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java.lang.Objectorg.biojava.bio.program.gff.SequencesAsGFF
public class SequencesAsGFF
Turns a sequence database into a GFF event stream.
Constructor Summary | |
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SequencesAsGFF()
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Method Summary | |
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protected SimpleGFFRecord |
createGFFRecord(Feature feature,
String id)
Internal method to create a GFFRecord from an individual Feature. |
protected void |
doPreProcessSequence(Sequence seq,
GFFDocumentHandler handler,
String id)
Emit any per-sequence header information. |
protected void |
doProcessFeature(Feature feature,
GFFDocumentHandler handler,
String id)
Internal method to process an individual Feature. |
protected void |
doProcessSequence(Sequence seq,
GFFDocumentHandler handler,
String id)
Internal method to process an individual Sequence. |
FeatureFilter |
getFeatureFilter()
Return the current FeatureFilter. |
boolean |
getGenerateSequenceHeader()
Discover if per-sequence header lines will be generated. |
boolean |
getRecurse()
Return whether features will be filtered recursively or not. |
boolean |
getShatter()
Determine if features with non-contiguous locations will be broken into multiple GFF records. |
void |
processDB(SequenceDB seqDB,
GFFDocumentHandler handler)
Process all Sequences within a SequenceDB, informing handler of any suitable features. |
void |
processSequence(Sequence seq,
GFFDocumentHandler handler)
Process an individual Sequence, informing handler of any suitable features. |
void |
setFeatureFilter(FeatureFilter filter)
Replace the current FeatureFilter with filter. |
void |
setGenerateSequenceHeader(boolean b)
Specify whether a per-sequence header line, giving the length of the sequence, should be generated. |
void |
setRecurse(boolean recurse)
Set whether features will be filtered recursively to recurse. |
void |
setShatter(boolean b)
Specify whether features with non-contiguous locations should be broken up such that a GFF feature line is emitted for each contiguous block. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public SequencesAsGFF()
Method Detail |
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public void setShatter(boolean b)
b
- public boolean getShatter()
public void setGenerateSequenceHeader(boolean b)
public boolean getGenerateSequenceHeader()
public FeatureFilter getFeatureFilter()
This is the object that will accept or reject individual features.
public void setFeatureFilter(FeatureFilter filter)
filter
- the new FeatureFilterpublic boolean getRecurse()
public void setRecurse(boolean recurse)
recurse
- true if you want to recurse,
false otherwiseprotected void doPreProcessSequence(Sequence seq, GFFDocumentHandler handler, String id) throws BioException
BioException
protected void doProcessSequence(Sequence seq, GFFDocumentHandler handler, String id) throws BioException
seq
- the Sequence to GFFifyhandler
- the GFFDocumentHandler that will
receive the GFF for all suitable features within
seqid
- the value of the seqName field in any
GFFRecords produced
BioException
protected void doProcessFeature(Feature feature, GFFDocumentHandler handler, String id) throws BioException
feature
- the Feature to GFFifyhandler
- the GFFDocumentHandler that will
receive the GFF for this featureid
- the value of the seqName field in any
GFFRecords produced
BioException
protected SimpleGFFRecord createGFFRecord(Feature feature, String id) throws BioException
feature
- the Feature to GFFifyid
- the value of the seqName field in any
GFFRecords produced
BioException
public void processSequence(Sequence seq, GFFDocumentHandler handler) throws BioException
seq
- the Sequence to GFFifyhandler
- the GFFDocumentHandler that will
receive the GFF for all suitable features within
seq
BioException
public void processDB(SequenceDB seqDB, GFFDocumentHandler handler) throws BioException
seqDB
- the SequenceDB to GFFifyhandler
- the GFFDocumentHandler that will
receive the GFF for all suitable features within
seqDB
BioException
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