charite.christo.metannogen
Interface Reaction

All Known Implementing Classes:

MReaction

public interface Reaction

This object holds a biochemical conversion reactants into products.

Field Summary

static int	DIRECTION_BACKWARD
static int	DIRECTION_FORWARD
static int	DIRECTION_REVERSIBLE
static int	EQUALS_IGNORE_COMPARTMENT
static int	EQUALS_IGNORE_ORIENTATION
static int	EQUALS_IGNORE_PROTON
static int	EQUALS_IGNORE_STOICHIOMETRY
static int	EQUALS_RECORD_DIFFERENCES
static long	FILTER_NOT_EXCLUDED
static long	FILTER_REJECTED_DATASETS
static int	TEXT_HUMAN_READABLE
static int	TEXT_NO_COMPARTMENT
static int	TEXT_SORT_METABOLITES
static long	UNIQUE

Method Summary

boolean	areAllSpeciesTranslated() Short for Integer.parsInt(getAttribute(key)).
boolean	equals(Reaction equat1, long options) Comparison
String	getAttribute(String key) The network can contain additional implementation specific data.
double	getAttributeF(String key) Short for Double.parsDouble(getAttribute(key)).
int	getAttributeI(String key)
Map<String,String>	getAttributes()
Object	getClientProperty(Object o) This method is similar to JComponent#getClientProperty(Object)
ReactionCollection	getCollection() Returns the reference of the containing network object.
String	getCompartmentOfSpeciesP(String m)
String	getCompartmentOfSpeciesS(String m) Returns null if the given metabolite is not part of the reaction.
String[]	getCompartmentsP() List of Compartments for products.
String[]	getCompartmentsS() List of reactants
String[]	getCompartmentsWithEnzyme() Alle compartments fur diese Reaktionsgleichung, sorted alphabetically In der Implementierung wird getReactionsWithThisStoichiometry() iteriert und eine Liste aller compartments erstellt.
int	getConfidence()
String[]	getDatasetFields() If the reaction is created from a Dataset then return the dataset fields.
float	getDeltaG()
int	getDirection() See DIRECTION_FORWARD, DIRECTION_BACKWARD, DIRECTION_REVERSIBLE
String[]	getEC() Array of EC-numbers or an array of length 0.
String	getID() The Identifier.
String	getName() The human readable name of the reaction.
String[]	getProducts() List of products The following Arrays have exactly the same size: getCompartmentsP() getProducts() getSpeciesP() getStoichiometriesP()
Reaction[]	getReactionsWithThisStoichiometry() Die Grundidee ist, dass initial ein Array von Reaktionen generiert wird, bei der jede Stoichiometrie nur einmal auftaucht.
Species[]	getSpeciesP() List of products
Species[]	getSpeciesS() List of reactants
int[]	getStoichiometriesP() Stoichiometries of products.
int[]	getStoichiometriesS() Stoichiometries of reactants.
int	getStoichiometryP(String metabolite, String compartment)
int	getStoichiometryS(String metabolite, String compartment) Compartment may be null.
String[]	getSubstrates() List of reactants The following Arrays have exactly the same size: getCompartmentsS() getSubstrates() getSpeciesS() getStoichiometriesS()
String[]	getSubstratesAndProducts() Union set of getSubstrates() and getProducts()
String[]	getSubstratesAndProductsWithoutProton() Union of getSubstrates() and getProducts() skipping H2O and H+
int	getSubstratesAndProductsWithoutProtonHashCode() Dadurch wird die equals Methode extrem schnell
boolean	isBiomass()
boolean	isExcluded() Exists but should not be used in file export.
boolean	isReversible() Identical to getDirection()==DIRECTION_REVERSIBLE
boolean	isTransport() True if reactants and products have different compartments.
void	putClientProperty(Object key, Object value) This method allows to attach data.
void	setDeltaG(float f)
void	setDirection(int direction) See DIRECTION_FORWARD, DIRECTION_BACKWARD, DIRECTION_REVERSIBLE
void	setExcluded(boolean b) Exists but should not be used in file export
void	setReactionsWithThisStoichiometry(Reaction[] rr)
String	toText(int options) Options may be 0 or TEXT_HUMAN_READABLE

Field Detail

EQUALS_IGNORE_COMPARTMENT

static final int EQUALS_IGNORE_COMPARTMENT

See Also:

Constant Field Values

EQUALS_IGNORE_PROTON

static final int EQUALS_IGNORE_PROTON

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Constant Field Values

EQUALS_IGNORE_ORIENTATION

static final int EQUALS_IGNORE_ORIENTATION

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Constant Field Values

EQUALS_IGNORE_STOICHIOMETRY

static final int EQUALS_IGNORE_STOICHIOMETRY

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Constant Field Values

EQUALS_RECORD_DIFFERENCES

static final int EQUALS_RECORD_DIFFERENCES

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Constant Field Values

TEXT_HUMAN_READABLE

static final int TEXT_HUMAN_READABLE

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Constant Field Values

TEXT_NO_COMPARTMENT

static final int TEXT_NO_COMPARTMENT

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Constant Field Values

TEXT_SORT_METABOLITES

static final int TEXT_SORT_METABOLITES

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Constant Field Values

DIRECTION_FORWARD

static final int DIRECTION_FORWARD

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Constant Field Values

DIRECTION_BACKWARD

static final int DIRECTION_BACKWARD

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Constant Field Values

DIRECTION_REVERSIBLE

static final int DIRECTION_REVERSIBLE

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Constant Field Values

UNIQUE

static final long UNIQUE

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Constant Field Values

FILTER_REJECTED_DATASETS

static final long FILTER_REJECTED_DATASETS

See Also:

