org.dishevelled.bio.assembly.gfa2

Class Fragment

java.lang.Object

org.dishevelled.bio.assembly.gfa.GfaRecord

org.dishevelled.bio.assembly.gfa2.Gfa2Record

org.dishevelled.bio.assembly.gfa2.Fragment

@Immutable
public final class Fragment
extends Gfa2Record

Fragment GFA 2.0 record.

Author:

Michael Heuer

Constructor Summary

Constructors

Constructor and Description
Fragment(String segmentId, Reference external, Position segmentStart, Position segmentEnd, Position fragmentStart, Position fragmentEnd, Alignment alignment, Map<String,Tag> tags) Create a new fragment GFA 2.0 record.

Method Summary

Modifier and Type	Method and Description
boolean	containsTraceSpacing() Return true if the tags for this fragment contain the reserved key TS, for trace spacing.
boolean	containsTs() Return true if the tags for this fragment contain the reserved key TS.
boolean	equals(Object o)
Alignment	getAlignment() Return the alignment for this fragment, if any.
Optional<Alignment>	getAlignmentOpt() Return an optional wrapping the alignment for this fragment.
Reference	getExternal() Return the external reference for this fragment.
Position	getFragmentEnd() Return the fragment end position for this fragment.
Position	getFragmentStart() Return the fragment start position for this fragment.
Position	getSegmentEnd() Return the segment end position for this fragment.
String	getSegmentId() Return the segment identifier for this fragment.
Position	getSegmentStart() Return the segment start position for this fragment.
int	getTraceSpacing() Return the trace spacing for this fragment (Type=i value for the reserved key TS as an integer).
Optional<Integer>	getTraceSpacingOpt() Return an optional wrapping the trace spacing for this fragment (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 fragment has an alignment.
int	hashCode()
String	toString()
static Fragment	valueOf(String value) Parse a fragment 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

Fragment

public Fragment(String segmentId,
                Reference external,
                Position segmentStart,
                Position segmentEnd,
                Position fragmentStart,
                Position fragmentEnd,
                @Nullable
                Alignment alignment,
                Map<String,Tag> tags)

Create a new fragment GFA 2.0 record.

Parameters:

segmentId - segment identifier, must not be null

external - external reference, must not be null

segmentStart - segment start position, must not be null

segmentEnd - segment end position, must not be null

fragmentStart - fragment start position, must not be null

fragmentEnd - fragment end position, must not be null

alignment - alignment, if any

tags - tags, must not be null

Method Detail

getSegmentId

public String getSegmentId()

Return the segment identifier for this fragment.

Returns:

the segment identifier for this fragment

getExternal

public Reference getExternal()

Return the external reference for this fragment.

Returns:

the external reference for this fragment

getSegmentStart

public Position getSegmentStart()

Return the segment start position for this fragment.

Returns:

the segment start position for this fragment

getSegmentEnd

public Position getSegmentEnd()

Return the segment end position for this fragment.

Returns:

the segment end position for this fragment

getFragmentStart

public Position getFragmentStart()

Return the fragment start position for this fragment.

Returns:

the fragment start position for this fragment

getFragmentEnd

public Position getFragmentEnd()

Return the fragment end position for this fragment.

Returns:

the fragment end position for this fragment

hasAlignment

public boolean hasAlignment()

Return true if this fragment has an alignment.

Returns:

true if this fragment has an alignment

Since:

1.3.2

getAlignment

public Alignment getAlignment()

Return the alignment for this fragment, if any.

Returns:

the alignment for this fragment, if any

getAlignmentOpt

public Optional<Alignment> getAlignmentOpt()

Return an optional wrapping the alignment for this fragment.

Returns:

an optional wrapping the alignment for this fragment

containsTs

public boolean containsTs()

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

Returns:

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

Returns:

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

Since:

1.3.2

getTraceSpacing

public int getTraceSpacing()

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

Returns:

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

Returns:

an optional wrapping the trace spacing for this fragment (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 Fragment valueOf(String value)

Parse a fragment GFA 2.0 record from the specified value.

Parameters:

value - value, must not be null

Returns:

a fragment GFA 2.0 record parsed from the specified value