org.dishevelled.bio.assembly.gfa2

Class Edge

java.lang.Object

org.dishevelled.bio.assembly.gfa.GfaRecord

org.dishevelled.bio.assembly.gfa2.Gfa2Record

org.dishevelled.bio.assembly.gfa2.Edge

@Immutable
public final class Edge
extends Gfa2Record

Edge GFA 2.0 record.

Author:

Michael Heuer

Constructor Summary

Constructors

Constructor and Description
Edge(String id, Reference source, Reference target, Position sourceStart, Position sourceEnd, Position targetStart, Position targetEnd, Alignment alignment, Map<String,Tag> tags) Create a new edge GFA 2.0 record.

Method Summary

Modifier and Type	Method and Description
boolean	containsFc() Return true if the tags for this edge contain the reserved key FC.
boolean	containsFragmentCount() Return true if the tags for this edge contain the reserved key FC, for fragment count.
boolean	containsKc() Return true if the tags for this edge contain the reserved key KC.
boolean	containsKmerCount() Return true if the tags for this edge contain the reserved key KC, for k-mer count.
boolean	containsMappingQuality() Return true if the tags for this edge contain the reserved key MQ, for mapping quality.
boolean	containsMismatchCount() Return true if the tags for this edge contain the reserved key NM, for mismatch count.
boolean	containsMq() Return true if the tags for this edge contain the reserved key MQ.
boolean	containsNm() Return true if the tags for this edge contain the reserved key NM.
boolean	containsRc() Return true if the tags for this edge contain the reserved key RC.
boolean	containsReadCount() Return true if the tags for this edge contain the reserved key RC, for read count.
boolean	containsTraceSpacing() Return true if the tags for this edge contain the reserved key TS, for trace spacing.
boolean	containsTs() Return true if the tags for this edge contain the reserved key TS.
boolean	equals(Object o)
Alignment	getAlignment() Return the alignment for this edge, if any.
Optional<Alignment>	getAlignmentOpt() Return an optional wrapping the alignment for this edge.
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 edge (Type=i value for the reserved key FC as an integer).
Optional<Integer>	getFragmentCountOpt() Return an optional wrapping the fragment count for this edge (Type=i value for the reserved key FC as an integer).
String	getId() Return the identifier for this edge, if any.
Optional<String>	getIdOpt() Return an optional wrapping the identifier for this edge.
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 edge (Type=i value for the reserved key KC as an integer).
Optional<Integer>	getKmerCountOpt() Return an optional wrapping the k-mer count for this edge (Type=i value for the reserved key KC as an integer).
int	getMappingQuality() Return the mapping quality for this edge (Type=i value for the reserved key MQ as an integer).
Optional<Integer>	getMappingQualityOpt() Return an optional wrapping the mapping quality for this edge (Type=i value for the reserved key MQ as an integer).
int	getMismatchCount() Return the mismatch count for this edge (Type=i value for the reserved key NM as an integer).
Optional<Integer>	getMismatchCountOpt() Return an optional wrapping the mismatch count for this edge (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.
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 edge (Type=i value for the reserved key RC as an integer).
Optional<Integer>	getReadCountOpt() Return an optional wrapping the read count for this edge (Type=i value for the reserved key RC as an integer).
Reference	getSource() Return the source reference for this edge.
Position	getSourceEnd() Return the source end position for this edge.
Position	getSourceStart() Return the source start position for this edge.
Reference	getTarget() Return the target reference for this edge.
Position	getTargetEnd() Return the target end position for this edge.
Position	getTargetStart() Return the target start position for this edge.
int	getTraceSpacing() Return the trace spacing for this edge (Type=i value for the reserved key TS as an integer).
Optional<Integer>	getTraceSpacingOpt() Return an optional wrapping the trace spacing for this edge (Type=i value for the reserved key TS as an integer).
int	getTs() Return the Type=i value for the reserved key TS as an integer.
Optional<Integer>	getTsOpt() Return an optional Type=i value for the reserved key TS as an integer.
boolean	hasAlignment() Return true if this edge has an alignment.
int	hashCode()
boolean	hasId() Return true if this edge has an identifier.
String	toString()
static Edge	valueOf(String value) Parse an edge 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

Edge

public Edge(@Nullable
            String id,
            Reference source,
            Reference target,
            Position sourceStart,
            Position sourceEnd,
            Position targetStart,
            Position targetEnd,
            @Nullable
            Alignment alignment,
            Map<String,Tag> tags)

Create a new edge GFA 2.0 record.

