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Hierarchy For All Packages
Package Hierarchies:
umich.ms.datatypes
,
umich.ms.datatypes.index
,
umich.ms.datatypes.index.impl
,
umich.ms.datatypes.lcmsrun
,
umich.ms.datatypes.scan
,
umich.ms.datatypes.scan.impl
,
umich.ms.datatypes.scan.props
,
umich.ms.datatypes.scancollection
,
umich.ms.datatypes.scancollection.impl
,
umich.ms.datatypes.spectrum
,
umich.ms.datatypes.spectrum.impl
,
umich.ms.external
,
umich.ms.external.apache.cassandra.io
,
umich.ms.external.msnumpress
,
umich.ms.fileio
,
umich.ms.fileio.chunk
,
umich.ms.fileio.exceptions
,
umich.ms.fileio.filetypes
,
umich.ms.fileio.filetypes.agilent.cef
,
umich.ms.fileio.filetypes.agilent.cef.example
,
umich.ms.fileio.filetypes.gpmdb
,
umich.ms.fileio.filetypes.mzidentml
,
umich.ms.fileio.filetypes.mzidentml.example
,
umich.ms.fileio.filetypes.mzml
,
umich.ms.fileio.filetypes.mzml.util
,
umich.ms.fileio.filetypes.mzxml
,
umich.ms.fileio.filetypes.mzxml.example
,
umich.ms.fileio.filetypes.pepxml
,
umich.ms.fileio.filetypes.pepxml.example
,
umich.ms.fileio.filetypes.protxml
,
umich.ms.fileio.filetypes.protxml.example
,
umich.ms.fileio.filetypes.thermo.raw
,
umich.ms.fileio.filetypes.thermo.raw.test
,
umich.ms.fileio.filetypes.xmlbased
,
umich.ms.logging
,
umich.ms.msfiletoolbox
,
umich.ms.util
,
umich.ms.util.base64
,
umich.ms.util.file
,
umich.ms.util.xml
Class Hierarchy
java.lang.
Object
umich.ms.util.file.
AbstractFile
(implements java.io.
Closeable
)
umich.ms.fileio.filetypes.
AbstractLCMSDataSource
<T> (implements umich.ms.fileio.filetypes.
LCMSDataSource
<T>, java.io.
Serializable
)
umich.ms.fileio.filetypes.xmlbased.
AbstractXMLBasedDataSource
<E,I>
umich.ms.fileio.filetypes.mzml.
MZMLFile
umich.ms.fileio.filetypes.mzxml.
MZXMLFile
umich.ms.fileio.filetypes.thermo.raw.
ThermoRawFile
umich.ms.fileio.filetypes.gpmdb.
GPMDBFile
umich.ms.datatypes.scan.
AbstractScan
(implements umich.ms.datatypes.scan.
IScan
)
umich.ms.datatypes.scan.impl.
ScanDefault
umich.ms.datatypes.spectrum.
AbstractSpectrum
(implements umich.ms.datatypes.spectrum.
ISpectrum
, java.io.
Serializable
)
umich.ms.datatypes.spectrum.impl.
SpectrumDefault
(implements java.io.
Serializable
)
umich.ms.datatypes.scan.props.
ActivationInfo
umich.ms.fileio.filetypes.agilent.cef.example.
AgilentCefFile
umich.ms.fileio.filetypes.agilent.cef.example.
AgilentCefTest
umich.ms.fileio.filetypes.agilent.cef.example.
AgilentCompound
umich.ms.fileio.filetypes.agilent.cef.example.
AgilentCompounds
umich.ms.fileio.filetypes.agilent.cef.example.
AgilentMSPeak
(implements java.lang.
Comparable
<T>)
umich.ms.util.base64.
Base64
umich.ms.util.base64.
Base64Context
umich.ms.util.base64.
Base64ContextPooled
umich.ms.util.base64.
Base64Slow
org.apache.commons.pool2.BasePooledObjectFactory<T> (implements org.apache.commons.pool2.PooledObjectFactory<T>)
umich.ms.util.
ByteArrayHolderFactory
umich.ms.fileio.filetypes.xmlbased.
XMLStreamReaderFactory
umich.ms.fileio.chunk.
ChunkedFile
(implements umich.ms.fileio.chunk.
FileChunkSource
)
umich.ms.fileio.filetypes.mzml.util.
CvAttrs
umich.ms.fileio.filetypes.mzml.util.
CVTerm
umich.ms.fileio.filetypes.mzml.util.
ActivationCVTerm
umich.ms.fileio.filetypes.mzml.util.
InstrumentModelCVTerm
umich.ms.fileio.filetypes.mzxml.example.
Example
umich.ms.fileio.filetypes.mzxml.example.
Example2
umich.ms.fileio.filetypes.mzxml.example.
Example3
umich.ms.fileio.filetypes.mzxml.example.
Example4
umich.ms.fileio.chunk.
FileChunk
umich.ms.util.file.
FileListing
umich.ms.fileio.filetypes.gpmdb.
GPMDBParser
umich.ms.datatypes.lcmsrun.
