java.lang.Object
- org.biojava.bio.seq.io.agave.SimpleAnnotFilter

All Implemented Interfaces:

AGAVEAnnotFilter

Direct Known Subclasses:

Agave2AgaveAnnotFilter, Embl2AgaveAnnotFilter
```
public class SimpleAnnotFilter
extends java.lang.Object
implements AGAVEAnnotFilter
```
Basic implementation of AGAVEAnnotFilter

Author:

Hanning Ni Doubletwist Inc

Field Summary

Fields
Modifier and Type Field Description

static AGAVEAnnotFilterFactory SIMPLE_ANNOT_FILTER_FACTORY
- Fields inherited from interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
  BOTH_FORWARD_COMPLEMENT, COMPLEMENT, FORWARD

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`java.lang.String`	`getAccession(Annotation annot)`
`java.lang.String`	`getAlignLength(Annotation annot)`
`java.lang.String`	`getAlignUnits(Annotation annot)`
`AGAVEDbId[]`	`getAltIds(Annotation annot)`
`java.lang.String`	`getChromNum(Annotation annot)`
`java.lang.String`	`getChromosome(Annotation annot)`
`java.lang.String`	`getClassifyId(Annotation annot)`
`java.lang.String`	`getClassifySystem(Annotation annot)`
`java.lang.String`	`getClassifyType(Annotation annot)`
`java.lang.String`	`getCloneId(Annotation annot)`
`java.lang.String`	`getCloneLibrary(Annotation annot)`
`java.lang.String`	`getConfidence(Annotation annot)`
`java.lang.String`	`getCreateDate(Annotation annot)`
`AGAVEDbId`	`getDbId(Annotation annot)`
`java.lang.String`	`getDescription(Annotation annot)`
`java.lang.String`	`getEcNumber(Annotation annot)`
`java.lang.String`	`getElementId(Annotation annot)`
`java.lang.String[]`	`getElementIds(Annotation annot)`
`java.lang.String[]`	`getExonIds(Annotation annot)`
`java.lang.String`	`getFeatureType(Annotation annot)`
`java.lang.String`	`getGroupOrder(Annotation annot)`
`AGAVEIdAlias[]`	`getIdAlias(Annotation annot)`
`java.lang.String`	`getKeyword(Annotation annot)`
`java.lang.String`	`getLabel(Annotation annot)`
`AGAVEMapLocation[]`	`getMapLocation(Annotation annot)`
`java.lang.String`	`getMapPosition(Annotation annot)`
`java.lang.String`	`getMatchAlign(Annotation annot)`
`java.lang.String`	`getMatchDesc(Annotation annot)`
`AGAVEMatchRegion`	`getMatchRegion(Annotation annot)`
`java.lang.String`	`getMolType(Annotation annot)`
`java.lang.String`	`getNote(Annotation annot)`
`java.lang.String`	`getOrganism(Annotation annot)`
`java.lang.String`	`getOS(Annotation annot)`
`AGAVEProperty[]`	`getProperty(Annotation annot, java.lang.String type)`	ThomasD made this a bit safer...
`AGAVEQueryRegion`	`getQueryRegion(Annotation annot)`
`AGAVERelatedAnnot[]`	`getRelatedAnnot(Annotation annot)`
`java.lang.String`	`getResultType(Annotation annot)`
`java.lang.String`	`getSequenceId(Annotation annot)`
`java.lang.String`	`getTaxonId(Annotation annot)`
`java.lang.String`	`getUpdateDate(Annotation annot)`
`java.lang.String`	`getVersion(Annotation annot)`
`AGAVEXrefs[]`	`getXrefs(Annotation annot)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - SIMPLE_ANNOT_FILTER_FACTORY
```
public static final AGAVEAnnotFilterFactory SIMPLE_ANNOT_FILTER_FACTORY
```
- Method Detail
  - getAccession
```
public java.lang.String getAccession(Annotation annot)
```
    Specified by:
    
