public class MzXmlControllerImpl extends CachedDataAccessController
DataAccessController.ContentCategory, DataAccessController.Type
CHROMATOGRAM_TYPE, MZGRAPH_TYPE, SPECTRUM_TYPE
Constructor and Description |
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MzXmlControllerImpl(File file) |
Modifier and Type | Method and Description |
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void |
close()
Close data access controller by resetting the data reader first
|
ParamGroup |
getAdditional()
Get additional details, the mzXML is like mzML the Additional is the combination of FileContent
and StartTime.
|
Chromatogram |
getChromatogramById(Comparable id,
boolean useCache)
Get chromatogram using a chromatogram id, gives the option to choose whether to use cache.
|
List<DataProcessing> |
getDataProcessings()
Get a list of data processings by checking the cache first
|
ExperimentMetaData |
getExperimentMetaData()
The Experiment Metadata supported for MzXML is only the name of the files,
the type of the file, the instrument, the person contacts.
|
ParamGroup |
getFileContent()
This will be summarize the different parent file formats.
|
IdentificationMetaData |
getIdentificationMetaData()
The identification MetaData is not supported for mzXML files
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List<InstrumentConfiguration> |
getInstrumentConfigurations()
Get a list of instrument configurations.
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MzGraphMetaData |
getMzGraphMetaData()
Get the MzGraphMetaData support the dataProcessing Metadata, the Instrument Configuration
and do not contains scanSetting information for mzXML files.
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List<Person> |
getPersonContacts()
Get a list of person contacts
|
List<Software> |
getSoftwares()
The softwares on mzXml are annotated with their names, the type, and the execution
time processing the data.
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List<SourceFile> |
getSourceFiles()
Get a list of Source Files.
|
String |
getUid()
Get the unique id for this data access controller
It generates a MD5 hash using the absolute path of the file
This will guarantee the same id if the file path is the same
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MzXmlUnmarshallerAdaptor |
getUnmarshaller()
Get the backend data reader
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static boolean |
isValidFormat(File file)
Check a file is mzML file
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getAvailablePeptideLevelScores, getAvailableProteinLevelScores, getCache, getCachingStrategy, getChromatogramById, getChromatogramIds, getMode, getNumberOfFragmentIons, getNumberOfPeptides, getNumberOfPTMs, getNumberOfPTMs, getNumberOfSpectrumPeaks, getNumberOfUniquePeptides, getPeptideByIndex, getPeptideByIndex, getPeptideIds, getPeptidePrecursorCharge, getPeptidePrecursorMz, getPeptideQuantUnit, getPeptidesBySpectrum, getPeptideScore, getPeptideSequence, getPeptideSequenceEnd, getPeptideSequences, getPeptideSequenceStart, getPeptideSpectrumId, getProteinAccession, getProteinAccessionVersion, getProteinAmbiguityGroupById, getProteinAmbiguityGroupIds, getProteinById, getProteinIds, getProteinQuantUnit, getProteinScore, getProteinThreshold, getPTMs, getSearchDatabase, getSearchDatabaseVersion, getSearchEngineCvTermReferences, getSpectraDataBasedOnTitle, getSpectrumById, getSpectrumIdForPeptide, getSpectrumIds, getSpectrumMsLevel, getSpectrumPrecursorCharge, getSpectrumPrecursorIntensity, getSpectrumPrecursorMz, getSumOfIntensity, isSpectrumBasedOnTitle, populateCache, setCachingStrategy, setMode
getAvailableQuantPeptideLevelScores, getChromatogramByIndex, getChromatogramIndex, getContentCategories, getFragmentIons, getIsotopeLabellingQuantMethods, getLabelFreeQuantMethods, getName, getNumberOfChromatograms, getNumberOfIdentifiedSpectra, getNumberOfPeptides, getNumberOfPeptidesByRank, getNumberOfProteinAmbiguityGroups, getNumberOfProteins, getNumberOfQuantPeptides, getNumberOfQuantPeptides, getNumberOfQuantPTMs, getNumberOfQuantPTMs, getNumberOfReagents, getNumberOfSpectra, getNumberOfSubstitutionPTMs, getNumberOfSubstitutionPTMs, getNumberOfUniqueQuantPeptides, getPeptideEvidences, getPeptideIsotopeLabellingQuantMethods, getPeptideLabelFreeQuantMethods, getPeptideQuantData, getPeptideQuantStudyData, getPeptideRank, getPeptideTheoreticalMz, getProteinByIndex, getProteinCoverage, getProteinIsotopeLabellingQuantMethods, getProteinLabelFreeQuantMethods, getProteinQuantData, getProteinQuantStudyData, getProteinScores, getProteinSequence, getQuantMethods, getQuantPeptideByIndex, getQuantPeptideEvidences, getQuantPeptideIds, getQuantPeptideQuantScore, getQuantPeptideScore, getQuantPeptideSequence, getQuantPeptideSequences, getQuantPeptideSpectrumId, getQuantPTMs, getQuantSample, getReferenceSubSampleIndex, getSamples, getSource, getSpectraByIndex, getSpectrumIndex, getStudyVariables, getSubstitutionPTMs, getType, hasChromatogram, hasDecoyInformation, hasIsotopeLabellingQuantMethods, hasLabelFreeQuantMethods, hasMetaDataInformation, hasPeptide, hasPeptideQuantData, hasPeptideTotalIntensities, hasProtein, hasProteinAmbiguityGroup, hasProteinQuantData, hasProteinSequence, hasProteinTotalIntensities, hasQuantData, hasQuantPeptide, hasSpectrum, indexOfProtein, isIdentifiedSpectrum, proteinsAreInferred, setContentCategories, setInferredProteinGroups, setName, setSource, setType, setUid
public MzXmlControllerImpl(File file)
public MzXmlUnmarshallerAdaptor getUnmarshaller()
public String getUid()
getUid
in interface DataAccessController
getUid
in class AbstractDataAccessController
public List<Person> getPersonContacts()
public List<SourceFile> getSourceFiles()
public ParamGroup getFileContent()
public List<Software> getSoftwares()
public List<InstrumentConfiguration> getInstrumentConfigurations()
public List<DataProcessing> getDataProcessings()
public ParamGroup getAdditional()
getAdditional
in class AbstractDataAccessController
public Chromatogram getChromatogramById(Comparable id, boolean useCache)
getChromatogramById
in class CachedDataAccessController
id
- chromatogram iduseCache
- true means to use cachepublic void close()
close
in interface DataAccessController
close
in class CachedDataAccessController
public ExperimentMetaData getExperimentMetaData()
getExperimentMetaData
in interface MetaDataAccess
getExperimentMetaData
in class CachedDataAccessController
public MzGraphMetaData getMzGraphMetaData()
getMzGraphMetaData
in interface MetaDataAccess
getMzGraphMetaData
in class CachedDataAccessController
public IdentificationMetaData getIdentificationMetaData()
getIdentificationMetaData
in interface MetaDataAccess
getIdentificationMetaData
in class CachedDataAccessController
public static boolean isValidFormat(File file)
file
- input fileCopyright © 2015 European Bioinformatics Institute. All Rights Reserved.