org.dishevelled.bio.assembly.gfa1

Class Link

java.lang.Object

org.dishevelled.bio.assembly.gfa.GfaRecord

org.dishevelled.bio.assembly.gfa1.Gfa1Record

org.dishevelled.bio.assembly.gfa1.Link

@Immutable
public final class Link
extends Gfa1Record

Link GFA 1.0 record.

Author:

Michael Heuer

Constructor Summary

Constructors

Constructor and Description
Link(Reference source, Reference target, String overlap, Map<String,Tag> tags) Create a new link GFA 1.0 record.

Method Summary

Modifier and Type	Method and Description
boolean	containsFc() Return true if the tags for this link contain the reserved key FC.
boolean	containsFragmentCount() Return true if the tags for this link contain the reserved key FC, for fragment count.
boolean	containsId() Return true if the tags for this segment contain the reserved key ID.
boolean	containsKc() Return true if the tags for this link contain the reserved key KC.
boolean	containsKmerCount() Return true if the tags for this link contain the reserved key KC, for k-mer count.
boolean	containsMappingQuality() Return true if the tags for this link contain the reserved key MQ, for mapping quality.
boolean	containsMismatchCount() Return true if the tags for this link contain the reserved key NM, for mismatch count.
boolean	containsMq() Return true if the tags for this link contain the reserved key MQ.
boolean	containsNm() Return true if the tags for this link contain the reserved key NM.
boolean	containsRc() Return true if the tags for this link contain the reserved key RC.
boolean	containsReadCount() Return true if the tags for this link contain the reserved key RC, for read count.
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 the fragment count for this link (Type=i value for the reserved key FC as an integer).
Optional<Integer>	getFragmentCountOpt() Return an optional wrapping the fragment count for this link (Type=i value for the reserved key FC as an integer).
String	getId() Return the Type=Z value for the reserved key ID as a string.
Optional<String>	getIdOpt() Return an optional Type=Z value for the reserved key ID as a string.
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 link (Type=i value for the reserved key KC as an integer).
Optional<Integer>	getKmerCountOpt() Return an optional wrapping the k-mer count for this link (Type=i value for the reserved key KC as an integer).
int	getMappingQuality() Return the mapping quality for this link (Type=i value for the reserved key MQ as an integer).
Optional<Integer>	getMappingQualityOpt() Return an optional wrapping the mapping quality for this link (Type=i value for the reserved key MQ as an integer).
int	getMismatchCount() Return the mismatch count for this link (Type=i value for the reserved key NM as an integer).
Optional<Integer>	getMismatchCountOpt() Return an optional wrapping the mismatch count for this link (Type=i value for the reserved key NM as an integer).
int	getMq() Return the Type=i value for the reserved key MQ as an integer.
Optional<Integer>	getMqOpt() Return an optional Type=i value for the reserved key MQ as an integer.
int	getNm() Return the Type=i value for the reserved key NM as an integer.
Optional<Integer>	getNmOpt() Return an optional Type=i value for the reserved key NM as an integer.
String	getOverlap() Return the overlap in cigar format for this link, if any.
Optional<String>	getOverlapOpt() Return an optional wrapping the overlap in cigar format for this link.
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 link (Type=i value for the reserved key RC as an integer).
Optional<Integer>	getReadCountOpt() Return an optional wrapping the read count for this link (Type=i value for the reserved key RC as an integer).
Reference	getSource() Return the source reference for this link.
Reference	getTarget() Return the target reference for this link.
int	hashCode()
boolean	hasOverlap() Return true if this link has an overlap in cigar format.
String	toString()
static Link	valueOf(String value) Parse a link 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

Link

public Link(Reference source,
            Reference target,
            @Nullable
            String overlap,
            Map<String,Tag> tags)

Create a new link GFA 1.0 record.

Parameters:

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

getSource

public Reference getSource()

Return the source reference for this link.

Returns:

the source reference for this link

getTarget

public Reference getTarget()

Return the target reference for this link.

Returns:

the target reference for this link

hasOverlap

public boolean hasOverlap()

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

Returns:

true if this link has an overlap in cigar format.

getOverlap

public String getOverlap()

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

Returns:

the overlap in cigar format for this link, if any

getOverlapOpt

public Optional<String> getOverlapOpt()

Return an optional wrapping the overlap in cigar format for this link.

Returns:

an optional wrapping the overlap in cigar format for this link

containsMq

public boolean containsMq()

Return true if the tags for this link contain the reserved key MQ.

Returns:

true if the tags for this link contain the reserved key MQ

getMq

public int getMq()

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

Returns:

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

getMqOpt

public Optional<Integer> getMqOpt()

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

Returns:

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

containsMappingQuality

public boolean containsMappingQuality()

Return true if the tags for this link contain the reserved key MQ, for mapping quality.

Returns:

true if the tags for this link contain the reserved key MQ, for mapping quality

getMappingQuality

public int getMappingQuality()

Return the mapping quality for this link (Type=i value for the reserved key MQ as an integer).

Returns:

the mapping quality for this link (Type=i value for the reserved key MQ as an integer)

getMappingQualityOpt

public Optional<Integer> getMappingQualityOpt()

Return an optional wrapping the mapping quality for this link (Type=i value for the reserved key MQ as an integer).

Returns:

an optional wrapping the mapping quality for this link (Type=i value for the reserved key MQ as an integer)

containsNm

public boolean containsNm()

Return true if the tags for this link contain the reserved key NM.

Returns:

true if the tags for this link contain the reserved key NM

getNm

public int getNm()

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

Returns:

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

getNmOpt

public Optional<Integer> getNmOpt()

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

Returns:

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

containsMismatchCount

public boolean containsMismatchCount()

Return true if the tags for this link contain the reserved key NM, for mismatch count.

Returns:

true if the tags for this link contain the reserved key NM, for mismatch count

getMismatchCount

public int getMismatchCount()

Return the mismatch count for this link (Type=i value for the reserved key NM as an integer).

Returns:

the mismatch count for this link (Type=i value for the reserved key NM as an integer)

getMismatchCountOpt

public Optional<Integer> getMismatchCountOpt()

Return an optional wrapping the mismatch count for this link (Type=i value for the reserved key NM as an integer).

Returns:

an optional wrapping the mismatch count for this link (Type=i value for the reserved key NM as an integer)

containsRc

public boolean containsRc()

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

Returns:

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

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

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

containsReadCount

public boolean containsReadCount()

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

Returns:

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

getReadCount

public int getReadCount()

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

Returns:

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

getReadCountOpt

public Optional<Integer> getReadCountOpt()

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

Returns:

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

containsFc

public boolean containsFc()

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

Returns:

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

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

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

containsFragmentCount

public boolean containsFragmentCount()

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

Returns:

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

getFragmentCount

public int getFragmentCount()

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

Returns:

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

getFragmentCountOpt

public Optional<Integer> getFragmentCountOpt()

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

Returns:

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

containsKc

public boolean containsKc()

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

Returns:

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

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

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

containsKmerCount

public boolean containsKmerCount()

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

Returns:

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

getKmerCount

public int getKmerCount()

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

Returns:

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

getKmerCountOpt

public Optional<Integer> getKmerCountOpt()

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

Returns:

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

containsId

public boolean containsId()

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

Returns:

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

getId

public String getId()

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

Returns:

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

getIdOpt

public Optional<String> getIdOpt()

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

Returns:

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

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 Link valueOf(String value)

Parse a link GFA 1.0 record from the specified value.

Parameters:

value - value, must not be null

Returns:

a link GFA 1.0 record parsed from the specified value