java.lang.Object

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

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 final 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 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, 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 Details
- INDENT
  
  public static final String INDENT
  
  use a two space indent
  See Also:
  
  Constant Field Values
- mOut
  
  protected 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 Details
- 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 Details
- 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, PrintStream os) throws 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:
  
  IOException
- writeHeader
  
  protected void writeHeader()
  
  Write <sciobj>
- writeFooter
  
  protected void writeFooter()
  
  Write </sciobj>
- write
  
  protected void write(Sequence seq) throws IOException
  
  Writing Sequence.
  
  Parameters:
  
  seq - is simple sequence or simple assembly
  
  Throws:
  
  IOException
- writeContig
  
  protected void writeContig(Annotatable seq) throws IOException
  
  Throws:
  
  IOException
- writeAssembly
  
  protected void writeAssembly(Annotatable seq) throws IOException
  
  Throws:
  
  IOException
- writeBioSequence
  
  protected void writeBioSequence(Annotatable seq) throws IOException
  
  Throws:
  
  IOException
- writeSequenceMap
  
  protected void writeSequenceMap(Annotatable seq) throws IOException
  
  group sequence_map by getSource()
  
  Throws:
  
  IOException
- writeClassification
  
  protected void writeClassification(Annotatable seq) throws IOException
  
  Throws:
  
  IOException
- writeSequenceMap2
  
  protected void writeSequenceMap2(Annotatable f) throws IOException
  
  Write SequenceMap XML
  
  Throws:
  
  IOException
- writeAnnotations
  
  protected void writeAnnotations(FeatureHolder f) throws IOException
  
  Throws:
  
  IOException
- writeGene
  
  protected void writeGene(Annotatable f) throws IOException
  
  Throws:
  
  IOException
- writeTranscript
  
  protected void writeTranscript(Annotatable f) throws IOException
  
  Throws:
  
  IOException
- writeSeqFeature
  
  protected void writeSeqFeature(Annotatable f) throws IOException
  
  Write SeqFeature XML
  
  Throws:
  
  IOException
- writeCompResult
  
  protected void writeCompResult(Annotatable f) throws IOException
  
  Throws:
  
  IOException

Class AgaveWriter

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

INDENT

mOut

mIndent

mFilter

mAnnotFilter

mWriteDocType

Constructor Details

AgaveWriter

AgaveWriter

Method Details

setWriteDocType

writeSequence

writeHeader

writeFooter

write

writeContig

writeAssembly

writeBioSequence

writeSequenceMap

writeClassification

writeSequenceMap2

writeAnnotations

writeGene

writeTranscript

writeSeqFeature

writeCompResult