }
+ }
+ }
+ }
+ //note: treeclimber had the code below added - not sure why?
+ 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);
+ readOk = -1; return -1;
+ }
+ lc = rc = -1;
+ }
+
+ while((ch=filehandle.get())!=';'){;}
+ 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) {
+ 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 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);
+ 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()==')'){
+ error = readSpecialChar(f,')',"right parenthesis");
+ if (error == -1) { readOk = -1; return -1; }
+ }
+
+ 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); }
+
+ T->tree[n].setChildren(lc,rc);
+ T->tree[lc].setParent(n);
+ T->tree[rc].setParent(n);
+
+ return n++;
+ }else{
+ f.putback(c);
+ string name = "";
+ char d=f.get();
+ while(d != ':' && d != ',' && d!=')' && d!='\n'){
+ name += d;
+ d=f.get();
+ }
+
+ int blen = 0;
+ if(d == ':') { blen = 1; }
+
+ f.putback(d);
+
+ //set group info
+ string group = globaldata->gTreemap->getGroup(name);
+
+ //find index in tree of name
+ 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;
+
+ //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;
+ }
+
+ T->tree[n1].setGroup(group);
+ 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);
+ }else{
+ T->tree[n1].setBranchLength(0.0);
+ }
+
+ while((c=f.get())!=0 && (c != ':' && c != ',' && c!=')') ) {;}
+ f.putback(c);
+
+ return n1;
+ }
+ }
+ 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";
+ 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