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java.lang.Objectorg.biojava.bio.seq.io.agave.AgaveWriter
public class AgaveWriter
Writes Sequence into AGAVE XML document. The AGAVE format is defined in agave.dtd which can be downloaded from http://www.agavexml.org.
Nested Class Summary | |
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protected class |
AgaveWriter.Indent
Implements indenting for elements. |
Field Summary | |
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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 | |
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AgaveWriter()
Default constructor uses generic annotation to attribute mapping. |
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AgaveWriter(AGAVEAnnotFilter filter)
Construct with data source specific annotation to attribute mapping. |
Method Summary | |
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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)
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protected void |
writeAssembly(Annotatable seq)
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protected void |
writeBioSequence(Annotatable seq)
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protected void |
writeClassification(Annotatable seq)
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protected void |
writeCompResult(Annotatable f)
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protected void |
writeContig(Annotatable seq)
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protected void |
writeFooter()
Write </sciobj> |
protected void |
writeGene(Annotatable f)
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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)
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final java.lang.String INDENT
protected java.io.PrintWriter mOut
protected AgaveWriter.Indent mIndent
protected org.biojava.bio.seq.io.agave.PCDATAFilterWriter mFilter
protected AGAVEAnnotFilter mAnnotFilter
protected boolean mWriteDocType
Constructor Detail |
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public AgaveWriter()
public AgaveWriter(AGAVEAnnotFilter filter)
Method Detail |
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public void setWriteDocType(boolean writeDocType)
public void writeSequence(Sequence seq, java.io.PrintStream os) throws java.io.IOException
seq
- maybe the or simple sequence
if annotation of seq has chromosome information , generatetag if seq is SimpleAssembly, generate tag otherwise, generate tag currently each top-level sequence is wrapped into seperated sciobj xml file
java.io.IOException
protected void writeHeader()
protected void writeFooter()
protected void write(Sequence seq) throws java.io.IOException
seq
- is simple sequence or simple assembly
java.io.IOException
protected void writeContig(Annotatable seq) throws java.io.IOException
java.io.IOException
protected void writeAssembly(Annotatable seq) throws java.io.IOException
java.io.IOException
protected void writeBioSequence(Annotatable seq) throws java.io.IOException
java.io.IOException
protected void writeSequenceMap(Annotatable seq) throws java.io.IOException
java.io.IOException
protected void writeClassification(Annotatable seq) throws java.io.IOException
java.io.IOException
protected void writeSequenceMap2(Annotatable f) throws java.io.IOException
java.io.IOException
protected void writeAnnotations(FeatureHolder f) throws java.io.IOException
java.io.IOException
protected void writeGene(Annotatable f) throws java.io.IOException
java.io.IOException
protected void writeTranscript(Annotatable f) throws java.io.IOException
java.io.IOException
protected void writeSeqFeature(Annotatable f) throws java.io.IOException
java.io.IOException
protected void writeCompResult(Annotatable f) throws java.io.IOException
java.io.IOException
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