htsjdk.tribble.gff.Gff3Writer

All Implemented Interfaces:: Closeable, AutoCloseable

public class Gff3Writer extends Object implements Closeable

A class to write out gff3 files. Features are added using addFeature(Gff3Feature), directives using addDirective(Gff3Codec.Gff3Directive), and comments using addComment(String). Note that the version 3 directive is automatically added at creation, so should not be added separately.

Constructor Summary

Constructors

Constructor

Description

Gff3Writer(OutputStream stream)

Gff3Writer(Path path)
Method Summary

Modifier and Type

Method

Description

void

addComment(String comment)

Add comment line

void

addDirective(Gff3Codec.Gff3Directive directive)

Add a directive

void

addDirective(Gff3Codec.Gff3Directive directive, Object object)

Add a directive with an object

void

addFeature(Gff3Feature feature)

add a feature

void

close()

protected String

escapeString(String s)

escape a String.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- Gff3Writer
  
  public Gff3Writer(Path path) throws IOException
  
  Throws:
  
  IOException
- Gff3Writer
  
  public Gff3Writer(OutputStream stream)
Method Details
- addFeature
  
  public void addFeature(Gff3Feature feature) throws IOException
  
  add a feature
  
  Parameters:
  
  feature - the feature to be added
  
  Throws:
  
  IOException
- escapeString
  
  protected String escapeString(String s)
  
  escape a String. Default behavior is to call encodeString(String)
  
  Parameters:
  
  s - the string to be escaped
  
  Returns:
  
  the escaped string
- addDirective
  
  public void addDirective(Gff3Codec.Gff3Directive directive, Object object) throws IOException
  
  Add a directive with an object
  
  Parameters:
  
  directive - the directive to be added
  
  object - the object to be encoded with the directive
  
  Throws:
  
  IOException
- addDirective
  
  public void addDirective(Gff3Codec.Gff3Directive directive) throws IOException
  
  Add a directive
  
  Parameters:
  
  directive - the directive to be added
  
  Throws:
  
  IOException
- addComment
  
  public void addComment(String comment) throws IOException
  
  Add comment line
  
  Parameters:
  
  comment - the comment line (not including leading #)
  
  Throws:
  
  IOException
- close
  
  public void close() throws IOException
  
  Specified by:
  
  close in interface AutoCloseable
  
  Specified by:
  
  close in interface Closeable
  
  Throws:
  
  IOException

Class Gff3Writer

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

Gff3Writer

Gff3Writer

Method Details

addFeature

escapeString

addDirective

addDirective

addComment

close