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java.lang.Objectsbrt.shell.io.fba.FluxIntervalInputFile
public class FluxIntervalInputFile
This class is used to read flux interval input files.
Constructor Summary | |
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FluxIntervalInputFile(java.lang.String fileName,
FileFormat fileFormat,
java.util.Set<LinearComb<java.lang.String>> requiredVariables,
MapFormat<LinearComb<java.lang.String>,Interval> mapFormat,
Fluxome fluxome,
double tolerance)
Constructs a new flux-interval input file. |
Method Summary | |
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void |
close()
Closes this file. |
static FluxConstraints |
convertConstraints(java.util.Map<LinearComb<java.lang.String>,Interval> intervals,
Fluxome fluxome,
double tolerance)
Converts the provided intervals into a FluxConstraints object. |
static java.util.Set<LinearComb<java.lang.String>> |
convertVariables(java.util.Set<java.lang.String> rxnNames)
Converts a set of reaction names to a set of single-term linear combinations. |
java.lang.String |
getCanonicalName()
Returns the canonical name of this file. |
java.lang.String |
getOriginalName()
Returns the provided name of this file. |
double |
getTolerance()
Returns the constraint tolerance. |
boolean |
isClosed()
Indicates if this file has already been closed. |
java.util.Iterator<FluxConstraints> |
iterator()
Returns an iterator over the flux intervals contained in this file. |
static void |
verifyFluxConstraints(java.util.Map<java.lang.String,Interval> fluxConsts,
Fluxome fluxome,
double tolerance)
Verifies that the provided constraints are legitimate for the provided fluxome. |
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 FluxIntervalInputFile(java.lang.String fileName, FileFormat fileFormat, java.util.Set<LinearComb<java.lang.String>> requiredVariables, MapFormat<LinearComb<java.lang.String>,Interval> mapFormat, Fluxome fluxome, double tolerance)
fileName
- the name of the file to be read.fileFormat
- the format of the file to be read.requiredVariables
- the variables that must be contained in the file
to be read.mapFormat
- the format of data strings in the file to be read.fluxome
- the fluxome for which flux intervals correspond.tolerance
- the constraint tolerance.Method Detail |
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public double getTolerance()
public void close()
close
in interface SbrtFile
public final java.lang.String getOriginalName()
getOriginalName
in interface SbrtFile
public final java.lang.String getCanonicalName()
getCanonicalName
in interface SbrtFile
File.getCanonicalPath()
public boolean isClosed()
isClosed
in interface SbrtFile
true
if this file is closed; false
othewise.public java.util.Iterator<FluxConstraints> iterator()
iterator
in interface java.lang.Iterable<FluxConstraints>
public static java.util.Set<LinearComb<java.lang.String>> convertVariables(java.util.Set<java.lang.String> rxnNames)
rxnNames
- the reaction names to be used for constructing
single-term linear combinations.
public static FluxConstraints convertConstraints(java.util.Map<LinearComb<java.lang.String>,Interval> intervals, Fluxome fluxome, double tolerance)
FluxConstraints
object. If
a provided linear combination contains a single term, with coefficient
equal to 1, and constant equal to 0, the interval will be applied to the
variable itself (not the linear combination), which is retrievable using
FluxConstraints.getConstraint(String) and
FluxConstraints.getFluxConstraints(). The flux intervals are
also verified against the provided fluxome.
intervals
- reaction name expressions mapped to their corresponding
interval.fluxome
- the fluxome for which flux intervals correspond.tolerance
- the contraint tolerance.
FluxConstraints
object corresponding to the provided
input.public static void verifyFluxConstraints(java.util.Map<java.lang.String,Interval> fluxConsts, Fluxome fluxome, double tolerance)
fluxConsts
- reaction named mapped to flux constraints.fluxome
- the fluxome for which the flux constraints correspond.tolerance
- the constraint tolerance.
ApplicationException
- if the provided flux constraints are not
valid for the provided fluxome.Fluxome.isValid(Interval, String, double)
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