com.hfg.bio

Class DigestSettings

java.lang.Object

com.hfg.setting.Settings

com.hfg.bio.DigestSettings

All Implemented Interfaces:

Cloneable

public class DigestSettings
extends Settings
implements Cloneable

Settings for protein digestion via protease(s).

Field Summary

Fields

Modifier and Type	Field and Description
static String	ALKYLATED_CYS
static String	MAX_FRAG_LENGTH
static String	MAX_FRAG_MASS
static String	MAX_MISSED_CLEAVAGES
static String	MIN_FRAG_LENGTH
static String	MIN_FRAG_MASS
static String	PROTEASE

Constructor Summary

Constructors

Constructor and Description
DigestSettings()

Method Summary

Modifier and Type	Method and Description
DigestSettings	clone()
AminoAcid	getAlkylatedCys()
Integer	getMaxFragmentLength()
Float	getMaxFragmentMass()
Integer	getMaxMissedCleavages()
Integer	getMinFragmentLength()
Float	getMinFragmentMass()
Set<Protease>	getProteases()
protected void	init() For subclasses to override.
boolean	meetsCriteria(DigestFragment inFrag) Returns whether the specified DigestFragment meets criteria for inclusion.
DigestSettings	setAlkylatedCys(AminoAcid inValue) By specifying a modified cysteine a "virtual reduction" will be performed on the protein before digestion.
DigestSettings	setMaxFragmentLength(Integer inValue)
DigestSettings	setMaxFragmentMass(Float inValue)
DigestSettings	setMaxMissedCleavages(int inValue)
DigestSettings	setMinFragmentLength(Integer inValue)
DigestSettings	setMinFragmentMass(Float inValue)
DigestSettings	setProtease(Protease inValue)
DigestSettings	setProteases(Collection<Protease> inValues)

Methods inherited from class com.hfg.setting.Settings

add, get, name, setName, setTagName, size, toXMLTag

Methods inherited from class java.lang.Object

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

Field Detail

PROTEASE

public static final String PROTEASE

See Also:

Constant Field Values

MAX_MISSED_CLEAVAGES

public static final String MAX_MISSED_CLEAVAGES

See Also:

Constant Field Values

MIN_FRAG_LENGTH

public static final String MIN_FRAG_LENGTH

See Also:

Constant Field Values

MAX_FRAG_LENGTH

public static final String MAX_FRAG_LENGTH

See Also:

Constant Field Values

MIN_FRAG_MASS

public static final String MIN_FRAG_MASS

See Also:

Constant Field Values

MAX_FRAG_MASS

public static final String MAX_FRAG_MASS

See Also:

Constant Field Values

ALKYLATED_CYS

public static final String ALKYLATED_CYS

See Also:

Constant Field Values

Constructor Detail

DigestSettings

public DigestSettings()

Method Detail

init

protected void init()

Description copied from class: Settings

For subclasses to override.

Overrides:

init in class Settings

setProtease

public DigestSettings setProtease(Protease inValue)

setProteases

public DigestSettings setProteases(Collection<Protease> inValues)

getProteases

public Set<Protease> getProteases()

setMaxMissedCleavages

public DigestSettings setMaxMissedCleavages(int inValue)

getMaxMissedCleavages

public Integer getMaxMissedCleavages()

setMinFragmentLength

public DigestSettings setMinFragmentLength(Integer inValue)

getMinFragmentLength

public Integer getMinFragmentLength()

setMaxFragmentLength

public DigestSettings setMaxFragmentLength(Integer inValue)

getMaxFragmentLength

public Integer getMaxFragmentLength()

setMinFragmentMass

public DigestSettings setMinFragmentMass(Float inValue)

getMinFragmentMass

public Float getMinFragmentMass()

setMaxFragmentMass

public DigestSettings setMaxFragmentMass(Float inValue)

getMaxFragmentMass

public Float getMaxFragmentMass()

setAlkylatedCys

public DigestSettings setAlkylatedCys(AminoAcid inValue)

By specifying a modified cysteine a "virtual reduction" will be performed on the protein before digestion.

Parameters:

inValue - AminoAcid to substitute for x-linked or free cysteines

Returns:

this DigestSettings object to enable method chaining

getAlkylatedCys

public AminoAcid getAlkylatedCys()

meetsCriteria

public boolean meetsCriteria(DigestFragment inFrag)

Returns whether the specified DigestFragment meets criteria for inclusion.

Parameters:

inFrag - the DigestFragment to test for inclusion

Returns:

whether the specified DigestFragment meets criteria for inclusion

clone

public DigestSettings clone()

Overrides:

clone in class Settings