Package org.snpeff.interval
Class GffMarker
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.Custom
org.snpeff.interval.GffMarker
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<Interval>
,Iterable<KeyValue<String,
,String>> TxtSerializable
- Direct Known Subclasses:
Gtf2Marker
An interval intended as a mark
- Author:
- pcingola
- See Also:
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
Add key value pairstatic boolean
canParseLine
(String line) Can this line (form a GFF file) be parsed? Note: Returns false for headers, empty lines and lines having less number of fields than expectedprotected String
protected BioType
int
getFrame()
getGffParentId
(boolean doNotRecurse) String[]
Parent can have multiple, comma separated entriesgetTags()
boolean
When annotating a VCF file, add fields from this GFFboolean
boolean
isMultipleValues
(String key) Does the key have mutiple valuesboolean
Is biotType considered 'protein coding'?iterator()
protected void
Parse an entry (line) from a GFF fileprotected void
parseAttributes
(String attrStr) Parse attributes (key-value pairs) from a line in a GFF fileprotected String
parseId()
Obtain or create an IDtoString()
Methods inherited from class org.snpeff.interval.Custom
cloneShallow, getLabel, getScore, setLabel, setScore, variantEffect
Methods inherited from class org.snpeff.interval.Marker
adjust, apply, applyDel, applyDup, applyIns, applyMixed, clone, codonTable, compareTo, compareToPos, distance, distanceBases, getParent, getType, idChain, idChain, idChain, includes, intersect, isAdjustIfParentDoesNotInclude, isDeferredAnalysis, isShowWarningIfParentDoesNotInclude, minus, query, query, readTxt, serializeParse, serializeSave, shouldApply, union, variantEffectNonRef
Methods inherited from class org.snpeff.interval.Interval
equals, findParent, getChromosome, getChromosomeName, getChromosomeNameOri, getChromosomeNum, getEnd, getGenome, getGenomeName, getId, getStart, getStrand, hashCode, intersects, intersects, intersects, intersects, intersectSize, isCircular, isSameChromo, isStrandMinus, isStrandPlus, isValid, setChromosomeNameOri, setEnd, setId, setParent, setStart, setStrandMinus, shiftCoordinates, size, toStr, toStringAsciiArt, toStrPos
Methods inherited from class java.lang.Object
equals, finalize, getClass, notify, notifyAll, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Field Details
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MULTIPLE_VALUES_SEPARATOR
- See Also:
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FIELD_BIOTYPE
- See Also:
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FIELD_DB_XREF
- See Also:
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FIELD_EXON_ID
- See Also:
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FIELD_GENE
- See Also:
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FIELD_GENE_BIOTYPE
- See Also:
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FIELD_GENE_ID
- See Also:
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FIELD_GENE_NAME
- See Also:
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FIELD_GENE_TYPE
- See Also:
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FIELD_ID
- See Also:
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FIELD_NAME
- See Also:
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FIELD_NAMEU
- See Also:
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FIELD_PARENT
- See Also:
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FIELD_PROTEIN_ID
- See Also:
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FIELD_TAG
- See Also:
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FIELD_TRANSCRIPT_ID
- See Also:
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FIELD_TRANSCRIPT_TSL
- See Also:
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FIELD_TRANSCRIPT_VERSION
- See Also:
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Constructor Details
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GffMarker
public GffMarker() -
GffMarker
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GffMarker
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Method Details
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canParseLine
Can this line (form a GFF file) be parsed? Note: Returns false for headers, empty lines and lines having less number of fields than expected -
add
Add key value pair -
getAttr
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getBiotype
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getBioType
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getBiotypeGeneric
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getFrame
public int getFrame() -
getGeneBiotype
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getGeneId
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getGeneName
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getGffParentId
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getGffParentIds
Parent can have multiple, comma separated entries -
getGffType
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getProteinId
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getTranscriptBiotype
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getTags
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getTranscriptTsl
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getTranscriptId
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getTranscriptVersion
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hasAnnotations
public boolean hasAnnotations()When annotating a VCF file, add fields from this GFF- Overrides:
hasAnnotations
in classCustom
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hasAttr
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isMultipleValues
Does the key have mutiple values -
isProteingCoding
public boolean isProteingCoding()Is biotType considered 'protein coding'? -
iterator
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parse
Parse an entry (line) from a GFF file -
parseAttributes
Parse attributes (key-value pairs) from a line in a GFF file -
parseId
Obtain or create an ID -
toString
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