X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedordervector.cpp;h=3944212ea99e688cea1e04af5bd559044869505d;hb=6446d2e9713a95db5f772135b7aa3387f7ebf7bb;hp=973f69553a476c4e67f72c4b9f10cecae0bc32b6;hpb=37a229b590342d94cd22bb1f7f4127e85197a27f;p=mothur.git diff --git a/sharedordervector.cpp b/sharedordervector.cpp index 973f695..3944212 100644 --- a/sharedordervector.cpp +++ b/sharedordervector.cpp @@ -7,9 +7,6 @@ * */ -using namespace std; - - #include "sharedordervector.h" #include "sharedutilities.h" @@ -36,7 +33,7 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() { //reads in a if (globaldata->gGroupmap == NULL) { groupmap = new GroupMap(); } - int num, inputData, pos, count; + int num, inputData, count; count = 0; numSeqs = 0; string holdLabel, nextLabel, groupN; individual newguy; @@ -60,8 +57,7 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() { //reads in a } } - //save position in file in case next line is a new label. - pos = f.tellg(); + m->gobble(f); if (f.eof() != true) { f >> nextLabel; } @@ -85,15 +81,14 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() { //reads in a } } - //save position in file in case next line is a new label. - pos = f.tellg(); - + m->gobble(f); + if (f.eof() != true) { f >> nextLabel; } } //put file pointer back since you are now at a new distance label - f.seekg(pos, ios::beg); + for (int i = 0; i < nextLabel.length(); i++) { f.unget(); } if (globaldata->gGroupmap == NULL) { globaldata->gGroupmap = groupmap; } @@ -101,11 +96,7 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() { //reads in a } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function SharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedOrderVector class function SharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedOrderVector", "SharedOrderVector"); exit(1); } } @@ -149,7 +140,7 @@ individual SharedOrderVector::get(int index){ /***********************************************************************/ - +//commented updateStats out to improve speed, but whoever calls this must remember to update when they are done with all the pushbacks they are doing void SharedOrderVector::push_back(int binNumber, int abund, string groupName){ individual newGuy; newGuy.group = groupName; @@ -159,7 +150,8 @@ void SharedOrderVector::push_back(int binNumber, int abund, string groupName){ //numSeqs++; //numBins++; //if (abund > maxRank) { maxRank = abund; } - updateStats(); + + //updateStats(); } /***********************************************************************/ @@ -174,11 +166,7 @@ void SharedOrderVector::print(ostream& output){ output << endl; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedOrderVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedOrderVector", "print"); exit(1); } } @@ -187,7 +175,7 @@ void SharedOrderVector::print(ostream& output){ /***********************************************************************/ void SharedOrderVector::resize(int){ - cout << "resize() did nothing in class SharedOrderVector"; + m->mothurOut("resize() did nothing in class SharedOrderVector"); } /***********************************************************************/ @@ -230,13 +218,9 @@ RAbundVector SharedOrderVector::getRAbundVector(){ return rav; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedOrderVector", "getRAbundVector"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the SharedOrderVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /***********************************************************************/ @@ -254,11 +238,7 @@ OrderVector SharedOrderVector::getOrderVector(map* nameMap = NULL) { return ov; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedOrderVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedOrderVector", "getOrderVector"); exit(1); } } @@ -288,14 +268,9 @@ SharedRAbundVector SharedOrderVector::getSharedRAbundVector(string group) { return sharedRav; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedOrderVector", "getSharedRAbundVector"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the SharedOrderVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - } /***********************************************************************/ vector SharedOrderVector::getSharedRAbundVector() { @@ -310,14 +285,9 @@ vector SharedOrderVector::getSharedRAbundVector() { return lookup; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedOrderVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedOrderVector", "getSharedRAbundVector"); exit(1); } - } /***********************************************************************/ SharedSAbundVector SharedOrderVector::getSharedSAbundVector(string group) { @@ -328,14 +298,9 @@ SharedSAbundVector SharedOrderVector::getSharedSAbundVector(string group) { } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedOrderVector", "getSharedSAbundVector"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the SharedOrderVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - } /***********************************************************************/ @@ -354,34 +319,23 @@ void SharedOrderVector::updateStats(){ numBins = 0; maxRank = 0; - for(int i=0;i hold(numSeqs, 0); - - //for(int i=0;i hold(numSeqs, 0); for(int i=0;i numBins) { numBins = data[i].bin; } - if(data[i].abundance > maxRank) { maxRank = data[i].abundance; } + hold[data[i].bin] = hold[data[i].bin]+1; + } + + for(int i=0;i 0) { numBins++; } + if(hold[i] > maxRank) { maxRank = hold[i]; } } - numBins++; //if you have 10 bins largest .bin is 9 since we start at 0. + } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function updateStats. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedOrderVector", "updateStats"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the SharedOrderVector class function updateStats. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /***********************************************************************/