org.dishevelled.bio.assembly.gfa2

Class Alignment

java.lang.Object

org.dishevelled.bio.assembly.gfa2.Alignment

@Immutable
public final class Alignment
extends Object

Alignment.

Author:

Michael Heuer

Constructor Summary

Constructors

Constructor and Description
Alignment(List<Integer> trace) Create a new aligment with the specified trace.
Alignment(String cigar) Create a new alignment with the specified cigar.

Method Summary

Modifier and Type	Method and Description
boolean	equals(Object o)
String	getCigar() Return the cigar for this alignment, if any.
Optional<String>	getCigarOpt() Return an optional wrapping the cigar for this alignment.
List<Integer>	getTrace() Return the trace as an immutable list of Integers, or null if this alignment does not have a trace.
Optional<List<Integer>>	getTraceOpt() Return an optional wrapping the trace for this alignment.
boolean	hasCigar() Return true if this alignment has a cigar.
int	hashCode()
boolean	hasTrace() Return true if this alignment has a trace.
String	toString()
static Alignment	valueOf(String value) Parse an alignment from the specified value.

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

Alignment

public Alignment(String cigar)

Create a new alignment with the specified cigar.

Parameters:

cigar - cigar, if any

Alignment

public Alignment(List<Integer> trace)

Create a new aligment with the specified trace.

Parameters:

trace - trace, if any

Method Detail

hasCigar

public boolean hasCigar()

Return true if this alignment has a cigar.

Returns:

true if this alignment has a cigar

getCigar

public String getCigar()

Return the cigar for this alignment, if any.

Returns:

the cigar for this alignment, if any

getCigarOpt

public Optional<String> getCigarOpt()

Return an optional wrapping the cigar for this alignment.

Returns:

an optional wrapping the cigar for this alignment

hasTrace

public boolean hasTrace()

Return true if this alignment has a trace.

Returns:

true if this alignment has a trace

getTrace

public List<Integer> getTrace()

Return the trace as an immutable list of Integers, or null if this alignment does not have a trace.

Returns:

the trace as an immutable list of Integers, or null if this alignment does not have a trace

getTraceOpt

public Optional<List<Integer>> getTraceOpt()

Return an optional wrapping the trace for this alignment.

Returns:

an optional wrapping the trace for this alignment

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object

toString

public String toString()

Overrides:

toString in class Object

valueOf

public static Alignment valueOf(String value)

Parse an alignment from the specified value.

Parameters:

value - value, must not be null

Returns:

an alignment parsed from the specified value