org.dishevelled.bio.assembly.gfa1

Class Path

java.lang.Object

org.dishevelled.bio.assembly.gfa.GfaRecord

org.dishevelled.bio.assembly.gfa1.Gfa1Record

org.dishevelled.bio.assembly.gfa1.Path

@Immutable
public final class Path
extends Gfa1Record

Path GFA 1.0 record.

Author:

Michael Heuer

Constructor Summary

Constructors

Constructor and Description
Path(String name, List<Reference> segments, List<String> overlaps, Map<String,Tag> tags) Create a new path GFA 1.0 record.

Method Summary

Modifier and Type	Method and Description
boolean	equals(Object o)
String	getName() Return the name for this path.
List<String>	getOverlaps() Return an immutable list of overlaps in cigar format for this path, or null if none exist.
Optional<List<String>>	getOverlapsOpt() Return an optional wrapping the list of overlaps in cigar format for this path.
List<Reference>	getSegments() Return an immutable list of segment references for this path.
int	hashCode()
boolean	hasOverlaps() Return true if this path has any overlaps.
String	toString()
static Path	valueOf(String value) Parse a path 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

Path

public Path(String name,
            List<Reference> segments,
            @Nullable
            List<String> overlaps,
            Map<String,Tag> tags)

Create a new path GFA 1.0 record.

Parameters:

name - name, must not be null

segments - list of segment references, must not be null

overlaps - list of overlaps, if any

tags - tags, must not be null

Method Detail

getName

public String getName()

Return the name for this path.

Returns:

the name for this path

getSegments

public List<Reference> getSegments()

Return an immutable list of segment references for this path.

Returns:

an immutable list of segment references for this path

hasOverlaps

public boolean hasOverlaps()

Return true if this path has any overlaps.

Returns:

true if this path has any overlaps

getOverlaps

public List<String> getOverlaps()

Return an immutable list of overlaps in cigar format for this path, or null if none exist.

Returns:

an immutable list of overlaps in cigar format for this path, or null if none exist

getOverlapsOpt

public Optional<List<String>> getOverlapsOpt()

Return an optional wrapping the list of overlaps in cigar format for this path.

Returns:

an optional wrapping the list of overlap in cigar format for this path

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 Path valueOf(String value)

Parse a path GFA 1.0 record from the specified value.

Parameters:

value - value, must not be null

Returns:

a path GFA 1.0 record parsed from the specified value