+++ /dev/null
-/*
- * readtree.cpp
- * Mothur
- *
- * Created by Sarah Westcott on 1/22/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "readtree.h"
-
-/***********************************************************************/
-ReadTree::ReadTree() {
- try {
- m = MothurOut::getInstance();
- }
- catch(exception& e) {
- m->errorOut(e, "ReadTree", "ReadTree");
- exit(1);
- }
-}
-/***********************************************************************/
-int ReadTree::AssembleTrees(map<string, string> nameMap) {
- try {
- //assemble users trees
- for (int i = 0; i < Trees.size(); i++) {
- if (m->control_pressed) { return 0; }
- Trees[i]->assembleTree(nameMap);
- }
- 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(TreeMap* tmap) {
- 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(tmap);
-
- numNodes = T->getNumNodes();
- numLeaves = T->getNumLeaves();
-
- error = readTreeString(tmap);
-
- //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(tmap); delete temp;
-
- nexusTranslation(tmap); //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(tmap);
- numNodes = T->getNumNodes();
- numLeaves = T->getNumLeaves();
-
- //read tree info
- error = readTreeString(tmap);
-
- //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(TreeMap* tmap) {
- 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;}
- }
-
- //update treemap
- tmap->namesOfSeqs.clear();
-
- /*char c;
- string number, name;
- while ((c = filehandle.peek()) != EOF) {
-
- filehandle >> number;
-
- if ((number == "tree") || (number == ";") ) { name = number; break; }
-
- filehandle >> name;
-
- char lastChar;
- if (name.length() != 0) { lastChar = name[name.length()-1]; }
-
- if ((name == "tree") || (name == ";") ) { break; }
-
- if (lastChar == ',') { name.erase(name.end()-1); } //erase the comma
- */
-
- string number, name;
- for(int i=0;i<numSeqs;i++){
-
- filehandle >> number;
- filehandle >> name;
- name.erase(name.end()-1); //erase the comma
-
- //insert new one with new name
- string group = tmap->getGroup(name);
- tmap->treemap[toString(number)].groupname = group;
- tmap->treemap[toString(number)].vectorIndex = tmap->getIndex(name);
- //erase old one. so treemap[sarah].groupnumber is now treemap[1].groupnumber. if number is 1 and name is sarah.
- tmap->treemap.erase(name);
- tmap->namesOfSeqs.push_back(number);
- }
-
- return name;
- }
- catch(exception& e) {
- m->errorOut(e, "ReadNewickTree", "nexusTranslation");
- exit(1);
- }
-}
-
-/**************************************************************************************************/
-int ReadNewickTree::readTreeString(TreeMap* tmap) {
- 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, tmap);
- 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, tmap);
- 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{
- 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, TreeMap* tmap) {
- 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, tmap);
- 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);
- }
-
- //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 = "";
- 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
- string group = tmap->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(group == "not found") {
- m->mothurOut("Name: " + name + " is not in your groupfile, and will be disregarded. \n"); //readOk = -1; return n1;
-
- tmap->namesOfSeqs.push_back(name);
- tmap->treemap[name].groupname = "xxx";
-
- map<string, int>::iterator it;
- it = tmap->seqsPerGroup.find("xxx");
- if (it == tmap->seqsPerGroup.end()) { //its a new group
- tmap->addGroup("xxx");
- tmap->seqsPerGroup["xxx"] = 1;
- }else {
- tmap->seqsPerGroup["xxx"]++;
- }
-
- group = "xxx";
- }
-
- vector<string> tempGroup; tempGroup.push_back(group);
-
- T->tree[n1].setGroup(tempGroup);
- 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