GencodeGtfFeature (gatk 4.2.0.0 API)

java.lang.Object
- org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature

All Implemented Interfaces:

htsjdk.samtools.util.Locatable, htsjdk.tribble.Feature, java.lang.Comparable<GencodeGtfFeature>

Direct Known Subclasses:

GencodeGtfCDSFeature, GencodeGtfExonFeature, GencodeGtfGeneFeature, GencodeGtfSelenocysteineFeature, GencodeGtfStartCodonFeature, GencodeGtfStopCodonFeature, GencodeGtfTranscriptFeature, GencodeGtfUTRFeature
```
public abstract class GencodeGtfFeature
extends java.lang.Object
implements htsjdk.tribble.Feature, java.lang.Comparable<GencodeGtfFeature>
```
A GencodeGtfFeature represents data in a GENCODE GTF file. Features are grouped logically by related data. While the abstract class GencodeGtfFeature represents a single line of a GENCODE GTF File, the concrete instantiations represent at least one line, and often more than one. For example, a GencodeGtfGeneFeature represents all lines in the given data file with information on a particular gene. This includes all transcripts, exons, coding regions, etc. in that gene. Similarly, a GencodeGtfTranscriptFeature represents all lines in the given data file with information on a particular transcript. However, a GencodeGtfSelenocysteineFeature represents a particular line in the given data file that contains information on a specific selenocysteine. The specification of a GTF file is defined here: http://mblab.wustl.edu/GTF22.html Currently only supports GENCODE versions 19-26. Created by jonn on 7/21/17.

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`static class`	`GencodeGtfFeature.AnnotationSource` Keyword identifying the source of the feature, like a program (e.g.
`static class`	`GencodeGtfFeature.FeatureTag` Additional relevant information appended to a feature.
`static class`	`GencodeGtfFeature.FeatureType` Type of the feature represented in a single line of a GENCODE GTF File.
`static class`	`GencodeGtfFeature.GeneTranscriptStatus` Indication of whether a feature is new, tenatative, or already known.
`static class`	`GencodeGtfFeature.GeneTranscriptType` Biotype / transcript type for the transcript or gene represented in a feature.
`static class`	`GencodeGtfFeature.GenomicPhase` Whether the first base of the CDS segment is the first (frame 0), second (frame 1) or third (frame 2) \ in the codon of the ORF.
`static class`	`GencodeGtfFeature.LocusLevel` Status of how a position was annotated / verified: 1 - verified locus 2 - manually annotated locus 3 - automatically annotated locus For more information, see: https://www.gencodegenes.org/data_format.html https://en.wikipedia.org/wiki/General_feature_format
`static class`	`GencodeGtfFeature.OptionalField<T>`
`static class`	`GencodeGtfFeature.RemapStatus` Attribute that indicates the status of the mapping.
`static class`	`GencodeGtfFeature.RemapTargetStatus` Attribute that compares the mapping to the existing target annotations.
`static class`	`GencodeGtfFeature.TranscriptSupportLevel` Transcript score according to how well mRNA and EST alignments match over its full length.

Field Summary

Fields
Modifier and Type	Field and Description
`static java.lang.String`	`ANNOTATION_SOURCE_ENA`
`static java.lang.String`	`ANNOTATION_SOURCE_ENSEMBL`
`static java.lang.String`	`ANNOTATION_SOURCE_HAVANA`
`static java.lang.String`	`EXTRA_FIELD_KEY_VALUE_SPLITTER`
`static int`	`NO_EXON_NUMBER`
`static int`	`NO_FEATURE_ORDER`

