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

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

public class CofoofSource<F extends Fluxome>
extends java.lang.Object
implements java.util.Iterator<ColumnOrFbaOptOutputFile<F>>

This class is used to provide a source of column-oriented FBA optimization output files.

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

Constructor Summary
CofoofSource(java.util.Iterator<java.lang.String> fileNameSource, FileFormat fileFormat, java.util.Set<java.lang.String> columnHeaders, FbaOptFileLineFormat fbaFormat)
          Constructs a new source of column-oriented FBA optimization output files.
CofoofSource(java.util.Iterator<java.lang.String> fileNameSource, java.lang.String fileNameSourceName, FileFormat fileFormat, java.util.Set<java.lang.String> columnHeaders, FbaOptFileLineFormat fbaFormat)
          Constructs a new source of column-oriented FBA optimization output files.
 
Method Summary
 FbaOptFileLineFormat getFbaOptFileLineFormat()
          Returns the FBA optimization file line format used to write data strings to files produced by this source.
 FileFormat getFileFormat()
          Returns the file format used to create files of type ColumnOrFbaOptOutputFile.
 boolean hasNext()
          Indicates if this iterator can return another file using the next() method.
 ColumnOrFbaOptOutputFile<F> next()
          Returns the next column-oriented 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

CofoofSource

public CofoofSource(java.util.Iterator<java.lang.String> fileNameSource,
                    FileFormat fileFormat,
                    java.util.Set<java.lang.String> columnHeaders,
                    FbaOptFileLineFormat fbaFormat)
Constructs a new source of column-oriented FBA optimization output files.

Parameters:
fileNameSource - the file name source.
fileFormat - the file format used to write files.
columnHeaders - a set of valid column headers that will appear in the files produced by this source. This set can consist of reaction names and the objective function header. If null, all values from every added set of results will be written to this file.
fbaFormat - the map format used to write data strings to the files produced by this source.
Throws:
java.lang.NullPointerException - if any argument except columnHeaders is null.

CofoofSource

public CofoofSource(java.util.Iterator<java.lang.String> fileNameSource,
                    java.lang.String fileNameSourceName,
                    FileFormat fileFormat,
                    java.util.Set<java.lang.String> columnHeaders,
                    FbaOptFileLineFormat fbaFormat)
Constructs a new source of column-oriented 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.
columnHeaders - a set of valid column headers that will appear in the files produced by this source. This set can consist of reaction names and the objective function header. If null, all values from every added set of results will be written to this file.
fbaFormat - the map format used to write data strings to the files produced by this source.
Throws:
java.lang.NullPointerException - if any argument except columnHeaders is null.
Method Detail

getFileFormat

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

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

getFbaOptFileLineFormat

public FbaOptFileLineFormat getFbaOptFileLineFormat()
Returns the FBA optimization file line format used to write data strings to files produced by this source.

Returns:
the FBA optimization file line format used to write data strings to files produced by this source.

hasNext

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

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

next

public ColumnOrFbaOptOutputFile<F> next()
Returns the next column-oriented map output file with the next name returned by the file name source.

Specified by:
next in interface java.util.Iterator<ColumnOrFbaOptOutputFile<F extends Fluxome>>
Returns:
the next column-oriented map output file.

remove

public void remove()
Throws UnsupportedOperationException.

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