org.dishevelled.bio.assembly.gfa2

Class Segment

java.lang.Object

org.dishevelled.bio.assembly.gfa.GfaRecord

org.dishevelled.bio.assembly.gfa2.Gfa2Record

org.dishevelled.bio.assembly.gfa2.Segment

@Immutable
public final class Segment
extends Gfa2Record

Segment GFA 2.0 record.

Author:

Michael Heuer

Constructor Summary

Constructors

Constructor and Description
Segment(String id, int length, String sequence, Map<String,Tag> tags) Create a new segment GFA 2.0 record.

Method Summary

Modifier and Type	Method and Description
boolean	containsFc() Return true if the tags for this segment contain the reserved key FC.
boolean	containsFragmentCount() Return true if the tags for this segment contain the reserved key FC, for fragment count.
boolean	containsKc() Return true if the tags for this segment contain the reserved key KC.
boolean	containsKmerCount() Return true if the tags for this segment contain the reserved key KC, for k-mer count.
boolean	containsRc() Return true if the tags for this segment contain the reserved key RC.
boolean	containsReadCount() Return true if the tags for this segment contain the reserved key RC, for read count.
boolean	containsSequenceChecksum() Return true if the tags for this segment contain the reserved key SH, for SHA-256 checksum of the sequence.
boolean	containsSequenceUri() Return true if the tags for this segment contain the reserved key UR.
boolean	containsSh() Return true if the tags for this segment contain the reserved key SH.
boolean	containsUr() Return true if the tags for this segment contain the reserved key UR.
boolean	equals(Object o)
int	getFc() Return the Type=i value for the reserved key FC as an integer.
Optional<Integer>	getFcOpt() Return an optional Type=i value for the reserved key FC as an integer.
int	getFragmentCount() Return true if the tags for this segment contain the reserved key FC, for fragment count.
Optional<Integer>	getFragmentCountOpt() Return an optional wrapping the fragment count for this segment (Type=i value for the reserved key FC as an integer).
String	getId() Return the identifier for this segment.
Optional<String>	getIdOpt() Deprecated. will be removed in 2.0, identifier is always non-null
int	getKc() Return the Type=i value for the reserved key KC as an integer.
Optional<Integer>	getKcOpt() Return an optional Type=i value for the reserved key KC as an integer.
int	getKmerCount() Return the k-mer count for this segment (Type=i value for the reserved key KC as an integer).
Optional<Integer>	getKmerCountOpt() Return an optional wrapping the k-mer count for this segment (Type=i value for the reserved key KC as an integer).
int	getLength() Return the length for this segment.
int	getRc() Return the Type=i value for the reserved key RC as an integer.
Optional<Integer>	getRcOpt() Return an optional Type=i value for the reserved key RC as an integer.
int	getReadCount() Return the read count for this segment (Type=i value for the reserved key RC as an integer).
Optional<Integer>	getReadCountOpt() Return an optional wrapping the read count for this segment (Type=i value for the reserved key RC as an integer).
String	getSequence() Return the sequence for this segment, if any.
byte[]	getSequenceChecksum() Return the SHA-256 checksum of the sequence for this segment (Type=H value for the reserved key SH as a byte array).
Optional<byte[]>	getSequenceChecksumOpt() Return an optional wrapping the SHA-256 checksum of the sequence for this segment (Type=H value for the reserved key SH as a byte array).
Optional<String>	getSequenceOpt() Return an optional wrapping the sequence for this segment.
String	getSequenceUri() Return the URI or local file-system path of the sequence for this segment (Type=Z value for the reserved key UR as a string).
Optional<String>	getSequenceUriOpt() Return an optional wrapping the URI or local file-system path of the sequence for this segment (Type=Z value for the reserved key UR as a string).
byte[]	getSh() Return the Type=H value for the reserved key SH as a byte array.
Optional<byte[]>	getShOpt() Return an optional Type=H value for the reserved key SH as a byte array.
String	getUr() Return the Type=Z value for the reserved key UR as a string.
Optional<String>	getUrOpt() Return an optional Type=Z value for the reserved key UR as a string.
int	hashCode()
boolean	hasSequence() Return true if this segment has a sequence.
String	toString()
static Segment	valueOf(String value) Parse a segment GFA 2.0 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

Segment

public Segment(String id,
               int length,
               @Nullable
               String sequence,
               Map<String,Tag> tags)

Create a new segment GFA 2.0 record.

