info.bioinfweb.libralign.model.adapters

Class InvalidUnderlyingTokenException

java.lang.Object

java.lang.Throwable

java.lang.Exception

java.lang.RuntimeException

info.bioinfweb.libralign.model.adapters.InvalidUnderlyingTokenException

All Implemented Interfaces:

java.io.Serializable

public class InvalidUnderlyingTokenException
extends java.lang.RuntimeException

Exception that indicates that a token that could not be translated by a SingleSequenceDataAdapter was found.

In case of a SingleCharSequenceAdapter this happens if a token which has a string representation that is not exactly one character long was tried to convert and SingleCharSequenceAdapter.isCutLongRepresentations() was set to false.

In case of SingleBioJavaSequenceAdapter this happens if no compound could be found in the specified compound set which was associated with the string representation of the token in question and SingleBioJavaSequenceAdapter#isAllowUnkownCompounds() was false.

Other implementations in- and outside LibrAlign might also throw this exception for similar reasons.

Since:

0.1.0

Author:

Ben Stöver

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
InvalidUnderlyingTokenException(SingleSequenceDataAdapter<?> adapter, java.lang.Object token, java.lang.String representation) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
SingleSequenceDataAdapter<?>	getAdapter()
java.lang.String	getRepresentation()
java.lang.Object	getToken()

Methods inherited from class java.lang.Throwable

addSuppressed, fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, getSuppressed, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

InvalidUnderlyingTokenException

public InvalidUnderlyingTokenException(SingleSequenceDataAdapter<?> adapter,
                                       java.lang.Object token,
                                       java.lang.String representation)

Creates a new instance of this class.

Parameters:

adapter - the adapter that tries to convert the token to a character

token - the token that could not be converted

representation - the invalid representation of that token

Method Detail

getAdapter

public SingleSequenceDataAdapter<?> getAdapter()

getToken

public java.lang.Object getToken()

getRepresentation

public java.lang.String getRepresentation()