X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=inputdata.cpp;h=8e54ab787c683535dd132caf0881aab3399945b9;hb=b447f829850ae054e42560c7c3ed71b14f3f40bb;hp=b237bb4fc55b0bacafa3815f9619f0345bd31492;hpb=753dc84cf289b1d5dc0ca5b0c043640927aa951a;p=mothur.git diff --git a/inputdata.cpp b/inputdata.cpp index b237bb4..8e54ab7 100644 --- a/inputdata.cpp +++ b/inputdata.cpp @@ -15,8 +15,9 @@ /***********************************************************************/ InputData::InputData(string fName, string f) : format(f){ - + m = MothurOut::getInstance(); openInputFile(fName, fileHandle); + filename = fName; } @@ -33,7 +34,7 @@ InputData::~InputData(){ InputData::InputData(string fName, string orderFileName, string f) : format(f){ try { - + m = MothurOut::getInstance(); ifstream ofHandle; openInputFile(orderFileName, ofHandle); string name; @@ -51,13 +52,9 @@ InputData::InputData(string fName, string orderFileName, string f) : format(f){ openInputFile(fName, fileHandle); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function InputData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "InputData", "InputData"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the InputData class function InputData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /***********************************************************************/ @@ -66,25 +63,60 @@ ListVector* InputData::getListVector(){ if(fileHandle){ if(format == "list") { list = new ListVector(fileHandle); - } + }else{ list = NULL; } gobble(fileHandle); return list; } else{ - return 0; + return NULL; } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "InputData", "getListVector"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the InputData class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} + +/***********************************************************************/ + +ListVector* InputData::getListVector(string label){ + try { + ifstream in; + string thisLabel; + openInputFile(filename, in); + + if(in){ + + if (format == "list") { + + while (in.eof() != true) { + + list = new ListVector(in); + thisLabel = list->getLabel(); + + //if you are at the last label + if (thisLabel == label) { break; } + //so you don't loose this memory + else { delete list; } + gobble(in); + } + }else{ list = NULL; } + + in.close(); + return list; + } + else{ + return NULL; + } + } + catch(exception& e) { + m->errorOut(e, "InputData", "getListVector"); exit(1); - } + } } + /***********************************************************************/ SharedListVector* InputData::getSharedListVector(){ @@ -92,25 +124,61 @@ SharedListVector* InputData::getSharedListVector(){ if(fileHandle){ if (format == "shared") { SharedList = new SharedListVector(fileHandle); - } + }else{ SharedList = NULL; } gobble(fileHandle); return SharedList; } else{ - return 0; + return NULL; } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "InputData", "getSharedListVector"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the InputData class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +/***********************************************************************/ + +SharedListVector* InputData::getSharedListVector(string label){ + try { + ifstream in; + string thisLabel; + openInputFile(filename, in); + + if(in){ + + if (format == "shared") { + + while (in.eof() != true) { + + SharedList = new SharedListVector(in); + thisLabel = SharedList->getLabel(); + + //if you are at the last label + if (thisLabel == label) { break; } + //so you don't loose this memory + else { delete SharedList; } + gobble(in); + } + + }else{ SharedList = NULL; } + + in.close(); + return SharedList; + + }else{ + return NULL; + } + } + catch(exception& e) { + m->errorOut(e, "InputData", "getSharedListVector"); exit(1); - } + } } + + /***********************************************************************/ SharedOrderVector* InputData::getSharedOrderVector(){ @@ -118,23 +186,58 @@ SharedOrderVector* InputData::getSharedOrderVector(){ if(fileHandle){ if (format == "sharedfile") { SharedOrder = new SharedOrderVector(fileHandle); - } + }else{ SharedOrder = NULL; } gobble(fileHandle); return SharedOrder; }else{ - return 0; + return NULL; } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "InputData", "getSharedOrderVector"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the InputData class function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} + +/***********************************************************************/ + +SharedOrderVector* InputData::getSharedOrderVector(string label){ + try { + ifstream in; + string thisLabel; + openInputFile(filename, in); + + if(in){ + + if (format == "sharedfile") { + + while (in.eof() != true) { + + SharedOrder = new SharedOrderVector(in); + thisLabel = SharedOrder->getLabel(); + + //if