    getAccession in interface AGAVEAnnotFilter
  - getKeyword
```
public java.lang.String getKeyword(Annotation annot)
```
    Specified by:
    
    getKeyword in interface AGAVEAnnotFilter
  - getElementId
```
public java.lang.String getElementId(Annotation annot)
```
    Specified by:
    
    getElementId in interface AGAVEAnnotFilter
  - getOrganism
```
public java.lang.String getOrganism(Annotation annot)
```
    Specified by:
    
    getOrganism in interface AGAVEAnnotFilter
  - getLabel
```
public java.lang.String getLabel(Annotation annot)
```
    Specified by:
    
    getLabel in interface AGAVEAnnotFilter
  - getDescription
```
public java.lang.String getDescription(Annotation annot)
```
    Specified by:
    
    getDescription in interface AGAVEAnnotFilter
  - getMatchAlign
```
public java.lang.String getMatchAlign(Annotation annot)
```
    Specified by:
    
    getMatchAlign in interface AGAVEAnnotFilter
  - getMatchRegion
```
public AGAVEMatchRegion getMatchRegion(Annotation annot)
```
    Specified by:
    
    getMatchRegion in interface AGAVEAnnotFilter
  - getQueryRegion
```
public AGAVEQueryRegion getQueryRegion(Annotation annot)
```
    Specified by:
    
    getQueryRegion in interface AGAVEAnnotFilter
  - getClassifySystem
```
public java.lang.String getClassifySystem(Annotation annot)
```
    Specified by:
    
    getClassifySystem in interface AGAVEAnnotFilter
  - getClassifyId
```
public java.lang.String getClassifyId(Annotation annot)
```
    Specified by:
    
    getClassifyId in interface AGAVEAnnotFilter
  - getClassifyType
```
public java.lang.String getClassifyType(Annotation annot)
```
    Specified by:
    
    getClassifyType in interface AGAVEAnnotFilter
  - getExonIds
```
public java.lang.String[] getExonIds(Annotation annot)
```
    Specified by:
    
    getExonIds in interface AGAVEAnnotFilter
  - getChromNum
```
public java.lang.String getChromNum(Annotation annot)
```
    Specified by:
    
    getChromNum in interface AGAVEAnnotFilter
  - getIdAlias
```
public AGAVEIdAlias[] getIdAlias(Annotation annot)
```
    Specified by:
    
    getIdAlias in interface AGAVEAnnotFilter
  - getNote
```
public java.lang.String getNote(Annotation annot)
```
    Specified by:
    
    getNote in interface AGAVEAnnotFilter
  - getAltIds
```
public AGAVEDbId[] getAltIds(Annotation annot)
```
    Specified by:
    
    getAltIds in interface AGAVEAnnotFilter
  - getMapLocation
```
public AGAVEMapLocation[] getMapLocation(Annotation annot)
```
    Specified by:
    
    getMapLocation in interface AGAVEAnnotFilter
  - getRelatedAnnot
```
public AGAVERelatedAnnot[] getRelatedAnnot(Annotation annot)
```
    Specified by:
    
    getRelatedAnnot in interface AGAVEAnnotFilter
  - getElementIds
```
public java.lang.String[] getElementIds(Annotation annot)
```
    Specified by:
    
    getElementIds in interface AGAVEAnnotFilter
  - getGroupOrder
```
public java.lang.String getGroupOrder(Annotation annot)
```
    Specified by:
    
    getGroupOrder in interface AGAVEAnnotFilter
  - getMatchDesc
```
public java.lang.String getMatchDesc(Annotation annot)
```
    Specified by:
    
    getMatchDesc in interface AGAVEAnnotFilter
  - getFeatureType
```
public java.lang.String getFeatureType(Annotation annot)
```
    Specified by:
    
    getFeatureType in interface AGAVEAnnotFilter
  - getResultType
```
public java.lang.String getResultType(Annotation annot)
```
    Specified by:
    
