org.dishevelled.bio.assembly.gfa1

Class Traversal

java.lang.Object

org.dishevelled.bio.assembly.gfa.GfaRecord

org.dishevelled.bio.assembly.gfa1.Gfa1Record

org.dishevelled.bio.assembly.gfa1.Traversal

@Immutable
public final class Traversal
extends Gfa1Record

Traversal.

Author:

Michael Heuer

Constructor Summary

Constructors

Constructor and Description
Traversal(String pathName, int ordinal, Reference source, Reference target, String overlap, Map<String,Tag> tags) Create a new traversal GFA 1.0 record.

Method Summary

Modifier and Type	Method and Description
boolean	equals(Object o)
int	getOrdinal() Return the ordinal for this traversal.
String	getOverlap() Return the overlap in cigar format for this traversal, if any.
Optional<String>	getOverlapOpt() Return an optional wrapping the overlap for this traversal.
String	getPathName() Return the path name for this traversal.
Reference	getSource() Return the source reference for this traversal.
Reference	getTarget() Return the target reference for this traversal.
int	hashCode()
boolean	hasOverlap() Return true if this traversal has an overlap in cigar format.
String	toString()
static Traversal	valueOf(String value) Parse a traversal GFA 1.0 record from the specified value.

Methods inherited from class org.dishevelled.bio.assembly.gfa.GfaRecord

containsTagKey, getTagByteArray, getTagByteArrayOpt, getTagBytes, getTagBytesOpt, getTagCharacter, getTagCharacterOpt, getTagFloat, getTagFloatOpt, getTagFloats, getTagFloatsOpt, getTagInteger, getTagIntegerOpt, getTagIntegers, getTagIntegersOpt, getTags, getTagString, getTagStringOpt

Methods inherited from class java.lang.Object

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

Constructor Detail

Traversal

public Traversal(String pathName,
                 int ordinal,
                 Reference source,
                 Reference target,
                 @Nullable
                 String overlap,
                 Map<String,Tag> tags)

Create a new traversal GFA 1.0 record.

Parameters:

pathName - path name, must not be null

ordinal - ordinal, must be at least zero

source - source reference, must not be null

target - target reference, must not be null

overlap - overlap, if any

tags - tags, must not be null

Method Detail

getPathName

public String getPathName()

Return the path name for this traversal.

Returns:

the path name for ths traversal

getOrdinal

public int getOrdinal()

Return the ordinal for this traversal.

Returns:

the ordinal for this traversal

getSource

public Reference getSource()

Return the source reference for this traversal.

Returns:

the source reference for this traversal

getTarget

public Reference getTarget()

Return the target reference for this traversal.

Returns:

the target reference for this traversal

hasOverlap

public boolean hasOverlap()

Return true if this traversal has an overlap in cigar format.

Returns:

true if this traversal has an overlap in cigar format.

getOverlap

public String getOverlap()

Return the overlap in cigar format for this traversal, if any.

Returns:

the overlap in cigar format for this traversal, if any

getOverlapOpt

public Optional<String> getOverlapOpt()

Return an optional wrapping the overlap for this traversal.

Returns:

an optional wrapping the overlap for this traversal

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 Traversal valueOf(String value)

Parse a traversal GFA 1.0 record from the specified value.

Parameters:

value - value, must not be null

Returns:

a traversal GFA 1.0 record parsed from the specified value