Constant Field Values

FILTER_NOT_EXCLUDED

static final long FILTER_NOT_EXCLUDED

See Also:

Constant Field Values

Method Detail

getReactionsWithThisStoichiometry

Reaction[] getReactionsWithThisStoichiometry()

Die Grundidee ist, dass initial ein Array von Reaktionen generiert wird, bei der jede Stoichiometrie nur einmal auftaucht. Fur die mitochondriale und Cytosolische Variante einer Reaktion wird nur ein Vertreter in das Array aufgenommen. Mit dieser Abfrage kommt man an die Reaktionen aller Compartments.

getCompartmentsWithEnzyme

String[] getCompartmentsWithEnzyme()

Alle compartments fur diese Reaktionsgleichung, sorted alphabetically In der Implementierung wird getReactionsWithThisStoichiometry() iteriert und eine Liste aller compartments erstellt. In diesem Bsp {"cyto","mitoMx"}

toText

String toText(int options)

Options may be 0 or TEXT_HUMAN_READABLE

setDeltaG

void setDeltaG(float f)

getDeltaG

float getDeltaG()

isTransport

boolean isTransport()

True if reactants and products have different compartments. Bug: ficytC[m] + h2o[c] + so3[c] --> (2) focytC[m] + (2) h[c] + so4[c] is falsly a transport

isBiomass

boolean isBiomass()

getSubstratesAndProducts

String[] getSubstratesAndProducts()

Union set of getSubstrates() and getProducts()

getSubstratesAndProductsWithoutProton

String[] getSubstratesAndProductsWithoutProton()

Union of getSubstrates() and getProducts() skipping H2O and H+

getSubstratesAndProductsWithoutProtonHashCode

int getSubstratesAndProductsWithoutProtonHashCode()

Dadurch wird die equals Methode extrem schnell

getSubstrates

String[] getSubstrates()

List of reactants The following Arrays have exactly the same size: getCompartmentsS() getSubstrates() getSpeciesS() getStoichiometriesS()

getProducts

String[] getProducts()

List of products The following Arrays have exactly the same size: getCompartmentsP() getProducts() getSpeciesP() getStoichiometriesP()

getSpeciesS

Species[] getSpeciesS()

List of reactants

getSpeciesP

Species[] getSpeciesP()

List of products

getCompartmentsP

String[] getCompartmentsP()

List of Compartments for products.

getCompartmentsS

String[] getCompartmentsS()

List of reactants

getCompartmentOfSpeciesS

String getCompartmentOfSpeciesS(String m)

Returns null if the given metabolite is not part of the reaction.

getCompartmentOfSpeciesP

String getCompartmentOfSpeciesP(String m)

getStoichiometriesS

int[] getStoichiometriesS()

Stoichiometries of reactants.

getStoichiometriesP

int[] getStoichiometriesP()

Stoichiometries of products.

getStoichiometryS

int getStoichiometryS(String metabolite,
                      String compartment)

Compartment may be null. Returns 0 if the metabolite is not in the reaction.

getStoichiometryP

int getStoichiometryP(String metabolite,
                      String compartment)

equals

boolean equals(Reaction equat1,
               long options)

Comparison

Returns:

true if both Reactions are identical

putClientProperty

void putClientProperty(Object key,
                       Object value)

This method allows to attach data. It is similar to JComponent#putClientProperty(Object,Object)

getClientProperty

Object getClientProperty(Object o)

This method is similar to JComponent#getClientProperty(Object)

getAttribute

String getAttribute(String key)

The network can contain additional implementation specific data. In Metannogen this data is entered into the text pane or is provided by additional plain text files specified by command line parmeters. Syntax:

       $DEPENDSON="FAD"       
       

The method call getAttribute("DEPENDSON") would return "FAD"

getAttributes

Map<String,String> getAttributes()

getAttributeF

double getAttributeF(String key)

Short for Double.parsDouble(getAttribute(key)).

getAttributeI

int getAttributeI(String key)

areAllSpeciesTranslated

boolean areAllSpeciesTranslated()

Short for Integer.parsInt(getAttribute(key)).

getID

String getID()

The Identifier. For reactions from Dataset the ID is formed from the Dataset ID At-sign and compartment.

getName

String getName()

The human readable name of the reaction.

getConfidence

int getConfidence()

getEC

String[] getEC()

Array of EC-numbers or an array of length 0.

getCollection

ReactionCollection getCollection()

Returns the reference of the containing network object.

setReactionsWithThisStoichiometry

void setReactionsWithThisStoichiometry(Reaction[] rr)

setDirection

void setDirection(int direction)

See DIRECTION_FORWARD, DIRECTION_BACKWARD, DIRECTION_REVERSIBLE

getDirection

int getDirection()

See DIRECTION_FORWARD, DIRECTION_BACKWARD, DIRECTION_REVERSIBLE

setExcluded

void setExcluded(boolean b)

Exists but should not be used in file export

isExcluded

boolean isExcluded()

Exists but should not be used in file export. See FILTER_NOT_EXCLUDED.

isReversible

boolean isReversible()

Identical to getDirection()==DIRECTION_REVERSIBLE

getDatasetFields

String[] getDatasetFields()

If the reaction is created from a Dataset then return the dataset fields. This method, can be used to check the data that was entered user.