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java.lang.Objectsbrt.kernel.fba.RxnComparer
public class RxnComparer
This class is used to compare chemical reactions. Read the documentation for each of these methods carefully, because similarly named methods can perform very different operations.
Constructor Summary | |
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RxnComparer()
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Method Summary | ||
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static boolean |
equivChemRxns(ChemRxn rxn1,
ChemRxn rxn2)
Indicates if the provided chemical reactions are stoichiometrically equivalent. |
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static boolean |
equivIrrevRxns(IrrevRxn rxn1,
IrrevRxn rxn2)
Indicates if the provided irreversible reactions are stoichiometrically equivalent. |
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static boolean |
equivRevExchRxns(RevExchRxn rxn1,
RevExchRxn rxn2)
Indicates if the provided reversible exchange reactions are stoichiometrically equivalent. |
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static boolean |
equivRevRxns(RevRxn rxn1,
RevRxn rxn2)
Indicates if the provided reversible reactions are stoichiometrically equivalent. |
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static boolean |
equivSinkRxns(SinkRxn rxn1,
SinkRxn rxn2)
Indicates if the provided sink reactions are stoichiometrically equivalent. |
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static boolean |
equivSourceRxns(SourceRxn rxn1,
SourceRxn rxn2)
Indicates if the provided source reactions are stoichiometrically equivalent. |
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static
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getEquivIrrevRxnIds(java.util.Map<T,IrrevRxn> rxns)
Returns a collection of sets of the names of stoichiometrically equivalent reactions contained in the provided map. |
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static
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getEquivIrrevRxnIds(T rxnId,
java.util.Map<T,IrrevRxn> rxns)
Returns the keys in the provided map that correspond to reactions that are stoichiometrically equivalent to the reaction in the map with the specified map key. |
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static
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getEquivIrrevRxns(T rxnId,
java.util.Map<T,IrrevRxn> rxns)
Returns the reactions in the provided map that are stoichiometrically equivalent to the reaction in the map with the provided map key. |
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static
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getEquivRevExchRxnIds(java.util.Map<T,RevExchRxn> rxns)
Returns a collection of sets of the names of stoichiometrically equivalent reactions contained in the provided map. |
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static
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getEquivRevRxnIds(java.util.Map<T,RevRxn> rxns)
Returns a collection of sets of the names of stoichiometrically equivalent reactions contained in the provided map. |
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static
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getEquivRevRxnIds(T rxnId,
java.util.Map<T,RevRxn> rxns)
Returns the keys in the provided map that correspond to reactions that are stoichiometrically equivalent to the reaction in the map with the specified map key. |
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static
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getEquivRevRxns(T rxnId,
java.util.Map<T,RevRxn> rxns)
Returns the reactions in the provided map that are stoichiometrically equivalent to the reaction in the map with the provided map key. |
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static
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getEquivSinkRxnIds(java.util.Map<T,SinkRxn> rxns)
Returns a collection of sets of the names of stoichiometrically equivalent reactions contained in the provided map. |
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static
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getEquivSourceRxnIds(java.util.Map<T,SourceRxn> rxns)
Returns a collection of sets of the names of stoichiometrically equivalent reactions contained in the provided map. |
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static
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getReverseIrrevRxnIds(T rxnId,
java.util.Map<T,IrrevRxn> rxns)
Returns all of the keys in the provided map that correspond to reactions that are the reverse of the reaction specified by the provided key. |
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static
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getReverseIrrevRxns(T rxnId,
java.util.Map<T,IrrevRxn> rxns)
Returns all of the reactions in the provided map that are the reverse of the reaction specified by the provided key. |
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static
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getReverseSinkRxnIds(SourceRxn source,
java.util.Map<T,SinkRxn> rxns)
Returns all of the keys in the provided map that correspond to the sink reactions that are the reverse of the provided source reaction. |
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static
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getReverseSinkRxns(SourceRxn source,
java.util.Map<T,SinkRxn> rxns)
Returns all of the sink reactions in the provided map that are the reverse of the provided source reaction. |
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static
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getReverseSourceRxnIds(SinkRxn sink,
java.util.Map<T,SourceRxn> rxns)
Returns all of the keys in the provided map that correspond to the source reactions that are the reverse of the provided sink reaction. |
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static
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getReverseSourceRxns(SinkRxn sink,
java.util.Map<T,SourceRxn> rxns)
Returns all of the source reactions in the provided map that are the reverse of the provided sink reaction. |
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static boolean |
reverseChemRxns(ChemRxn rxn1,
ChemRxn rxn2)
Indicates if the provided chemical reactions are the reverse of each other. |
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static boolean |
reverseExchangeRxns(SinkRxn rxn1,
SourceRxn rxn2)
Indicates if the provided exchange reactions are the reverse of each other. |
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static boolean |
reverseExchangeRxns(SourceRxn rxn1,
SinkRxn rxn2)
Indicates if the provided exchange reactions are the reverse of each other. |
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static boolean |
reverseIrrevRxns(IrrevRxn rxn1,
IrrevRxn rxn2)
Indicates if the provided chemical reactions are the reverse of each other. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public RxnComparer()
Method Detail |
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public static boolean equivChemRxns(ChemRxn rxn1, ChemRxn rxn2)
A <==> B
and (2) A --> (2) B
are considered
stoichiometrically equivalent by this method, but A <==> B
and
B <==> A
are not.
