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Packages that use org.biojava.bio.seq.io.agave | |
org.biojava.bio.seq.io.agave | Classes for converting between AGAVE XML and BioJava objects. |
Classes in org.biojava.bio.seq.io.agave used by org.biojava.bio.seq.io.agave | |
AGAVEAnnotFilter
This interface defines mapping from BioJava into AGAVE format. |
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AGAVEAnnotFilterFactory
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AGAVEBioSeqCallbackItf
An interface that can be tested for by nested handlers when trying to do a callback. |
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AGAVECallbackItf
An interface that can be tested for by nested handlers when trying to do a callback. |
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AGAVEChromosomeCallbackItf
An interface that can be tested for by nested handlers when trying to do a callback. |
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AGAVEContigCallbackItf
An interface that can be tested for by nested handlers when trying to do a callback. |
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AGAVEDbId
* @author Hanning Ni Doubletwist Inc * @author Greg Cox |
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AGAVEDbIdCallbackItf
this is the interface implemented by several classes |
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AGAVEDbIdPropCallbackItf
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AGAVEEvidenceCallbackItf
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AGAVEFeatureCallbackItf
An interface that can be tested for by nested handlers when trying to do a callback. |
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AGAVEIdAlias
* @author Hanning Ni Doubletwist Inc * @author Greg Cox |
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AGAVEIdAliasCallbackItf
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AGAVEMapLocation
* @author Hanning Ni Doubletwist Inc * @author Greg Cox |
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AGAVEMapPosition
* * @author Hanning Ni Doubletwist Inc * @author Greg Cox |
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AGAVEMatchRegion
* match_region * * @author Hanning Ni Doubletwist Inc * @author Greg Cox |
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AGAVEProperty
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AGAVEQueryRegion
* * @author Hanning Ni Doubletwist Inc * @author Greg Cox |
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AGAVERelatedAnnot
* * @author Hanning Ni Doubletwist Inc * @author Greg Cox |
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AgaveWriter.Indent
Implements indenting for elements. |
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AGAVEXref
xref |
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AGAVEXrefCallbackItf
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AGAVEXrefs
* xrefs * * @author Hanning Ni Doubletwist Inc * @author Greg Cox |
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DelegationManager
Interface which exposes delegation services offered by a StAX event source. |
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ElementRecognizer
This class is copied to agave package Simple interface for filtering SAX/StAX startElement events |
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SequenceHandler
mark interface |
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SimpleAnnotFilter
Basic implementation of AGAVEAnnotFilter |
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StAXContentHandler
Interface for StAX content handlers. |
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StAXContentHandlerBase
Simple implementation of the StAXContentHandler
interface, with empty implementations for all the methods. |
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StAXFeatureHandler
StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler. |
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StAXHandlerFactory
Factory for StAX content handlers. |
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StAXPropertyHandler
StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler. |
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