public interface AGAVEAnnotFilter
This interface defines mapping from BioJava into AGAVE format. As data from different sources is stored differently in BioJava it is impossible to define universal mapping from BioJava to Agave. Currently I implemented two mappings:
( embl -> )biojava -> agave
( agave -> )biojava -> agave
Modifier and Type | Field and Description |
---|---|
static int |
BOTH_FORWARD_COMPLEMENT |
static int |
COMPLEMENT |
static int |
FORWARD |
static final int FORWARD
static final int COMPLEMENT
static final int BOTH_FORWARD_COMPLEMENT
String getAccession(Annotation annot)
String getLabel(Annotation annot)
String getElementId(Annotation annot)
String getSequenceId(Annotation annot)
String getKeyword(Annotation annot)
String getOrganism(Annotation annot)
String getDescription(Annotation annot)
String getNote(Annotation annot)
String getVersion(Annotation annot)
String getOS(Annotation annot)
String getMolType(Annotation annot)
String getTaxonId(Annotation annot)
String getCloneId(Annotation annot)
String getCloneLibrary(Annotation annot)
String getChromosome(Annotation annot)
String getMapPosition(Annotation annot)
String getEcNumber(Annotation annot)
String getCreateDate(Annotation annot)
String getUpdateDate(Annotation annot)
AGAVEDbId[] getAltIds(Annotation annot)
AGAVEXrefs[] getXrefs(Annotation annot)
AGAVEMapLocation[] getMapLocation(Annotation annot)
AGAVERelatedAnnot[] getRelatedAnnot(Annotation annot)
String[] getElementIds(Annotation annot)
String[] getExonIds(Annotation annot)
String getChromNum(Annotation annot)
AGAVEProperty[] getProperty(Annotation annot, String type)
AGAVEDbId getDbId(Annotation annot)
String getGroupOrder(Annotation annot)
String getFeatureType(Annotation annot)
String getResultType(Annotation annot)
String getConfidence(Annotation annot)
String getAlignLength(Annotation annot)
String getAlignUnits(Annotation annot)
String getMatchDesc(Annotation annot)
String getMatchAlign(Annotation annot)
AGAVEQueryRegion getQueryRegion(Annotation annot)
AGAVEMatchRegion getMatchRegion(Annotation annot)
AGAVEIdAlias[] getIdAlias(Annotation annot)
String getClassifySystem(Annotation annot)
String getClassifyId(Annotation annot)
String getClassifyType(Annotation annot)
Copyright © 2014 BioJava. All rights reserved.