Hash
umich.ms.fileio.filetypes.xmlbased.
IndexBuilder.Info
umich.ms.fileio.filetypes.xmlbased.
IndexBuilder.Result
<T>
umich.ms.datatypes.index.impl.
IndexDefault
<T> (implements umich.ms.datatypes.index.
Index
<T>)
umich.ms.fileio.filetypes.mzml.
MZMLIndex
umich.ms.fileio.filetypes.mzxml.
MZXMLIndex
umich.ms.fileio.filetypes.thermo.raw.
ThermoRawIndex
umich.ms.datatypes.index.impl.
IndexElementDefault
(implements umich.ms.datatypes.index.
IndexElement
)
umich.ms.fileio.filetypes.xmlbased.
AbstractXMLBasedIndexElement
(implements umich.ms.fileio.filetypes.xmlbased.
XMLBasedIndexElement
)
umich.ms.fileio.filetypes.mzml.
MZMLIndexElement
umich.ms.fileio.filetypes.mzxml.
MZXMLIndexElement
umich.ms.fileio.filetypes.thermo.raw.
ThermoRawIndexElement
umich.ms.datatypes.scan.props.
InjectionInfo
java.io.
InputStream
(implements java.io.
Closeable
)
umich.ms.util.
ReverseLineInputStream
umich.ms.datatypes.scan.props.
Instrument
(implements java.io.
Serializable
)
umich.ms.util.
Interval1D
<V> (implements java.lang.
Comparable
<T>)
umich.ms.util.
DoubleRange
umich.ms.util.
IntervalST
<K,V> (implements java.lang.
Iterable
<T>)
umich.ms.util.
IntervalST.Node
<U,W>
umich.ms.fileio.filetypes.agilent.cef.example.
IonId
umich.ms.datatypes.
LCMSData
(implements java.io.
Serializable
)
umich.ms.fileio.filetypes.
LCMSDataSourceFactory
umich.ms.datatypes.
LCMSDataSubset
(implements java.io.
Serializable
)
umich.ms.datatypes.
LCMSRange
(implements java.io.
Serializable
)
umich.ms.datatypes.
LCMSRangeSet
(implements java.io.
Serializable
)
umich.ms.datatypes.
LCMSRangeSet.MsLevelRangeSet
umich.ms.datatypes.lcmsrun.
LCMSRunInfo
(implements java.io.
Serializable
)
umich.ms.fileio.filetypes.mzml.
MZMLRunInfo
umich.ms.logging.
LogHelper
umich.ms.util.
MathHelper
umich.ms.msfiletoolbox.
MsftbxInfo
umich.ms.external.msnumpress.
MSNumpress
umich.ms.datatypes.lcmsrun.
MsSoftware
umich.ms.fileio.filetypes.xmlbased.
MultiSpectraParser
(implements java.util.concurrent.
Callable
<V>)
umich.ms.fileio.filetypes.mzml.
MZMLMultiSpectraParser
umich.ms.fileio.filetypes.mzxml.
MZXMLMultiSpectraParser
umich.ms.fileio.filetypes.mzidentml.example.
MzIdentMlExample
umich.ms.fileio.filetypes.mzidentml.
MzIdentMLParser
umich.ms.fileio.filetypes.mzidentml.example.
MzIdentMlReadWriteExample
umich.ms.fileio.filetypes.mzml.
MZMLIndexBuilder
(implements umich.ms.fileio.filetypes.xmlbased.
IndexBuilder
<T>)
umich.ms.fileio.filetypes.mzml.
MZMLIndexParser
umich.ms.fileio.filetypes.mzml.
MZMLIndexParser.OffsetId
umich.ms.fileio.filetypes.mzml.
MZMLPeaksDecoder
umich.ms.fileio.filetypes.mzml.
MZMLPeaksDecoder.DecodedData
umich.ms.fileio.filetypes.mzml.
MZMLRunHeaderParser
(implements umich.ms.fileio.filetypes.mzxml.
XmlBasedRunHeaderParser
)
umich.ms.fileio.filetypes.mzml.
MzmlVars
umich.ms.fileio.filetypes.mzxml.
MZXMLIndexBuilder
(implements umich.ms.fileio.filetypes.xmlbased.
IndexBuilder
<T>)
umich.ms.fileio.filetypes.mzxml.
MZXMLIndexParser
umich.ms.fileio.filetypes.mzxml.
MZXMLPeaksDecoder
umich.ms.fileio.filetypes.mzxml.
MZXMLPeaksDecoder.DecodedData
umich.ms.fileio.filetypes.mzxml.
MZXMLRunHeaderParser
(implements umich.ms.fileio.filetypes.mzxml.
XmlBasedRunHeaderParser
)
umich.ms.util.
OffsetLength
umich.ms.fileio.
Opts
umich.ms.datatypes.lcmsrun.
OriginalFile
java.io.
OutputStream
(implements java.io.
Closeable
, java.io.
Flushable
)
umich.ms.util.
