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java.lang.Objectsbrt.shell.io.fba.ColumnOrFbaOptOutputFile<F>
F
- the fluxome type.public class ColumnOrFbaOptOutputFile<F extends Fluxome>
This class is used to write column-oriented output files containing FBA optimization data.
Constructor Summary | |
---|---|
ColumnOrFbaOptOutputFile(java.lang.String fileName,
FileFormat fileFormat,
java.util.Set<java.lang.String> columnHeaders,
FbaOptFileLineFormat fbaFormat)
Constructs a new column-oriented FBA optimization output file. |
Method Summary | ||
---|---|---|
void |
addData(java.util.Map<java.lang.String,java.lang.Double> results)
Writes the appropriate values in the provided map to this file. |
|
|
addData(S results)
Writes the appropriate values in the provided FbaOptimizer.Results 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. |
|
java.util.Set<java.lang.String> |
getColumnHeaders()
Returns the set of column headers that are written to this file. |
|
FbaOptFileLineFormat |
getFbaOptFileLineFormat()
Returns the FBA optimization file line format used to write data strings to this file. |
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java.lang.String |
getName()
Returns the canonical name of this file. |
|
java.lang.String |
getOriginalName()
Returns the provided name of this file. |
|
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 |
Constructor Detail |
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public ColumnOrFbaOptOutputFile(java.lang.String fileName, FileFormat fileFormat, java.util.Set<java.lang.String> columnHeaders, FbaOptFileLineFormat fbaFormat)
fileName
- the name of the file to create.fileFormat
- the format of the file to create.columnHeaders
- a set of valid column headers that will appear
in the file. This set can consist of reaction names and the
objective function header.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> getColumnHeaders()
public <S extends FbaOptimizer.Results> void addData(S results)
FbaOptimizer.Results
to this file.
The appropriates values are those returned by
getColumnHeaders().
addData
in interface ResultsManager<FbaOptimizer.Results>
S
- a type extending FbaOptimizer.Results
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 getColumnHeaders().
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 getColumnHeaders().
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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