C++ FileHandler::loadFeatures方法代码示例

本文整理汇总了C++中FileHandler::loadFeatures方法的典型用法代码示例。如果您正苦于以下问题：C++ FileHandler::loadFeatures方法的具体用法？C++ FileHandler::loadFeatures怎么用？C++ FileHandler::loadFeatures使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类FileHandler的用法示例。

在下文中一共展示了FileHandler::loadFeatures方法的3个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C++代码示例。

示例1: main_

  ExitCodes main_(int, const char**)
  {
    //-------------------------------------------------------------
    // parameter handling
    //-------------------------------------------------------------

    //input file names
    String in = getStringOption_("in");

    //input file type
    FileHandler fh;
    FileTypes::Type in_type = FileTypes::nameToType(getStringOption_("in_type"));

    if (in_type == FileTypes::UNKNOWN)
    {
      in_type = fh.getType(in);
      writeDebug_(String("Input file type: ") + FileTypes::typeToName(in_type), 2);
    }

    if (in_type == FileTypes::UNKNOWN)
    {
      writeLog_("Error: Could not determine input file type!");
      return PARSE_ERROR;
    }


    //output file names and types
    String out = getStringOption_("out");
    FileTypes::Type out_type = FileTypes::nameToType(getStringOption_("out_type"));

    if (out_type == FileTypes::UNKNOWN)
    {
      out_type = fh.getTypeByFileName(out);
    }

    if (out_type == FileTypes::UNKNOWN)
    {
      writeLog_("Error: Could not determine output file type!");
      return PARSE_ERROR;
    }

    bool TIC_DTA2D = getFlag_("TIC_DTA2D");

    writeDebug_(String("Output file type: ") + FileTypes::typeToName(out_type), 1);

    //-------------------------------------------------------------
    // reading input
    //-------------------------------------------------------------
    typedef MSExperiment<Peak1D> MSExperimentType;
    MSExperimentType exp;

    typedef MSExperimentType::SpectrumType SpectrumType;

    typedef FeatureMap<> FeatureMapType;

    FeatureMapType fm;
    ConsensusMap cm;

    writeDebug_(String("Loading input file"), 1);

    if (in_type == FileTypes::CONSENSUSXML)
    {
      ConsensusXMLFile().load(in, cm);
      cm.sortByPosition();
      if ((out_type != FileTypes::FEATUREXML) &&
          (out_type != FileTypes::CONSENSUSXML))
      {
        // You you will lose information and waste memory. Enough reasons to issue a warning!
        writeLog_("Warning: Converting consensus features to peaks. You will lose information!");
        exp.set2DData(cm);
      }
    }
    else if (in_type == FileTypes::EDTA)
    {
      EDTAFile().load(in, cm);
      cm.sortByPosition();
      if ((out_type != FileTypes::FEATUREXML) &&
          (out_type != FileTypes::CONSENSUSXML))
      {
        // You you will lose information and waste memory. Enough reasons to issue a warning!
        writeLog_("Warning: Converting consensus features to peaks. You will lose information!");
        exp.set2DData(cm);
      }
    }
    else if (in_type == FileTypes::FEATUREXML ||
             in_type == FileTypes::TSV ||
             in_type == FileTypes::PEPLIST ||
             in_type == FileTypes::KROENIK)
    {
      fh.loadFeatures(in, fm, in_type);
      fm.sortByPosition();
      if ((out_type != FileTypes::FEATUREXML) &&
          (out_type != FileTypes::CONSENSUSXML))
      {
        // You will lose information and waste memory. Enough reasons to issue a warning!
        writeLog_("Warning: Converting features to peaks. You will lose information! Mass traces are added, if present as 'num_of_masstraces' and 'masstrace_intensity_<X>' (X>=0) meta values.");
        exp.set2DData<true>(fm);
      }
    }
    else
//.........这里部分代码省略.........

开发者ID:BioITer，项目名称:OpenMS，代码行数:101，代码来源:FileConverter.C

示例2: getOptions

START_SECTION((const PeakFileOptions &getOptions() const))
FileHandler a;
TEST_EQUAL(a.getOptions().hasMSLevels(), false)
END_SECTION

START_SECTION((PeakFileOptions & getOptions()))
FileHandler a;
a.getOptions().addMSLevel(1);
TEST_EQUAL(a.getOptions().hasMSLevels(), true);
END_SECTION

