Package org.snpeff.pdb

Class IdMapper

java.lang.Object

org.snpeff.pdb.IdMapper

public class IdMapper
extends java.lang.Object

Map IDs

Author:

pcingola

Constructor Summary

Constructors

Constructor	Description
IdMapper()

Method Summary

Modifier and Type	Method	Description
void	add(IdMapperEntry ime)
void	addAll(java.util.Collection<IdMapperEntry> imes)
java.util.List<IdMapperEntry>	getByPdbId(java.lang.String id)
java.util.List<IdMapperEntry>	getByPdbId(java.lang.String id, java.lang.String chainId)
java.util.List<IdMapperEntry>	getByTrId(java.lang.String id)
java.util.Collection<IdMapperEntry>	getEntries()
void	load(java.lang.String fileName)
void	setVerbose(boolean verbose)
java.lang.String	toString()
static java.lang.String	transcriptIdNoVersion(java.lang.String trId)	Remove version form transcript ID
static java.util.Set<java.lang.String>	transcriptIds(java.util.List<IdMapperEntry> ids)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

IdMapper

public IdMapper()

Method Detail

transcriptIdNoVersion

public static java.lang.String transcriptIdNoVersion(java.lang.String trId)

Remove version form transcript ID

transcriptIds

public static java.util.Set<java.lang.String> transcriptIds(java.util.List<IdMapperEntry> ids)

add

public void add(IdMapperEntry ime)

addAll

public void addAll(java.util.Collection<IdMapperEntry> imes)

getByPdbId

public java.util.List<IdMapperEntry> getByPdbId(java.lang.String id)

getByPdbId

public java.util.List<IdMapperEntry> getByPdbId(java.lang.String id,
                                                java.lang.String chainId)

getByTrId

public java.util.List<IdMapperEntry> getByTrId(java.lang.String id)

getEntries

public java.util.Collection<IdMapperEntry> getEntries()

load

public void load(java.lang.String fileName)

setVerbose

public void setVerbose(boolean verbose)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object