X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=readtree.cpp;h=b9c38e973f2cea531c03c17071ed65a155bf65a3;hp=81a7729ffb474294502407eec1c44620bfff3378;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=06da1833191d5dee7e206f436d9631680f1e7c42 diff --git a/readtree.cpp b/readtree.cpp index 81a7729..b9c38e9 100644 --- a/readtree.cpp +++ b/readtree.cpp @@ -12,69 +12,71 @@ /***********************************************************************/ ReadTree::ReadTree() { try { - globaldata = GlobalData::getInstance(); - globaldata->gTree.clear(); + m = MothurOut::getInstance(); } 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"; + m->errorOut(e, "ReadTree", "ReadTree"); 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"; +} +/***********************************************************************/ +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 { - gobble(f); + m->gobble(f); char d = f.get(); if(d == EOF){ - cerr << "Error: Input file ends prematurely, expecting a " << name << "\n"; + m->mothurOut("Error: Input file ends prematurely, expecting a " + name + "\n"); exit(1); } if(d != c){ - cerr << "Error: Expected " << name << " in input file. Found " << d << ".\n"; + m->mothurOut("Error: Expected " + name + " in input file. Found " + toString(d) + ".\n"); exit(1); } if(d == ')' && f.peek() == '\n'){ - gobble(f); + m->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"; + m->errorOut(e, "ReadTree", "readSpecialChar"); 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); + m->gobble(f); char d = f.get(); if(d == EOF){ - cerr << "Error: Input file ends prematurely, expecting a left parenthesis\n"; + m->mothurOut("Error: Input file ends prematurely, expecting a left parenthesis\n"); 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"; + m->errorOut(e, "ReadTree", "readNodeChar"); 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); - } } /**************************************************************************************************/ @@ -84,57 +86,73 @@ float ReadTree::readBranchLength(istream& f) { float b; if(!(f >> b)){ - cerr << "Error: Missing branch length in input tree.\n"; + m->mothurOut("Error: Missing branch length in input tree.\n"); exit(1); } - gobble(f); + m->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"; + m->errorOut(e, "ReadTree", "readBranchLength"); 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. -void ReadNewickTree::read() { +int ReadNewickTree::read(CountTable* ct) { try { - int c; + 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) { + 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(); + T = new Tree(ct); + numNodes = T->getNumNodes(); numLeaves = T->getNumLeaves(); - readTreeString(); + error = readTreeString(ct); + //save trees for later commands - globaldata->gTree.push_back(T); - gobble(filehandle); + Trees.push_back(T); + m->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 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) { + while ((c = filehandle.peek()) != EOF) { + if (m->control_pressed) { filehandle.close(); return 0; } if(holder == "[" || holder == "[!"){ comment = 1; } @@ -152,34 +170,36 @@ void ReadNewickTree::read() { filehandle.putback(c); //put back first ( of tree. //make new tree - T = new Tree(); + T = new Tree(ct); numNodes = T->getNumNodes(); numLeaves = T->getNumLeaves(); //read tree info - readTreeString(); + error = readTreeString(ct); + //save trees for later commands - globaldata->gTree.push_back(T); + Trees.push_back(T); } } + if (error != 0) { readOk = error; } + + filehandle.close(); + + 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"; + m->errorOut(e, "ReadNewickTree", "read"); 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() { +string ReadNewickTree::nexusTranslation(CountTable* ct) { 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 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 @@ -191,36 +211,28 @@ void ReadNewickTree::nexusTranslation() { comment = 0; } filehandle >> holder; - if(holder == "tree" && comment != 1){return;} + if(holder == "tree" && comment != 1){return holder;} } - - //update treemap - globaldata->gTreemap->namesOfSeqs.clear(); + + 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 - 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); + ct->renameSeq(name, toString(number)); } + + return name; } 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"; + m->errorOut(e, "ReadNewickTree", "nexusTranslation"); 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); - } } /**************************************************************************************************/ -void ReadNewickTree::readTreeString() { +int ReadNewickTree::readTreeString(CountTable* ct) { try { int n = 0; @@ -233,21 +245,24 @@ void ReadNewickTree::readTreeString() { if(ch == '('){ n = numLeaves; //number of leaves / sequences, we want node 1 to start where the leaves left off - lc = readNewickInt(filehandle, n, T); - + 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); + 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{ @@ -259,13 +274,15 @@ void ReadNewickTree::readTreeString() { n = T->getIndex(name); if(n!=0){ - cerr << "Internal error: The only taxon is not taxon 0.\n"; - exit(1); + 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())!=';'){;} + while(((ch=filehandle.get())!=';') && (filehandle.eof() != true)){;} + if(rooted != 1){ T->tree[n].setChildren(lc,rc); T->tree[n].setBranchLength(0); @@ -273,44 +290,82 @@ void ReadNewickTree::readTreeString() { 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) { - cout << "Standard Error: " << e.what() << " has occurred in the ReadNewickTree class Function readTreeString. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ReadNewickTree", "readTreeString"); 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) { +int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T, CountTable* ct) { try { + + if (m->control_pressed) { return -1; } + int c = readNodeChar(f); - - if(c == '('){ - int lc = readNewickInt(f, n, T); - readSpecialChar(f,',',"comma"); - int rc = readNewickInt(f, n, T); + 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"); + 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){ cerr << "Error: Too many nodes in input tree\n"; exit(1); } + 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); - + }else{ + T->tree[n].setBranchLength(0.0); + } + return n++; + }else{ f.putback(c); string name = ""; @@ -319,64 +374,54 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) { name += d; d=f.get(); } - +//cout << name << endl; int blen = 0; - if(d == ':') { blen = 1; } + if(d == ':') { blen = 1; } f.putback(d); //set group info - string group = globaldata->gTreemap->getGroup(name); - + 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(n1 == -1) { - cerr << "Name: " << name << " not found in your groupfile and it will be ignored. \n"; - globaldata->gTreemap->namesOfSeqs.push_back(name); - globaldata->gTreemap->treemap[name].groupname = "xxx"; - globaldata->gTreemap->treemap[name].vectorIndex = (globaldata->gTreemap->namesOfSeqs.size() - 1); + if(group.size() == 0) { + m->mothurOut("Name: " + name + " is not in your groupfile, and will be disregarded. \n"); //readOk = -1; return n1; - map::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"; - } - + 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(); + 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) { - cout << "Standard Error: " << e.what() << " has occurred in the ReadNewickTree class Function readNewickInt. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ReadNewickTree", "readNewickInt"); 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); - } } /**************************************************************************************************/ /**************************************************************************************************/