fr.profi.mzdb.io.reader.cache

Class AbstractSpectrumHeaderReader

java.lang.Object

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

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

Direct Known Subclasses:

SpectrumHeaderAsyncReader, SpectrumHeaderReader

public abstract class AbstractSpectrumHeaderReader
extends MzDbEntityCacheContainer

Author:

David Bouyssie

Field Summary

Fields

Modifier and Type	Field and Description
protected static int	TIME_INDEX_WIDTH The time index width.

Constructor Summary

Constructors

Constructor and Description
AbstractSpectrumHeaderReader(AbstractMzDbReader mzDbReader, AbstractDataEncodingReader dataEncodingReader)

Method Summary

Modifier and Type	Method and Description
Map<Long,SpectrumHeader>	getMs1SpectrumHeaderById(com.almworks.sqlite4java.SQLiteConnection connection) Gets the MS1 spectrum header by id.
protected SpectrumHeader[]	getMs1SpectrumHeaders(com.almworks.sqlite4java.SQLiteConnection connection) Gets the MS1 spectrum headers.
Map<Long,SpectrumHeader>	getMs2SpectrumHeaderById(com.almworks.sqlite4java.SQLiteConnection connection) Gets the MS2 spectrum header by id.
protected SpectrumHeader[]	getMs2SpectrumHeaders(com.almworks.sqlite4java.SQLiteConnection connection) Gets the MS2 spectrum headers.
Map<Long,SpectrumHeader>	getMs3SpectrumHeaderById(com.almworks.sqlite4java.SQLiteConnection connection) Gets the MS2 spectrum header by id.
protected SpectrumHeader[]	getMs3SpectrumHeaders(com.almworks.sqlite4java.SQLiteConnection connection) Gets the MS2 spectrum headers.
SpectrumHeader	getSpectrumHeader(long id, com.almworks.sqlite4java.SQLiteConnection connection) /** Gets the spectrum header.
Map<Long,SpectrumHeader>	getSpectrumHeaderById(com.almworks.sqlite4java.SQLiteConnection connection) Gets the spectrum headers by id.
protected SpectrumHeader	getSpectrumHeaderForTime(float time, int msLevel, com.almworks.sqlite4java.SQLiteConnection connection) Gets the spectrum header for time.
protected SpectrumHeader[]	getSpectrumHeaders(com.almworks.sqlite4java.SQLiteConnection connection) Gets the spectrum headers.
protected long[]	getSpectrumIdsForTimeRange(float minRT, float maxRT, int msLevel, com.almworks.sqlite4java.SQLiteConnection connection) Gets the spectrum ids for time range.
protected Map<Long,Float>	getSpectrumTimeById(com.almworks.sqlite4java.SQLiteConnection connection) Gets the spectrum time by id.

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

getEntityCache, getMzDbReader

Methods inherited from class java.lang.Object

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

Field Detail

TIME_INDEX_WIDTH

protected static final int TIME_INDEX_WIDTH

The time index width.

See Also:

Constant Field Values

Constructor Detail

AbstractSpectrumHeaderReader

public AbstractSpectrumHeaderReader(AbstractMzDbReader mzDbReader,
                                    AbstractDataEncodingReader dataEncodingReader)
                             throws com.almworks.sqlite4java.SQLiteException

Parameters:

mzDbReader -

Throws:

com.almworks.sqlite4java.SQLiteException

Method Detail

getSpectrumHeaders

protected SpectrumHeader[] getSpectrumHeaders(com.almworks.sqlite4java.SQLiteConnection connection)
                                       throws com.almworks.sqlite4java.SQLiteException

Gets the spectrum headers.

Parameters:

connection - the connection

Returns:

the spectrum headers

Throws:

com.almworks.sqlite4java.SQLiteException - the SQ lite exception

getSpectrumHeaderById

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

Gets the spectrum headers by id.

Parameters:

connection - the connection

Returns:

the spectrum header by id

Throws:

com.almworks.sqlite4java.SQLiteException - the SQ lite exception

getMs1SpectrumHeaders

protected SpectrumHeader[] getMs1SpectrumHeaders(com.almworks.sqlite4java.SQLiteConnection connection)
                                          throws com.almworks.sqlite4java.SQLiteException

Gets the MS1 spectrum headers.

Parameters:

connection - the connection

Returns:

the spectrum headers

Throws:

com.almworks.sqlite4java.SQLiteException - the SQ lite exception

getMs1SpectrumHeaderById

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

Gets the MS1 spectrum header by id.

Parameters:

connection - the connection

Returns:

the spectrum header by id

Throws:

com.almworks.sqlite4java.SQLiteException - the SQ lite exception

getMs2SpectrumHeaders

protected SpectrumHeader[] getMs2SpectrumHeaders(com.almworks.sqlite4java.SQLiteConnection connection)
                                          throws com.almworks.sqlite4java.SQLiteException

Gets the MS2 spectrum headers.

Parameters:

connection - the connection

Returns:

the spectrum headers

Throws:

com.almworks.sqlite4java.SQLiteException - the SQ lite exception

getMs2SpectrumHeaderById

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

Gets the MS2 spectrum header by id.

Parameters:

connection - the connection

Returns:

the spectrum header by id

Throws:

com.almworks.sqlite4java.SQLiteException - the SQ lite exception

getMs3SpectrumHeaders

protected SpectrumHeader[] getMs3SpectrumHeaders(com.almworks.sqlite4java.SQLiteConnection connection)
                                          throws com.almworks.sqlite4java.SQLiteException

Gets the MS2 spectrum headers.

Parameters:

connection - the connection

Returns:

the spectrum headers

Throws:

com.almworks.sqlite4java.SQLiteException - the SQ lite exception

getMs3SpectrumHeaderById

public Map<Long,SpectrumHeader> getMs3SpectrumHeaderById(com.almworks.sqlite4java.SQLiteConnection connection)
                                                  throws com.almworks.sqlite4java.SQLiteException

Gets the MS2 spectrum header by id.

Parameters:

connection - the connection

Returns:

the spectrum header by id

Throws:

com.almworks.sqlite4java.SQLiteException - the SQ lite exception

getSpectrumHeader

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

/** Gets the spectrum header.

Parameters:

id - the id

connection - the connection

Returns:

spectrum header

Throws:

com.almworks.sqlite4java.SQLiteException - the SQ lite exception

getSpectrumTimeById

protected Map<Long,Float> getSpectrumTimeById(com.almworks.sqlite4java.SQLiteConnection connection)
                                       throws com.almworks.sqlite4java.SQLiteException

Gets the spectrum time by id.

Parameters:

connection - the connection

Returns:

the spectrum time mapped by the spectrum id

Throws:

com.almworks.sqlite4java.SQLiteException - the SQLite exception

getSpectrumHeaderForTime

protected SpectrumHeader getSpectrumHeaderForTime(float time,
                                                  int msLevel,
                                                  com.almworks.sqlite4java.SQLiteConnection connection)
                                           throws Exception

Gets the spectrum header for time.

Parameters:

time - the time

msLevel - the ms level

connection - the connection

Returns:

SpectrumHeader the closest to the time input parameter

Throws:

Exception - the exception

getSpectrumIdsForTimeRange

protected long[] getSpectrumIdsForTimeRange(float minRT,
                                            float maxRT,
                                            int msLevel,
                                            com.almworks.sqlite4java.SQLiteConnection connection)
                                     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

connection - the connection

Returns:

array of integers corresponding to the ids of matching spectrum

Throws:

com.almworks.sqlite4java.SQLiteException - the SQ lite exception