org.dishevelled.bio.assembly.gfa2

Class Gap

java.lang.Object

org.dishevelled.bio.assembly.gfa.GfaRecord

org.dishevelled.bio.assembly.gfa2.Gfa2Record

org.dishevelled.bio.assembly.gfa2.Gap

@Immutable
public final class Gap
extends Gfa2Record

Gap GFA 2.0 record.

Author:

Michael Heuer

Constructor Summary

Constructors

Constructor and Description
Gap(String id, Reference source, Reference target, int distance, Integer variance, Map<String,Tag> tags) Create a new gap GFA 2.0 record.

Method Summary

Modifier and Type	Method and Description
boolean	containsTraceSpacing() Return true if the tags for this gap contain the reserved key TS, for trace spacing.
boolean	containsTs() Return true if the tags for this gap contain the reserved key TS.
boolean	equals(Object o)
int	getDistance() Return the distance for this gap.
String	getId() Return the identifier for this gap, if any.
Optional<String>	getIdOpt() Return an optional wrapping the identifier for this gap.
Reference	getSource() Return the source reference for this gap.
Reference	getTarget() Return the target reference for this gap.
int	getTraceSpacing() Return the trace spacing for this gap (Type=i value for the reserved key TS as an integer).
Optional<Integer>	getTraceSpacingOpt() Return an optional wrapping the trace spacing for this gap (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.
Integer	getVariance() Return the variance for this gap, if any.
Optional<Integer>	getVarianceOpt() Return an optional wrapping the variance for this gap.
int	hashCode()
boolean	hasId() Return true if this gap has an identifier.
boolean	hasVariance() Return true if this gap has a variance.
String	toString()
static Gap	valueOf(String value) Parse a gap 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

Gap

public Gap(@Nullable
           String id,
           Reference source,
           Reference target,
           int distance,
           @Nullable
           Integer variance,
           Map<String,Tag> tags)

Create a new gap GFA 2.0 record.

Parameters:

id - identifier, if any

source - source reference, must not be null

target - target reference, must not be null

distance - distance, must be at least zero

variance - variance, if any

tags - tags, must not be null

Method Detail

hasId

public boolean hasId()

Return true if this gap has an identifier.

Returns:

true if this gap has an identifier

getId

public String getId()

Return the identifier for this gap, if any.

Returns:

the identifier for this gap, if any

getIdOpt

public Optional<String> getIdOpt()

Return an optional wrapping the identifier for this gap.

Returns:

an optional wrapping the identifier for this gap

getSource

public Reference getSource()

Return the source reference for this gap.

Returns:

the source reference for this gap

getTarget

public Reference getTarget()

Return the target reference for this gap.

Returns:

the target reference for this gap

getDistance

public int getDistance()

Return the distance for this gap.

Returns:

the distance for this gap

hasVariance

public boolean hasVariance()

Return true if this gap has a variance.

Returns:

true if this gap has a variance

getVariance

public Integer getVariance()

Return the variance for this gap, if any.

Returns:

the variance for this gap, if any

getVarianceOpt

public Optional<Integer> getVarianceOpt()

Return an optional wrapping the variance for this gap.

Returns:

an optional wrapping the variance for this gap

containsTs

public boolean containsTs()

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

Returns:

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

Returns:

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

Since:

1.3.2

getTraceSpacing

public int getTraceSpacing()

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

Returns:

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

Returns:

an optional wrapping the trace spacing for this gap (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 Gap valueOf(String value)

Parse a gap GFA 2.0 record from the specified value.

Parameters:

value - value, must not be null

Returns:

a gap GFA 2.0 record parsed from the specified value