Package org.snpeff.interval
Class GffMarker
- java.lang.Object
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- org.snpeff.interval.Interval
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- org.snpeff.interval.Marker
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- org.snpeff.interval.Custom
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- org.snpeff.interval.GffMarker
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,java.lang.Iterable<KeyValue<java.lang.String,java.lang.String>>
,TxtSerializable
- Direct Known Subclasses:
Gtf2Marker
public class GffMarker extends Custom
An interval intended as a mark- Author:
- pcingola
- See Also:
- Serialized Form
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Field Summary
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Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
add(java.lang.String key, java.lang.String value)
Add key value pairstatic boolean
canParseLine(java.lang.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 expectedjava.lang.String
getAttr(java.lang.String key)
BioType
getBiotype()
protected java.lang.String
getBioType()
protected BioType
getBiotypeGeneric()
int
getFrame()
BioType
getGeneBiotype()
java.lang.String
getGeneId()
java.lang.String
getGeneName()
java.lang.String
getGffParentId(boolean fromGeneId)
java.lang.String[]
getGffParentIds()
Parent can have multiple, comma separated entriesGffType
getGffType()
BioType
getTranscriptBiotype()
java.lang.String
getTranscriptId()
java.lang.String
getTranscriptVersion()
boolean
hasAnnotations()
When annotating a VCF file, add fields from this GFFboolean
hasAttr(java.lang.String key)
boolean
isProteingCoding()
Is biotType considered 'protein coding'?java.util.Iterator<KeyValue<java.lang.String,java.lang.String>>
iterator()
protected void
parse(Genome genome, java.lang.String line)
Parse an entry (line) from a GFF fileprotected void
parseAttributes(java.lang.String attrStr)
Parse attributes (key-value pairs) from a line in a GFF fileprotected java.lang.String
parseId()
Obtain or create an IDjava.lang.String
toString()
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Methods inherited from class org.snpeff.interval.Custom
cloneShallow, getLabel, getScore, setLabel, setScore, variantEffect
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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, isShowWarningIfParentDoesNotInclude, minus, query, query, readTxt, serializeParse, serializeSave, shouldApply, union, variantEffectNonRef
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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
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Method Detail
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canParseLine
public static boolean canParseLine(java.lang.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 expected
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add
public void add(java.lang.String key, java.lang.String value)
Add key value pair
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getAttr
public java.lang.String getAttr(java.lang.String key)
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getBiotype
public BioType getBiotype()
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getBioType
protected java.lang.String getBioType()
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getBiotypeGeneric
protected BioType getBiotypeGeneric()
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getFrame
public int getFrame()
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getGeneBiotype
public BioType getGeneBiotype()
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getGeneId
public java.lang.String getGeneId()
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getGeneName
public java.lang.String getGeneName()
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getGffParentId
public java.lang.String getGffParentId(boolean fromGeneId)
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getGffParentIds
public java.lang.String[] getGffParentIds()
Parent can have multiple, comma separated entries
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getGffType
public GffType getGffType()
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getTranscriptBiotype
public BioType getTranscriptBiotype()
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getTranscriptId
public java.lang.String getTranscriptId()
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getTranscriptVersion
public java.lang.String 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
public boolean hasAttr(java.lang.String key)
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isProteingCoding
public boolean isProteingCoding()
Is biotType considered 'protein coding'?
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iterator
public java.util.Iterator<KeyValue<java.lang.String,java.lang.String>> iterator()
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parse
protected void parse(Genome genome, java.lang.String line)
Parse an entry (line) from a GFF file
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parseAttributes
protected void parseAttributes(java.lang.String attrStr)
Parse attributes (key-value pairs) from a line in a GFF file
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parseId
protected java.lang.String parseId()
Obtain or create an ID
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