Package uk.ac.ebi.pride.jmztab2.utils.errors

Class MZTabError

java.lang.Object

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError

All Implemented Interfaces:

Serializable

public class MZTabError
extends Object
implements Serializable

mzTab files can be validated to ensure that they comply with the latest version of the format specification. The process includes two steps: first of all the basic model architecture is created, including the metadata section and the generation of the table column headers. The second step is the validation of the column rows, which take most of the processing time. The class MZTabFileParser is used to parse and validate the mzTab files. If the validation is successful, an MZTabFile model will be then generated. A series of messages are then reported, which can help to diagnose different types of format-related (reporting format problems) and/or logical (reporting errors related to the logical relationships among the different sections in a file) errors. At the moment of writing, there are about sixty types of error messages (http://mztab.googlecode.com/wiki/jmzTab_message). The validation messages have a unique identifier and are classified in three levels: Info, Warn and Error, according to the requirements included in the specification document.

Since:

06/02/13

Author:

qingwei

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
MZTabError(MZTabErrorType type, int lineNumber, String... values)	System will fill a couple of values one by one, and generate a concrete error message during parse lineNumber line in mzTab file.

Method Summary

Modifier and Type	Method	Description
int	getLineNumber()	Getter for the field lineNumber.
String	getMessage()	Getter for the field message.
MZTabErrorType	getType()	Getter for the field type.
String	toString()	Code: Unique number for error/warn Category: Currently, there are three types of messages: Format, Logical Original: Message expression pattern. "{?}"
ValidationMessage	toValidationMessage()

Methods inherited from class java.lang.Object

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

Constructor Detail

MZTabError

public MZTabError(MZTabErrorType type,
                  int lineNumber,
                  String... values)

System will fill a couple of values one by one, and generate a concrete error message during parse lineNumber line in mzTab file.

Parameters:

type - SHOULD NOT null.

lineNumber - SHOULD be positive integer. Except "-1", which means the line number unknown.

values - May be null, if no variable in error's original pattern.

Method Detail

getType

public MZTabErrorType getType()

Getter for the field type.

Returns:

MZTabErrorType

See Also:

FormatErrorType, LogicalErrorType

getMessage

public String getMessage()

Getter for the field message.

Returns:

a concrete error/warn message.

getLineNumber

public int getLineNumber()

Getter for the field lineNumber.

Returns:

the line number.

toString

public String toString()

Code: Unique number for error/warn Category: Currently, there are three types of messages: Format, Logical Original: Message expression pattern. "{?}" is a couple of parameters which can be filled during validate processing. Cause: A readable text to describe the reason why raise this error/warn. Currently, these cause message coming from mztab specification mainly.

Overrides:

toString in class Object

toValidationMessage

public ValidationMessage toValidationMessage()
                                      throws IllegalStateException

Throws:

IllegalStateException