Package htsjdk.tribble.gff

Class Gff3Writer

java.lang.Object

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