Serialized Form

Package org.biojava.nbio.core.alignment

Class org.biojava.nbio.core.alignment.SimpleAlignedSequence

class SimpleAlignedSequence extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

alignmentFromSequence

int[] alignmentFromSequence

length

int length

location

Location location

numAfter

int numAfter

numBefore

int numBefore

numGapPositions

int numGapPositions

numGaps

int numGaps

original

S extends Sequence<C> original

prev

AlignedSequence<S extends Sequence<C>,C extends Compound> prev

sequenceFromAlignment

int[] sequenceFromAlignment

Class org.biojava.nbio.core.alignment.SimpleProfile

class SimpleProfile extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

length

int length

list

List<AlignedSequence<S extends Sequence<C>,C extends Compound>> list

originals

List<S extends Sequence<C>> originals

Class org.biojava.nbio.core.alignment.SimpleProfilePair

class SimpleProfilePair extends SimpleProfile<S extends Sequence<C>,C extends Compound> implements Serializable

serialVersionUID:

1L

Serialized Fields

query

Profile<S extends Sequence<C>,C extends Compound> query

target

Profile<S extends Sequence<C>,C extends Compound> target

Class org.biojava.nbio.core.alignment.SimpleSequencePair

class SimpleSequencePair extends SimpleProfile<S extends Sequence<C>,C extends Compound> implements Serializable

serialVersionUID:

1L

Serialized Fields

identicals

int identicals

similars

int similars

Package org.biojava.nbio.core.alignment.matrices

Class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix

class SimpleSubstitutionMatrix extends Object implements Serializable

serialVersionUID:

-2645265638108462479L

Serialized Fields

cols

List<C extends Compound> cols

compoundSet

CompoundSet<C extends Compound> compoundSet

description

String description

matrix

short[][] matrix

max

short max

min

short min

name

String name

rows

List<C extends Compound> rows

Class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper

class SubstitutionMatrixHelper extends Object implements Serializable

serialVersionUID:

148491724604653225L

Package org.biojava.nbio.core.exceptions

Exception org.biojava.nbio.core.exceptions.CompoundNotFoundException

class CompoundNotFoundException extends Exception implements Serializable

serialVersionUID:

1L

Exception org.biojava.nbio.core.exceptions.ParserException

class ParserException extends RuntimeException implements Serializable

serialVersionUID:

-4101924035353204493L

Exception org.biojava.nbio.core.exceptions.TranslationException

class TranslationException extends RuntimeException implements Serializable

serialVersionUID:

-3017433758219757440L

Package org.biojava.nbio.core.sequence

Class org.biojava.nbio.core.sequence.CDSComparator

class CDSComparator extends Object implements Serializable

serialVersionUID:

1L

Class org.biojava.nbio.core.sequence.ExonComparator

class ExonComparator extends Object implements Serializable

serialVersionUID:

1L

Class org.biojava.nbio.core.sequence.SequenceComparator

class SequenceComparator extends Object implements Serializable

serialVersionUID:

1L

Package org.biojava.nbio.core.sequence.compound

Class org.biojava.nbio.core.sequence.compound.AminoAcidCompound

class AminoAcidCompound extends AbstractCompound implements Serializable

serialVersionUID:

-1955116496725902319L

Serialized Fields

compoundSet

AminoAcidCompoundSet compoundSet

Class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet

class AminoAcidCompoundSet extends Object implements Serializable

serialVersionUID:

4000344194364133456L

Serialized Fields

aminoAcidCompoundCache

Map<String,AminoAcidCompound> aminoAcidCompoundCache

aminoAcidCompoundCache3Letter

Map<String,AminoAcidCompound> aminoAcidCompoundCache3Letter

equivalentsCache

Map<AminoAcidCompound,Set<AminoAcidCompound>> equivalentsCache

Package org.biojava.nbio.core.sequence.location

Class org.biojava.nbio.core.sequence.location.FuzzyPoint

class FuzzyPoint extends SimplePoint implements Serializable

Serialized Fields

max

int max

min

int min

resolver

Point.Resolver<FuzzyPoint> resolver

Class org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation

class BondLocation extends AbstractLocation implements Serializable

Class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation

class GroupLocation extends SimpleLocation implements Serializable

Class org.biojava.nbio.core.sequence.location.InsdcLocations.OneOfLocation

class OneOfLocation extends AbstractLocation implements Serializable

Class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation

class OrderLocation extends SimpleLocation implements Serializable

Class org.biojava.nbio.core.sequence.location.SequenceLocation

class SequenceLocation extends SimpleLocation implements Serializable

Serialized Fields

sequence

S extends AbstractSequence<C> sequence

Class org.biojava.nbio.core.sequence.location.SimpleLocation

class SimpleLocation extends AbstractLocation implements Serializable

Class org.biojava.nbio.core.sequence.location.SimplePoint

class SimplePoint extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

position

int position

uncertain

boolean uncertain

unknown

boolean unknown

Package org.biojava.nbio.core.sequence.location.template

Class org.biojava.nbio.core.sequence.location.template.AbstractLocation

class AbstractLocation extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

accession

AccessionID accession

betweenCompounds

boolean betweenCompounds

circular

boolean circular

end

Point end

partialOn3prime

boolean partialOn3prime

partialOn5prime

boolean partialOn5prime

start

Point start

strand

Strand strand

subLocations

List<Location> subLocations