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java.lang.Objectsbrt.shell.io.fba.RowOrFbaOptOutputFile<F>
F
- the fluxome type.public class RowOrFbaOptOutputFile<F extends Fluxome>
This class is used to write row-oriented output files containing FBA optimization data.
Constructor Summary | |
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RowOrFbaOptOutputFile(java.lang.String fileName,
FileFormat fileFormat,
FbaOptFileLineFormat fbaFormat)
Constructs a new row-oriented FBA optimization output file. |
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RowOrFbaOptOutputFile(java.lang.String fileName,
FileFormat fileFormat,
java.util.Set<java.lang.String> rowHeaders,
FbaOptFileLineFormat fbaFormat)
Constructs a new row-oriented FBA optimization output file. |
Method Summary | |
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void |
addData(FbaOptimizer.Results results)
Writes the appropriate values in the provided FbaOptimizer.Results to this file. |
void |
addData(java.util.Map<java.lang.String,java.lang.Double> results)
Writes the appropriate values in the provided map to this file. |
void |
breakPoint()
Writes a line of # symbols to this file. |
void |
close()
Closes this file. |
java.lang.String |
getCanonicalName()
Returns the canonical name of this file. |
FbaOptFileLineFormat |
getFbaOptFileLineFormat()
Returns the FBA optimization file line format used to write data strings to this file. |
java.lang.String |
getName()
Returns the canonical name of this file. |
java.lang.String |
getOriginalName()
Returns the provided name of this file. |
java.util.Set<java.lang.String> |
getRowHeaders()
Returns the set of row headers whose values will be written to this output file when results are added. |
boolean |
isClosed()
Indicates if this file has already been closed. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface sbrt.kernel.io.ResultsManager |
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addData |
Constructor Detail |
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public RowOrFbaOptOutputFile(java.lang.String fileName, FileFormat fileFormat, java.util.Set<java.lang.String> rowHeaders, FbaOptFileLineFormat fbaFormat)
fileName
- the name of the file to create.fileFormat
- the format of the file to create.rowHeaders
- a set of valid row headers that will appear
in the file. 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 file.public RowOrFbaOptOutputFile(java.lang.String fileName, FileFormat fileFormat, FbaOptFileLineFormat fbaFormat)
fileName
- the name of the file to create.fileFormat
- the format of the file to create.fbaFormat
- the map format used to write data strings
to the file.Method Detail |
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public FbaOptFileLineFormat getFbaOptFileLineFormat()
getFbaOptFileLineFormat
in interface FbaOptOutputFile<F extends Fluxome>
public java.util.Set<java.lang.String> getRowHeaders()
null
if every value in an added set of
results will be written to this file.public void addData(FbaOptimizer.Results results)
FbaOptimizer.Results
to this file.
The appropriates values are those returned by
getRowHeaders().
results
- the results to write to this file.
java.lang.IllegalArgumentException
- if the provided
results object does not contain all the variables in the
set returned by getRowHeaders().
java.lang.IllegalStateException
- if close()
has already been called.public void addData(java.util.Map<java.lang.String,java.lang.Double> results)
results
- the results vector to write to this file.
java.lang.IllegalArgumentException
- if the provided
map does not contain all the keys in the
set returned by getRowHeaders().
java.lang.IllegalStateException
- if close()
has already been called.public void close()
close
in interface ResultsManager<FbaOptimizer.Results>
close
in interface SbrtFile
public final java.lang.String getName()
getName
in interface ResultsManager<FbaOptimizer.Results>
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 ResultsManager<FbaOptimizer.Results>
isClosed
in interface SbrtFile
true
if this file is closed;
false
othewise.ResultsManager.close()
public void breakPoint()
#
symbols to this file.
breakPoint
in interface ResultsManager<FbaOptimizer.Results>
java.lang.IllegalStateException
- if close()
has already been called.
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