X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtree.cpp;h=1df49b5502f405bf29b31ee585fb5d6a264f9cda;hb=6de5adaae66b28aa60a75f123005cede410c156c;hp=cdaa38701e0593817d5af7b415e308429fe2e6a1;hpb=5a1e62397b91f57d0d3aff635891df04b8999a88;p=mothur.git diff --git a/readtree.cpp b/readtree.cpp index cdaa387..1df49b5 100644 --- a/readtree.cpp +++ b/readtree.cpp @@ -13,10 +13,11 @@ ReadTree::ReadTree() { try { globaldata = GlobalData::getInstance(); + m = MothurOut::getInstance(); globaldata->gTree.clear(); } catch(exception& e) { - errorOut(e, "ReadTree", "ReadTree"); + m->errorOut(e, "ReadTree", "ReadTree"); exit(1); } } @@ -28,11 +29,11 @@ int ReadTree::readSpecialChar(istream& f, char c, string name) { char d = f.get(); if(d == EOF){ - mothurOut("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){ - mothurOut("Error: Expected " + name + " in input file. Found " + toString(d) + ".\n"); + m->mothurOut("Error: Expected " + name + " in input file. Found " + toString(d) + ".\n"); exit(1); } if(d == ')' && f.peek() == '\n'){ @@ -41,7 +42,7 @@ int ReadTree::readSpecialChar(istream& f, char c, string name) { return d; } catch(exception& e) { - errorOut(e, "ReadTree", "readSpecialChar"); + m->errorOut(e, "ReadTree", "readSpecialChar"); exit(1); } } @@ -54,13 +55,13 @@ int ReadTree::readNodeChar(istream& f) { char d = f.get(); if(d == EOF){ - mothurOut("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) { - errorOut(e, "ReadTree", "readNodeChar"); + m->errorOut(e, "ReadTree", "readNodeChar"); exit(1); } } @@ -72,14 +73,14 @@ float ReadTree::readBranchLength(istream& f) { float b; if(!(f >> b)){ - mothurOut("Error: Missing branch length in input tree.\n"); + m->mothurOut("Error: Missing branch length in input tree.\n"); exit(1); } gobble(f); return b; } catch(exception& e) { - errorOut(e, "ReadTree", "readBranchLength"); + m->errorOut(e, "ReadTree", "readBranchLength"); exit(1); } } @@ -167,7 +168,7 @@ int ReadNewickTree::read() { return readOk; } catch(exception& e) { - errorOut(e, "ReadNewickTree", "read"); + m->errorOut(e, "ReadNewickTree", "read"); exit(1); } } @@ -208,7 +209,7 @@ void ReadNewickTree::nexusTranslation() { } } catch(exception& e) { - errorOut(e, "ReadNewickTree", "nexusTranslation"); + m->errorOut(e, "ReadNewickTree", "nexusTranslation"); exit(1); } } @@ -228,8 +229,8 @@ int ReadNewickTree::readTreeString() { 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) { mothurOut("error with lc"); mothurOutEndLine(); return -1; } //reports an error in reading - + if (lc == -1) { m->mothurOut("error with lc"); m->mothurOutEndLine(); return -1; } //reports an error in reading + if(filehandle.peek()==','){ readSpecialChar(filehandle,',',"comma"); } @@ -239,7 +240,7 @@ int ReadNewickTree::readTreeString() { } if(rooted != 1){ rc = readNewickInt(filehandle, n, T); - if (rc == -1) { mothurOut("error with rc"); mothurOutEndLine(); return -1; } //reports an error in reading + if (rc == -1) { m->mothurOut("error with rc"); m->mothurOutEndLine(); return -1; } //reports an error in reading if(filehandle.peek() == ')'){ readSpecialChar(filehandle,')',"right parenthesis"); } @@ -255,7 +256,7 @@ int ReadNewickTree::readTreeString() { n = T->getIndex(name); if(n!=0){ - mothurOut("Internal error: The only taxon is not taxon 0.\n"); + m->mothurOut("Internal error: The only taxon is not taxon 0.\n"); //exit(1); readOk = -1; return -1; } @@ -274,7 +275,7 @@ int ReadNewickTree::readTreeString() { } catch(exception& e) { - errorOut(e, "ReadNewickTree", "readTreeString"); + m->errorOut(e, "ReadNewickTree", "readTreeString"); exit(1); } } @@ -282,15 +283,20 @@ int ReadNewickTree::readTreeString() { int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) { 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 + 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 @@ -303,17 +309,60 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) { if(f.peek() == ':'){ readSpecialChar(f,':',"colon"); - if(n >= numNodes){ 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 + while(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); + + T->printTree(); cout << endl; + lc = n; + n++; + + readSpecialChar(f,',',"comma"); + + int rc = readNewickInt(f, n, T); + cout << n << '\t' << lc << '\t' << rc << endl; + if (rc == -1) { return -1; } //reports an error in reading + + if(f.peek()==')'){ + string k; + k = f.peek(); + cout << "in here " << k << endl; + readSpecialChar(f,')',"right parenthesis"); + //to pass over labels in trees + c=filehandle.get(); + while((c!=',') && (c != -1) && (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); + } + + break; + } + } + cout << n << '\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; + return n++; }else{ f.putback(c); @@ -323,7 +372,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) { name += d; d=f.get(); } - + cout << name << endl; int blen = 0; if(d == ':') { blen = 1; } @@ -337,7 +386,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) { //adds sequence names that are not in group file to the "xxx" group if(group == "not found") { - mothurOut("Name: " + name + " is not in your groupfile, and will be disregarded. \n"); //readOk = -1; return n1; + 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"; @@ -373,7 +422,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) { } } catch(exception& e) { - errorOut(e, "ReadNewickTree", "readNewickInt"); + m->errorOut(e, "ReadNewickTree", "readNewickInt"); exit(1); } }