Parameters:

id - identifier, must not be null

length - length, must be at least zero

sequence - sequence, if any

tags - tags, must not be null

Method Detail

getId

public String getId()

Return the identifier for this segment.

Returns:

the identifier for this segment

getIdOpt

public Optional<String> getIdOpt()

Deprecated. will be removed in 2.0, identifier is always non-null

Return an optional wrapping the identifier for this segment.

Returns:

an optional wrapping the identifier for this segment

getLength

public int getLength()

Return the length for this segment.

Returns:

the length for this segment

hasSequence

public boolean hasSequence()

Return true if this segment has a sequence.

Returns:

true if this segment has a sequence

Since:

1.3.2

getSequence

public String getSequence()

Return the sequence for this segment, if any.

Returns:

the sequence for this segment, if any

getSequenceOpt

public Optional<String> getSequenceOpt()

Return an optional wrapping the sequence for this segment.

Returns:

an optional wrapping the sequence for this segment

containsRc

public boolean containsRc()

Return true if the tags for this segment contain the reserved key RC.

Returns:

true if the tags for this segment contain the reserved key RC

Since:

1.3.2

getRc

public int getRc()

Return the Type=i value for the reserved key RC as an integer.

Returns:

the Type=i value for the reserved key RC as an integer

Since:

1.3.2

getRcOpt

public Optional<Integer> getRcOpt()

Return an optional Type=i value for the reserved key RC as an integer.

Returns:

an optional Type=i value for the reserved key RC as an integer

Since:

1.3.2

containsReadCount

public boolean containsReadCount()

Return true if the tags for this segment contain the reserved key RC, for read count.

Returns:

true if the tags for this segment contain the reserved key RC, for read count

Since:

1.3.2

getReadCount

public int getReadCount()

Return the read count for this segment (Type=i value for the reserved key RC as an integer).

Returns:

the read count for this segment (Type=i value for the reserved key RC as an integer)

Since:

1.3.2

getReadCountOpt

public Optional<Integer> getReadCountOpt()

Return an optional wrapping the read count for this segment (Type=i value for the reserved key RC as an integer).

Returns:

an optional wrapping the read count for this segment (Type=i value for the reserved key RC as an integer)

Since:

1.3.2

containsFc

public boolean containsFc()

Return true if the tags for this segment contain the reserved key FC.

Returns:

true if the tags for this segment contain the reserved key FC

Since:

1.3.2

getFc

public int getFc()

Return the Type=i value for the reserved key FC as an integer.

Returns:

the Type=i value for the reserved key FC as an integer

Since:

1.3.2

getFcOpt

public Optional<Integer> getFcOpt()

Return an optional Type=i value for the reserved key FC as an integer.

Returns:

an optional Type=i value for the reserved key FC as an integer

Since:

1.3.2

containsFragmentCount

public boolean containsFragmentCount()

Return true if the tags for this segment contain the reserved key FC, for fragment count.

Returns:

true if the tags for this segment contain the reserved key FC, for fragment count

Since:

1.3.2

getFragmentCount

public int getFragmentCount()

Return true if the tags for this segment contain the reserved key FC, for fragment count.

Returns:

if the tags for this segment contain the reserved key FC, for fragment count

Since:

1.3.2

getFragmentCountOpt

public Optional<Integer> getFragmentCountOpt()

Return an optional wrapping the fragment count for this segment (Type=i value for the reserved key FC as an integer).

Returns:

an optional wrapping the fragment count for this segment (Type=i value for the reserved key FC as an integer)

Since:

1.3.2

containsKc

public boolean containsKc()

Return true if the tags for this segment contain the reserved key KC.

Returns:

true if the tags for this segment contain the reserved key KC

Since:

1.3.2

getKc

public int getKc()

Return the Type=i value for the reserved key KC as an integer.

Returns:

the Type=i value for the reserved key KC as an integer

Since:

1.3.2

getKcOpt

public Optional<Integer> getKcOpt()

Return an optional Type=i value for the reserved key KC as an integer.

