X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=readtree.cpp;h=b9c38e973f2cea531c03c17071ed65a155bf65a3;hp=51f44e217899c3acebc1a34879b31d6624389191;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=2a7d1455e8cfe4f67a7173f3a7249762c5436217 diff --git a/readtree.cpp b/readtree.cpp index 51f44e2..b9c38e9 100644 --- a/readtree.cpp +++ b/readtree.cpp @@ -12,9 +12,7 @@ /***********************************************************************/ ReadTree::ReadTree() { try { - globaldata = GlobalData::getInstance(); m = MothurOut::getInstance(); - globaldata->gTree.clear(); } catch(exception& e) { m->errorOut(e, "ReadTree", "ReadTree"); @@ -22,10 +20,25 @@ ReadTree::ReadTree() { } } /***********************************************************************/ +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){ @@ -37,7 +50,7 @@ int ReadTree::readSpecialChar(istream& f, char c, string name) { exit(1); } if(d == ')' && f.peek() == '\n'){ - gobble(f); + m->gobble(f); } return d; } @@ -51,7 +64,7 @@ int ReadTree::readSpecialChar(istream& f, char c, string name) { int ReadTree::readNodeChar(istream& f) { try { // while(isspace(d=f.get())) {;} - gobble(f); + m->gobble(f); char d = f.get(); if(d == EOF){ @@ -76,7 +89,7 @@ float ReadTree::readBranchLength(istream& f) { m->mothurOut("Error: Missing branch length in input tree.\n"); exit(1); } - gobble(f); + m->gobble(f); return b; } catch(exception& e) { @@ -94,7 +107,7 @@ float ReadTree::readBranchLength(istream& f) { /***********************************************************************/ //This class reads a file in Newick form and stores it in a tree. -int ReadNewickTree::read() { +int ReadNewickTree::read(CountTable* ct) { try { holder = ""; int c, error; @@ -102,8 +115,10 @@ int ReadNewickTree::read() { //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; @@ -116,23 +131,28 @@ int ReadNewickTree::read() { } //make new tree - T = new Tree(); + T = new Tree(ct); numNodes = T->getNumNodes(); numLeaves = T->getNumLeaves(); - error = 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; } @@ -150,21 +170,22 @@ int 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 - error = 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) { @@ -174,11 +195,11 @@ int ReadNewickTree::read() { } /**************************************************************************************************/ //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 @@ -190,23 +211,19 @@ 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) { m->errorOut(e, "ReadNewickTree", "nexusTranslation"); @@ -215,7 +232,7 @@ void ReadNewickTree::nexusTranslation() { } /**************************************************************************************************/ -int ReadNewickTree::readTreeString() { +int ReadNewickTree::readTreeString(CountTable* ct) { try { int n = 0; @@ -228,8 +245,8 @@ int 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); - if (lc == -1) { m->mothurOut("error with lc"); m->mothurOutEndLine(); return -1; } //reports an error in reading + 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"); @@ -237,14 +254,15 @@ int ReadNewickTree::readTreeString() { // ';' means end of tree. else if((ch=filehandle.peek())==';' || ch=='['){ rooted = 1; - } + } + if(rooted != 1){ - rc = readNewickInt(filehandle, n, T); - if (rc == -1) { m->mothurOut("error with rc"); m->mothurOutEndLine(); return -1; } //reports an error in reading + 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{ @@ -263,7 +281,8 @@ int ReadNewickTree::readTreeString() { lc = rc = -1; } - while(((ch=filehandle.get())!=';') && (filehandle.eof() != true)){;} + while(((ch=filehandle.get())!=';') && (filehandle.eof() != true)){;} + if(rooted != 1){ T->tree[n].setChildren(lc,rc); T->tree[n].setBranchLength(0); @@ -271,6 +290,8 @@ int ReadNewickTree::readTreeString() { if(lc!=-1){ T->tree[lc].setParent(n); } if(rc!=-1){ T->tree[rc].setParent(n); } } + + //T->printTree(); cout << endl; return 0; } @@ -281,59 +302,70 @@ int ReadNewickTree::readTreeString() { } /**************************************************************************************************/ -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); - if (lc == -1) { return -1; } //reports an error in reading + + //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--; - readSpecialChar(f,',',"comma"); - - int rc = readNewickInt(f, n, T); - if (rc == -1) { return -1; } //reports an error in reading if(f.peek()==')'){ readSpecialChar(f,')',"right parenthesis"); //to pass over labels in trees c=filehandle.get(); - while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ 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; } + 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); } - - //to account for multifurcating trees generated by fasttree, we are forcing them to be bifurcating - /* if(f.peek() == ','){ - - //force this node to be left child and read new rc - T->tree[n].setChildren(lc,rc); - T->tree[lc].setParent(n); - T->tree[rc].setParent(n); - - n++; - - - - }*/ - - T->tree[n].setChildren(lc,rc); - T->tree[lc].setParent(n); - T->tree[rc].setParent(n); - + return n++; + }else{ f.putback(c); string name = ""; @@ -342,40 +374,34 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) { name += d; d=f.get(); } - +//cout << name << endl; int blen = 0; 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(group == "not found") { + if(group.size() == 0) { m->mothurOut("Name: " + name + " is not in your groupfile, and will be disregarded. \n"); //readOk = -1; return n1; - globaldata->gTreemap->namesOfSeqs.push_back(name); - globaldata->gTreemap->treemap[name].groupname = "xxx"; - - 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"]++; - } - - group = "xxx"; - } - - vector tempGroup; tempGroup.push_back(group); - - T->tree[n1].setGroup(tempGroup); + 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){ @@ -386,6 +412,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) { } while((c=f.get())!=0 && (c != ':' && c != ',' && c!=')') ) {;} + f.putback(c); return n1;