START_SECTION((template <class FeatureType> bool loadFeatures(const String &filename, FeatureMap<FeatureType>&map, FileTypes::Type force_type = FileTypes::UNKNOWN)))
FileHandler tmp;
FeatureMap map;
TEST_EQUAL(tmp.loadFeatures("test.bla", map), false)
TEST_EQUAL(tmp.loadFeatures(OPENMS_GET_TEST_DATA_PATH("FeatureXMLFile_2_options.featureXML"), map), true)
TEST_EQUAL(map.size(), 7);
TEST_EQUAL(tmp.loadFeatures(OPENMS_GET_TEST_DATA_PATH("FeatureXMLFile_2_options.featureXML"), map), true)
TEST_EQUAL(map.size(), 7);
END_SECTION

START_SECTION((template <class PeakType> void storeExperiment(const String &filename, const MSExperiment<PeakType>&exp, ProgressLogger::LogType log = ProgressLogger::NONE)))
FileHandler fh;
PeakMap exp;
fh.loadExperiment(OPENMS_GET_TEST_DATA_PATH("MzMLFile_1.mzML"), exp);

//test mzML
String filename;
NEW_TMP_FILE(filename)
fh.storeExperiment(filename, exp);

开发者ID:burlab，项目名称:OpenMS，代码行数:30，代码来源:FileHandler_test.cpp

示例3: main_

  ExitCodes main_(int, const char**)
  {
    //-------------------------------------------------------------
    // parameter handling
    //-------------------------------------------------------------

    //input file names
    String in = getStringOption_("in");
    bool write_mzML_index = getFlag_("write_mzML_index");

    //input file type
    FileHandler fh;
    FileTypes::Type in_type = FileTypes::nameToType(getStringOption_("in_type"));

    if (in_type == FileTypes::UNKNOWN)
    {
      in_type = fh.getType(in);
      writeDebug_(String("Input file type: ") + FileTypes::typeToName(in_type), 2);
    }

    if (in_type == FileTypes::UNKNOWN)
    {
      writeLog_("Error: Could not determine input file type!");
      return PARSE_ERROR;
    }


    //output file names and types
    String out = getStringOption_("out");
    FileTypes::Type out_type = FileTypes::nameToType(getStringOption_("out_type"));

    if (out_type == FileTypes::UNKNOWN)
    {
      out_type = fh.getTypeByFileName(out);
    }

    if (out_type == FileTypes::UNKNOWN)
    {
      writeLog_("Error: Could not determine output file type!");
      return PARSE_ERROR;
    }

    bool TIC_DTA2D = getFlag_("TIC_DTA2D");
    bool process_lowmemory = getFlag_("process_lowmemory");

    writeDebug_(String("Output file type: ") + FileTypes::typeToName(out_type), 1);

    String uid_postprocessing = getStringOption_("UID_postprocessing");
    //-------------------------------------------------------------
    // reading input
    //-------------------------------------------------------------
    typedef MSExperiment<Peak1D> MSExperimentType;
    MSExperimentType exp;

    typedef MSExperimentType::SpectrumType SpectrumType;

    typedef FeatureMap FeatureMapType;

    FeatureMapType fm;
    ConsensusMap cm;

    writeDebug_(String("Loading input file"), 1);

    if (in_type == FileTypes::CONSENSUSXML)
    {
      ConsensusXMLFile().load(in, cm);
      cm.sortByPosition();
      if ((out_type != FileTypes::FEATUREXML) &&
          (out_type != FileTypes::CONSENSUSXML))
      {
        // You you will lose information and waste memory. Enough reasons to issue a warning!
        writeLog_("Warning: Converting consensus features to peaks. You will lose information!");
        exp.set2DData(cm);
      }
    }
    else if (in_type == FileTypes::EDTA)
    {
      EDTAFile().load(in, cm);
      cm.sortByPosition();
      if ((out_type != FileTypes::FEATUREXML) &&
          (out_type != FileTypes::CONSENSUSXML))
      {
        // You you will lose information and waste memory. Enough reasons to issue a warning!
        writeLog_("Warning: Converting consensus features to peaks. You will lose information!");
        exp.set2DData(cm);
      }
    }
    else if (in_type == FileTypes::FEATUREXML ||
             in_type == FileTypes::TSV ||
             in_type == FileTypes::PEPLIST ||
             in_type == FileTypes::KROENIK)
    {
      fh.loadFeatures(in, fm, in_type);
      fm.sortByPosition();
      if ((out_type != FileTypes::FEATUREXML) &&
          (out_type != FileTypes::CONSENSUSXML))
      {
        // You will lose information and waste memory. Enough reasons to issue a warning!
        writeLog_("Warning: Converting features to peaks. You will lose information! Mass traces are added, if present as 'num_of_masstraces' and 'masstrace_intensity_<X>' (X>=0) meta values.");
        exp.set2DData<true>(fm);
//.........这里部分代码省略.........

开发者ID:BioinformaticsArchive，项目名称:OpenMS，代码行数:101，代码来源:FileConverter.cpp

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