TranscriptSet (SnpEff 5.2 API)

java.lang.Object

org.snpeff.spliceSites.TranscriptSet

All Implemented Interfaces:: Iterable<Transcript>

public class TranscriptSet extends Object implements Iterable<Transcript>

A set of transcripts

Author:: pablocingolani

Field Summary

Fields

Modifier and Type

Field

Description

static final int

MAX_TRANSCRIPTS_PER_GENE
Constructor Summary

Constructors

Constructor

Description

TranscriptSet(Genome genome)
Method Summary

Modifier and Type

Method

Description

void

filter()

Filter out "bad transcripts"

List<Transcript>

getByChromo(String chrName)

Iterator<Transcript>

iterator()

void

setDebug(boolean debug)

void

setVerbose(boolean verbose)

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

Methods inherited from interface java.lang.Iterable
forEach, spliterator

Field Details
- MAX_TRANSCRIPTS_PER_GENE
  
  public static final int MAX_TRANSCRIPTS_PER_GENE
  See Also:
  
  Constant Field Values
Constructor Details
- TranscriptSet
  
  public TranscriptSet(Genome genome)
Method Details
- filter
  
  public void filter()
  
  Filter out "bad transcripts"
- getByChromo
  
  public List<Transcript> getByChromo(String chrName)
- iterator
  
  public Iterator<Transcript> iterator()
  
  Specified by:
  
  iterator in interface Iterable<Transcript>
- setDebug
  
  public void setDebug(boolean debug)
- setVerbose
  
  public void setVerbose(boolean verbose)