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java.lang.Objectsbrt.shell.io.fba.FluxCapInputFile
public class FluxCapInputFile
This class is used to read files containing flux caps. Flux caps are used in Mahadevan-Schilling flux interval processes.
Constructor Summary | |
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FluxCapInputFile(java.lang.String fileName,
FluxCapFormat lineFormat)
Constructs a new flux cap input file. |
Method Summary | |
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void |
close()
Closes this file. |
java.lang.String |
getCanonicalName()
Returns the canonical name of this file. |
UnmodifiableMap<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> |
getFluxCaps()
Returns the flux caps contained in this file. |
Fluxome |
getFluxome()
Returns the fluxome used to verify reaction names. |
MapFormat<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> |
getMapFormat()
Returns the map format used to parse this file. |
java.lang.String |
getOriginalName()
Returns the provided name of this file. |
boolean |
isClosed()
Indicates if this file has already been closed. |
java.util.Iterator<java.util.Map<java.lang.String,java.util.Set<LinearComb<java.lang.String>>>> |
iterator()
Returns an iterator over this file. |
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 FluxCapInputFile(java.lang.String fileName, FluxCapFormat lineFormat)
fileName
- the name of the file to read.lineFormat
- the format used to parse the data strings in this
file.Method Detail |
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public Fluxome getFluxome()
public UnmodifiableMap<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> getFluxCaps()
public MapFormat<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> getMapFormat()
getMapFormat
in interface MapTextFile<java.lang.String,java.util.Set<LinearComb<java.lang.String>>>
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<java.util.Map<java.lang.String,java.util.Set<LinearComb<java.lang.String>>>> iterator()
iterator
in interface java.lang.Iterable<java.util.Map<java.lang.String,java.util.Set<LinearComb<java.lang.String>>>>
getFluxCaps()
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