Package org.snpeff.interval
Class Genes
java.lang.Object
org.snpeff.interval.Genes
- All Implemented Interfaces:
Serializable
,Iterable<Gene>
A collection of genes (marker intervals)
Note: It is assumed that all genes belong to the same genome
- Author:
- pcingola
- See Also:
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
Add a gene interval to this collectionvoid
In a circular genome, a gene can have negative coordinates or crosses over chromosome end.Creates a list of Intergenic regionsvoid
createSpliceSites
(int spliceSiteSize, int spliceRegionExonSize, int spliceRegionIntronMin, int spliceRegionIntronMax) Create splice sites.createUpDownStream
(int upDownLength) Creates a list of UP/DOWN stream regions (for each transcript) Upstream (downstream) stream is defined as upDownLength before (after) transcript Note: If upDownLength <=0 no interval is createdfindTranscript
(String trId) Find a transcript by IDObtain a gene intervalgetGeneByName
(String geneName) Obtain a gene by GeneName WARNING: The first match is returned.iterator()
int
size()
sorted()
toString()
values()
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Field Details
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debug
public boolean debug
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Constructor Details
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Genes
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Method Details
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add
Add a gene interval to this collection -
createCircularGenes
public void createCircularGenes()In a circular genome, a gene can have negative coordinates or crosses over chromosome end. These genes are mirrored to the opposite end of the chromosome so that they can be referenced by both circular coordinates. -
createIntergenic
Creates a list of Intergenic regions -
createSpliceSites
public void createSpliceSites(int spliceSiteSize, int spliceRegionExonSize, int spliceRegionIntronMin, int spliceRegionIntronMax) Create splice sites.- Parameters:
createIfMissing
- : If true, create canonical splice sites if they are missing. For a definition of splice site, see comments at the beginning of SpliceSite.java
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createUpDownStream
Creates a list of UP/DOWN stream regions (for each transcript) Upstream (downstream) stream is defined as upDownLength before (after) transcript Note: If upDownLength <=0 no interval is created -
findTranscript
Find a transcript by ID -
get
Obtain a gene interval -
getGeneByName
Obtain a gene by GeneName WARNING: The first match is returned. If multiple genes share the same gene name, no order can be expected for this method. -
iterator
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size
public int size() -
sorted
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toString
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values
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