rxn1
- a chemical reaction.rxn2
- a chemical reaction.
true
if the reactions are equivalent; false
otherwise.public static boolean equivIrrevRxns(IrrevRxn rxn1, IrrevRxn rxn2)
A --> B
and (2) A --> (2) B
are considered
stoichiometrically equivalent by this method.
rxn1
- an irreversible reaction.rxn2
- an irreversible reaction.
true
if the irreversible reactions are equivalent;
false
otherwise.public static boolean equivSourceRxns(SourceRxn rxn1, SourceRxn rxn2)
rxn1
- a source reaction.rxn2
- a source reaction.
true
if the source reactions are equivalent; false
otherwise.public static boolean equivSinkRxns(SinkRxn rxn1, SinkRxn rxn2)
rxn1
- a sink reaction.rxn2
- a sink reaction.
true
if the sink reactions are equivalent; false
otherwise.public static boolean equivRevExchRxns(RevExchRxn rxn1, RevExchRxn rxn2)
rxn1
- a reversible exchange reaction.rxn2
- a reversible exchange reaction.
true
if the reversible exchange reactions are equivalent;
false
otherwise.public static boolean equivRevRxns(RevRxn rxn1, RevRxn rxn2)
rxn1
must be
equivalent to either the reactants or products of rxn2
.
The products of rxn1
must also be equivalent to either the
reactants or products of rxn2
, but not equivlent to the
reactants of rxn1
. For example, (2) A <==> (2) B
and
B <==> A
are considered stoichiometrically equivalent by this
method.
rxn1
- a reversible exchange reaction.rxn2
- a reversible exchange reaction.
true
if the reversible exchange reactions are equivalent;
false
otherwise.public static boolean reverseChemRxns(ChemRxn rxn1, ChemRxn rxn2)
rxn1
must be
stoichiometrically equivalent to the products and reactants,
respectively, of rxn2
. For example, A <==> B
and
(2) B --> (2) A
are considered to be the reverse of each other
by this method.
rxn1
- a reaction.rxn2
- a reaction.
true
if the provided reactions are the reverse of each
other; false
otherwise.public static boolean reverseIrrevRxns(IrrevRxn rxn1, IrrevRxn rxn2)
rxn1
must be
stoichiometrically equivalent to the products and reactants,
respectively, of rxn2
. For example, A --> B
and
(2) B --> (2) A
are considered to be the reverse of each other
by this method.
rxn1
- a reaction.rxn2
- a reaction.
true
if the provided reactions are the reverse of each
other; false
otherwise.public static boolean reverseExchangeRxns(SourceRxn rxn1, SinkRxn rxn2)
rxn1
- a source reaction.rxn2
- a sink reaction.
true
if the exchange reactions are associated with the same
chemical species; false
otherwise.public static boolean reverseExchangeRxns(SinkRxn rxn1, SourceRxn rxn2)
rxn1
- a sink reaction.rxn2
- a source reaction.
true
if the exchange reactions are associated with the same
chemical species; false
otherwise.public static <T extends java.lang.Comparable<? super T>> java.util.Map<T,IrrevRxn> getEquivIrrevRxns(T rxnId, java.util.Map<T,IrrevRxn> rxns)
T
- a comparable type.rxnId
- the map key of the reaction whose
stoichiometrically equivalent reactions will be returned.rxns
- keys mapped to reactions.
equivIrrevRxns(IrrevRxn, IrrevRxn)
public static <T extends java.lang.Comparable<? super T>> java.util.Map<T,RevRxn> getEquivRevRxns(T rxnId, java.util.Map<T,RevRxn> rxns)
T
- a comparable type.rxnId
- the map key of the reaction whose
stoichiometrically equivalent reactions will be returned.rxns
- keys mapped to reactions.
equivRevRxns(RevRxn, RevRxn)
public static <T extends java.lang.Comparable<? super T>> java.util.Set<T> getEquivIrrevRxnIds(T rxnId, java.util.Map<T,IrrevRxn> rxns)
T
- a comparable type.rxnId
- the map key of the reaction whose stoichiometrically
equivalent reaction keys will be returned.rxns
- keys mapped to reactions.
