X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=fileoutput.cpp;h=a4a68a8ef25a66ca52052faf8a1e8e6221bec4af;hp=597a05a6ad9a892caff5f0b6f69269ae6af4013d;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=5a9f3cce3e2e053c249e3e97507ce180f0854d76 diff --git a/fileoutput.cpp b/fileoutput.cpp index 597a05a..a4a68a8 100644 --- a/fileoutput.cpp +++ b/fileoutput.cpp @@ -15,7 +15,7 @@ ThreeColumnFile::~ThreeColumnFile(){ inFile.close(); outFile.close(); - remove(outName.c_str()); + m->mothurRemove(outName); } /***********************************************************************/ @@ -23,16 +23,16 @@ ThreeColumnFile::~ThreeColumnFile(){ void ThreeColumnFile::initFile(string label){ try { if(counter != 0){ - openOutputFile(outName, outFile); - openInputFile(inName, inFile); + m->openOutputFile(outName, outFile); + m->openInputFile(inName, inFile); string inputBuffer; - inputBuffer = getline(inFile); + inputBuffer = m->getline(inFile); outFile << inputBuffer << '\t' << label << "\tlci\thci" << endl; } else{ - openOutputFile(outName, outFile); + m->openOutputFile(outName, outFile); outFile << "numsampled\t" << label << "\tlci\thci" << endl; } @@ -40,7 +40,7 @@ void ThreeColumnFile::initFile(string label){ outFile.setf(ios::showpoint); } catch(exception& e) { - errorOut(e, "ThreeColumnFile", "initFile"); + m->errorOut(e, "ThreeColumnFile", "initFile"); exit(1); } } @@ -51,7 +51,7 @@ void ThreeColumnFile::output(int nSeqs, vector data){ try { if(counter != 0){ string inputBuffer; - inputBuffer = getline(inFile); + inputBuffer = m->getline(inFile); outFile << inputBuffer << setprecision(4) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl; } @@ -60,7 +60,7 @@ void ThreeColumnFile::output(int nSeqs, vector data){ } } catch(exception& e) { - errorOut(e, "ThreeColumnFile", "output"); + m->errorOut(e, "ThreeColumnFile", "output"); exit(1); } } @@ -78,15 +78,19 @@ void ThreeColumnFile::resetFile(){ } counter = 1; - remove(inName.c_str()); + m->mothurRemove(inName); renameOk = rename(outName.c_str(), inName.c_str()); + //renameFile(outName, inName); + //checks to make sure user was able to rename and remove successfully - if ((renameOk != 0)) { mothurOut("Unable to rename necessary files."); mothurOutEndLine(); } - + if ((renameOk != 0)) { + m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine(); + perror(" : "); + } } catch(exception& e) { - errorOut(e, "ThreeColumnFile", "resetFile"); + m->errorOut(e, "ThreeColumnFile", "resetFile"); exit(1); } } @@ -98,7 +102,7 @@ ColumnFile::~ColumnFile(){ inFile.close(); outFile.close(); - remove(outName.c_str()); + m->mothurRemove(outName); } /***********************************************************************/ @@ -106,11 +110,11 @@ ColumnFile::~ColumnFile(){ void ColumnFile::initFile(string label, vector tags){ try { if(counter != 0){ - openOutputFile(outName, outFile); - openInputFile(inName, inFile); + m->openOutputFile(outName, outFile); + m->openInputFile(inName, inFile); string inputBuffer; - inputBuffer = getline(inFile); + inputBuffer = m->getline(inFile); outFile << inputBuffer << '\t'; for(int i = 0; i < tags.size(); i++) { @@ -119,7 +123,7 @@ void ColumnFile::initFile(string label, vector tags){ outFile << endl; } else{ - openOutputFile(outName, outFile); + m->openOutputFile(outName, outFile); for(int i = 0; i < tags.size(); i++) { outFile << label + tags[i] << '\t'; } @@ -130,7 +134,7 @@ void ColumnFile::initFile(string label, vector tags){ outFile.setf(ios::showpoint); } catch(exception& e) { - errorOut(e, "ColumnFile", "initFile"); + m->errorOut(e, "ColumnFile", "initFile"); exit(1); } } @@ -142,7 +146,7 @@ void ColumnFile::output(vector data){ if(counter != 0){ string inputBuffer; - inputBuffer = getline(inFile); + inputBuffer = m->getline(inFile); outFile << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(iters.length()); for (int i = 1; i< data.size(); i++) { @@ -160,7 +164,7 @@ void ColumnFile::output(vector data){ } catch(exception& e) { - errorOut(e, "ColumnFile", "output"); + m->errorOut(e, "ColumnFile", "output"); exit(1); } } @@ -178,15 +182,19 @@ void ColumnFile::resetFile(){ } counter = 1; - remove(inName.c_str()); + m->mothurRemove(inName); renameOk = rename(outName.c_str(), inName.c_str()); + //renameFile(outName, inName); + //checks to make sure user was able to rename and remove successfully - if ((renameOk != 0)) { mothurOut("Unable to rename necessary files."); mothurOutEndLine(); } - + if ((renameOk != 0)) { + m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine(); + perror(" : "); + } } catch(exception& e) { - errorOut(e, "ColumnFile", "resetFile"); + m->errorOut(e, "ColumnFile", "resetFile"); exit(1); } } @@ -198,7 +206,7 @@ SharedThreeColumnFile::~SharedThreeColumnFile(){ inFile.close(); outFile.close(); - remove(outName.c_str()); + m->mothurRemove(outName); } /***********************************************************************/ @@ -206,16 +214,16 @@ SharedThreeColumnFile::~SharedThreeColumnFile(){ void SharedThreeColumnFile::initFile(string label){ try { if(counter != 0){ - openOutputFile(outName, outFile); - openInputFile(inName, inFile); + m->openOutputFile(outName, outFile); + m->openInputFile(inName, inFile); string inputBuffer; - inputBuffer = getline(inFile); + inputBuffer = m->getline(inFile); outFile << inputBuffer << '\t' << label << "\tlci\thci" << endl; } else{ - openOutputFile(outName, outFile); + m->openOutputFile(outName, outFile); outFile << "numsampled\t" << groupLabel << '\t' << label << "\tlci\thci" << endl; } @@ -223,7 +231,7 @@ void SharedThreeColumnFile::initFile(string label){ outFile.setf(ios::showpoint); } catch(exception& e) { - errorOut(e, "SharedThreeColumnFile", "initFile"); + m->errorOut(e, "SharedThreeColumnFile", "initFile"); exit(1); } } @@ -234,7 +242,7 @@ void SharedThreeColumnFile::output(int nSeqs, vector data){ try { if(counter != 0){ string inputBuffer; - inputBuffer = getline(inFile); + inputBuffer = m->getline(inFile); outFile << inputBuffer << setprecision(4) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl; } @@ -244,7 +252,7 @@ void SharedThreeColumnFile::output(int nSeqs, vector data){ } } catch(exception& e) { - errorOut(e, "SharedThreeColumnFile", "output"); + m->errorOut(e, "SharedThreeColumnFile", "output"); exit(1); } } @@ -261,15 +269,20 @@ void SharedThreeColumnFile::resetFile(){ outFile.close(); } counter = 1; - remove(inName.c_str()); + + m->mothurRemove(inName); renameOk = rename(outName.c_str(), inName.c_str()); + //renameFile(outName, inName); + //checks to make sure user was able to rename and remove successfully - if ((renameOk != 0)) { mothurOut("Unable to rename necessary files."); mothurOutEndLine(); } - + if ((renameOk != 0)) { + m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine(); + perror(" : "); + } } catch(exception& e) { - errorOut(e, "SharedThreeColumnFile", "resetFile"); + m->errorOut(e, "SharedThreeColumnFile", "resetFile"); exit(1); } } @@ -282,7 +295,7 @@ OneColumnFile::~OneColumnFile(){ inFile.close(); outFile.close(); - remove(outName.c_str()); + m->mothurRemove(outName); } /***********************************************************************/ @@ -290,24 +303,24 @@ OneColumnFile::~OneColumnFile(){ void OneColumnFile::initFile(string label){ try { if(counter != 0){ - openOutputFile(outName, outFile); - openInputFile(inName, inFile); + m->openOutputFile(outName, outFile); + m->openInputFile(inName, inFile); string inputBuffer; - inputBuffer = getline(inFile); + inputBuffer = m->getline(inFile); outFile << inputBuffer << '\t' << label << endl; } else{ - openOutputFile(outName, outFile); - outFile << "numsequences\t" << label << endl; + m->openOutputFile(outName, outFile); + outFile << "numsampled\t" << label << endl; } outFile.setf(ios::fixed, ios::floatfield); outFile.setf(ios::showpoint); } catch(exception& e) { - errorOut(e, "OneColumnFile", "initFile"); + m->errorOut(e, "OneColumnFile", "initFile"); exit(1); } } @@ -318,7 +331,7 @@ void OneColumnFile::output(int nSeqs, vector data){ try { if(counter != 0){ string inputBuffer; - inputBuffer = getline(inFile); + inputBuffer = m->getline(inFile); outFile << inputBuffer << setprecision(4) << '\t' << data[0] << endl; } @@ -327,7 +340,7 @@ void OneColumnFile::output(int nSeqs, vector data){ } } catch(exception& e) { - errorOut(e, "OneColumnFile", "output"); + m->errorOut(e, "OneColumnFile", "output"); exit(1); } } @@ -339,20 +352,25 @@ void OneColumnFile::resetFile(){ if(counter != 0){ outFile.close(); inFile.close(); - } - else{ + }else{ outFile.close(); } counter = 1; - remove(inName.c_str()); + + m->mothurRemove(inName); renameOk = rename(outName.c_str(), inName.c_str()); + //renameFile(outName, inName); + //checks to make sure user was able to rename and remove successfully - if ((renameOk != 0)) { mothurOut("Unable to rename necessary files."); mothurOutEndLine(); } + if ((renameOk != 0)) { + m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine(); + perror(" : "); + } } catch(exception& e) { - errorOut(e, "OneColumnFile", "resetFile"); + m->errorOut(e, "OneColumnFile", "resetFile"); exit(1); } } @@ -364,7 +382,7 @@ SharedOneColumnFile::~SharedOneColumnFile(){ inFile.close(); outFile.close(); - remove(outName.c_str()); + m->mothurRemove(outName); } /***********************************************************************/ @@ -372,17 +390,17 @@ SharedOneColumnFile::~SharedOneColumnFile(){ void SharedOneColumnFile::initFile(string label){ try { if(counter != 0){ - openOutputFile(outName, outFile); - openInputFile(inName, inFile); + m->openOutputFile(outName, outFile); + m->openInputFile(inName, inFile); string inputBuffer; - inputBuffer = getline(inFile); + inputBuffer = m->getline(inFile); outFile << inputBuffer << '\t' << label << endl; } else{ - openOutputFile(outName, outFile); + m->openOutputFile(outName, outFile); outFile << "sampled\t" << label << endl; } @@ -391,7 +409,7 @@ void SharedOneColumnFile::initFile(string label){ outFile.setf(ios::showpoint); } catch(exception& e) { - errorOut(e, "SharedOneColumnFile", "initFile"); + m->errorOut(e, "SharedOneColumnFile", "initFile"); exit(1); } } @@ -409,7 +427,7 @@ void SharedOneColumnFile::output(int nSeqs, vector data){ } if(counter != 0){ string inputBuffer; - inputBuffer = getline(inFile); + inputBuffer = m->getline(inFile); outFile << inputBuffer << setprecision(2) << '\t' << dataOutput << endl; } @@ -418,7 +436,7 @@ void SharedOneColumnFile::output(int nSeqs, vector data){ } } catch(exception& e) { - errorOut(e, "SharedOneColumnFile", "output"); + m->errorOut(e, "SharedOneColumnFile", "output"); exit(1); } } @@ -435,17 +453,20 @@ void SharedOneColumnFile::resetFile(){ outFile.close(); } counter = 1; - - remove(inName.c_str()); + + m->mothurRemove(inName); renameOk = rename(outName.c_str(), inName.c_str()); - //checks to make sure user was able to rename and remove successfully - if ((renameOk != 0)) { mothurOut("Unable to rename necessary files."); mothurOutEndLine(); } - + //renameFile(outName, inName); + //checks to make sure user was able to rename and remove successfully + if ((renameOk != 0)) { + m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine(); + perror(" : "); + } } catch(exception& e) { - errorOut(e, "SharedOneColumnFile", "resetFile"); + m->errorOut(e, "SharedOneColumnFile", "resetFile"); exit(1); } }