org.dishevelled.bio.assembly.gfa1

Class Containment

java.lang.Object

org.dishevelled.bio.assembly.gfa.GfaRecord

org.dishevelled.bio.assembly.gfa1.Gfa1Record

org.dishevelled.bio.assembly.gfa1.Containment

@Immutable
public final class Containment
extends Gfa1Record

Containment GFA 1.0 record.

Author:

Michael Heuer

Constructor Summary

Constructors

Constructor and Description
Containment(Reference container, Reference contained, int position, String overlap, Map<String,Tag> tags) Create a new containment GFA 1.0 record.

Method Summary

Modifier and Type	Method and Description
boolean	containsId() Return true if the tags for this segment contain the reserved key ID.
boolean	containsMismatchCount() Return true if the tags for this containment contain the reserved key NM, for mismatch count.
boolean	containsNm() Return true if the tags for this containment contain the reserved key NM.
boolean	containsRc() Return true if the tags for this containment contain the reserved key RC.
boolean	containsReadCount() Return true if the tags for this containment contain the reserved key RC, for read count.
boolean	equals(Object o)
Reference	getContained() Return the contained reference for this containment.
Reference	getContainer() Return the container reference for this containment.
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	getMismatchCount() Return the mismatch count for this containment (Type=i value for the reserved key NM as an integer).
Optional<Integer>	getMismatchCountOpt() Return an optional wrapping the mismatch count for this containment (Type=i value for the reserved key NM 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 containment, if any.
Optional<String>	getOverlapOpt() Return an optional wrapping the overlap in cigar format for this containment.
int	getPosition() Return the position for this containment (0-based coordinate system).
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 containment (Type=i value for the reserved key RC as an integer).
Optional<Integer>	getReadCountOpt() Return an optional wrapping the read count for this containment (Type=i value for the reserved key RC as an integer).
int	hashCode()
boolean	hasOverlap() Return true if this containment has an overlap in cigar format.
String	toString()
static Containment	valueOf(String value) Parse a containment 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

Containment

public Containment(Reference container,
                   Reference contained,
                   int position,
                   @Nullable
                   String overlap,
                   Map<String,Tag> tags)

Create a new containment GFA 1.0 record.

Parameters:

container - container reference, must not be null

contained - contained reference, must not be null

position - position, must be at least zero

overlap - overlap in cigar format, if any

tags - tags, must not be null

Method Detail

getContainer

public Reference getContainer()

Return the container reference for this containment.

Returns:

the container reference for this containment

getContained

public Reference getContained()

Return the contained reference for this containment.

Returns:

the contained reference for this containment

getPosition

public int getPosition()

Return the position for this containment (0-based coordinate system). The position is the leftmost position of the contained segment in the container segment in its forward orientation (i.e. before this is oriented according to the container reference orientation).

Returns:

the position for this containment (0-based coordinate system)

hasOverlap

public boolean hasOverlap()

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

Returns:

true if this containment has an overlap in cigar format.

getOverlap

public String getOverlap()

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

Returns:

the overlap in cigar format for this containment, if any

getOverlapOpt

public Optional<String> getOverlapOpt()

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

Returns:

an optional wrapping the overlap in cigar format for this containment

containsRc

public boolean containsRc()

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

Returns:

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

Returns:

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

getReadCount

public int getReadCount()

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

Returns:

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

Returns:

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

containsNm

public boolean containsNm()

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

Returns:

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

Returns:

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

getMismatchCount

public int getMismatchCount()

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

Returns:

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

Returns:

an optional wrapping the mismatch count for this containment (Type=i value for the reserved key NM 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 Containment valueOf(String value)

Parse a containment GFA 1.0 record from the specified value.

Parameters:

value - value, must not be null

Returns:

a containment GFA 1.0 record parsed from the specified value