    getResultType in interface AGAVEAnnotFilter
  - getConfidence
```
public java.lang.String getConfidence(Annotation annot)
```
    Specified by:
    
    getConfidence in interface AGAVEAnnotFilter
  - getAlignLength
```
public java.lang.String getAlignLength(Annotation annot)
```
    Specified by:
    
    getAlignLength in interface AGAVEAnnotFilter
  - getAlignUnits
```
public java.lang.String getAlignUnits(Annotation annot)
```
    Specified by:
    
    getAlignUnits in interface AGAVEAnnotFilter
  - getXrefs
```
public AGAVEXrefs[] getXrefs(Annotation annot)
```
    Specified by:
    
    getXrefs in interface AGAVEAnnotFilter
  - getVersion
```
public java.lang.String getVersion(Annotation annot)
```
    Specified by:
    
    getVersion in interface AGAVEAnnotFilter
  - getSequenceId
```
public java.lang.String getSequenceId(Annotation annot)
```
    Specified by:
    
    getSequenceId in interface AGAVEAnnotFilter
  - getTaxonId
```
public java.lang.String getTaxonId(Annotation annot)
```
    Specified by:
    
    getTaxonId in interface AGAVEAnnotFilter
  - getCloneId
```
public java.lang.String getCloneId(Annotation annot)
```
    Specified by:
    
    getCloneId in interface AGAVEAnnotFilter
  - getCloneLibrary
```
public java.lang.String getCloneLibrary(Annotation annot)
```
    Specified by:
    
    getCloneLibrary in interface AGAVEAnnotFilter
  - getChromosome
```
public java.lang.String getChromosome(Annotation annot)
```
    Specified by:
    
    getChromosome in interface AGAVEAnnotFilter
  - getMapPosition
```
public java.lang.String getMapPosition(Annotation annot)
```
    Specified by:
    
    getMapPosition in interface AGAVEAnnotFilter
  - getEcNumber
```
public java.lang.String getEcNumber(Annotation annot)
```
    Specified by:
    
    getEcNumber in interface AGAVEAnnotFilter
  - getCreateDate
```
public java.lang.String getCreateDate(Annotation annot)
```
    Specified by:
    
    getCreateDate in interface AGAVEAnnotFilter
  - getUpdateDate
```
public java.lang.String getUpdateDate(Annotation annot)
```
    Specified by:
    
    getUpdateDate in interface AGAVEAnnotFilter
  - getOS
```
public java.lang.String getOS(Annotation annot)
```
    Specified by:
    
    getOS in interface AGAVEAnnotFilter
  - getMolType
```
public java.lang.String getMolType(Annotation annot)
```
    Specified by:
    
    getMolType in interface AGAVEAnnotFilter
  - getDbId
```
public AGAVEDbId getDbId(Annotation annot)
```
    Specified by:
    
    getDbId in interface AGAVEAnnotFilter
  - getProperty
```
public AGAVEProperty[] getProperty(Annotation annot,
                                   java.lang.String type)
```
    ThomasD made this a bit safer...
    
    Specified by:
    
    getProperty in interface AGAVEAnnotFilter

Class SimpleAnnotFilter

Field Summary

Fields inherited from interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

Method Summary

Methods inherited from class java.lang.Object

Field Detail

SIMPLE_ANNOT_FILTER_FACTORY

Method Detail

getAccession

getKeyword

getElementId

getOrganism

getLabel

getDescription

getMatchAlign

getMatchRegion

getQueryRegion

getClassifySystem

getClassifyId

getClassifyType

getExonIds

getChromNum

getIdAlias

getNote

getAltIds

getMapLocation

getRelatedAnnot

getElementIds

getGroupOrder

getMatchDesc

getFeatureType

getResultType

getConfidence

getAlignLength

getAlignUnits

getXrefs

getVersion

getSequenceId

getTaxonId

getCloneId

getCloneLibrary

getChromosome

getMapPosition

getEcNumber

getCreateDate

getUpdateDate

getOS

getMolType

getDbId

getProperty