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java.lang.Objectorg.biojava.bio.seq.io.agave.StAXContentHandlerBase
org.biojava.bio.seq.io.agave.StAXFeatureHandler
org.biojava.bio.seq.io.agave.AGAVEHandler
Handles the root AGAVE element modified for agave format
Field Summary |
Fields inherited from class org.biojava.bio.seq.io.agave.StAXFeatureHandler |
annot, callbackStack, endLoc, featureListener, featureTemplate, myLocalName, stackLevel, startLoc, staxenv, subFeatures |
Constructor Summary | |
AGAVEHandler()
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Method Summary | |
java.util.Iterator |
getSequences()
get all the top level sequences bio_sequence --> SimpleSequence contig --> SimpleAssembly --> SimpleSequence( if only one sequence ) chromosome -> SimpleAssembly -> SimpleSequence( if only one sequence) |
void |
reportSequence(Sequence sequence)
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void |
startElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
org.xml.sax.Attributes attrs,
DelegationManager dm)
|
Methods inherited from class org.biojava.bio.seq.io.agave.StAXFeatureHandler |
addFeatureToSequence, addHandler, createTemplate, endElement, endElementHandler, getFeatureListener, getHandlerStackIterator, getLevel, pop, push, realizeSubFeatures, setFeatureListener, setHandlerCharacteristics, setProperty, startElement, startElementHandler |
Methods inherited from class org.biojava.bio.seq.io.agave.StAXContentHandlerBase |
characters, endPrefixMapping, endTree, ignorableWhitespace, processingInstruction, setDocumentLocator, skippedEntity, startPrefixMapping, startTree |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
public AGAVEHandler()
Method Detail |
public void reportSequence(Sequence sequence)
reportSequence
in interface AGAVECallbackItf
sequence
- from sub-tag <bio_sequence>/<contig>/<chromosome>
bio_sequence --> SimpleSequence contig --> SimpleAssembly --> SimpleSequence( if only one sequence ) chromosome -> SimpleAssembly -> SimpleSequence( if only one sequence)
public java.util.Iterator getSequences()
public void startElementHandler(java.lang.String nsURI, java.lang.String localName, java.lang.String qName, org.xml.sax.Attributes attrs, DelegationManager dm) throws org.xml.sax.SAXException
org.xml.sax.SAXException
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