IdMapper (SnpEff 5.4 API)

java.lang.Object

org.snpeff.pdb.IdMapper

public class IdMapper extends Object

Map protein ID to transcript ID and vice versa

Constructor Summary

Constructors

Constructor

Description

IdMapper()
Method Summary

Modifier and Type

Method

Description

void

add(IdMapperEntry ime)

void

addAll(Collection<IdMapperEntry> imes)

List<IdMapperEntry>

getByPdbId(String id)

List<IdMapperEntry>

getByPdbId(String id, String chainId)

List<IdMapperEntry>

getByTrId(String id)

Collection<IdMapperEntry>

getEntries()

void

load(String fileName)

void

setVerbose(boolean verbose)

String

toString()

static String

transcriptIdNoVersion(String trId)

Remove version form transcript ID

static Set<String>

transcriptIds(List<IdMapperEntry> ids)

Methods inherited from class Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details
- IdMapper
  
  public IdMapper()
Method Details
- transcriptIdNoVersion
  
  public static String transcriptIdNoVersion(String trId)
  
  Remove version form transcript ID
- transcriptIds
  
  public static Set<String> transcriptIds(List<IdMapperEntry> ids)
- add
  
  public void add(IdMapperEntry ime)
- addAll
  
  public void addAll(Collection<IdMapperEntry> imes)
- getByPdbId
  
  public List<IdMapperEntry> getByPdbId(String id)
- getByPdbId
  
  public List<IdMapperEntry> getByPdbId(String id, String chainId)
- getByTrId
  
  public List<IdMapperEntry> getByTrId(String id)
- getEntries
  
  public Collection<IdMapperEntry> getEntries()
- load
  
  public void load(String fileName)
- setVerbose
  
  public void setVerbose(boolean verbose)
- toString
  
  public String toString()
  
  Overrides:
  
  toString in class Object