X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtree.cpp;h=3062f6677fa8527b4eb59a9ab979458465bfb777;hb=5c80ce8b80938d41cf6c64a017fa6fd50d45de5b;hp=d3790df170ab0651c24987bc3541b62f48197c5f;hpb=2e5ec5cbbd23637ed20da9bdd544d178a3b5d949;p=mothur.git diff --git a/readtree.cpp b/readtree.cpp index d3790df..3062f66 100644 --- a/readtree.cpp +++ b/readtree.cpp @@ -13,16 +13,13 @@ ReadTree::ReadTree() { try { globaldata = GlobalData::getInstance(); + m = MothurOut::getInstance(); globaldata->gTree.clear(); } 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"; - exit(1); - } } /***********************************************************************/ int ReadTree::readSpecialChar(istream& f, char c, string name) { @@ -32,11 +29,11 @@ int ReadTree::readSpecialChar(istream& f, char c, string name) { 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'){ @@ -45,13 +42,9 @@ int ReadTree::readSpecialChar(istream& f, char c, string name) { 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); - } } /**************************************************************************************************/ @@ -62,19 +55,15 @@ int ReadTree::readNodeChar(istream& 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); - } } /**************************************************************************************************/ @@ -84,20 +73,16 @@ 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); 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); - } } /***********************************************************************/ @@ -132,6 +117,7 @@ int ReadNewickTree::read() { //make new tree T = new Tree(); + numNodes = T->getNumNodes(); numLeaves = T->getNumLeaves(); @@ -177,16 +163,14 @@ int ReadNewickTree::read() { } 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. @@ -225,13 +209,9 @@ void ReadNewickTree::nexusTranslation() { } } 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); - } } /**************************************************************************************************/ @@ -249,7 +229,7 @@ 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) { cout << "error with lc" << endl; 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"); @@ -260,7 +240,7 @@ int ReadNewickTree::readTreeString() { } if(rooted != 1){ rc = readNewickInt(filehandle, n, T); - if (rc == -1) { cout << "error with rc" << endl; 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"); } @@ -276,14 +256,14 @@ int ReadNewickTree::readTreeString() { n = T->getIndex(name); if(n!=0){ - cerr << "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; } 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); @@ -295,19 +275,17 @@ int ReadNewickTree::readTreeString() { } 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) { try { + + if (m->control_pressed) { return -1; } + int c = readNodeChar(f); if(c == '('){ @@ -319,15 +297,22 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* 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(); } + filehandle.putback(c); + } if(f.peek() == ':'){ readSpecialChar(f,':',"colon"); - if(n >= numNodes){ cerr << "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); } + }else{ + T->tree[n].setBranchLength(0.0); + } T->tree[n].setChildren(lc,rc); T->tree[lc].setParent(n); @@ -356,7 +341,7 @@ 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") { - cout << "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 +358,9 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) { group = "xxx"; } - T->tree[n1].setGroup(group); + vector tempGroup; tempGroup.push_back(group); + + T->tree[n1].setGroup(tempGroup); T->tree[n1].setChildren(-1,-1); if(blen == 1){ @@ -390,13 +377,9 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) { } } 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); - } } /**************************************************************************************************/ /**************************************************************************************************/