sbrt.shell.proc.fba
Class PalssonSbmlReaderManager

java.lang.Object
  extended by sbrt.shell.mng.AbstractProcessManager
      extended by sbrt.shell.proc.fba.PalssonSbmlReaderManager
All Implemented Interfaces:
ProcessManager<java.lang.String,java.lang.String>, ShellProcessManager<java.lang.String,java.lang.String>

public final class PalssonSbmlReaderManager
extends AbstractProcessManager
implements ShellProcessManager<java.lang.String,java.lang.String>

This class is used to manage the reading of SBML files obtained from Palsson's website.

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

Field Summary
static java.lang.String FLUX_BOUNDS_FILE_NAME
          Used to denote the name of the file to which the flux bounds should be written.
static java.lang.String FLUX_VECTOR_FILE_NAME
          Used to denote the name of the file to which the flux vector should be written.
static java.lang.String GENE_FILE_NAME
          Used to denote the name of the file to which gene-reaction relationships should be written.
static UnmodifiableSet<java.lang.String> optionalKeywords
          The set of keywords understood, but not required, by this process manager.
static java.lang.String PROTEIN_FILE_NAME
          Used to denote the name of the file to which protein-reaction relationships should be written.
static UnmodifiableSet<java.lang.String> requiredKeywords
          The set of keywords required by this process manager.
static java.lang.String RXN_FILE_NAME
          Used to denote the name of the file to which chemical reactions should be written.
static java.lang.String SBML_INPUT_FILE
          The keyword used to denote the name of the SBML input file.
 
Fields inherited from class sbrt.shell.mng.AbstractProcessManager
ALGORITHM, COMPLETED, DATA_HEADERS, DEV_NULL, ELAPSED_TIME, FILE_FORMAT, INPUT_FILE, INPUT_FILE_NAME_FILE, ITERATIONS, OUTPUT_FILE_NAME, OUTPUT_FILE_NAME_FILE, PERCENT, PERCENT_COMPLETED, SEED, ZERO_CUTOFF
 
Constructor Summary
PalssonSbmlReaderManager()
           
 
Method Summary
 void execute(java.io.PrintWriter out)
          Executes the process this process manager controls and writes informative messages to the provided print writer.
 UnmodifiableSet<java.lang.String> getOptionalKeys()
          Returns the set of keywords understood, but not required, by this process manager.
 UnmodifiableSet<java.lang.String> getRequiredKeys()
          Returns the set of keywords required by this process manager.
 void setInput(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
          Uses the provided input to prepare this process manager for execution.
 
Methods inherited from class sbrt.shell.mng.AbstractProcessManager
check, closeFile, closeRm, execute, getFileFormat, getFileFormat, getFileNameSource, getIterations, getSeed, getTextFileFormat, getZeroCutoff, getZeroCutoff, parseInt, parseLong, printProgress, printProgress, printProgress, runProcess, setInput
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface sbrt.shell.mng.ProcessManager
check, execute, setInput
 

Field Detail

GENE_FILE_NAME

public static final java.lang.String GENE_FILE_NAME
Used to denote the name of the file to which gene-reaction relationships should be written.

See Also:
Constant Field Values

PROTEIN_FILE_NAME

public static final java.lang.String PROTEIN_FILE_NAME
Used to denote the name of the file to which protein-reaction relationships should be written.

See Also:
Constant Field Values

RXN_FILE_NAME

public static final java.lang.String RXN_FILE_NAME
Used to denote the name of the file to which chemical reactions should be written.

See Also:
Constant Field Values

FLUX_VECTOR_FILE_NAME

public static final java.lang.String FLUX_VECTOR_FILE_NAME
Used to denote the name of the file to which the flux vector should be written.

See Also:
Constant Field Values

FLUX_BOUNDS_FILE_NAME

public static final java.lang.String FLUX_BOUNDS_FILE_NAME
Used to denote the name of the file to which the flux bounds should be written.

See Also:
Constant Field Values

SBML_INPUT_FILE

public static final java.lang.String SBML_INPUT_FILE
The keyword used to denote the name of the SBML input file.

See Also:
Constant Field Values

requiredKeywords

public static final UnmodifiableSet<java.lang.String> requiredKeywords
The set of keywords required by this process manager.


optionalKeywords

public static final UnmodifiableSet<java.lang.String> optionalKeywords
The set of keywords understood, but not required, by this process manager.

Constructor Detail

PalssonSbmlReaderManager

public PalssonSbmlReaderManager()
Method Detail

getRequiredKeys

public UnmodifiableSet<java.lang.String> getRequiredKeys()
Returns the set of keywords required by this process manager.

Specified by:
getRequiredKeys in interface ProcessManager<java.lang.String,java.lang.String>
Returns:
the set of keywords required by this process manager.

getOptionalKeys

public UnmodifiableSet<java.lang.String> getOptionalKeys()
Returns the set of keywords understood, but not required, by this process manager.

Specified by:
getOptionalKeys in interface ProcessManager<java.lang.String,java.lang.String>
Returns:
the set of keywords understood, but not required, by this process manager.

setInput

public void setInput(ManagerInput<java.lang.String,java.lang.String> input,
                     java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. As the input is processed, informative messages are printed to the provided print writer.

Specified by:
setInput in interface ProcessManager<java.lang.String,java.lang.String>
Parameters:
input - all of the information required to prepare this process manager for execution.
out - the print writer to which all messages will be printed.

execute

public void execute(java.io.PrintWriter out)
Executes the process this process manager controls and writes informative messages to the provided print writer.

Specified by:
execute in interface ProcessManager<java.lang.String,java.lang.String>
Parameters:
out - the print writer where informative messagse will be written.
Throws:
java.lang.IllegalStateException - if no input was provided to this process manager.