X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=readtree.cpp;fp=readtree.cpp;h=0000000000000000000000000000000000000000;hp=6fa4c3da814347cc60c0807bd16cb373fff8c962;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76 diff --git a/readtree.cpp b/readtree.cpp deleted file mode 100644 index 6fa4c3d..0000000 --- a/readtree.cpp +++ /dev/null @@ -1,463 +0,0 @@ -/* - * 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 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> 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 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::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 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); - } -} -/**************************************************************************************************/ -/**************************************************************************************************/ -