X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=inputdata.cpp;h=8b1829a3db697df21b3d0f64bf6be6cfea15c536;hp=592367a5fbf0c07f0587a577551654173eb5e15a;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=f18d75f9c996cb619a5051a7664620c0c5ae05fb diff --git a/inputdata.cpp b/inputdata.cpp index 592367a..8b1829a 100644 --- a/inputdata.cpp +++ b/inputdata.cpp @@ -10,32 +10,30 @@ #include "inputdata.h" #include "ordervector.hpp" #include "listvector.hpp" -#include "utilities.hpp" +#include "rabundvector.hpp" /***********************************************************************/ InputData::InputData(string fName, string f) : format(f){ - - openInputFile(fName, fileHandle); - + m = MothurOut::getInstance(); + m->openInputFile(fName, fileHandle); + filename = fName; + m->saveNextLabel = ""; } - /***********************************************************************/ - InputData::~InputData(){ - -// delete output; - + fileHandle.close(); + m->saveNextLabel = ""; } /***********************************************************************/ InputData::InputData(string fName, string orderFileName, string f) : format(f){ try { - + m = MothurOut::getInstance(); ifstream ofHandle; - openInputFile(orderFileName, ofHandle); + m->openInputFile(orderFileName, ofHandle); string name; int count = 0; @@ -44,45 +42,110 @@ InputData::InputData(string fName, string orderFileName, string f) : format(f){ ofHandle >> name; orderMap[name] = count; count++; - gobble(ofHandle); + m->gobble(ofHandle); } ofHandle.close(); - openInputFile(fName, fileHandle); + m->openInputFile(fName, fileHandle); + m->saveNextLabel = ""; + } 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); - } } /***********************************************************************/ ListVector* InputData::getListVector(){ try { - if(fileHandle){ + if(!fileHandle.eof()){ if(format == "list") { list = new ListVector(fileHandle); - } + }else{ list = NULL; } - gobble(fileHandle); + m->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; + m->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; } + m->gobble(in); + } + }else{ list = NULL; } + + in.close(); + return list; + } + else{ + return NULL; + } + } + catch(exception& e) { + m->errorOut(e, "InputData", "getListVector"); + exit(1); + } +} +/***********************************************************************/ +ListVector* InputData::getListVector(string label, bool resetFP){ + try { + string thisLabel; + fileHandle.clear(); + fileHandle.seekg(0); + + if(fileHandle){ + + if (format == "list") { + + while (fileHandle.eof() != true) { + + list = new ListVector(fileHandle); m->gobble(fileHandle); + thisLabel = list->getLabel(); + + //if you are at the last label + if (thisLabel == label) { break; } + //so you don't loose this memory + else { delete list; } + } + }else{ list = NULL; } + + return list; + } + else{ + return NULL; + } + } + catch(exception& e) { + m->errorOut(e, "InputData", "getListVector"); exit(1); - } + } } /***********************************************************************/ @@ -92,25 +155,61 @@ SharedListVector* InputData::getSharedListVector(){ if(fileHandle){ if (format == "shared") { SharedList = new SharedListVector(fileHandle); - } + }else{ SharedList = NULL; } - gobble(fileHandle); + m->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; + m->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; } + m->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 +217,58 @@ SharedOrderVector* InputData::getSharedOrderVector(){ if(fileHandle){ if (format == "sharedfile") { SharedOrder = new SharedOrderVector(fileHandle); - } + }else{ SharedOrder = NULL; } - gobble(fileHandle); + m->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; + m->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; } + m->gobble(in); + } + + }else{ SharedOrder = NULL; } + + in.close(); + return SharedOrder; + + }else{ + return NULL; + } + } + catch(exception& e) { + m->errorOut(e, "InputData", "getSharedOrderVector"); exit(1); - } + } } @@ -144,7 +278,7 @@ 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") { @@ -159,30 +293,317 @@ OrderVector* InputData::getOrderVector(){ else if(format == "sabund"){ input = new SAbundVector(fileHandle); } - else if(format == "listorder"){ - input = new ListVector(fileHandle); - } + + m->gobble(fileHandle); + + output = new OrderVector(); + *output = (input->getOrderVector()); - gobble(fileHandle); + 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; + m->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; } + m->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; } + m->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; } + m->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; } + m->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; } + m->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"; +} + +/***********************************************************************/ +//this is used when you don't need the order vector +vector InputData::getSharedRAbundVectors(){ + try { + if(fileHandle){ + if (format == "sharedfile") { + SharedRAbundVector* SharedRAbund = new SharedRAbundVector(fileHandle); + if (SharedRAbund != NULL) { + return SharedRAbund->getSharedRAbundVectors(); + } + }else if (format == "shared") { + SharedList = new SharedListVector(fileHandle); + + if (SharedList != NULL) { + return SharedList->getSharedRAbundVector(); + } + } + m->gobble(fileHandle); + } + + //this is created to signal to calling function that the input file is at eof + vector null; null.push_back(NULL); + return