X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtree.cpp;h=5e909e620d237ed063d9a64bd191f707ddea1daa;hb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;hp=4d3bd6daa435e303f236b8ca9dd31385a2df21dd;hpb=8f92612d5a69f5245e63a20657e7d93519c0769e;p=mothur.git diff --git a/readtree.cpp b/readtree.cpp index 4d3bd6d..5e909e6 100644 --- a/readtree.cpp +++ b/readtree.cpp @@ -16,13 +16,9 @@ ReadTree::ReadTree() { 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"; + 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 +28,11 @@ 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"; + 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"; + mothurOut("Error: Expected " + name + " in input file. Found " + toString(d) + ".\n"); exit(1); } if(d == ')' && f.peek() == '\n'){ @@ -45,13 +41,9 @@ 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"; + 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 +54,15 @@ int ReadTree::readNodeChar(istream& f) { char d = f.get(); if(d == EOF){ - cerr << "Error: Input file ends prematurely, expecting a left parenthesis\n"; + 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"; + 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); - } } /**************************************************************************************************/ @@ -84,47 +72,54 @@ float ReadTree::readBranchLength(istream& f) { float b; if(!(f >> b)){ - cerr << "Error: Missing branch length in input tree.\n"; + 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"; + 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() { 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) { + // get past comments + if(c == '[') { + comment = 1; + } + if(c == ']'){ + comment = 0; + } + if((c == '(') && (comment != 1)){ break; } + filehandle.get(); + } + //make new tree T = new Tree(); numNodes = T->getNumNodes(); numLeaves = T->getNumLeaves(); - readTreeString(); + error = readTreeString(); //save trees for later commands globaldata->gTree.push_back(T); @@ -158,21 +153,22 @@ void ReadNewickTree::read() { numLeaves = T->getNumLeaves(); //read tree info - readTreeString(); + error = readTreeString(); //save trees for later commands globaldata->gTree.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"; + 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. @@ -211,17 +207,13 @@ 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"; + 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() { try { int n = 0; @@ -235,6 +227,7 @@ void 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(filehandle.peek()==','){ readSpecialChar(filehandle,',',"comma"); @@ -245,6 +238,7 @@ void 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(filehandle.peek() == ')'){ readSpecialChar(filehandle,')',"right parenthesis"); } @@ -260,32 +254,28 @@ void ReadNewickTree::readTreeString() { n = T->getIndex(name); if(n!=0){ - cerr << "Internal error: The only taxon is not taxon 0.\n"; - exit(1); + 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); T->tree[n].setParent(-1); if(lc!=-1){ T->tree[lc].setParent(n); } if(rc!=-1){ T->tree[rc].setParent(n); } - cout << "new loop "<< 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"; + 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); - } - } /**************************************************************************************************/ @@ -295,18 +285,29 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) { 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); + int rc = readNewickInt(f, n, T); + if (rc == -1) { return -1; } //reports an error in reading 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=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){ 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); @@ -323,7 +324,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) { } int blen = 0; - if(d == ':') { blen = 1; } + if(d == ':') { blen = 1; } f.putback(d); @@ -334,12 +335,11 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) { 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"; + if(group == "not found") { + 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"; - globaldata->gTreemap->treemap[name].vectorIndex = (globaldata->gTreemap->namesOfSeqs.size() - 1); map::iterator it; it = globaldata->gTreemap->seqsPerGroup.find("xxx"); @@ -350,20 +350,14 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) { globaldata->gTreemap->seqsPerGroup["xxx"]++; } - //find index in tree of name - n1 = T->getIndex(name); group = "xxx"; - numLeaves++; - numNodes = 2*numLeaves - 1; - T->resetTree(); } T->tree[n1].setGroup(group); - T->printTree(); 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); @@ -376,13 +370,9 @@ 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"; + 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); - } } /**************************************************************************************************/ /**************************************************************************************************/