ByteArrayHolder
umich.ms.fileio.filetypes.pepxml.example.
PepXmlAnalysisSummaryExample
umich.ms.fileio.filetypes.pepxml.example.
PepXmlExample
umich.ms.fileio.filetypes.pepxml.
PepXmlParser
umich.ms.fileio.filetypes.pepxml.example.
PepXmlSimpleExample
umich.ms.fileio.filetypes.pepxml.
PepXmlStream
(implements java.lang.
Iterable
<T>)
umich.ms.fileio.filetypes.pepxml.example.
PepXmlWriteExample
umich.ms.util.
PooledByteArrayHolders
umich.ms.datatypes.scan.props.
PrecursorInfo
(implements java.io.
Serializable
)
umich.ms.fileio.filetypes.protxml.example.
ProtXmlJaxbExample
umich.ms.fileio.filetypes.protxml.
ProtXmlParser
umich.ms.fileio.filetypes.protxml.example.
ProtXmlSimpleExample
java.io.
RandomAccessFile
(implements java.io.
Closeable
, java.io.
DataInput
, java.io.
DataOutput
)
umich.ms.external.apache.cassandra.io.
BufferedRandomAccessFile
umich.ms.external.
BufferedRandomAccessFile
java.lang.ref.
Reference
<T>
java.lang.ref.
PhantomReference
<T>
com.google.common.base.FinalizablePhantomReference<T> (implements com.google.common.base.FinalizableReference)
umich.ms.datatypes.
LCMSData.User
java.lang.ref.
WeakReference
<T>
umich.ms.util.
StrongReference
<T>
umich.ms.datatypes.scancollection.impl.
ScanCollectionDefault
(implements umich.ms.datatypes.scancollection.
IScanCollection
)
umich.ms.datatypes.scancollection.
ScanCollectionHelper
umich.ms.datatypes.scancollection.
ScanIndex
(implements java.io.
Serializable
)
umich.ms.datatypes.scancollection.
ScanIndexRoot
(implements java.io.
Serializable
)
umich.ms.util.
SpectrumUtils
umich.ms.util.
StringUtils
umich.ms.fileio.filetypes.thermo.raw.test.
ThermoTest
java.lang.
Throwable
(implements java.io.
Serializable
)
java.lang.
Exception
umich.ms.fileio.exceptions.
FileParsingException
umich.ms.fileio.exceptions.
RunHeaderParsingException
umich.ms.fileio.exceptions.
RunHeaderBoundsNotFound
umich.ms.fileio.exceptions.
IndexBrokenException
umich.ms.fileio.exceptions.
IndexNotFoundException
java.io.
IOException
umich.ms.util.base64.
Base64DecodingException
umich.ms.fileio.exceptions.
OutOfMemoryException
umich.ms.util.xml.
XmlUtils
umich.ms.util.
ZlibInflater
Interface Hierarchy
java.util.concurrent.
Callable
<V>
umich.ms.fileio.filetypes.xmlbased.
IndexBuilder
<T>
umich.ms.fileio.chunk.
FileChunkSource
umich.ms.datatypes.spectrum.
IIndexedSpectrum
umich.ms.fileio.filetypes.
LCMSDataSource
<T>
umich.ms.fileio.filetypes.
LCMSDataSourceDetector
umich.ms.fileio.filetypes.
SequentialScanReader
java.io.
Serializable
umich.ms.datatypes.index.
Index
<T>
umich.ms.datatypes.index.
IndexElement
umich.ms.fileio.filetypes.xmlbased.
XMLBasedIndexElement
umich.ms.datatypes.scan.
IScan
umich.ms.datatypes.scancollection.
IScanCollection
umich.ms.datatypes.spectrum.
ISpectrum
umich.ms.fileio.filetypes.xmlbased.
XMLBasedIndexElement
umich.ms.fileio.filetypes.mzxml.
XmlBasedRunHeaderParser
Enum Hierarchy
java.lang.
Object
java.lang.
Enum
<E> (implements java.lang.
Comparable
<T>, java.io.
Serializable
)
umich.ms.datatypes.lcmsrun.
Hash.TYPE
umich.ms.datatypes.scan.
StorageStrategy
umich.ms.datatypes.scan.
PeaksCompression
umich.ms.datatypes.scan.props.
ScanType
umich.ms.datatypes.scan.props.
Polarity
umich.ms.fileio.filetypes.mzml.
MzmlVars.BIN_DATA_TYPE
umich.ms.fileio.filetypes.mzml.
MZMLMultiSpectraParser.TAG
umich.ms.fileio.filetypes.mzml.
MZMLMultiSpectraParser.ATTR
umich.ms.fileio.filetypes.mzml.util.
UnitsCV
umich.ms.fileio.filetypes.mzml.util.
PSIMSCV
umich.ms.fileio.filetypes.mzxml.
MZXMLMultiSpectraParser.TAG
umich.ms.fileio.filetypes.mzxml.
MZXMLMultiSpectraParser.ATTR
umich.ms.util.xml.
TAG_TYPE
umich.ms.util.xml.
POSITION
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