Package org.biojava.bio.program.tagvalue

Class RegexParser

java.lang.Object
org.biojava.bio.program.tagvalue.RegexParser
All Implemented Interfaces:
TagValueParser
public class RegexParser extends Object implements TagValueParser

A TagValueParser that splits a line based upon a regular expression. There are configuration parameters analgous to those in LineSplitParser for configuring parsing details.

Since:
1.3
Author:
Matthew Pocock, Keith James (enabled empty line EOR)

  • Field Summary

    Fields inherited from interface org.biojava.bio.program.tagvalue.TagValueParser

    EMPTY_LINE_EOR

  • Constructor Summary

    Constructors
    Constructor
    Description
    RegexParser()
    Create a new RegexParser with all boolean values set to false.

  • Method Summary

    Modifier and Type
    Method
    Description
    boolean
    getContinueOnEmptyTag()
    Report whether empty tags will be treated as continuations of the last non -empty tag.
    String
    getEndOfRecord()
    Get the explicit end-of-record string.
    boolean
    getMergeSameTag()
    Report whether empty tags will be treated as continuations of the last non -empty tag.
    Pattern
    getPattern()
    Get the Pattern currently used to split lines.
    int
    getTagGroup()
    Get the group number that matches the tag.
    boolean
    getTrimTag()
    See if trimming of tags is enabled.
    boolean
    getTrimValue()
    See if trimming of values is enabled.
    int
    getValueGroup()
    Get the group number that matches the value.
    TagValue
    parse(Object o)
     
    void
    setContinueOnEmptyTag(boolean continueOnEmptyTag)
    Decide whether to treat empty tags as continuations of the previous non -empty tag.
    void
    setEndOfRecord(String endOfRecord)
    Set the explicit end-of-record string.
    void
    setMergeSameTag(boolean mergeSameTag)
    Decide if multiple examples of a single tag should be merged into a single start/endTag pair with multiple values, or multiple start/endTag pairs each with a single value.
    void
    setPattern(Pattern pattern)
    Set the Pattern used to split lines.
    void
    setTagGroup(int group)
    Set the group number that will match the tag.
    void
    setTrimTag(boolean trimTag)
    Enable trimming of the tag using String.trim().
    void
    setTrimValue(boolean trimValue)
    Enable trimming of the value using String.trim().
    void
    setValueGroup(int group)
    Set the group number that will match the value.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • RegexParser

      public RegexParser()
      Create a new RegexParser with all boolean values set to false.

  • Method Details

    • setPattern

      public void setPattern(Pattern pattern)
      Set the Pattern used to split lines.
      Parameters:
      pattern - the Pattern used to split lines

    • getPattern

      public Pattern getPattern()
      Get the Pattern currently used to split lines.
      Returns:
      the current Pattern

    • setTagGroup

      public void setTagGroup(int group)
      Set the group number that will match the tag.
      Parameters:
      group - the tag group number

    • getTagGroup

      public int getTagGroup()
      Get the group number that matches the tag.
      Returns:
      the tag group number

    • setValueGroup

      public void setValueGroup(int group)
      Set the group number that will match the value.
      Parameters:
      group - the value group number

    • getValueGroup

      public int getValueGroup()
      Get the group number that matches the value.
      Returns:
      the value group number

    • setEndOfRecord

      public void setEndOfRecord(String endOfRecord)
      Set the explicit end-of-record string.
      Parameters:
      endOfRecord - the new endOfRecord String

    • getEndOfRecord

      public String getEndOfRecord()
      Get the explicit end-of-record string.
      Returns:
      the current endOfRecord String

    • setTrimTag

      public void setTrimTag(boolean trimTag)
      Enable trimming of the tag using String.trim().
      Parameters:
      trimTag - true if tags should be trimmed, false otherwise

    • getTrimTag

      public boolean getTrimTag()
      See if trimming of tags is enabled.
      Returns:
      true if tag trimming is enabled, false otherwise

    • setTrimValue

      public void setTrimValue(boolean trimValue)
      Enable trimming of the value using String.trim().
      Parameters:
      trimValue - true if values should be trimmed, false otherwise

    • getTrimValue

      public boolean getTrimValue()
      See if trimming of values is enabled.
      Returns:
      true if value trimming is enabled, false otherwise

    • setContinueOnEmptyTag

      public void setContinueOnEmptyTag(boolean continueOnEmptyTag)
      Decide whether to treat empty tags as continuations of the previous non -empty tag.
      Parameters:
      continueOnEmptyTag - true if empty tags should be replaced, false otherwise

    • getContinueOnEmptyTag

      public boolean getContinueOnEmptyTag()
      Report whether empty tags will be treated as continuations of the last non -empty tag.
      Returns:
      true if empty tags will be replaced, false otherwise

    • setMergeSameTag

      public void setMergeSameTag(boolean mergeSameTag)
      Decide if multiple examples of a single tag should be merged into a single start/endTag pair with multiple values, or multiple start/endTag pairs each with a single value.
      Parameters:
      mergeSameTag - true if tags will be merged, false otherwise

    • getMergeSameTag

      public boolean getMergeSameTag()
      Report whether empty tags will be treated as continuations of the last non -empty tag.
      Returns:
      true if tags will be merged, false otherwise

    • parse

      public TagValue parse(Object o) throws ParserException
      Specified by:
      parse in interface TagValueParser
      Throws:
      ParserException