sbrt.shell.io.fba
Class SfoofSource<F extends Fluxome>

java.lang.Object
  extended by sbrt.shell.io.fba.SfoofSource<F>
Type Parameters:
F - the fluxome type.
All Implemented Interfaces:
java.util.Iterator<SerFbaOptOutputFile<F>>

public class SfoofSource<F extends Fluxome>
extends java.lang.Object
implements java.util.Iterator<SerFbaOptOutputFile<F>>

This class is used to provide a source of serialized FBA optimization output files.

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

Constructor Summary
SfoofSource(java.util.Iterator<java.lang.String> fileNameSource, FileFormat fileFormat, java.util.Set<java.lang.String> filterKeys, FbaOptFileLineFormat fbaFormat)
          Constructs a new source of serialized FBA optimization output files.
SfoofSource(java.util.Iterator<java.lang.String> fileNameSource, java.lang.String fileNameSourceName, FileFormat fileFormat, java.util.Set<java.lang.String> filterKeys, FbaOptFileLineFormat fbaFormat)
          Constructs a new source of serialized FBA optimization output files.
 
Method Summary
 FileFormat getFileFormat()
          Returns the file format used to create files of type SerFbaOptOutputFile.
 boolean hasNext()
          Indicates if this iterator can return another file using the next() method.
 SerFbaOptOutputFile<F> next()
          Returns the next serialized map output file with the next name returned by the file name source.
 void remove()
          Throws UnsupportedOperationException.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SfoofSource

public SfoofSource(java.util.Iterator<java.lang.String> fileNameSource,
                   FileFormat fileFormat,
                   java.util.Set<java.lang.String> filterKeys,
                   FbaOptFileLineFormat fbaFormat)
Constructs a new source of serialized FBA optimization output files.

Parameters:
fileNameSource - the file name source.
fileFormat - the file format used to write files.
filterKeys - a set of valid keys that will appear in the files produced by this source. This set can consist of reaction names and the objective function header.
fbaFormat - the map format used to supply a header object for objective values.
Throws:
java.lang.NullPointerException - if any argument except filterKeys is null.

SfoofSource

public SfoofSource(java.util.Iterator<java.lang.String> fileNameSource,
                   java.lang.String fileNameSourceName,
                   FileFormat fileFormat,
                   java.util.Set<java.lang.String> filterKeys,
                   FbaOptFileLineFormat fbaFormat)
Constructs a new source of serialized FBA optimization output files.

Parameters:
fileNameSource - the file name source.
fileNameSourceName - the name of the file name source.
fileFormat - the file format used to write files.
filterKeys - a set of valid keys that will appear in the files produced by this source. This set can consist of reaction names and the objective function header.
fbaFormat - the map format used to supply a header object for objective values.
Throws:
java.lang.NullPointerException - if any argument except filterKeys is null.
Method Detail

getFileFormat

public FileFormat getFileFormat()
Returns the file format used to create files of type SerFbaOptOutputFile.

Returns:
the file format used to create files of type SerFbaOptOutputFile.

hasNext

public boolean hasNext()
Indicates if this iterator can return another file using the next() method.

Specified by:
hasNext in interface java.util.Iterator<SerFbaOptOutputFile<F extends Fluxome>>
Returns:
true if this iterator can return another file; false otherwise.

next

public SerFbaOptOutputFile<F> next()
Returns the next serialized map output file with the next name returned by the file name source.

Specified by:
next in interface java.util.Iterator<SerFbaOptOutputFile<F extends Fluxome>>
Returns:
the next serialized map output file.

remove

public void remove()
Throws UnsupportedOperationException.

Specified by:
remove in interface java.util.Iterator<SerFbaOptOutputFile<F extends Fluxome>>
Throws:
java.lang.UnsupportedOperationException