sbrt.shell.io.fba
Class FluxCapInputFile

java.lang.Object
  extended by sbrt.shell.io.fba.FluxCapInputFile
All Implemented Interfaces:
java.lang.Iterable<java.util.Map<java.lang.String,java.util.Set<LinearComb<java.lang.String>>>>, InputFile<java.util.Map<java.lang.String,java.util.Set<LinearComb<java.lang.String>>>>, MapInputFile<java.lang.String,java.util.Set<LinearComb<java.lang.String>>>, MapTextFile<java.lang.String,java.util.Set<LinearComb<java.lang.String>>>, MapTextInputFile<java.lang.String,java.util.Set<LinearComb<java.lang.String>>>, SbrtFile

public class FluxCapInputFile
extends java.lang.Object
implements MapTextInputFile<java.lang.String,java.util.Set<LinearComb<java.lang.String>>>

This class is used to read files containing flux caps. Flux caps are used in Mahadevan-Schilling flux interval processes.

Author:
This class was written and documented by Jeremiah Wright while in the Wagner lab.

Constructor Summary
FluxCapInputFile(java.lang.String fileName, FluxCapFormat lineFormat)
          Constructs a new flux cap input file.
 
Method Summary
 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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

FluxCapInputFile

public FluxCapInputFile(java.lang.String fileName,
                        FluxCapFormat lineFormat)
Constructs a new flux cap input file.

Parameters:
fileName - the name of the file to read.
lineFormat - the format used to parse the data strings in this file.
Method Detail

getFluxome

public Fluxome getFluxome()
Returns the fluxome used to verify reaction names.

Returns:
the fluxome used to verify reaction names.

getFluxCaps

public UnmodifiableMap<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> getFluxCaps()
Returns the flux caps contained in this file.

Returns:
the flux caps contained in this file.

getMapFormat

public MapFormat<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> getMapFormat()
Returns the map format used to parse this file.

Specified by:
getMapFormat in interface MapTextFile<java.lang.String,java.util.Set<LinearComb<java.lang.String>>>
Returns:
the map format used to parse this file.

close

public void close()
Closes this file. If this file is already closed, then invoking this method has no effect.

Specified by:
close in interface SbrtFile

getOriginalName

public final java.lang.String getOriginalName()
Returns the provided name of this file.

Specified by:
getOriginalName in interface SbrtFile
Returns:
the provided name of this file.

getCanonicalName

public final java.lang.String getCanonicalName()
Returns the canonical name of this file.

Specified by:
getCanonicalName in interface SbrtFile
Returns:
the canonical name of this file.
See Also:
File.getCanonicalPath()

isClosed

public boolean isClosed()
Indicates if this file has already been closed.

Specified by:
isClosed in interface SbrtFile
Returns:
true if this file is closed; false othewise.

iterator

public java.util.Iterator<java.util.Map<java.lang.String,java.util.Set<LinearComb<java.lang.String>>>> iterator()
Returns an iterator over this file. This iterator returns only a single map.

Specified by:
iterator in interface java.lang.Iterable<java.util.Map<java.lang.String,java.util.Set<LinearComb<java.lang.String>>>>
Returns:
an iterator over this file.
See Also:
getFluxCaps()