charite.christo.metannogen
Class MReaction

java.lang.Object
  charite.christo.metannogen.MObject
      charite.christo.metannogen.MReaction

All Implemented Interfaces:

DialogStringMatch.Interface, Colored, HasChildren, HasID, HasName, HasRendererText, HasInfoText, Reaction, TabItemTipIcon.Interface, Cloneable

public class MReaction
extends MObject
implements Reaction, TabItemTipIcon.Interface, HasRendererText, Colored, HasChildren, HasInfoText, HasID, DialogStringMatch.Interface

First invokation of a getter my take several Mikroseconds. Then all outputs are cached and take Nanos. All metabolite and compartment Strings are finalized and can be compared by identity instead of equals which is faster.

Field Summary

static MReaction[]

NONE

Fields inherited from interface charite.christo.metannogen.Reaction

DIRECTION_BACKWARD, DIRECTION_FORWARD, DIRECTION_REVERSIBLE, EQUALS_IGNORE_COMPARTMENT, EQUALS_IGNORE_ORIENTATION, EQUALS_IGNORE_PROTON, EQUALS_IGNORE_STOICHIOMETRY, EQUALS_RECORD_DIFFERENCES, FILTER_NOT_EXCLUDED, FILTER_REJECTED_DATASETS, TEXT_HUMAN_READABLE, TEXT_NO_COMPARTMENT, TEXT_SORT_METABOLITES, UNIQUE

Fields inherited from interface charite.christo.interfaces.HasRendererText

JLIST

Constructor Summary

MReaction()

MReaction(byte[] text)

MReaction(byte[] txt, int begin, int end)

MReaction(CharSequence text)

MReaction(String[] mmS, int[] stoichS, String[] ccS, String[] mmP, int[] stoichP, String[] ccP)

Method Summary

boolean	areAllCompartmentsTranslated()
boolean	areAllSpeciesTranslated() Short for Integer.parsInt(getAttribute(key)).
boolean	assertIntern() Checks whether the arrays have the same length and whether for all Strings s=s.intern();
boolean	equals(Reaction r, long options) Comparison
static String	equationHumanReadable(ByteArray ba, boolean sumFormula)
float[]	floatValues()
String[]	getAllNames()
String[]	getBraceExpansionID()
Object[]	getChildren()
Color	getColor()
CharSequence	getComment()
String	getCompartmentOfSpecies(String m)
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
EC_Class[]	getEC_classes()
String[]	getEC() Array of EC-numbers or an array of length 0.
MReaction[]	getIdenticalReactionsNC()
static String[]	getIDsForProton()
String	getInfoText()
static String[]	getLastEqualsDifferingMetabolite()
String	getName() The human readable name of the reaction.
String[]	getOrthologies()
Pathway[]	getPathways()
String[]	getProducts() List of products The following Arrays have exactly the same size: getCompartmentsP() getProducts() getSpeciesP() getStoichiometriesP()
MReaction	getReactionMetabolitesMappedNC(Map<String,String> mapMetabolites)
MReaction[]	getReactionsWithThisStoichiometry() Die Grundidee ist, dass initial ein Array von Reaktionen generiert wird, bei der jede Stoichiometrie nur einmal auftaucht.
String	getRendererText(int options)
MSpecies[]	getSpecies()
MSpecies[]	getSpeciesP() List of products
MSpecies[]	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() All metabolites as a unique sorted list
String[]	getSubstratesAndProductsWithoutProton() Metabolite IDs, skip hydrogen
int	getSubstratesAndProductsWithoutProtonHashCode() Dadurch wird die equals Methode extrem schnell
String[]	getSubstratesAndProductsWithoutProtonMapped()
TabItemTipIcon	getTabItemTipIcon(MouseEvent ev)
boolean	hasChildren()
int	hashCode(Object o)
boolean	isAlreadyInOtherNetwork()
boolean	isBiomass()
boolean	isExcluded() Exists but should not be used in file export.
boolean	isGeneral()
boolean	isReversible() Identical to getDirection()==DIRECTION_REVERSIBLE
boolean	isTransport() True if reactants and products have different compartments.
static void	main(String[] argv)
void	setAlreadyInOtherNetwork(boolean b)
void	setBraceExpansionID(String[] braceID)
void	setColor(Color color)
void	setComment(CharSequence s)
MReaction	setCompartmentDictionary(Map<String,String> map)
void	setConfidence(int c)
void	setDatasetFields(String[] fields)
MReaction	setDefaultCompartment(String compartment) When parsing from text, metabolites without underscor_compartment are assigned the default compartment.
void	setDefinition(CharSequence s)
void	setDeltaG(float dg)
void	setDirection(int dir) See DIRECTION_FORWARD, DIRECTION_BACKWARD, DIRECTION_REVERSIBLE
void	setEC(CharSequence s)
void	setEC(String[] ec)
void	setEquation(CharSequence text)
void	setExcluded(boolean yesNo) Exists but should not be used in file export
static void	setIDsForProton(String[] idsOfProton)
MReaction	setMetaboliteDictionary(Map<String,String> map) Used to convert metabolite ID's when parsing from String
void	setOrthologies(CharSequence s)
void	setPathways(Pathway[] ss)
void	setReactionsWithThisStoichiometry(Reaction[] rr)
void	setSubstratesOrProducts(String[] metabolite, int[] stoich, String[] compart, boolean isProduct)
MSpecies	speciesForID(CharSequence id)
MSpecies[]	speciesFromIDs(CharSequence[] ss)
String	toText(int options) Options may be 0 or TEXT_HUMAN_READABLE
String	toTextSorted(long options)
MReaction	translateMetabolitesAndCompartments(Map<String,String> mapM, Map<String,String> mapC)

