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java.lang.Objectsbrt.kernel.fba.proc.RevRxnBreakerProcess
public final class RevRxnBreakerProcess
This class is used to break reversible reactions into pairs of irreversible
reactions. Reactions of type RevRxn
are broken apart into a pair of
"forward" and "reverse" reactions of type IrrevRxn
. Reactions of
type RevExchRxn
are broken apart in a pair of "source" and "sink"
reactions of types SourceRxn
and SinkRxn
.
Field Summary | |
---|---|
static java.lang.String |
FORWARD_SUFFIX
The default suffix added to the names or IDs of forward reactions. |
static java.lang.String |
REVERSE_SUFFIX
The default suffix added to the names or IDs of reverse reactions. |
static java.lang.String |
SINK_SUFFIX
The default suffix added to the names or IDs of sink reactions. |
static java.lang.String |
SOURCE_SUFFIX
The default suffix added to the names or IDs of source reactions. |
Constructor Summary | |
---|---|
RevRxnBreakerProcess()
Constructs a new reversible reaction breaker process. |
Method Summary | |
---|---|
java.util.Map<java.lang.String,ExchangeRxn> |
breakRxn(java.lang.String rxnId,
RevExchRxn rxn)
Breaks a reversible exchange reaction into a pair of irreversible source and sink exchange reactions. |
java.util.Map<java.lang.String,IrrevRxn> |
breakRxn(java.lang.String rxnId,
RevRxn rxn)
Breaks a reversible reaction into a pair of irreversible reactions. |
java.util.Map<java.lang.String,ChemRxn> |
breakRxns(java.util.Map<java.lang.String,ChemRxn> rxns)
Breaks reversible reactions into pairs of irreversible reactions. |
void |
run(ResultsManager<java.util.Map<java.lang.String,ChemRxn>> resultsManager)
Breaks the reversible reactions supplied to this process and adds the result to the provided manager. |
void |
setForwardSuffix(java.lang.String suffix)
Sets the forward suffix if a non-default value is desired. |
void |
setReverseSuffix(java.lang.String suffix)
Sets the reverse suffix if a non-default value is desired. |
void |
setRxns(java.util.Map<java.lang.String,? extends ChemRxn> rxns)
Sets the reactions for which reversible reactions will be broken. |
void |
setSinkSuffix(java.lang.String suffix)
Sets the sink suffix if a non-default value is desired. |
void |
setSourceSuffix(java.lang.String suffix)
Sets the source suffix if a non-default value is desired. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
public static final java.lang.String FORWARD_SUFFIX
public static final java.lang.String REVERSE_SUFFIX
public static final java.lang.String SOURCE_SUFFIX
public static final java.lang.String SINK_SUFFIX
Constructor Detail |
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public RevRxnBreakerProcess()
Method Detail |
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public void setForwardSuffix(java.lang.String suffix)
suffix
- the string to be appended to the names of forward reactions.public void setReverseSuffix(java.lang.String suffix)
suffix
- the string to be appended to the names of reverse reactions.public void setSourceSuffix(java.lang.String suffix)
suffix
- the string to be appended to the names of source reactions.public void setSinkSuffix(java.lang.String suffix)
suffix
- the string to be appended to the names of sink reactions.public void setRxns(java.util.Map<java.lang.String,? extends ChemRxn> rxns)
rxns
- reactions names mapped to their corresponding reaction.public void run(ResultsManager<java.util.Map<java.lang.String,ChemRxn>> resultsManager)
run
in interface KernelProcess<java.util.Map<java.lang.String,ChemRxn>>
resultsManager
- the results manager to which all reactions
will be added.public java.util.Map<java.lang.String,ChemRxn> breakRxns(java.util.Map<java.lang.String,ChemRxn> rxns)
rxns
- reaction names mapped to their corresponding reaction.
public java.util.Map<java.lang.String,IrrevRxn> breakRxn(java.lang.String rxnId, RevRxn rxn)
rxnId
- the reaction name or ID.rxn
- the reversible reaction.
public java.util.Map<java.lang.String,ExchangeRxn> breakRxn(java.lang.String rxnId, RevExchRxn rxn)
rxnId
- the reaction name or ID.rxn
- the reversible exchange reaction.
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