X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=readtree.cpp;h=b9c38e973f2cea531c03c17071ed65a155bf65a3;hp=3a9aa51c5052ea331592f4e9ee51164b69f1170c;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=4761e165b4a196fefa57755d3176d9ced19df6b1 diff --git a/readtree.cpp b/readtree.cpp index 3a9aa51..b9c38e9 100644 --- a/readtree.cpp +++ b/readtree.cpp @@ -9,3 +9,420 @@ #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> 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 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 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 currentGroups = ct->getNamesOfGroups(); + if (!m->inUsersGroups("xxx", currentGroups)) { ct->addGroup("xxx"); } + currentGroups = ct->getNamesOfGroups(); + vector 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); + } +} +/**************************************************************************************************/ +/**************************************************************************************************/ +