Package org.biojava.bio.seq.io.agave
package org.biojava.bio.seq.io.agave
Classes for converting between AGAVE XML and BioJava objects. Use AGAVEHandler with a SAX parser to
parse AGAVE XML into BioJava Sequences, and use AgaveWriter to write BioJava Sequences into AGAVE format.
When writing BioJava to AGAVE we need to specify how the data in BioJava stored.
Two conversion filters are implemented. The Agave2AgaveAnnotFilter helps write data that was parsed from
AGAVE, and Embl2AgaveAnnotFilter helps write data that was parsed from EMBL.
This package uses a modified version of the BioJava StAX parser architecture that
supports nested features.
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ClassDescriptionDumping the data from biojava with source of agave into agave formatDeals with alternate sequence IDsThis interface defines mapping from BioJava into AGAVE format.An interface that can be tested for by nested handlers when trying to do a callback.Handles the AGAVE <bio_sequence> elementHandles the AGAVE <bio_sequence> elementAn interface that can be tested for by nested handlers when trying to do a callback.Handles the AGAVE <cds> elementAn interface that can be tested for by nested handlers when trying to do a callback.Handles the AGAVE <chromosome> elementAn interface that can be tested for by nested handlers when trying to do a callback.Handles the AGAVE <contig> elementthis is the interface implemented by several classesDeals with database crossreferencesDeals with database crossreferencesAn interface that can be tested for by nested handlers when trying to do a callback.Handles the root AGAVE element modified for agave formatDeals with AGAVE keywordsDeals with match_alignDeals with match_descmatch_regionDeals with match_regionHandles the AGAVE <mrna> elementDeals with noteHandles the AGAVE <predicted_protein> elementsci_propertyseq_featureseq_locationsequence_mapDeals with sequence codetranscriptunordered_fragmentsMoves view attributes into annotation properties.Writes Sequence into AGAVE XML document.xrefhandle AGAVE xrefxref_propertyxrefsDeals with database crossreferences (xrefs)Interface which exposes delegation services offered by a StAX event source.This class is copied to agave package Simple interface for filtering SAX/StAX startElement eventsFilter elements by local name (not recommended).Filter elements by name and namespace.Filter elements on the existence of a specified attribute.Map EMBL data into AGAVE formatLightweight adaptor which translates SAX content events into StAX form, and provides delegation services.mark interfaceBasic implementation of AGAVEAnnotFilterInterface for StAX content handlers.Simple implementation of the
StAXContentHandler
interface, with empty implementations for all the methods.StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.Factory for StAX content handlers.StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.Just make the property follow the common case