Constructor Summary

Constructors
Modifier	Constructor and Description
`protected`	`GencodeGtfFeature(GencodeGtfFeatureBaseData baseData)` Populate this GencodeGtfFeature with the given data.
`protected`	`GencodeGtfFeature(java.lang.String[] gtfFields, java.lang.String gtfFileType)` Populate this GencodeGtfFeature with the given data.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`compareTo(GencodeGtfFeature other)` Comparable interface implementation for `GencodeGtfFeature`.
`boolean`	`contains(htsjdk.samtools.util.Locatable other)` Checks if `other` is contained within this `GencodeGtfFeature`.
`static GencodeGtfFeature`	`create(GencodeGtfFeatureBaseData baseData)` Create the appropriate `GencodeGtfFeature` object based on the given `baseData`
`static GencodeGtfFeature`	`create(java.lang.String[] gtfFields, java.lang.String gtfFileType)` Create a `GencodeGtfFeature` based on a line from a Gencode GTF File.
`static GencodeGtfFeature`	`create(java.lang.String gtfLine, java.lang.String gtfFileType)` Create a `GencodeGtfFeature` based on a line from a Gencode GTF File.
`boolean`	`equals(java.lang.Object that)`
`java.lang.String`	`getAnnotationSource()`
`java.lang.String`	`getAnonymousOptionalFields()`
`java.lang.String`	`getChromosomeName()`
`java.lang.String`	`getContig()`
`int`	`getEnd()`
`java.lang.String`	`getExonId()`
`int`	`getExonNumber()`
`int`	`getFeatureOrderNumber()`
`GencodeGtfFeature.FeatureType`	`getFeatureType()`
`java.lang.String`	`getGeneId()`
`java.lang.String`	`getGeneName()`
`GencodeGtfFeature.GeneTranscriptStatus`	`getGeneStatus()`
`GencodeGtfFeature.GeneTranscriptType`	`getGeneType()`
`int`	`getGenomicEndLocation()`
`GencodeGtfFeature.GenomicPhase`	`getGenomicPhase()`
`SimpleInterval`	`getGenomicPosition()`
`int`	`getGenomicStartLocation()`
`htsjdk.tribble.annotation.Strand`	`getGenomicStrand()`
`java.lang.String`	`getGtfSourceFileType()`
`GencodeGtfFeature.LocusLevel`	`getLocusLevel()`
`GencodeGtfFeature.OptionalField<?>`	`getOptionalField(java.lang.String key)`
`java.util.List<GencodeGtfFeature.OptionalField<?>>`	`getOptionalFields()`
`int`	`getStart()`
`java.lang.String`	`getTranscriptId()`
`java.lang.String`	`getTranscriptName()`
`GencodeGtfFeature.GeneTranscriptStatus`	`getTranscriptStatus()`
`GencodeGtfFeature.GeneTranscriptType`	`getTranscriptType()`
`java.lang.String`	`getUcscGenomeVersion()`
`int`	`hashCode()`
`boolean`	`overlaps(htsjdk.samtools.util.Locatable other)` Checks if `other` overlaps with this `GencodeGtfFeature`.
`java.lang.String`	`serializeToString()` Serializes all data in `GencodeGtfFeature` to a string.
`void`	`setFeatureOrderNumber(int featureOrderNumber)`
`void`	`setUcscGenomeVersion(java.lang.String ucscGenomeVersion)`
`java.lang.String`	`toString()`

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

Methods inherited from interface htsjdk.tribble.Feature
getChr

Methods inherited from interface htsjdk.samtools.util.Locatable
contigsMatch, getLengthOnReference, withinDistanceOf

- Field Detail
  - ANNOTATION_SOURCE_ENSEMBL
```
public static final java.lang.String ANNOTATION_SOURCE_ENSEMBL
```
    See Also:
    
    Constant Field Values
  - ANNOTATION_SOURCE_HAVANA
```
public static final java.lang.String ANNOTATION_SOURCE_HAVANA
```
    See Also:
    
    Constant Field Values
  - ANNOTATION_SOURCE_ENA
```
public static final java.lang.String ANNOTATION_SOURCE_ENA
```
    See Also:
    
    Constant Field Values
  - NO_FEATURE_ORDER
```
public static final int NO_FEATURE_ORDER
```
    See Also:
    
    Constant Field Values
  - NO_EXON_NUMBER
```
public static final int NO_EXON_NUMBER
```
    See Also:
    