you are at the last label + if (thisLabel == label) { break; } + //so you don't loose this memory + else { delete SharedOrder; } + gobble(in); + } + + }else{ SharedOrder = NULL; } + + in.close(); + return SharedOrder; + + }else{ + return NULL; + } + } + catch(exception& e) { + m->errorOut(e, "InputData", "getSharedOrderVector"); exit(1); - } + } } @@ -144,7 +247,7 @@ SharedOrderVector* InputData::getSharedOrderVector(){ OrderVector* InputData::getOrderVector(){ try { if(fileHandle){ - if(format == "list") { + if((format == "list") || (format == "listorder")) { input = new ListVector(fileHandle); } else if (format == "shared") { @@ -159,29 +262,127 @@ OrderVector* InputData::getOrderVector(){ else if(format == "sabund"){ input = new SAbundVector(fileHandle); } - else if(format == "listorder"){ - input = new ListVector(fileHandle); - } - + gobble(fileHandle); + + output = new OrderVector(); + *output = (input->getOrderVector()); + + return output; + } + else{ + return NULL; + } + } + catch(exception& e) { + m->errorOut(e, "InputData", "getOrderVector"); + exit(1); + } +} + +/***********************************************************************/ +OrderVector* InputData::getOrderVector(string label){ + try { + + ifstream in; + string thisLabel; + openInputFile(filename, in); + + if(in){ + if((format == "list") || (format == "listorder")) { + + while (in.eof() != true) { + + input = new ListVector(in); + thisLabel = input->getLabel(); + + //if you are at the last label + if (thisLabel == label) { break; } + //so you don't loose this memory + else { delete input; } + gobble(in); + } + } + else if (format == "shared") { + + while (in.eof() != true) { + + input = new SharedListVector(in); + thisLabel = input->getLabel(); + + //if you are at the last label + if (thisLabel == label) { break; } + //so you don't loose this memory + else { delete input; } + gobble(in); + } + + } + else if(format == "rabund"){ + + while (in.eof() != true) { + + input = new RAbundVector(in); + thisLabel = input->getLabel(); + + //if you are at the last label + if (thisLabel == label) { break; } + //so you don't loose this memory + else { delete input; } + gobble(in); + } + + } + else if(format == "order"){ + + while (in.eof() != true) { + + input = new OrderVector(in); + thisLabel = input->getLabel(); + + //if you are at the last label + if (thisLabel == label) { break; } + //so you don't loose this memory + else { delete input; } + gobble(in); + } + + } + else if(format == "sabund"){ + + while (in.eof() != true) { + + input = new SAbundVector(in); + thisLabel = input->getLabel(); + + //if you are at the last label + if (thisLabel == label) { break; } + //so you don't loose this memory + else { delete input; } + gobble(in); + + } + + } + + in.close(); + output = new OrderVector(); *output = (input->getOrderVector()); return output; + } else{ - return 0; + return NULL; } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "InputData", "getOrderVector"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the InputData class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } + /***********************************************************************/ //this is used when you don't need the order vector vector InputData::getSharedRAbundVectors(){ @@ -207,13 +408,67 @@ vector InputData::getSharedRAbundVectors(){ } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getSharedRAbundVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "InputData", "getSharedRAbundVectors"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the InputData class function getSharedRAbundVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +/***********************************************************************/ +vector InputData::getSharedRAbundVectors(string label){ + try { + ifstream in; + string thisLabel; + + openInputFile(filename, in); + + if(in){ + if (format == "sharedfile") { + while (in.eof() != true) { + + SharedRAbundVector* SharedRAbund = new SharedRAbundVector(in); + if (SharedRAbund != NULL) { + thisLabel = SharedRAbund->getLabel(); + //if you are at the last label + if (thisLabel == label) { in.close(); return SharedRAbund->getSharedRAbundVectors(); } + else { + //so you don't loose this memory + vector lookup = SharedRAbund->getSharedRAbundVectors(); + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + delete SharedRAbund; + } + }else{ break; } + gobble(in); + + } + }else if (format == "shared") { + while (in.eof() != true) { + + SharedList = new SharedListVector(in); + if (SharedList != NULL) { + thisLabel = SharedList->getLabel(); + //if you are at the last label + if (thisLabel == label) { in.close(); return SharedList->getSharedRAbundVector(); } + else { + //so you don't loose this memory + delete SharedList; + } + }else{ break; } + gobble(in); + + } + + } + } + + //this is created to signal to calling function that the input file is at eof + vector null; null.push_back(NULL); + in.close(); + return null; + + } + catch(exception& e) { + m->errorOut(e, "InputData", "getSharedRAbundVectors"); exit(1); - } + } } @@ -246,17 +501,115 @@ SAbundVector* InputData::getSAbundVector(){ return sabund; } else{ - return 0; + return NULL; } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "InputData", "getSAbundVector"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the InputData class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +/***********************************************************************/ +SAbundVector* InputData::getSAbundVector(string label){ + try { + + ifstream in; + string thisLabel; + openInputFile(filename, in); + + if(in){ + if (format == "list") { + + while (in.eof() != true) { + + input = new ListVector(in); + thisLabel = input->getLabel(); + + //if you are at the last label + if (thisLabel == label) { break; } + //so you don't loose this memory + else { delete input; } + gobble(in); + } + } + else if (format == "shared") { + + while (in.eof() != true) { + + input = new SharedListVector(in); + thisLabel = input->getLabel(); + + //if you are at the last label + if (thisLabel == label) { break; } + //so you don't loose this memory + else { delete input; } + gobble(in); + } + + } + else if(format == "rabund"){ + + while (in.eof() != true) { + + input = new RAbundVector(in); + thisLabel = input->getLabel(); + + //if you are at the last label + if (thisLabel == label) { break; } + //so you don't loose this memory + else { delete input; } + gobble(in); + } + + } + else if(format == "order"){ + + while (in.eof() != true) { + + input = new OrderVector(in); + thisLabel = input->getLabel(); + + //if you are at the last label + if (thisLabel == label) { break; } + //so you don't loose this memory + else { delete input; } + gobble(in); + } + + } + else if(format == "sabund"){ + + while (in.eof() != true) { + + input = new SAbundVector(in); + thisLabel = input->getLabel(); + + //if you are at the last label + if (thisLabel == label) { break; } + //so you don't loose this memory + else { delete input; } + gobble(in); + + } + + } + + in.close(); + + sabund = new SAbundVector(); + *sabund = (input->getSAbundVector()); + + return sabund; + + } + else{ + return NULL; + } + } + catch(exception& e) { + m->errorOut(e, "InputData", "getSAbundVector"); exit(1); - } + } } /***********************************************************************/ @@ -291,14 +644,112 @@ RAbundVector* InputData::getRAbundVector(){ } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "InputData", "getRAbundVector"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the InputData class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +/***********************************************************************/ +RAbundVector* InputData::getRAbundVector(string label){ + try { + + ifstream in; + string thisLabel; + openInputFile(filename, in); + + if(in){ + if (format == "list") { + + while (in.eof() != true) { + + input = new ListVector(in); + thisLabel = input->getLabel(); + + //if you are at the last label + if (thisLabel == label) { break; } + //so you don't loose this memory + else { delete input; } + gobble(in); + } + } + else if (format == "shared") { + + while (in.eof() != true) { + + input = new SharedListVector(in); + thisLabel = input->getLabel(); + + //if you are at the last label + if (thisLabel == label) { break; } + //so you don't loose this memory + else { delete input; } + gobble(in); + } + + } + else if(format == "rabund"){ + + while (in.eof() != true) { + + input = new RAbundVector(in); + thisLabel = input->getLabel(); + + //if you are at the last label + if (thisLabel == label) { break; } + //so you don't loose this memory + else { delete input; } + gobble(in); + } + + } + else if(format == "order"){ + + while (in.eof() != true) { + + input = new OrderVector(in); + thisLabel = input->getLabel(); + + //if you are at the last label + if (thisLabel == label) { break; } + //so you don't loose this memory + else { delete input; } + gobble(in); + } + + } + else if(format == "sabund"){ + + while (in.eof() != true) { + + input = new SAbundVector(in); + thisLabel = input->getLabel(); + + //if you are at the last label + if (thisLabel == label) { break; } + //so you don't loose this memory + else { delete input; } + gobble(in); + + } + + } + + in.close(); + + rabund = new RAbundVector(); + *rabund = (input->getRAbundVector()); + + return rabund; + } + else{ + return NULL; + } + } + catch(exception& e) { + m->errorOut(e, "InputData", "getRAbundVector"); exit(1); - } + } } + /***********************************************************************/