jp.sbi.celldesigner.plugin.util

Class PluginReactionSymbolType

java.lang.Object

jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType

public class PluginReactionSymbolType
extends java.lang.Object

This class defines ReactionType for PluginReaction.

Author:

The Systems Biology Institute

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	ADD_PRODUCT ADD_PRODUCT
static java.lang.String	ADD_REACTANT ADD_REACTANT
static java.lang.String	BOOLEAN_LOGIC_GATE_AND BOOLEAN_LOGIC_GATE_AND
static java.lang.String	BOOLEAN_LOGIC_GATE_NOT
static java.lang.String	BOOLEAN_LOGIC_GATE_OR BOOLEAN_LOGIC_GATE_OR
static java.lang.String	BOOLEAN_LOGIC_GATE_UNKNOWN BOOLEAN_LOGIC_GATE_UNKNOWN
static java.lang.String	CATALYSIS CATALYSIS
static java.lang.String	DEGRADATION DEGRADATION
static java.lang.String	DISSOCIATION DISSOCIATION
static java.lang.String	HETERODIMER_ASSOCIATION HETERODIMER_ASSOCIATION
static java.lang.String	HOMODIMER_FORMATION HOMODIMER_FORMATION
static java.lang.String	INHIBITION INHIBITION
static java.lang.String	KNOWN_TRANSITION_OMITTED KNOWN_TRANSITION_OMITTED
static java.lang.String	MODULATION
static java.lang.String	NEGATIVE_INFLUENCE
static java.lang.String	PHYSICAL_STIMULATION
static java.lang.String	POSITIVE_INFLUENCE
static java.lang.String	REDUCED_MODULATION
static java.lang.String	REDUCED_PHYSICAL_STIMULATION
static java.lang.String	REDUCED_TRIGGER
static java.lang.String	STATE_TRANSITION STATE_TRANSITION
static java.lang.String	TRANSCRIPTION TRANSCRIPTION
static java.lang.String	TRANSLATION TRANSLATION
static java.lang.String	TRANSPORT TRANSPORT
static java.lang.String	TRIGGER
static java.lang.String	TRUNCATION TRUNCATION
static java.lang.String	UNKNOWN_CATALYSIS UNKNOWN_CATALYSIS
static java.lang.String	UNKNOWN_INHIBITION UNKNOWN_INHIBITION
static java.lang.String	UNKNOWN_NEGATIVE_INFLUENCE
static java.lang.String	UNKNOWN_POSITIVE_INFLUENCE
static java.lang.String	UNKNOWN_REDUCED_MODULATION
static java.lang.String	UNKNOWN_REDUCED_PHYSICAL_STIMULATION
static java.lang.String	UNKNOWN_REDUCED_TRIGGER
static java.lang.String	UNKNOWN_TRANSITION UNKNOWN_TRANSITION

Constructor Summary

Constructors

Constructor and Description
PluginReactionSymbolType()

Method Summary

Modifier and Type	Method and Description
static boolean	isValidModifierType(PluginSimpleSpeciesReference sp)
static boolean	isValidReaction(PluginReaction re)
static boolean	isValidReactionType(PluginReaction sp)

