Package com.biomatters.geneious.publicapi.utilities

Enum ImportUtilities.ActionWhenInvalid

java.lang.Object

java.lang.Enum<ImportUtilities.ActionWhenInvalid>

com.biomatters.geneious.publicapi.utilities.ImportUtilities.ActionWhenInvalid

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<ImportUtilities.ActionWhenInvalid>

Enclosing class:

ImportUtilities

public static enum ImportUtilities.ActionWhenInvalid
extends java.lang.Enum<ImportUtilities.ActionWhenInvalid>

Specifies what to do when a sequence with invalid bases/residues is encountered during import

Enum Constant Summary

Enum Constants

Enum Constant	Description
DiscardSequence	Discard the sequence but continue importing
ImportWithInvalidBases	Leave invalid bases/residues in the sequence.
RemoveInvalidBases	Remove all invalid bases/residues (may change the length of sequences)
ReplaceInvalidBases	Replace all invalid bases/residues with ambiguities (X for amino acid, N for DNA)
ReplaceInvalidBasesWithGaps	Replace all invalid bases/residues with gaps (-)

Method Summary

Modifier and Type	Method	Description
static ImportUtilities.ActionWhenInvalid	valueOf(java.lang.String name)	Returns the enum constant of this type with the specified name.
static ImportUtilities.ActionWhenInvalid[]	values()	Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

DiscardSequence

public static final ImportUtilities.ActionWhenInvalid DiscardSequence

Discard the sequence but continue importing

ReplaceInvalidBases

public static final ImportUtilities.ActionWhenInvalid ReplaceInvalidBases

Replace all invalid bases/residues with ambiguities (X for amino acid, N for DNA)

ReplaceInvalidBasesWithGaps

public static final ImportUtilities.ActionWhenInvalid ReplaceInvalidBasesWithGaps

Replace all invalid bases/residues with gaps (-)

RemoveInvalidBases

public static final ImportUtilities.ActionWhenInvalid RemoveInvalidBases

Remove all invalid bases/residues (may change the length of sequences)

ImportWithInvalidBases

public static final ImportUtilities.ActionWhenInvalid ImportWithInvalidBases

Leave invalid bases/residues in the sequence. This should only be used internally to a plugin because the core of Geneious will not accept sequences containing invalid bases/residues.

Method Detail

values

public static ImportUtilities.ActionWhenInvalid[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (ImportUtilities.ActionWhenInvalid c : ImportUtilities.ActionWhenInvalid.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static ImportUtilities.ActionWhenInvalid valueOf(java.lang.String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

java.lang.IllegalArgumentException - if this enum type has no constant with the specified name

java.lang.NullPointerException - if the argument is null