null; + + } + catch(exception& e) { + m->errorOut(e, "InputData", "getSharedRAbundVectors"); exit(1); - } + } +} +/***********************************************************************/ +vector InputData::getSharedRAbundVectors(string label){ + try { + ifstream in; + string thisLabel; + + m->openInputFile(filename, in); + m->saveNextLabel = ""; + + 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; } + m->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; } + m->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); + } } +/***********************************************************************/ +//this is used when you don't need the order vector +vector InputData::getSharedRAbundFloatVectors(){ + try { + if(fileHandle){ + if (format == "relabund") { + SharedRAbundFloatVector* SharedRelAbund = new SharedRAbundFloatVector(fileHandle); + if (SharedRelAbund != NULL) { + return SharedRelAbund->getSharedRAbundFloatVectors(); + } + }else if (format == "sharedfile") { + SharedRAbundVector* SharedRAbund = new SharedRAbundVector(fileHandle); + if (SharedRAbund != NULL) { + vector lookup = SharedRAbund->getSharedRAbundVectors(); + vector lookupFloat = SharedRAbund->getSharedRAbundFloatVectors(lookup); + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup.clear(); + return lookupFloat; + } + + } + m->gobble(fileHandle); + } + + //this is created to signal to calling function that the input file is at eof + vector null; null.push_back(NULL); + return null; + + } + catch(exception& e) { + m->errorOut(e, "InputData", "getSharedRAbundFloatVectors"); + exit(1); + } +} +/***********************************************************************/ +vector InputData::getSharedRAbundFloatVectors(string label){ + try { + ifstream in; + string thisLabel; + + m->openInputFile(filename, in); + m->saveNextLabel = ""; + + if(in){ + if (format == "relabund") { + while (in.eof() != true) { + + SharedRAbundFloatVector* SharedRelAbund = new SharedRAbundFloatVector(in); + if (SharedRelAbund != NULL) { + thisLabel = SharedRelAbund->getLabel(); + //if you are at the last label + if (thisLabel == label) { in.close(); return SharedRelAbund->getSharedRAbundFloatVectors(); } + else { + //so you don't loose this memory + vector lookup = SharedRelAbund->getSharedRAbundFloatVectors(); + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + delete SharedRelAbund; + } + }else{ break; } + m->gobble(in); + } + }else 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(); + vector lookup = SharedRAbund->getSharedRAbundVectors(); + vector lookupFloat = SharedRAbund->getSharedRAbundFloatVectors(lookup); + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup.clear(); + return lookupFloat; + }else { + //so you don't loose this memory + vector lookup = SharedRAbund->getSharedRAbundVectors(); + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup.clear(); + delete SharedRAbund; + } + }else{ break; } + m->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", "getSharedRAbundFloatVectors"); + exit(1); + } +} /***********************************************************************/ SAbundVector* InputData::getSAbundVector(){ @@ -202,27 +623,266 @@ SAbundVector* InputData::getSAbundVector(){ } else if(format == "sabund"){ input = new SAbundVector(fileHandle); + } + m->gobble(fileHandle); + + sabund = new SAbundVector(); + *sabund = (input->getSAbundVector()); + + return sabund; + } + else{ + return NULL; + } + } + catch(exception& e) { + m->errorOut(e, "InputData", "getSAbundVector"); + exit(1); + } +} +/***********************************************************************/ +SAbundVector* InputData::getSAbundVector(string label){ + try { + + ifstream in; + string thisLabel; + m->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; } + m->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; } + m->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; } + m->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; } + m->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; } + m->gobble(in); - gobble(fileHandle); + } + + } + + in.close(); sabund = new SAbundVector(); *sabund = (input->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"; +} + +/***********************************************************************/ +RAbundVector* InputData::getRAbundVector(){ + try { + if(fileHandle){ + if (format == "list") { + input = new ListVector(fileHandle); + } + else if (format == "shared") { + input = new SharedListVector(fileHandle); + } + else if(format == "rabund"){ + input = new RAbundVector(fileHandle); + } + else if(format == "order"){ + input = new OrderVector(fileHandle); + } + else if(format == "sabund"){ + input = new SAbundVector(fileHandle); + } + + m->gobble(fileHandle); + + rabund = new RAbundVector(); + *rabund = (input->getRAbundVector()); + + return rabund; + } + else{ + return NULL; + } + } + catch(exception& e) { + m->errorOut(e, "InputData", "getRAbundVector"); exit(1); - } + } +} +/***********************************************************************/ +RAbundVector* InputData::getRAbundVector(string label){ + try { + + ifstream in; + string thisLabel; + m->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; } + m->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; } + m->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; } + m->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; } + m->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; } + m->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); + } } /***********************************************************************/ + + +