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

Class MZTabError

  • All Implemented Interfaces:
    java.io.Serializable
    public class MZTabError
extends java.lang.Object
implements java.io.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, java.lang.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

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int getLineNumber()
      Getter for the field lineNumber.
      java.lang.String getMessage()
      Getter for the field message.
      MZTabErrorType getType()
      Getter for the field type.
      java.lang.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,
                  java.lang.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

      • getMessage

        public java.lang.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 java.lang.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 java.lang.Object

      • toValidationMessage

        public ValidationMessage toValidationMessage()
                                      throws java.lang.IllegalStateException
        Throws:
        java.lang.IllegalStateException