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java.lang.Objectsbrt.shell.text.fba.RxnNameSetFormatV1
public final class RxnNameSetFormatV1
This class is a concrete implemenation of RxnNameSetFormat.
Field Summary | |
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static java.lang.String |
ALL_RXNS
The string used to indicate every reaction in a fluxome. |
Constructor Summary | |
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RxnNameSetFormatV1(Fluxome fluxome)
Constructs a new reaction name collection format using the provided fluxome. |
Method Summary | |
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java.lang.String |
format(java.util.Set<java.lang.String> reactionNames)
Returns a formatted string representation of the provided set of reaction names. |
Fluxome |
getFluxome()
Returns the fluxome used to verify reaction names. |
RxnNameVerifier |
getRxnNameChecker()
Returns the reaction name verifier. |
PipeSetFormat<java.lang.String> |
getSetFormat()
Returns the format used for sets of reaction names. |
java.util.LinkedHashSet<java.lang.String> |
parse(java.lang.String set)
Parses the provided string and returns its corresponding collection of reaction names as a LinkedHashSet . |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface sbrt.shell.text.Formatter |
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format |
Field Detail |
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public static final java.lang.String ALL_RXNS
Constructor Detail |
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public RxnNameSetFormatV1(Fluxome fluxome)
fluxome
- the fluxome used to verify reaction
names.Method Detail |
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public Fluxome getFluxome()
getFluxome
in interface RxnNameSetFormat
public PipeSetFormat<java.lang.String> getSetFormat()
public RxnNameVerifier getRxnNameChecker()
public java.lang.String format(java.util.Set<java.lang.String> reactionNames)
format
in interface RxnNameSetFormat
reactionNames
- the set of reaction names to be formatted.
public java.util.LinkedHashSet<java.lang.String> parse(java.lang.String set)
LinkedHashSet
. If the string ALL_RXNS
is present the set will contain the name of
every reaction in this format's fluxome.
parse
in interface RxnNameSetFormat
parse
in interface Parser<java.util.Set<java.lang.String>>
set
- the string to be parsed.
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