Methods inherited from class java.lang.Object

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

Field Detail

STATE_TRANSITION

public static final java.lang.String STATE_TRANSITION

STATE_TRANSITION

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Constant Field Values

KNOWN_TRANSITION_OMITTED

public static final java.lang.String KNOWN_TRANSITION_OMITTED

KNOWN_TRANSITION_OMITTED

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Constant Field Values

UNKNOWN_TRANSITION

public static final java.lang.String UNKNOWN_TRANSITION

UNKNOWN_TRANSITION

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Constant Field Values

CATALYSIS

public static final java.lang.String CATALYSIS

CATALYSIS

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Constant Field Values

UNKNOWN_CATALYSIS

public static final java.lang.String UNKNOWN_CATALYSIS

UNKNOWN_CATALYSIS

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Constant Field Values

INHIBITION

public static final java.lang.String INHIBITION

INHIBITION

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Constant Field Values

UNKNOWN_INHIBITION

public static final java.lang.String UNKNOWN_INHIBITION

UNKNOWN_INHIBITION

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Constant Field Values

TRANSPORT

public static final java.lang.String TRANSPORT

TRANSPORT

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Constant Field Values

TRANSCRIPTION

public static final java.lang.String TRANSCRIPTION

TRANSCRIPTION

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Constant Field Values

TRANSLATION

public static final java.lang.String TRANSLATION

TRANSLATION

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Constant Field Values

ADD_REACTANT

public static final java.lang.String ADD_REACTANT

ADD_REACTANT

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Constant Field Values

ADD_PRODUCT

public static final java.lang.String ADD_PRODUCT

ADD_PRODUCT

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Constant Field Values

HETERODIMER_ASSOCIATION

public static final java.lang.String HETERODIMER_ASSOCIATION

HETERODIMER_ASSOCIATION

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Constant Field Values

DISSOCIATION

public static final java.lang.String DISSOCIATION

DISSOCIATION

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Constant Field Values

TRUNCATION

public static final java.lang.String TRUNCATION

TRUNCATION

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Constant Field Values

HOMODIMER_FORMATION

public static final java.lang.String HOMODIMER_FORMATION

HOMODIMER_FORMATION

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Constant Field Values

DEGRADATION

public static final java.lang.String DEGRADATION

DEGRADATION

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Constant Field Values

BOOLEAN_LOGIC_GATE_AND

public static final java.lang.String BOOLEAN_LOGIC_GATE_AND

BOOLEAN_LOGIC_GATE_AND

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Constant Field Values

BOOLEAN_LOGIC_GATE_OR

public static final java.lang.String BOOLEAN_LOGIC_GATE_OR

BOOLEAN_LOGIC_GATE_OR

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Constant Field Values

BOOLEAN_LOGIC_GATE_UNKNOWN

public static final java.lang.String BOOLEAN_LOGIC_GATE_UNKNOWN

BOOLEAN_LOGIC_GATE_UNKNOWN

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Constant Field Values

BOOLEAN_LOGIC_GATE_NOT

public static final java.lang.String BOOLEAN_LOGIC_GATE_NOT

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Constant Field Values

TRIGGER

public static final java.lang.String TRIGGER

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Constant Field Values

PHYSICAL_STIMULATION

public static final java.lang.String PHYSICAL_STIMULATION

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Constant Field Values

MODULATION

public static final java.lang.String MODULATION

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Constant Field Values

NEGATIVE_INFLUENCE

public static final java.lang.String NEGATIVE_INFLUENCE

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Constant Field Values

POSITIVE_INFLUENCE

public static final java.lang.String POSITIVE_INFLUENCE

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Constant Field Values

REDUCED_MODULATION

public static final java.lang.String REDUCED_MODULATION

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Constant Field Values

REDUCED_PHYSICAL_STIMULATION

public static final java.lang.String REDUCED_PHYSICAL_STIMULATION

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Constant Field Values

REDUCED_TRIGGER

public static final java.lang.String REDUCED_TRIGGER

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Constant Field Values

UNKNOWN_NEGATIVE_INFLUENCE

public static final java.lang.String UNKNOWN_NEGATIVE_INFLUENCE

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Constant Field Values

UNKNOWN_POSITIVE_INFLUENCE

public static final java.lang.String UNKNOWN_POSITIVE_INFLUENCE

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Constant Field Values

UNKNOWN_REDUCED_MODULATION

public static final java.lang.String UNKNOWN_REDUCED_MODULATION

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Constant Field Values

UNKNOWN_REDUCED_PHYSICAL_STIMULATION

public static final java.lang.String UNKNOWN_REDUCED_PHYSICAL_STIMULATION

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Constant Field Values

UNKNOWN_REDUCED_TRIGGER

public static final java.lang.String UNKNOWN_REDUCED_TRIGGER

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Constant Field Values

Constructor Detail

PluginReactionSymbolType

public PluginReactionSymbolType()

Method Detail

isValidReaction

public static boolean isValidReaction(PluginReaction re)

Parameters:

re - PluginReaction

Returns:

true if isValidReactionType is true, and the number of reactants and products is valid, false otherwise. The valid number is the following:
For HETERODIMER_ASSOCIATION reactants>=2 and products>=1
For DISSOCIATION and TRUNCATION reactants>=1 and products>=2
For the other types reactants>=1 and products>=1

isValidModifierType

public static boolean isValidModifierType(PluginSimpleSpeciesReference sp)

Parameters:

sp - PluginSimpleSpeciesReference

Returns:

true if the modification type of the given PluginSpeciesReference is the one of the following fields of this PluginReactionSymbolType: CATALYSIS, INHIBITION, KNOWN_TRANSITION_OMITTED, STATE_TRANSITION, RANSCRIPTIONAL_ACTIVATION, RANSCRIPTIONAL_INHIBITION, TRANSLATIONAL_ACTIVATION, RANSLATIONAL_INHIBITION, TRANSPORT, UNKNOWN_CATALYSIS, UNKNOWN_INHIBITION and UNKNOWN_TRANSITION, BOOLEAN_LOGIC_GATE_AND, BOOLEAN_LOGIC_GATE_OR, BOOLEAN_LOGIC_GATE_UNKNOWN NEGATIVE_INFLUENCE, POSITIVE_INFLUENCE, REDUCED_MODULATION, REDUCED_PHYSICAL_STIMULATION, REDUCED_TRIGGER, UNKNOWN_NEGATIVE_INFLUENCE, UNKNOWN_POSITIVE_INFLUENCE, UNKNOWN_REDUCED_MODULATION, UNKNOWN_REDUCED_PHYSICAL_STIMULATION, UNKNOWN_REDUCED_TRIGGER false otherwise.

isValidReactionType

public static boolean isValidReactionType(PluginReaction sp)

Parameters:

sp - PluginReaction

Returns:

true if the reaction type of the given PluginReaction is the one of the following fields of the PluginReactionSymbolType: CATALYSIS, DEGRADATION, DISSOCIATION, HETERODIMER_ASSOCIATION, HOMODIMER_FORMATION, HOMODIMER_FORMATION, INHIBITION, KNOWN_TRANSITION_OMITTED, STATE_TRANSITION, RANSCRIPTIONAL_ACTIVATION, TRANSCRIPTIONAL_INHIBITION, TRANSLATIONAL_ACTIVATION, TRANSLATIONAL_INHIBITION, TRANSPORT, TRUNCATION, UNKNOWN_CATALYSIS, UNKNOWN_INHIBITION and UNKNOWN_TRANSITION, NEGATIVE_INFLUENCE, POSITIVE_INFLUENCE, REDUCED_MODULATION, REDUCED_PHYSICAL_STIMULATION, REDUCED_TRIGGER, UNKNOWN_NEGATIVE_INFLUENCE, UNKNOWN_POSITIVE_INFLUENCE, UNKNOWN_REDUCED_MODULATION, UNKNOWN_REDUCED_PHYSICAL_STIMULATION, UNKNOWN_REDUCED_TRIGGER , or the reaction type is PHYSICAL_STIMULATION and PHENOTYPE isn't the reactant but the product, false otherwise.