    Constant Field Values
  - EXTRA_FIELD_KEY_VALUE_SPLITTER
```
public static final java.lang.String EXTRA_FIELD_KEY_VALUE_SPLITTER
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - GencodeGtfFeature
```
protected GencodeGtfFeature(java.lang.String[] gtfFields,
                            java.lang.String gtfFileType)
```
    Populate this GencodeGtfFeature with the given data.
    
    Parameters:
    
    gtfFields - String[] containing an ordered list of fields to use to populate this GencodeGtfFeature.
    
    gtfFileType - A String containing the file type of the GTF data that created this GencodeGtfFeature.
  - GencodeGtfFeature
```
protected GencodeGtfFeature(GencodeGtfFeatureBaseData baseData)
```
    Populate this GencodeGtfFeature with the given data.
- Method Detail
  - create
```
public static GencodeGtfFeature create(GencodeGtfFeatureBaseData baseData)
```
    Create the appropriate GencodeGtfFeature object based on the given baseData
    
    Parameters:
    
    baseData - A GencodeGtfFeatureBaseData object containing all data for a single line in a GENCODE GTF File.
    
    Returns:
    
    A GencodeGtfFeature containing the data in baseData
  - create
```
public static GencodeGtfFeature create(java.lang.String gtfLine,
                                       java.lang.String gtfFileType)
```
    Create a GencodeGtfFeature based on a line from a Gencode GTF File.
    
    Parameters:
    
    gtfLine - A line from a Gencode GTF File to convert into a GencodeGtfFeature object.
    
    gtfFileType - A String containing the file type of the GTF data that created this GencodeGtfFeature.
    
    Returns:
    
    The GencodeGtfFeature representing the information in gtfLine
  - create
```
public static GencodeGtfFeature create(java.lang.String[] gtfFields,
                                       java.lang.String gtfFileType)
```
    Create a GencodeGtfFeature based on a line from a Gencode GTF File.
    
    Parameters:
    
    gtfFields - A line from a Gencode GTF File split on the FIELD_DELIMITER character.
    
    gtfFileType - A String containing the file type of the GTF data that created this GencodeGtfFeature.
    
    Returns:
    
    The GencodeGtfFeature representing the information in gtfLine
  - getContig
```
public java.lang.String getContig()
```
    Specified by:
    
    getContig in interface htsjdk.samtools.util.Locatable
  - getStart
```
public int getStart()
```
    Specified by:
    
    getStart in interface htsjdk.samtools.util.Locatable
  - getEnd
```
public int getEnd()
```
    Specified by:
    
    getEnd in interface htsjdk.samtools.util.Locatable
  - serializeToString
```
public java.lang.String serializeToString()
```
    Serializes all data in GencodeGtfFeature to a string. This includes all subfields of child classes.
    
    Returns:
    
    a String representing this GencodeGtfFeature
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object
  - getGtfSourceFileType
```
public java.lang.String getGtfSourceFileType()
```
  - getUcscGenomeVersion
```
public java.lang.String getUcscGenomeVersion()
```
  - setUcscGenomeVersion
```
public void setUcscGenomeVersion(java.lang.String ucscGenomeVersion)
```
  - getGenomicPosition
```
public SimpleInterval getGenomicPosition()
```
  - getFeatureOrderNumber
```
public int getFeatureOrderNumber()
```
  - getChromosomeName
```
public java.lang.String getChromosomeName()
```
  - getAnnotationSource
```
public java.lang.String getAnnotationSource()
```
  - getFeatureType
```
public GencodeGtfFeature.FeatureType getFeatureType()
```
  - getGenomicStartLocation
```
public int getGenomicStartLocation()
```
  - getGenomicEndLocation
```
public int getGenomicEndLocation()
```
  - getGenomicStrand
```
public htsjdk.tribble.annotation.Strand getGenomicStrand()
```
  - getGenomicPhase
```
public GencodeGtfFeature.GenomicPhase getGenomicPhase()
```
  - getGeneId
```
