Serialized Form (biojava-core 6.0.3 API)

Package org.biojava.nbio.core.alignment
- Class org.biojava.nbio.core.alignment.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 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 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 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 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 extends Object implements Serializable
  
  serialVersionUID:
  
  148491724604653225L
Package org.biojava.nbio.core.exceptions
- Class org.biojava.nbio.core.exceptions.CompoundNotFoundException extends Exception implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.core.exceptions.ParserException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -4101924035353204493L
- Class org.biojava.nbio.core.exceptions.TranslationException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -3017433758219757440L
Package org.biojava.nbio.core.sequence
- Class org.biojava.nbio.core.sequence.CDSComparator extends Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.core.sequence.ExonComparator extends Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.core.sequence.SequenceComparator extends Object implements Serializable
  
  serialVersionUID:
  
  1L
Package org.biojava.nbio.core.sequence.compound
- Class org.biojava.nbio.core.sequence.compound.AminoAcidCompound extends AbstractCompound implements Serializable
  
  serialVersionUID:
  
  -1955116496725902319L
  - Serialized Fields
    - compoundSet
      
      AminoAcidCompoundSet compoundSet
- Class org.biojava.nbio.core.sequence.compound.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 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 extends AbstractLocation implements Serializable
- Class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation extends SimpleLocation implements Serializable
- Class org.biojava.nbio.core.sequence.location.InsdcLocations.OneOfLocation extends AbstractLocation implements Serializable
- Class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation extends SimpleLocation implements Serializable
- Class org.biojava.nbio.core.sequence.location.SequenceLocation extends SimpleLocation implements Serializable
  - Serialized Fields
    - sequence
      
      S extends AbstractSequence<C> sequence
- Class org.biojava.nbio.core.sequence.location.SimpleLocation extends AbstractLocation implements Serializable
- Class org.biojava.nbio.core.sequence.location.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 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

Serialized Form

Package org.biojava.nbio.core.alignment

Class org.biojava.nbio.core.alignment.SimpleAlignedSequence extends Object implements Serializable

Serialized Fields

alignmentFromSequence

length

location

numAfter

numBefore

numGapPositions

numGaps

original

prev

sequenceFromAlignment

Class org.biojava.nbio.core.alignment.SimpleProfile extends Object implements Serializable

Serialized Fields

length

list

originals

Class org.biojava.nbio.core.alignment.SimpleProfilePair extends SimpleProfile<S extends Sequence<C>,​C extends Compound> implements Serializable

Serialized Fields

query

target

Class org.biojava.nbio.core.alignment.SimpleSequencePair extends SimpleProfile<S extends Sequence<C>,​C extends Compound> implements Serializable

Serialized Fields

identicals

similars

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

Class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix extends Object implements Serializable

Serialized Fields

cols

compoundSet

description

matrix

max

min

name

rows

Class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper extends Object implements Serializable

Package org.biojava.nbio.core.exceptions

Class org.biojava.nbio.core.exceptions.CompoundNotFoundException extends Exception implements Serializable

Class org.biojava.nbio.core.exceptions.ParserException extends RuntimeException implements Serializable

Class org.biojava.nbio.core.exceptions.TranslationException extends RuntimeException implements Serializable

Package org.biojava.nbio.core.sequence

Class org.biojava.nbio.core.sequence.CDSComparator extends Object implements Serializable

Class org.biojava.nbio.core.sequence.ExonComparator extends Object implements Serializable

Class org.biojava.nbio.core.sequence.SequenceComparator extends Object implements Serializable

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

Class org.biojava.nbio.core.sequence.compound.AminoAcidCompound extends AbstractCompound implements Serializable

Serialized Fields

compoundSet

Class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet extends Object implements Serializable

Serialized Fields

aminoAcidCompoundCache

aminoAcidCompoundCache3Letter

equivalentsCache

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

Class org.biojava.nbio.core.sequence.location.FuzzyPoint extends SimplePoint implements Serializable

Serialized Fields

max

min

resolver

Class org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation extends AbstractLocation implements Serializable

Class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation extends SimpleLocation implements Serializable

Class org.biojava.nbio.core.sequence.location.InsdcLocations.OneOfLocation extends AbstractLocation implements Serializable

Class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation extends SimpleLocation implements Serializable

Class org.biojava.nbio.core.sequence.location.SequenceLocation extends SimpleLocation implements Serializable

Serialized Fields

sequence

Class org.biojava.nbio.core.sequence.location.SimpleLocation extends AbstractLocation implements Serializable

Class org.biojava.nbio.core.sequence.location.SimplePoint extends Object implements Serializable

Serialized Fields

position

uncertain

unknown

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

Class org.biojava.nbio.core.sequence.location.template.AbstractLocation extends Object implements Serializable

Serialized Fields

accession

betweenCompounds

Class org.biojava.nbio.core.alignment.SimpleProfilePair extends SimpleProfile<S extends Sequence<C>,C extends Compound> implements Serializable

Class org.biojava.nbio.core.alignment.SimpleSequencePair extends SimpleProfile<S extends Sequence<C>,C extends Compound> implements Serializable