fr.profi.mzdb.io.reader.cache

Class SpectrumHeaderReader

java.lang.Object

fr.profi.mzdb.io.reader.cache.MzDbEntityCacheContainer

fr.profi.mzdb.io.reader.cache.AbstractSpectrumHeaderReader

fr.profi.mzdb.io.reader.cache.SpectrumHeaderReader

public class SpectrumHeaderReader
extends AbstractSpectrumHeaderReader

Author:

David Bouyssie

Field Summary

Fields inherited from class fr.profi.mzdb.io.reader.cache.AbstractSpectrumHeaderReader

TIME_INDEX_WIDTH

Constructor Summary

Constructors

Constructor and Description
SpectrumHeaderReader(MzDbReader mzDbReader, AbstractDataEncodingReader dataEncodingReader)

Method Summary

Modifier and Type	Method and Description
Map<Long,SpectrumHeader>	getMs1SpectrumHeaderById() Gets the MS1 spectrum header by id.
SpectrumHeader[]	getMs1SpectrumHeaders() Gets the MS1 spectrum headers.
Map<Long,SpectrumHeader>	getMs2SpectrumHeaderById() Gets the MS2 spectrum header by id.
SpectrumHeader[]	getMs2SpectrumHeaders() Gets the MS2 spectrum headers.
MzDbReader	getMzDbReader() specialized getter
SpectrumHeader	getSpectrumHeader(long id) /** Gets the spectrum header.
Map<Long,SpectrumHeader>	getSpectrumHeaderById() Gets the spectrum headers by id.
SpectrumHeader	getSpectrumHeaderForTime(float time, int msLevel) Gets the spectrum header for time.
SpectrumHeader[]	getSpectrumHeaders() Gets the spectrum headers.
long[]	getSpectrumIdsForTimeRange(float minRT, float maxRT, int msLevel) Gets the spectrum ids for time range.
Map<Long,Float>	getSpectrumTimeById() Gets the spectrum time by id.

Methods inherited from class fr.profi.mzdb.io.reader.cache.AbstractSpectrumHeaderReader

getMs1SpectrumHeaderById, getMs1SpectrumHeaders, getMs2SpectrumHeaderById, getMs2SpectrumHeaders, getMs3SpectrumHeaderById, getMs3SpectrumHeaders, getSpectrumHeader, getSpectrumHeaderById, getSpectrumHeaderForTime, getSpectrumHeaders, getSpectrumIdsForTimeRange, getSpectrumTimeById

Methods inherited from class fr.profi.mzdb.io.reader.cache.MzDbEntityCacheContainer

getEntityCache

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SpectrumHeaderReader

public SpectrumHeaderReader(MzDbReader mzDbReader,
                            AbstractDataEncodingReader dataEncodingReader)
                     throws com.almworks.sqlite4java.SQLiteException

Parameters:

mzDbReader -

Throws:

com.almworks.sqlite4java.SQLiteException

Method Detail

getMzDbReader

public MzDbReader getMzDbReader()

specialized getter

Specified by:

getMzDbReader in class MzDbEntityCacheContainer

Returns:

reader

getSpectrumHeaders

public SpectrumHeader[] getSpectrumHeaders()
                                    throws com.almworks.sqlite4java.SQLiteException

Gets the spectrum headers.

Returns:

the spectrum headers

Throws:

com.almworks.sqlite4java.SQLiteException

getSpectrumHeaderById

public Map<Long,SpectrumHeader> getSpectrumHeaderById()
                                               throws com.almworks.sqlite4java.SQLiteException

Gets the spectrum headers by id.

Returns:

the spectrum header by id

Throws:

com.almworks.sqlite4java.SQLiteException

getMs1SpectrumHeaders

public SpectrumHeader[] getMs1SpectrumHeaders()
                                       throws com.almworks.sqlite4java.SQLiteException

Gets the MS1 spectrum headers.

Returns:

the spectrum headers

Throws:

com.almworks.sqlite4java.SQLiteException

getMs1SpectrumHeaderById

public Map<Long,SpectrumHeader> getMs1SpectrumHeaderById()
                                                  throws com.almworks.sqlite4java.SQLiteException

Gets the MS1 spectrum header by id.

Returns:

the spectrum header by id

Throws:

com.almworks.sqlite4java.SQLiteException

getMs2SpectrumHeaders

public SpectrumHeader[] getMs2SpectrumHeaders()
                                       throws com.almworks.sqlite4java.SQLiteException

Gets the MS2 spectrum headers.

Returns:

the spectrum headers

Throws:

com.almworks.sqlite4java.SQLiteException

getMs2SpectrumHeaderById

public Map<Long,SpectrumHeader> getMs2SpectrumHeaderById()
                                                  throws com.almworks.sqlite4java.SQLiteException

Gets the MS2 spectrum header by id.

Returns:

the spectrum header by id

Throws:

com.almworks.sqlite4java.SQLiteException

getSpectrumHeader

public SpectrumHeader getSpectrumHeader(long id)
                                 throws com.almworks.sqlite4java.SQLiteException

/** Gets the spectrum header.

Parameters:

id - the id

Returns:

spectrum header

Throws:

com.almworks.sqlite4java.SQLiteException

getSpectrumTimeById

public Map<Long,Float> getSpectrumTimeById()
                                    throws com.almworks.sqlite4java.SQLiteException

Gets the spectrum time by id.

Returns:

the spectrum time mapped by the spectrum id

Throws:

com.almworks.sqlite4java.SQLiteException - the SQLite exception

getSpectrumHeaderForTime

public SpectrumHeader getSpectrumHeaderForTime(float time,
                                               int msLevel)
                                        throws Exception

Gets the spectrum header for time.

Parameters:

time - the time

msLevel - the ms level

Returns:

SpectrumHeader the closest to the time input parameter

Throws:

Exception

getSpectrumIdsForTimeRange

public long[] getSpectrumIdsForTimeRange(float minRT,
                                         float maxRT,
                                         int msLevel)
                                  throws com.almworks.sqlite4java.SQLiteException

Gets the spectrum ids for time range.

Parameters:

minRT - the min rt

maxRT - the max rt

msLevel - the ms level

Returns:

array of integers corresponding to the ids of matching spectrum

Throws:

com.almworks.sqlite4java.SQLiteException