Returns:

an optional Type=i value for the reserved key KC as an integer

Since:

1.3.2

containsKmerCount

public boolean containsKmerCount()

Return true if the tags for this segment contain the reserved key KC, for k-mer count.

Returns:

true if the tags for this segment contain the reserved key KC, for k-mer count

Since:

1.3.2

getKmerCount

public int getKmerCount()

Return the k-mer count for this segment (Type=i value for the reserved key KC as an integer).

Returns:

the k-mer count for this segment (Type=i value for the reserved key KC as an integer)

Since:

1.3.2

getKmerCountOpt

public Optional<Integer> getKmerCountOpt()

Return an optional wrapping the k-mer count for this segment (Type=i value for the reserved key KC as an integer).

Returns:

an optional wrapping the k-mer count for this segment (Type=i value for the reserved key KC as an integer)

Since:

1.3.2

containsSh

public boolean containsSh()

Return true if the tags for this segment contain the reserved key SH.

Returns:

true if the tags for this segment contain the reserved key SH

Since:

1.3.2

getSh

public byte[] getSh()

Return the Type=H value for the reserved key SH as a byte array.

Returns:

the Type=Z value for the reserved key SH as a byte array

Since:

1.3.2

getShOpt

public Optional<byte[]> getShOpt()

Return an optional Type=H value for the reserved key SH as a byte array.

Returns:

an optional Type=H value for the reserved key SH as a byte array

Since:

1.3.2

containsSequenceChecksum

public boolean containsSequenceChecksum()

Return true if the tags for this segment contain the reserved key SH, for SHA-256 checksum of the sequence.

Returns:

true if the tags for this segment contain the reserved key SH, for SHA-256 checksum of the sequence

Since:

1.3.2

getSequenceChecksum

public byte[] getSequenceChecksum()

Return the SHA-256 checksum of the sequence for this segment (Type=H value for the reserved key SH as a byte array).

Returns:

the SHA-256 checksum of the sequence for this segment (Type=H value for the reserved key SH as a byte array)

Since:

1.3.2

getSequenceChecksumOpt

public Optional<byte[]> getSequenceChecksumOpt()

Return an optional wrapping the SHA-256 checksum of the sequence for this segment (Type=H value for the reserved key SH as a byte array).

Returns:

an optional wrapping the SHA-256 checksum of the sequence for this segment (Type=H value for the reserved key SH as a byte array)

Since:

1.3.2

containsUr

public boolean containsUr()

Return true if the tags for this segment contain the reserved key UR.

Returns:

true if the tags for this segment contain the reserved key UR

Since:

1.3.2

getUr

public String getUr()

Return the Type=Z value for the reserved key UR as a string.

Returns:

the Type=Z value for the reserved key UR as a string

Since:

1.3.2

getUrOpt

public Optional<String> getUrOpt()

Return an optional Type=Z value for the reserved key UR as a string.

Returns:

an optional Type=Z value for the reserved key UR as a string

Since:

1.3.2

containsSequenceUri

public boolean containsSequenceUri()

Return true if the tags for this segment contain the reserved key UR.

Returns:

true if the tags for this segment contain the reserved key UR

Since:

1.3.2

getSequenceUri

public String getSequenceUri()

Return the URI or local file-system path of the sequence for this segment (Type=Z value for the reserved key UR as a string). If it does not start with a standard protocol (e.g. ftp), it is assumed to be a local path.

Returns:

the URI or local file-system path of the sequence for this segment (Type=Z value for the reserved key UR as a string)

Since:

1.3.2

getSequenceUriOpt

public Optional<String> getSequenceUriOpt()

Return an optional wrapping the URI or local file-system path of the sequence for this segment (Type=Z value for the reserved key UR as a string). If it does not start with a standard protocol (e.g. ftp), it is assumed to be a local path.

Returns:

an optional wrapping the URI or local file-system path of the sequence for this segment (Type=Z value for the reserved key UR as a string)

Since:

1.3.2

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 Segment valueOf(String value)

Parse a segment GFA 2.0 record from the specified value.

Parameters:

value - value, must not be null

Returns:

a segment GFA 2.0 record parsed from the specified value