Parameters:

id - identifier, if any

source - source reference, must not be null

target - target reference, must not be null

sourceStart - source start position, must not be null

sourceEnd - source end position, must not be null

targetStart - target start position, must not be null

targetEnd - target end position, must not be null

alignment - alignment, if any

tags - tags, must not be null

Method Detail

hasId

public boolean hasId()

Return true if this edge has an identifier.

Returns:

true if this edge has an identifier

Since:

1.3.2

getId

public String getId()

Return the identifier for this edge, if any.

Returns:

the identifier for this edge, if any

getIdOpt

public Optional<String> getIdOpt()

Return an optional wrapping the identifier for this edge.

Returns:

an optional wrapping the identifier for this edge

Since:

1.3.2

getSource

public Reference getSource()

Return the source reference for this edge.

Returns:

the source reference for this edge

getTarget

public Reference getTarget()

Return the target reference for this edge.

Returns:

the target reference for this edge

getSourceStart

public Position getSourceStart()

Return the source start position for this edge.

Returns:

the source start position for this edge

getSourceEnd

public Position getSourceEnd()

Return the source end position for this edge.

Returns:

the source end position for this edge

getTargetStart

public Position getTargetStart()

Return the target start position for this edge.

Returns:

the target start position for this edge

getTargetEnd

public Position getTargetEnd()

Return the target end position for this edge.

Returns:

the target end position for this edge

hasAlignment

public boolean hasAlignment()

Return true if this edge has an alignment.

Returns:

true if this edge has an alignment

Since:

1.3.2

getAlignment

public Alignment getAlignment()

Return the alignment for this edge, if any.

Returns:

the alignment for this edge, if any

getAlignmentOpt

public Optional<Alignment> getAlignmentOpt()

Return an optional wrapping the alignment for this edge.

Returns:

an optional wrapping the alignment for this edge

containsMq

public boolean containsMq()

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

Returns:

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

Since:

1.3.2

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

Since:

1.3.2

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

Since:

1.3.2

containsMappingQuality

public boolean containsMappingQuality()

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

Returns:

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

Since:

1.3.2

getMappingQuality

public int getMappingQuality()

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

Returns:

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

Since:

1.3.2

getMappingQualityOpt

public Optional<Integer> getMappingQualityOpt()

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

Returns:

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

Since:

1.3.2

containsNm

public boolean containsNm()

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

Returns:

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

Since:

1.3.2

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

Since:

1.3.2

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

Since:

1.3.2

containsMismatchCount

public boolean containsMismatchCount()

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

Returns:

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

Since:

1.3.2

getMismatchCount

public int getMismatchCount()

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

Returns:

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

Since:

1.3.2

getMismatchCountOpt

public Optional<Integer> getMismatchCountOpt()

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

Returns:

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

Since:

1.3.2

containsRc

public boolean containsRc()

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

Returns:

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

Returns:

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

Since:

1.3.2

getReadCount

public int getReadCount()

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

Returns:

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

Returns:

an optional wrapping the read count for this edge (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 edge contain the reserved key FC.

Returns:

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

Returns:

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

Since:

1.3.2

getFragmentCount

public int getFragmentCount()

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

Returns:

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

Since:

1.3.2

getFragmentCountOpt

public Optional<Integer> getFragmentCountOpt()

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

Returns:

an optional wrapping the fragment count for this edge (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 edge contain the reserved key KC.

Returns:

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

Returns:

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

Since:

1.3.2

getKmerCount

public int getKmerCount()

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

Returns:

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

Returns:

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

Since:

1.3.2

containsTs

public boolean containsTs()

Return true if the tags for this edge contain the reserved key TS.

Returns:

true if the tags for this edge contain the reserved key TS

Since:

1.3.2

getTs

public int getTs()

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

Returns:

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

Since:

1.3.2

getTsOpt

public Optional<Integer> getTsOpt()

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

Returns:

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

Since:

1.3.2

containsTraceSpacing

public boolean containsTraceSpacing()

Return true if the tags for this edge contain the reserved key TS, for trace spacing.

Returns:

true if the tags for this edge contain the reserved key TS, for trace spacing

Since:

1.3.2

getTraceSpacing

public int getTraceSpacing()

Return the trace spacing for this edge (Type=i value for the reserved key TS as an integer).

Returns:

the trace spacing for this edge (Type=i value for the reserved key TS as an integer)

Since:

1.3.2

getTraceSpacingOpt

public Optional<Integer> getTraceSpacingOpt()

Return an optional wrapping the trace spacing for this edge (Type=i value for the reserved key TS as an integer).

Returns:

an optional wrapping the trace spacing for this edge (Type=i value for the reserved key TS as an integer)

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 Edge valueOf(String value)

Parse an edge GFA 2.0 record from the specified value.

Parameters:

value - value, must not be null

Returns:

an edge GFA 2.0 record parsed from the specified value