Package org.biojava.bio.seq.io.agave

Class AgaveWriter

java.lang.Object

org.biojava.bio.seq.io.agave.AgaveWriter

public class AgaveWriter
extends java.lang.Object

Writes Sequence into AGAVE XML document. The AGAVE format is defined in agave.dtd which can be downloaded from http://www.agavexml.org.

Author:

Hanning Ni, Brian King

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
protected class	AgaveWriter.Indent	Implements indenting for elements.

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	INDENT	use a two space indent
protected AGAVEAnnotFilter	mAnnotFilter	The AnnotationMap to use for getting AGAVE XML attributes from a Sequence Annotation.
protected org.biojava.bio.seq.io.agave.PCDATAFilterWriter	mFilter	writes PCDATA replacing XML characters with escape entities
protected AgaveWriter.Indent	mIndent	indent
protected java.io.PrintWriter	mOut	Write to XML document
protected boolean	mWriteDocType	write DOCTYPE if true

Constructor Summary

Constructors

Constructor	Description
AgaveWriter()	Default constructor uses generic annotation to attribute mapping.
AgaveWriter(AGAVEAnnotFilter filter)	Construct with data source specific annotation to attribute mapping.

Method Summary

Modifier and Type	Method	Description
void	setWriteDocType(boolean writeDocType)	Set flag that determines if XML DOCTYPE is written or not.
protected void	write(Sequence seq)	Writing Sequence.
protected void	writeAnnotations(FeatureHolder f)
protected void	writeAssembly(Annotatable seq)
protected void	writeBioSequence(Annotatable seq)
protected void	writeClassification(Annotatable seq)
protected void	writeCompResult(Annotatable f)
protected void	writeContig(Annotatable seq)
protected void	writeFooter()	Write </sciobj>
protected void	writeGene(Annotatable f)
protected void	writeHeader()	Write <sciobj>
protected void	writeSeqFeature(Annotatable f)	Write SeqFeature XML
void	writeSequence(Sequence seq, java.io.PrintStream os)	Write sequence into AGAVE XML format.
protected void	writeSequenceMap(Annotatable seq)	group sequence_map by getSource()
protected void	writeSequenceMap2(Annotatable f)	Write SequenceMap XML
protected void	writeTranscript(Annotatable f)

Methods inherited from class java.lang.Object

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

Field Detail

INDENT

public static final java.lang.String INDENT

use a two space indent

See Also:

Constant Field Values

mOut

protected java.io.PrintWriter mOut

Write to XML document

mIndent

protected AgaveWriter.Indent mIndent

indent

mFilter

protected org.biojava.bio.seq.io.agave.PCDATAFilterWriter mFilter

writes PCDATA replacing XML characters with escape entities

mAnnotFilter

protected AGAVEAnnotFilter mAnnotFilter

The AnnotationMap to use for getting AGAVE XML attributes from a Sequence Annotation.

mWriteDocType

protected boolean mWriteDocType

write DOCTYPE if true

Constructor Detail

AgaveWriter

public AgaveWriter()

Default constructor uses generic annotation to attribute mapping.

AgaveWriter

public AgaveWriter(AGAVEAnnotFilter filter)

Construct with data source specific annotation to attribute mapping.

Method Detail

setWriteDocType

public void setWriteDocType(boolean writeDocType)

Set flag that determines if XML DOCTYPE is written or not. Default is true.

writeSequence

public void writeSequence(Sequence seq,
                          java.io.PrintStream os)
                   throws java.io.IOException

Write sequence into AGAVE XML format.

Parameters:

seq - maybe the or simple sequence

 if annotation of seq has chromosome information , generate  tag
 if seq is SimpleAssembly, generate  tag
 otherwise, generate  tag
 currently  each top-level sequence is wrapped into seperated sciobj xml file
 

Throws:

java.io.IOException

writeHeader

protected void writeHeader()

Write <sciobj>

writeFooter

protected void writeFooter()

Write </sciobj>

write

protected void write(Sequence seq)
              throws java.io.IOException

Writing Sequence.

Parameters:

seq - is simple sequence or simple assembly

Throws:

java.io.IOException

writeContig

protected void writeContig(Annotatable seq)
                    throws java.io.IOException

Throws:

java.io.IOException

writeAssembly

protected void writeAssembly(Annotatable seq)
                      throws java.io.IOException

Throws:

java.io.IOException

writeBioSequence

protected void writeBioSequence(Annotatable seq)
                         throws java.io.IOException

Throws:

java.io.IOException

writeSequenceMap

protected void writeSequenceMap(Annotatable seq)
                         throws java.io.IOException

group sequence_map by getSource()

Throws:

java.io.IOException

writeClassification

protected void writeClassification(Annotatable seq)
                            throws java.io.IOException

Throws:

java.io.IOException

writeSequenceMap2

protected void writeSequenceMap2(Annotatable f)
                          throws java.io.IOException

Write SequenceMap XML

Throws:

java.io.IOException

writeAnnotations

protected void writeAnnotations(FeatureHolder f)
                         throws java.io.IOException

Throws:

java.io.IOException

writeGene

protected void writeGene(Annotatable f)
                  throws java.io.IOException

Throws:

java.io.IOException

writeTranscript

protected void writeTranscript(Annotatable f)
                        throws java.io.IOException

Throws:

java.io.IOException

writeSeqFeature

protected void writeSeqFeature(Annotatable f)
                        throws java.io.IOException

Write SeqFeature XML

Throws:

java.io.IOException

writeCompResult

protected void writeCompResult(Annotatable f)
                        throws java.io.IOException

Throws:

java.io.IOException