de.charite.compbio.jannovar.impl.parse.ensembl

Class EnsemblParser

java.lang.Object

de.charite.compbio.jannovar.impl.parse.ensembl.EnsemblParser

All Implemented Interfaces:

TranscriptParser

public class EnsemblParser
extends Object
implements TranscriptParser

Parsing of ENSEMBL GTF files

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor and Description
EnsemblParser(ReferenceDictionary refDict, String basePath, org.ini4j.Profile.Section iniSection)

Method Summary

Modifier and Type	Method and Description
com.google.common.collect.ImmutableList<TranscriptModel>	run()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

EnsemblParser

public EnsemblParser(ReferenceDictionary refDict,
                     String basePath,
                     org.ini4j.Profile.Section iniSection)

Parameters:

refDict - path to ReferenceDictionary to use for name/id and id/length mapping.

basePath - path to where the to-be-parsed files live

iniSection - Profile.Section with configuration from INI file

Method Detail

run

public com.google.common.collect.ImmutableList<TranscriptModel> run()
                                                             throws TranscriptParseException

Specified by:

run in interface TranscriptParser

Returns:

list of TranscriptModel objects as parsed from the input.

Throws:

TranscriptParseException - on problems with parsing the transcript files