public java.lang.String getGeneId()
```
  - getTranscriptId
```
public java.lang.String getTranscriptId()
```
  - getGeneType
```
public GencodeGtfFeature.GeneTranscriptType getGeneType()
```
  - getGeneName
```
public java.lang.String getGeneName()
```
  - getTranscriptType
```
public GencodeGtfFeature.GeneTranscriptType getTranscriptType()
```
  - getTranscriptName
```
public java.lang.String getTranscriptName()
```
  - getGeneStatus
```
public GencodeGtfFeature.GeneTranscriptStatus getGeneStatus()
```
  - getTranscriptStatus
```
public GencodeGtfFeature.GeneTranscriptStatus getTranscriptStatus()
```
  - getExonNumber
```
public int getExonNumber()
```
  - getExonId
```
public java.lang.String getExonId()
```
  - getLocusLevel
```
public GencodeGtfFeature.LocusLevel getLocusLevel()
```
  - getOptionalFields
```
public java.util.List<GencodeGtfFeature.OptionalField<?>> getOptionalFields()
```
  - getAnonymousOptionalFields
```
public java.lang.String getAnonymousOptionalFields()
```
  - getOptionalField
```
public GencodeGtfFeature.OptionalField<?> getOptionalField(java.lang.String key)
```
  - compareTo
```
public int compareTo(GencodeGtfFeature other)
```
    Comparable interface implementation for GencodeGtfFeature. Order is determined by GencodeGtfFeatureBaseData.featureOrderNumber
    
    Specified by:
    
    compareTo in interface java.lang.Comparable<GencodeGtfFeature>
    
    Parameters:
    
    other - GencodeGtfFeature to which to compare
    
    Returns:
    
    -1 if this < other; 0 if this == other; 1 if this > other
  - equals
```
public boolean equals(java.lang.Object that)
```
    Overrides:
    
    equals in class java.lang.Object
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class java.lang.Object
  - contains
```
public boolean contains(htsjdk.samtools.util.Locatable other)
```
    Checks if other is contained within this GencodeGtfFeature. Comparison is made using SimpleInterval.contains(Locatable) ala GencodeGtfFeatureBaseData.genomicPosition
    
    Specified by:
    
    contains in interface htsjdk.samtools.util.Locatable
    
    Parameters:
    
    other - Locatable of which to check the bounds.
    
    Returns:
    
    true if other is contained within the bounds of this GencodeGtfFeature, false otherwise.
  - overlaps
```
public boolean overlaps(htsjdk.samtools.util.Locatable other)
```
    Checks if other overlaps with this GencodeGtfFeature. Comparison is made using SimpleInterval.overlaps(Locatable) ala GencodeGtfFeatureBaseData.genomicPosition
    
    Specified by:
    
    overlaps in interface htsjdk.samtools.util.Locatable
    
    Parameters:
    
    other - Locatable-derived class of which to check the bounds.
    
    Returns:
    
    true if other overlaps the bounds of this GencodeGtfFeature, false otherwise.
  - setFeatureOrderNumber
```
public void setFeatureOrderNumber(int featureOrderNumber)
```

Class GencodeGtfFeature

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface htsjdk.tribble.Feature

Methods inherited from interface htsjdk.samtools.util.Locatable

Field Detail

ANNOTATION_SOURCE_ENSEMBL

ANNOTATION_SOURCE_HAVANA

ANNOTATION_SOURCE_ENA

NO_FEATURE_ORDER

NO_EXON_NUMBER

EXTRA_FIELD_KEY_VALUE_SPLITTER

Constructor Detail

GencodeGtfFeature

GencodeGtfFeature

Method Detail

create

create

create

getContig

getStart

getEnd

serializeToString

toString

getGtfSourceFileType

getUcscGenomeVersion

setUcscGenomeVersion

getGenomicPosition

getFeatureOrderNumber

getChromosomeName

getAnnotationSource

getFeatureType

getGenomicStartLocation

getGenomicEndLocation

getGenomicStrand

getGenomicPhase

getGeneId

getTranscriptId

getGeneType

getGeneName

getTranscriptType

getTranscriptName

getGeneStatus

getTranscriptStatus

getExonNumber

getExonId

getLocusLevel

getOptionalFields

getAnonymousOptionalFields

getOptionalField

compareTo

equals

hashCode

contains

overlaps

setFeatureOrderNumber