org.sbml.jsbml

Class SBMLErrorLog

java.lang.Object

org.sbml.jsbml.SBMLErrorLog

public class SBMLErrorLog
extends java.lang.Object

Log of errors and other events encountered during SBML processing.

This class is used both to have the same API as the libSBML equivalent, and also to store the information sent by the SBML online validator.

See:

• libSBML SBMLErrorLog
• SBML Online Validator web API

Since:

0.8

Version:

$Rev$

Author:

Nicolas Rodriguez

Field Summary

Fields

Modifier and Type	Field and Description
private java.io.File	file
private java.util.List<Option>	options
private java.lang.String	status
private java.util.List<SBMLError>	validationErrors

Constructor Summary

Constructors

Constructor and Description
SBMLErrorLog()

Method Summary

Modifier and Type	Method and Description
boolean	add(Option option) Adds an option.
boolean	add(SBMLError e) Adds an error.
void	clearLog() Clears the log.
SBMLError	getError(long n) Returns the nth SBMLError object in this log.
int	getErrorCount() Returns the number of errors that have been logged.
java.util.List<SBMLError>	getErrorsBySeverity(SBMLError.SEVERITY severity)
(package private) java.io.File	getFile() Returns the file containing the xml error log representation.
int	getNumErrors() Returns the number of errors that have been logged.
int	getNumFailsWithSeverity(SBMLError.SEVERITY severity) Returns the number of errors that have been logged with the given severity code.
(package private) java.util.List<Option>	getOptions() Returns the list of options.
(package private) java.lang.String	getStatus() Returns the status of the error log.
java.util.List<SBMLError>	getValidationErrors() Returns the list of SBMLError
void	setFile(java.io.File file) Sets the file.
void	setOptions(java.util.List<Option> options) Sets the list of options.
void	setStatus(java.lang.String status) Sets the status.
(package private) void	setValidationErrors(java.util.List<SBMLError> validationErrors) Sets the list of errors.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

file

private java.io.File file

options

private java.util.List<Option> options

validationErrors

private java.util.List<SBMLError> validationErrors

status

private java.lang.String status

Constructor Detail

SBMLErrorLog

public SBMLErrorLog()

Method Detail

add

public boolean add(Option option)

Adds an option.

Parameters:

option -

Returns:

true if the option was added successfully.

add

public boolean add(SBMLError e)

Adds an error.

Parameters:

e -

Returns:

true if the error was added successfully.

clearLog

public void clearLog()

Clears the log.

getError

public SBMLError getError(long n)

Returns the nth SBMLError object in this log.

Index n is counted from 0. Callers should first inquire about the number of items in the log by using the getNumErrors() method. Attempts to use an error index number that exceeds the actual number of errors in the log will result in a null being returned.

Parameters:

n - the index number of the error to retrieve (with 0 being the first error).

Returns:

the nth SBMLError in this log, or null if n is greater than or equal to getNumErrors().

See Also:

getNumErrors()

getFile

java.io.File getFile()

Returns the file containing the xml error log representation.

Returns:

the file containing the xml error log representation.

getNumErrors

public int getNumErrors()

Returns the number of errors that have been logged.

To retrieve individual errors from the log, callers may use getError(long n).

Returns:

the number of errors that have been logged.

getErrorCount

public int getErrorCount()

Returns the number of errors that have been logged.

To retrieve individual errors from the log, callers may use getError(long n).

Returns:

the number of errors that have been logged.

getNumFailsWithSeverity

public int getNumFailsWithSeverity(SBMLError.SEVERITY severity)

Returns the number of errors that have been logged with the given severity code.

LibSBML associates severity levels with every SBMLError object to provide an indication of how serious the problem is. Severities range from informational diagnostics to fatal (irrecoverable) errors. Given an SBMLError object instance, a caller can interrogate it for its severity level using methods such as SBMLError.getSeverity(), SBMLError.isFatal(), and so on. The present method encapsulates iteration and interrogation of all objects in an SBMLErrorLog, making it easy to check for the presence of error objects with specific severity levels.

Parameters:

severity - a value from the enumeration SBMLError.SEVERITY

Returns:

a count of the number of errors with the given severity code.

See Also:

getNumErrors()

getErrorsBySeverity

public java.util.List<SBMLError> getErrorsBySeverity(SBMLError.SEVERITY severity)

Parameters:

severity -

Returns:

getOptions

java.util.List<Option> getOptions()

Returns the list of options.

Returns:

the list of options.

getStatus

java.lang.String getStatus()

Returns the status of the error log.

Returns:

the status of the error log.

getValidationErrors

public java.util.List<SBMLError> getValidationErrors()

Returns the list of SBMLError

Returns:

the list of SBMLError

setFile

public void setFile(java.io.File file)

Sets the file.

Parameters:

file -

setOptions

public void setOptions(java.util.List<Option> options)

Sets the list of options.

Parameters:

options -

setStatus

public void setStatus(java.lang.String status)

Sets the status.

Parameters:

status -

setValidationErrors

void setValidationErrors(java.util.List<SBMLError> validationErrors)

Sets the list of errors.

Parameters:

validationErrors -