IdMapper (SnpEff 5.1 API)

java.lang.Object

org.snpeff.pdb.IdMapper

public class IdMapper extends Object

Map IDs

Author:: pcingola

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 java.lang.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