equivIrrevRxns(IrrevRxn, IrrevRxn)
,
getEquivIrrevRxns(Comparable, Map)
public static <T extends java.lang.Comparable<? super T>> java.util.Set<T> getEquivRevRxnIds(T rxnId, java.util.Map<T,RevRxn> rxns)
T
- a comparable type.rxnId
- the map key of the reaction whose stoichiometrically
equivalent reaction keys will be returned.rxns
- keys mapped to reactions.
equivRevRxns(RevRxn, RevRxn)
,
getEquivRevRxns(Comparable, Map)
public static <T extends java.lang.Comparable<? super T>> java.util.Collection<java.util.Set<T>> getEquivIrrevRxnIds(java.util.Map<T,IrrevRxn> rxns)
T
- a comparable type.rxns
- IDs mapped to their corresponding reactions.
equivIrrevRxns(IrrevRxn, IrrevRxn)
public static <T extends java.lang.Comparable<? super T>> java.util.Collection<java.util.Set<T>> getEquivRevRxnIds(java.util.Map<T,RevRxn> rxns)
T
- a comparable type.rxns
- IDs mapped to their corresponding reactions.
equivRevRxns(RevRxn, RevRxn)
public static <T extends java.lang.Comparable<? super T>> java.util.Collection<java.util.Set<T>> getEquivSourceRxnIds(java.util.Map<T,SourceRxn> rxns)
T
- a comparable type.rxns
- IDs mapped to their corresponding reactions.
equivSourceRxns(SourceRxn, SourceRxn)
public static <T extends java.lang.Comparable<? super T>> java.util.Collection<java.util.Set<T>> getEquivSinkRxnIds(java.util.Map<T,SinkRxn> rxns)
T
- a comparable type.rxns
- IDs mapped to their corresponding reactions.
equivSinkRxns(SinkRxn, SinkRxn)
public static <T extends java.lang.Comparable<? super T>> java.util.Collection<java.util.Set<T>> getEquivRevExchRxnIds(java.util.Map<T,RevExchRxn> rxns)
T
- a comparable type.rxns
- IDs mapped to their corresponding reactions.
equivRevExchRxns(RevExchRxn, RevExchRxn)
public static <T extends java.lang.Comparable<? super T>> java.util.Set<T> getReverseIrrevRxnIds(T rxnId, java.util.Map<T,IrrevRxn> rxns)
T
- a comparable type.rxnId
- a key in the provided map that corresponds to the
reaction for which reverse reactions will be returned.rxns
- keys mapped to irreversible reactions.
reverseIrrevRxns(IrrevRxn, IrrevRxn)
,
getReverseIrrevRxns(Comparable, Map)
public static <T extends java.lang.Comparable<? super T>> java.util.Set<T> getReverseSourceRxnIds(SinkRxn sink, java.util.Map<T,SourceRxn> rxns)
T
- a comparable type.sink
- a sink reaction.rxns
- keys mapped to source reactions.
reverseExchangeRxns(SinkRxn, SourceRxn)
,
getReverseSourceRxns(SinkRxn, Map)
public static <T extends java.lang.Comparable<? super T>> java.util.Set<T> getReverseSinkRxnIds(SourceRxn source, java.util.Map<T,SinkRxn> rxns)
T
- a comparable type.source
- a source reaction.rxns
- keys mapped to sink reactions.
reverseExchangeRxns(SourceRxn, SinkRxn)
,
getReverseSinkRxns(SourceRxn, Map)
public static <T extends java.lang.Comparable<? super T>> java.util.Map<T,IrrevRxn> getReverseIrrevRxns(T rxnId, java.util.Map<T,IrrevRxn> rxns)
T
- a comparable type.rxnId
- a key in the provided map that corresponds to the
reaction for which reverse reactions will be returned.rxns
- keys mapped to irreversible reactions.
reverseIrrevRxns(IrrevRxn, IrrevRxn)
public static <T extends java.lang.Comparable<? super T>> java.util.Map<T,SourceRxn> getReverseSourceRxns(SinkRxn sink, java.util.Map<T,SourceRxn> rxns)
T
- a comparable type.sink
- a sink reaction.rxns
- keys mapped to source reactions.
reverseExchangeRxns(SinkRxn, SourceRxn)
public static <T extends java.lang.Comparable<? super T>> java.util.Map<T,SinkRxn> getReverseSinkRxns(SourceRxn source, java.util.Map<T,SinkRxn> rxns)
T
- a comparable type.source
- a source reaction.rxns
- keys mapped to sink reactions.
reverseExchangeRxns(SourceRxn, SinkRxn)
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