Methods inherited from class charite.christo.metannogen.MObject

clone, getAttribute, getAttributeF, getAttributeI, getAttributes, getClientProperty, getClientPropertyMapAsString, getCollection, getEntireText, getHaystacksForStringSearch, getID, getIDMapped, getIDMappedSimilar, getParent, getTopAncestor, getTopAncestorID, putClientProperty, setAttributes, setCollection, setID, setName, setParent, setTextBlock, toString

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface charite.christo.metannogen.Reaction

getAttribute, getAttributeF, getAttributeI, getAttributes, getClientProperty, getCollection, getID, putClientProperty

Methods inherited from interface charite.christo.interfaces.HasID

getID

Methods inherited from interface charite.christo.DialogStringMatch.Interface

getHaystacksForStringSearch

Field Detail

NONE

public static final MReaction[] NONE

Constructor Detail

MReaction

public MReaction()

MReaction

public MReaction(CharSequence text)

MReaction

public MReaction(byte[] text)

MReaction

public MReaction(byte[] txt,
                 int begin,
                 int end)

MReaction

public MReaction(String[] mmS,
                 int[] stoichS,
                 String[] ccS,
                 String[] mmP,
                 int[] stoichP,
                 String[] ccP)

Method Detail

setOrthologies

public void setOrthologies(CharSequence s)

setDefinition

public void setDefinition(CharSequence s)

setComment

public void setComment(CharSequence s)

getComment

public final CharSequence getComment()

getReactionsWithThisStoichiometry

public MReaction[] getReactionsWithThisStoichiometry()

Description copied from interface: Reaction

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.

Specified by:

getReactionsWithThisStoichiometry in interface Reaction

setReactionsWithThisStoichiometry

public void setReactionsWithThisStoichiometry(Reaction[] rr)

Specified by:

setReactionsWithThisStoichiometry in interface Reaction

getCompartmentsWithEnzyme

public String[] getCompartmentsWithEnzyme()

Description copied from interface: Reaction

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

Specified by:

getCompartmentsWithEnzyme in interface Reaction

isTransport

public boolean isTransport()

Description copied from interface: Reaction

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

Specified by:

isTransport in interface Reaction

isBiomass

public boolean isBiomass()

Specified by:

isBiomass in interface Reaction

getDeltaG

public float getDeltaG()

Specified by:

getDeltaG in interface Reaction

setDeltaG

public void setDeltaG(float dg)

