de.unirostock.sems.bives.ds.ontology

Class SBOTerm

java.lang.Object

de.unirostock.sems.bives.ds.ontology.SBOTerm

public class SBOTerm
extends Object

The Class SBOTerm representing a link into the Systems Biology Ontology.

Author:

Martin Scharm

Field Summary

Fields

Modifier and Type	Field and Description
static String	MOD_INHIBITOR The string defining an INHIBITOR.
static String	MOD_NONE The string defining no modification at all.
static String	MOD_STIMULATOR The string defining a STIMULATOR.
static String	MOD_UNKNOWN The string defining an UNKNOWN modifier.

Constructor Summary

Constructors

Constructor and Description
SBOTerm(String SBOTerm) Instantiates a new SBO term.

Method Summary

Modifier and Type	Method and Description
static SBOTerm	createInhibitor() Creates a dummy inhibitor.
static SBOTerm	createStimulator() Creates a dummy stimulator.
String	getSBOTerm() Gets the SBO term stored in here.
String	resolveModifier() Resolve this modifier.
static String	resolveModifier(String mod) Resolve a modifier.
static boolean	sameModifier(SBOTerm modTermA, SBOTerm modTermB) Check if modifiers are equal (in terms of chemical reaction networks).

Methods inherited from class java.lang.Object

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

Field Detail

MOD_STIMULATOR

public static final String MOD_STIMULATOR

The string defining a STIMULATOR.

See Also:

Constant Field Values

MOD_UNKNOWN

public static final String MOD_UNKNOWN

The string defining an UNKNOWN modifier.

See Also:

Constant Field Values

MOD_INHIBITOR

public static final String MOD_INHIBITOR

The string defining an INHIBITOR.

See Also:

Constant Field Values

MOD_NONE

public static final String MOD_NONE

The string defining no modification at all.

See Also:

Constant Field Values

Constructor Detail

SBOTerm

public SBOTerm(String SBOTerm)

Instantiates a new SBO term.

Parameters:

SBOTerm - the SBO term of the form SBO:[0-9]+

Method Detail

getSBOTerm

public String getSBOTerm()

Gets the SBO term stored in here.

Returns:

the SBO term

createStimulator

public static SBOTerm createStimulator()

Creates a dummy stimulator.

Returns:

the SBO term describing a stimulator

createInhibitor

public static SBOTerm createInhibitor()

Creates a dummy inhibitor.

Returns:

the SBO term describing an inhibitor

resolveModifier

public static String resolveModifier(String mod)

Resolve a modifier.

Parameters:

mod - the SBO term of the form SBO:[0-9]+

Returns:

the textual equivalent

resolveModifier

public String resolveModifier()

Resolve this modifier.

Returns:

the textual equivalent

sameModifier

public static boolean sameModifier(SBOTerm modTermA,
                                   SBOTerm modTermB)

Check if modifiers are equal (in terms of chemical reaction networks). They are equal if one of the following is true:

• both terms are null
• both terms encode for an inhibitor (no matter which kind)
• both terms encode for a stimulator (no matter which kind)

Parameters:

modTermA - the mod term a

modTermB - the mod term b

Returns:

true, if successful