Package org.proteios.io

Interface Summary

ExtensionDisableInterface	This interface is used to retrieve the disabled flag for an extension.
FileTypeInterface	This interface is used to get the file type a class i working on
FileValidationInterface
HitInterface
IdentificationFileInterface	This file API should be used to read files that contain identification search results.
MascotParameterFileUtilInterface	This file API should be used to get input data from Mascot input files.
OMSSAParameterFileUtilInterface	This file API should be used to get input data from OMSSA input files.
PeakListFileInterface	This file API should be used to get spectra from peak list files.
PickFileInterface	This file API should be used to read files that contain pick list information.
RobotFileInterface	This file API should be used to read files that contain robot pick results.
SpectrumFileAnalyzerInterface	This interface defines methods to access instrument analyzer information obtained from spectrum files.
SpectrumFileContactInterface	This interface defines methods to access spectrum file contact information.
SpectrumFileContactReaderInterface	This interface defines methods to access contact information obtained from spectrum files.
SpectrumFileInstrumentInterface	This interface defines methods to access instrument information obtained from spectrum files.
SpectrumFileInstrumentReaderInterface	This interface defines methods to access instrument information obtained from spectrum files.
SpectrumIdReaderInterface	This API should be used to get a list of spectrum id values.
SpectrumInterface	This interface defines methods to access an array of mass or intensity values for mass spectrometry peak lists.
StringPairInterface	This interface defines methods to access a name/value pair of strings.
XMLCrudeWriter	This interface defines crude XML writing.
XMLCrudeWriter2	This interface defines crude XML writing, with some added convenience methods.
XMLCrudeWriter3	This interface defines crude XML writing, with some added convenience methods.
XTandemParameterFileUtilInterface	This file API should be used to get input data from XTandem input files.

Class Summary

AHit
Base64Util	This class supports conversion to/from Base64-coded data.
ColumnPreferences	This class represents column preferences.
FileExtraUtil
FilenameParseUtil	This class supports simple extraction of data from filenames.
MailUtil	This class contains utilities for sending notification e-mails.
MascotFileReader	All methods assume that the input stream is at the the begining.
MascotParameterFileUtil	This class implements the MascotParameterFileUtilInterface that defines methods to access input data from a Mascot input file.
MascotParameterSet	This file API should be used to get parameter data from Mascot input files.
MascotParameterSetOptionsUtil
MascotServerIO	This class handles mascot search_form.pl transformation for easy parsing.
MgfFileReader	This class contains methods to access spectra from an MGF peak list file.
MzMLFileReader	This class contains methods to access spectra from an mzML file.
NotificationConfiguration	This class represents a notification configuration.
OMSSAParameterFileUtil	This class implements the OMSSAParameterFileUtilInterface that defines methods to access input data from an OMSSA input file.
OMSSAParameterSet	This file API should be used to get parameter data from OMSSA input files.
OMSSAParameterSetOptionsUtil
PeakListFileImpl	This class implements the PeakListFileInterface that defines methods to access spectra from an mzData file.
PeakListFileValidationFactory
PiumsPepfilReader
PklFileReader	This class contains methods to access spectra from a PKL peak list file.
PrecursorSelectedIon	This class contains spectrum precursor selected ion information in a spectrum file.
RobotFileImpl	This class implements the RobotFileInterface that defines methods to retrieve data from a Spot Handling Workstation robot file.
RobotFileSpotXY	This class imports gel spot coordinates from a Spot Handling Workstation log file.
SpectrumFileAnalyzer	This contains methods to access instrument analyzer information obtained from spectrum files.
SpectrumFileContact	This class contains spectrum file contact information.
SpectrumFileInstrument	This class contains methods to access instrument information obtained from spectrum files.
SpectrumImpl	This class implements the SpectrumInterface that defines methods to access an array of mass or intensity values for mass spectrometry peak lists.
SpectrumPrecursor	This class contains spectrum precursor information.
StringPair	This class contains methods to access a name/value pair of strings.
TablePreferences	This class represents table preferences.
TablePreferencesConfiguration	This class represents a table preferences configuration.
Tag	Extend this class if you want your classnames to match the tags.
TagFactory	Extend this factory when you want to read an xml file and create a set of objects out of each tag.
TandemFactory	Useful when reading tandem xml files
TandemFileReader	Reads a tandem xml file
XMLCrudeWriter2Impl	This class supports crude XML writing, with some added convenience methods.
XMLCrudeWriter3Impl	This class supports crude XML writing, with some added convenience methods.
XMLCrudeWriterImpl	This class supports crude XML writing.
XMLExportUtil	This class supports writing of special XML blocks.
XMLImportUtil	This class supports simple extraction of data from XML tags.
XMLReaderUtil	Use this class to simplify lookup and positioning of an XMLStreamReader
XMLTag	Defines an xml tag that is readable using a XMLReader and TagFactory.
XMLValidator	This class validates XML input (file, input stream, or SourceStream) against an XSD (XML Schema Definition) file.
XMLValidatorErrorHandler	This class handles errors when validating an XML file against an XSD (XML Schema Definition) file.
XMLValidatorLazyErrorHandler	This class handles errors when validating an XML file against an XSD (XML Schema Definition) file.
XTandemParameterFileUtil	This class implements the XTandemParameterFileUtilInterface that defines methods to access input data from an XTandem input file.
XTandemParameterSet	This file API should be used to get parameter data from XTandem input files.
XTandemParameterSetOptionsUtil

Enum Summary

NotificationConfiguration.Mode	The notification mode.
SpectrumPrecursor.FragmentationType	Precursor fragmentation type enum.
TablePreferencesConfiguration.Mode	The table preferences mode.