Specified by:

setDeltaG in interface Reaction

speciesForID

public MSpecies speciesForID(CharSequence id)

speciesFromIDs

public MSpecies[] speciesFromIDs(CharSequence[] ss)

getSpeciesS

public MSpecies[] getSpeciesS()

Description copied from interface: Reaction

List of reactants

Specified by:

getSpeciesS in interface Reaction

getSpeciesP

public MSpecies[] getSpeciesP()

Description copied from interface: Reaction

List of products

Specified by:

getSpeciesP in interface Reaction

getSpecies

public MSpecies[] getSpecies()

getSubstratesAndProductsWithoutProtonMapped

public String[] getSubstratesAndProductsWithoutProtonMapped()

getSubstratesAndProductsWithoutProton

public String[] getSubstratesAndProductsWithoutProton()

Metabolite IDs, skip hydrogen

Specified by:

getSubstratesAndProductsWithoutProton in interface Reaction

getConfidence

public int getConfidence()

Specified by:

getConfidence in interface Reaction

setConfidence

public void setConfidence(int c)

setDefaultCompartment

public MReaction setDefaultCompartment(String compartment)

When parsing from text, metabolites without underscor_compartment are assigned the default compartment.

setEquation

public void setEquation(CharSequence text)

setIDsForProton

public static void setIDsForProton(String[] idsOfProton)

getIDsForProton

public static String[] getIDsForProton()

setMetaboliteDictionary

public MReaction setMetaboliteDictionary(Map<String,String> map)

Used to convert metabolite ID's when parsing from String

setCompartmentDictionary

public MReaction setCompartmentDictionary(Map<String,String> map)

getSubstratesAndProducts

public String[] getSubstratesAndProducts()

All metabolites as a unique sorted list

Specified by:

getSubstratesAndProducts in interface Reaction

getProducts

public String[] getProducts()

Description copied from interface: Reaction

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

Specified by:

getProducts in interface Reaction

getSubstrates

public String[] getSubstrates()

Description copied from interface: Reaction

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

Specified by:

getSubstrates in interface Reaction

getCompartmentsP

public String[] getCompartmentsP()

Description copied from interface: Reaction

List of Compartments for products.

Specified by:

getCompartmentsP in interface Reaction

getCompartmentsS

public String[] getCompartmentsS()

Description copied from interface: Reaction

List of reactants

Specified by:

getCompartmentsS in interface Reaction

getCompartmentOfSpeciesS

public String getCompartmentOfSpeciesS(String m)

Description copied from interface: Reaction

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

Specified by:

getCompartmentOfSpeciesS in interface Reaction

getCompartmentOfSpeciesP

public String getCompartmentOfSpeciesP(String m)

Specified by:

getCompartmentOfSpeciesP in interface Reaction

getCompartmentOfSpecies

public String getCompartmentOfSpecies(String m)

getStoichiometriesS

public int[] getStoichiometriesS()

Description copied from interface: Reaction

Stoichiometries of reactants.

Specified by:

getStoichiometriesS in interface Reaction

getStoichiometriesP

public int[] getStoichiometriesP()

Description copied from interface: Reaction

Stoichiometries of products.

Specified by:

getStoichiometriesP in interface Reaction

getStoichiometryS

public int getStoichiometryS(String metabolite,
                             String compartment)

Description copied from interface: Reaction

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

Specified by:

getStoichiometryS in interface Reaction

getStoichiometryP

public int getStoichiometryP(String metabolite,
                             String compartment)

Specified by:

getStoichiometryP in interface Reaction

setSubstratesOrProducts

public void setSubstratesOrProducts(String[] metabolite,
                                    int[] stoich,
                                    String[] compart,
                                    boolean isProduct)

toText

public String toText(int options)

Description copied from interface: Reaction

Options may be 0 or TEXT_HUMAN_READABLE

Specified by:

toText in interface Reaction

getSubstratesAndProductsWithoutProtonHashCode

public int getSubstratesAndProductsWithoutProtonHashCode()

Description copied from interface: Reaction

Dadurch wird die equals Methode extrem schnell

Specified by:

getSubstratesAndProductsWithoutProtonHashCode in interface Reaction

equals

public boolean equals(Reaction r,
                      long options)

