com.compomics.util.experiment.identification.identification_parameters.tool_specific

Class MsAmandaParameters

java.lang.Object

com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsAmandaParameters

All Implemented Interfaces:

IdentificationAlgorithmParameter, Serializable

public class MsAmandaParameters
extends Object
implements IdentificationAlgorithmParameter

The MS Amanda specific parameters.

Author:

Harald Barsnes

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static int	MAX_MS_AMANDA_FASTA_FILE_NAME_LENGTH The maximum allowed length of the FASTA file name.

Constructor Summary

Constructors

Constructor and Description
MsAmandaParameters() Constructor.

Method Summary

Modifier and Type	Method and Description
boolean	equals(IdentificationAlgorithmParameter identificationAlgorithmParameter) Indicates whether another identificationAlgorithmParameter has the same parameters.
boolean	generateDecoy() Returns whether a decoy database shall be created and searched against.
Advocate	getAlgorithm() Returns the identification algorithm.
String	getInstrumentID() Return the instrument ID.
Integer	getMaxRank() Returns the maximum rank.
boolean	isLowMemoryMode() Returns whether the low memory mode is used.
boolean	isMonoIsotopic() Returns whether monoisotopic mass values shall be used (in contrast to average mass values).
void	setGenerateDecoyDatabase(boolean generateDecoy) Set whether a decoy database shall be created and searched against.
void	setInstrumentID(String instrumentID) Set the instrument ID.
void	setLowMemoryMode(boolean lowMemoryMode) Set whether the low memory mode is used.
void	setMaxRank(Integer maxRank) Set the maximum rank.
void	setMonoIsotopic(boolean monoisotopic) Set whether monoisotopic mass values shall be used (in contrast to average mass values).
String	toString(boolean html) Returns the parameters as a string.

Methods inherited from class java.lang.Object

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

Field Detail

MAX_MS_AMANDA_FASTA_FILE_NAME_LENGTH

public static final int MAX_MS_AMANDA_FASTA_FILE_NAME_LENGTH

The maximum allowed length of the FASTA file name.

See Also:

Constant Field Values

Constructor Detail

MsAmandaParameters

public MsAmandaParameters()

Constructor.

Method Detail

getAlgorithm

public Advocate getAlgorithm()

Description copied from interface: IdentificationAlgorithmParameter

Returns the identification algorithm.

Specified by:

getAlgorithm in interface IdentificationAlgorithmParameter

Returns:

the identification algorithm

equals

public boolean equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)

Description copied from interface: IdentificationAlgorithmParameter

Indicates whether another identificationAlgorithmParameter has the same parameters.

Specified by:

equals in interface IdentificationAlgorithmParameter

Parameters:

identificationAlgorithmParameter - the other identificationAlgorithmParameter

Returns:

true if the algorithm and parameters are the same

toString

public String toString(boolean html)

Description copied from interface: IdentificationAlgorithmParameter

Returns the parameters as a string.

Specified by:

toString in interface IdentificationAlgorithmParameter

Parameters:

html - use HTML formatting

Returns:

the parameters as a string

generateDecoy

public boolean generateDecoy()

Returns whether a decoy database shall be created and searched against.

Returns:

whether a decoy database shall be created and searched against

setGenerateDecoyDatabase

public void setGenerateDecoyDatabase(boolean generateDecoy)

Set whether a decoy database shall be created and searched against.

Parameters:

generateDecoy - the generateDecoy to set

isMonoIsotopic

public boolean isMonoIsotopic()

Returns whether monoisotopic mass values shall be used (in contrast to average mass values).

Returns:

monoisotopic mass values shall be used (in contrast to average mass values)

setMonoIsotopic

public void setMonoIsotopic(boolean monoisotopic)

Set whether monoisotopic mass values shall be used (in contrast to average mass values).

Parameters:

monoisotopic - the monoisotopic to set

getInstrumentID

public String getInstrumentID()

Return the instrument ID.

Returns:

the instrumentID

setInstrumentID

public void setInstrumentID(String instrumentID)

Set the instrument ID.

Parameters:

instrumentID - the instrumentID to set

getMaxRank

public Integer getMaxRank()

Returns the maximum rank.

Returns:

the maxRank

setMaxRank

public void setMaxRank(Integer maxRank)

Set the maximum rank.

Parameters:

maxRank - the maxRank to set

isLowMemoryMode

public boolean isLowMemoryMode()

Returns whether the low memory mode is used.

Returns:

the lowMemoryMode

setLowMemoryMode

public void setLowMemoryMode(boolean lowMemoryMode)

Set whether the low memory mode is used.

Parameters:

lowMemoryMode - the lowMemoryMode to set