#include "readtree.h"
+/***********************************************************************/
+ReadTree::ReadTree() {
+ try {
+ m = MothurOut::getInstance();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadTree", "ReadTree");
+ exit(1);
+ }
+}
+/***********************************************************************/
+int ReadTree::AssembleTrees() {
+ try {
+ //assemble users trees
+ for (int i = 0; i < Trees.size(); i++) {
+ if (m->control_pressed) { return 0; }
+ Trees[i]->assembleTree();
+ }
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadTree", "AssembleTrees");
+ exit(1);
+ }
+}
+/***********************************************************************/
+int ReadTree::readSpecialChar(istream& f, char c, string name) {
+ try {
+
+ m->gobble(f);
+ char d = f.get();
+
+ if(d == EOF){
+ m->mothurOut("Error: Input file ends prematurely, expecting a " + name + "\n");
+ exit(1);
+ }
+ if(d != c){
+ m->mothurOut("Error: Expected " + name + " in input file. Found " + toString(d) + ".\n");
+ exit(1);
+ }
+ if(d == ')' && f.peek() == '\n'){
+ m->gobble(f);
+ }
+ return d;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadTree", "readSpecialChar");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+int ReadTree::readNodeChar(istream& f) {
+ try {
+// while(isspace(d=f.get())) {;}
+ m->gobble(f);
+ char d = f.get();
+
+ if(d == EOF){
+ m->mothurOut("Error: Input file ends prematurely, expecting a left parenthesis\n");
+ exit(1);
+ }
+ return d;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadTree", "readNodeChar");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+float ReadTree::readBranchLength(istream& f) {
+ try {
+ float b;
+
+ if(!(f >> b)){
+ m->mothurOut("Error: Missing branch length in input tree.\n");
+ exit(1);
+ }
+ m->gobble(f);
+ return b;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadTree", "readBranchLength");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+/***********************************************************************/
+
+//Child Classes Below
+
+/***********************************************************************/
+/***********************************************************************/
+//This class reads a file in Newick form and stores it in a tree.
+
+int ReadNewickTree::read(CountTable* ct) {
+ try {
+ holder = "";
+ int c, error;
+ int comment = 0;
+
+ //if you are not a nexus file
+ if ((c = filehandle.peek()) != '#') {
+ while((c = filehandle.peek()) != EOF) {
+ if (m->control_pressed) { filehandle.close(); return 0; }
+ while ((c = filehandle.peek()) != EOF) {
+ if (m->control_pressed) { filehandle.close(); return 0; }
+ // get past comments
+ if(c == '[') {
+ comment = 1;
+ }
+ if(c == ']'){
+ comment = 0;
+ }
+ if((c == '(') && (comment != 1)){ break; }
+ filehandle.get();
+ }
+
+ //make new tree
+ T = new Tree(ct);
+
+ numNodes = T->getNumNodes();
+ numLeaves = T->getNumLeaves();
+
+ error = readTreeString(ct);
+
+ //save trees for later commands
+ Trees.push_back(T);
+ m->gobble(filehandle);
+ }
+ //if you are a nexus file
+ }else if ((c = filehandle.peek()) == '#') {
+ //get right number of seqs from nexus file.
+ Tree* temp = new Tree(ct); delete temp;
+
+ nexusTranslation(ct); //reads file through the translation and updates treemap
+ while((c = filehandle.peek()) != EOF) {
+ if (m->control_pressed) { filehandle.close(); return 0; }
+ // get past comments
+ while ((c = filehandle.peek()) != EOF) {
+ if (m->control_pressed) { filehandle.close(); return 0; }
+ 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(ct);
+ numNodes = T->getNumNodes();
+ numLeaves = T->getNumLeaves();
+
+ //read tree info
+ error = readTreeString(ct);
+
+ //save trees for later commands
+ Trees.push_back(T);
+ }
+ }
+
+ if (error != 0) { readOk = error; }
+
+ filehandle.close();
+
+ return readOk;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadNewickTree", "read");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+//This function read the file through the translation of the sequences names and updates treemap.
+string ReadNewickTree::nexusTranslation(CountTable* ct) {
+ try {
+
+ holder = "";
+ int numSeqs = m->Treenames.size(); //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 holder;}
+ }
+
+ string number, name;
+ for(int i=0;i<numSeqs;i++){
+
+ filehandle >> number;
+ filehandle >> name;
+ name.erase(name.end()-1); //erase the comma
+ ct->renameSeq(name, toString(number));
+ }
+
+ return name;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadNewickTree", "nexusTranslation");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+int ReadNewickTree::readTreeString(CountTable* ct) {
+ try {
+
+ int n = 0;
+ int lc, rc;
+
+ 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, ct);
+ if (lc == -1) { m->mothurOut("error with lc"); m->mothurOutEndLine(); m->control_pressed = true; 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, ct);
+ if (rc == -1) { m->mothurOut("error with rc"); m->mothurOutEndLine(); m->control_pressed = true; 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{
+ filehandle.putback(ch);
+ char name[MAX_LINE];
+ filehandle.get(name, MAX_LINE,'\n');
+ SKIPLINE(filehandle, ch);
+
+ n = T->getIndex(name);
+
+ if(n!=0){
+ 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)){;}
+
+ 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); }
+ }
+
+ //T->printTree(); cout << endl;
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadNewickTree", "readTreeString");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T, CountTable* ct) {
+ try {
+
+ if (m->control_pressed) { return -1; }
+
+ int c = readNodeChar(f);
+
+ 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, ct);
+ 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!=')')){ 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);
+ }
+
+ return n++;
+
+ }else{
+ f.putback(c);
+ string name = "";
+ char d=f.get();
+ while(d != ':' && d != ',' && d!=')' && d!='\n'){
+ name += d;
+ d=f.get();
+ }
+//cout << name << endl;
+ int blen = 0;
+ if(d == ':') { blen = 1; }
+
+ f.putback(d);
+
+ //set group info
+ vector<string> group = ct->getGroups(name);
+ //cout << name << endl;
+ //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(group.size() == 0) {
+ m->mothurOut("Name: " + name + " is not in your groupfile, and will be disregarded. \n"); //readOk = -1; return n1;
+
+ vector<string> currentGroups = ct->getNamesOfGroups();
+ if (!m->inUsersGroups("xxx", currentGroups)) { ct->addGroup("xxx"); }
+ currentGroups = ct->getNamesOfGroups();
+ vector<int> thisCounts; thisCounts.resize(currentGroups.size(), 0);
+ for (int h = 0; h < currentGroups.size(); h++) {
+ if (currentGroups[h] == "xxx") { thisCounts[h] = 1; break; }
+ }
+ ct->push_back(name, thisCounts);
+
+ group.push_back("xxx");
+ }
+ T->tree[n1].setGroup(group);
+ T->tree[n1].setChildren(-1,-1);
+
+ if(blen == 1){
+ f.get();
+ T->tree[n1].setBranchLength(readBranchLength(f));
+ }else{
+ T->tree[n1].setBranchLength(0.0);
+ }
+
+ while((c=f.get())!=0 && (c != ':' && c != ',' && c!=')') ) {;}
+
+ f.putback(c);
+
+ return n1;
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadNewickTree", "readNewickInt");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+/**************************************************************************************************/
+
projects / mothur.git / blobdiff