Description copied from interface: Reaction

Comparison

Specified by:

equals in interface Reaction

Returns:

true if both Reactions are identical

getLastEqualsDifferingMetabolite

public static final String[] getLastEqualsDifferingMetabolite()

areAllSpeciesTranslated

public boolean areAllSpeciesTranslated()

Description copied from interface: Reaction

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

Specified by:

areAllSpeciesTranslated in interface Reaction

areAllCompartmentsTranslated

public boolean areAllCompartmentsTranslated()

translateMetabolitesAndCompartments

public MReaction translateMetabolitesAndCompartments(Map<String,String> mapM,
                                                     Map<String,String> mapC)

main

public static void main(String[] argv)

getName

public final String getName()

Description copied from interface: Reaction

The human readable name of the reaction.

Specified by:

getName in interface HasName

Specified by:

getName in interface Reaction

Overrides:

getName in class MObject

hashCode

public final int hashCode(Object o)

toTextSorted

public String toTextSorted(long options)

floatValues

public final float[] floatValues()

isGeneral

public boolean isGeneral()

setDirection

public void setDirection(int dir)

Description copied from interface: Reaction

See DIRECTION_FORWARD, DIRECTION_BACKWARD, DIRECTION_REVERSIBLE

Specified by:

setDirection in interface Reaction

getDirection

public int getDirection()

Description copied from interface: Reaction

See DIRECTION_FORWARD, DIRECTION_BACKWARD, DIRECTION_REVERSIBLE

Specified by:

getDirection in interface Reaction

isReversible

public boolean isReversible()

Description copied from interface: Reaction

Identical to getDirection()==DIRECTION_REVERSIBLE

Specified by:

isReversible in interface Reaction

getEC

public String[] getEC()

Description copied from interface: Reaction

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

Specified by:

getEC in interface Reaction

setEC

public void setEC(CharSequence s)

setEC

public void setEC(String[] ec)

getEC_classes

public EC_Class[] getEC_classes()

getOrthologies

public String[] getOrthologies()

setPathways

public void setPathways(Pathway[] ss)

getPathways

public Pathway[] getPathways()

hasChildren

public boolean hasChildren()

Specified by:

hasChildren in interface HasChildren

getChildren

public Object[] getChildren()

Specified by:

getChildren in interface HasChildren

getIdenticalReactionsNC

public MReaction[] getIdenticalReactionsNC()

getInfoText

public final String getInfoText()

Specified by:

getInfoText in interface HasInfoText

getColor

public final Color getColor()

Specified by:

getColor in interface Colored

setColor

public final void setColor(Color color)

Specified by:

setColor in interface Colored

getRendererText

public String getRendererText(int options)

Specified by:

getRendererText in interface HasRendererText

getTabItemTipIcon

public TabItemTipIcon getTabItemTipIcon(MouseEvent ev)

Specified by:

getTabItemTipIcon in interface TabItemTipIcon.Interface

getReactionMetabolitesMappedNC

public MReaction getReactionMetabolitesMappedNC(Map<String,String> mapMetabolites)

setAlreadyInOtherNetwork

public void setAlreadyInOtherNetwork(boolean b)

isAlreadyInOtherNetwork

public boolean isAlreadyInOtherNetwork()

setExcluded

public void setExcluded(boolean yesNo)

Description copied from interface: Reaction

Exists but should not be used in file export

Specified by:

setExcluded in interface Reaction

isExcluded

public boolean isExcluded()

Description copied from interface: Reaction

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

Specified by:

isExcluded in interface Reaction

getDatasetFields

public String[] getDatasetFields()

Description copied from interface: Reaction

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.

Specified by:

getDatasetFields in interface Reaction

setDatasetFields

public void setDatasetFields(String[] fields)

assertIntern

public boolean assertIntern()

Checks whether the arrays have the same length and whether for all Strings s=s.intern();

equationHumanReadable

public static String equationHumanReadable(ByteArray ba,
                                           boolean sumFormula)

getAllNames

public String[] getAllNames()

setBraceExpansionID

public void setBraceExpansionID(String[] braceID)

getBraceExpansionID

public String[] getBraceExpansionID()