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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.deprecated
,
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.util
,
umich.ms.fileio.filetypes.xmlbased
,
umich.ms.fileio.util
,
umich.ms.logging
,
umich.ms.msfiletoolbox
,
umich.ms.util
,
umich.ms.util.base64
Class Hierarchy
java.lang.
Object
umich.ms.fileio.filetypes.util.
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.fileio.util.
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.fileio.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.util.
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.
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.xmlbased.
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.fileio.filetypes.mzxml.
XmlBasedRunHeaderParser
umich.ms.fileio.filetypes.mzml.
MZMLRunHeaderParser
umich.ms.fileio.filetypes.mzxml.
MZXMLRunHeaderParser
umich.ms.util.
XmlUtils
umich.ms.fileio.filetypes.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
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
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