Serialized Form (biojava-core 5.4.0 API)

Package org.biojava.nbio.core.alignment
- Class org.biojava.nbio.core.alignment.SimpleAlignedSequence extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - prev
```
AlignedSequence<S extends Sequence<C>,C extends Compound> prev
```
    - original
```
Sequence<C extends Compound> original
```
    - length
```
int length
```
    - numBefore
```
int numBefore
```
    - numAfter
```
int numAfter
```
    - location
```
Location location
```
    - numGaps
```
int numGaps
```
    - numGapPositions
```
int numGapPositions
```
    - alignmentFromSequence
```
int[] alignmentFromSequence
```
    - sequenceFromAlignment
```
int[] sequenceFromAlignment
```
- Class org.biojava.nbio.core.alignment.SimpleProfile extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - list
```
java.util.List<E> list
```
    - originals
```
java.util.List<E> originals
```
    - length
```
int length
```
- 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 java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -2645265638108462479L
  - Serialized Fields
    - compoundSet
```
CompoundSet<C extends Compound> compoundSet
```
    - description
```
java.lang.String description
```
    - name
```
java.lang.String name
```
    - matrix
```
short[][] matrix
```
    - max
```
short max
```
    - min
```
short min
```
    - rows
```
java.util.List<E> rows
```
    - cols
```
java.util.List<E> cols
```
- Class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  148491724604653225L
Package org.biojava.nbio.core.exceptions
- Class org.biojava.nbio.core.exceptions.CompoundNotFoundException extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.core.exceptions.ParserException extends java.lang.RuntimeException implements Serializable
  
  serialVersionUID:
  
  -4101924035353204493L
- Class org.biojava.nbio.core.exceptions.TranslationException extends java.lang.RuntimeException implements Serializable
  
  serialVersionUID:
  
  -3017433758219757440L
Package org.biojava.nbio.core.sequence
- Class org.biojava.nbio.core.sequence.CDSComparator extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.core.sequence.ExonComparator extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.core.sequence.SequenceComparator extends java.lang.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 java.lang.Object implements Serializable
  
  serialVersionUID:
  
  4000344194364133456L
  - Serialized Fields
    - aminoAcidCompoundCache
```
java.util.Map<K,V> aminoAcidCompoundCache
```
    - aminoAcidCompoundCache3Letter
```
java.util.Map<K,V> aminoAcidCompoundCache3Letter
```
    - equivalentsCache
```
java.util.Map<K,V> equivalentsCache
```
Package org.biojava.nbio.core.sequence.location
- Class org.biojava.nbio.core.sequence.location.FuzzyPoint extends SimplePoint implements Serializable
  - Serialized Fields
    - min
```
int min
```
    - max
```
int max
```
    - resolver
```
Point.Resolver<T extends Point> 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
```
AbstractSequence<C extends Compound> sequence
```
- Class org.biojava.nbio.core.sequence.location.SimpleLocation extends AbstractLocation implements Serializable
- Class org.biojava.nbio.core.sequence.location.SimplePoint extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - position
```
int position
```
    - unknown
```
boolean unknown
```
    - uncertain
```
boolean uncertain
```
Package org.biojava.nbio.core.sequence.location.template
- Class org.biojava.nbio.core.sequence.location.template.AbstractLocation extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - start
```
Point start
```
    - end
```
Point end
```
    - strand
```
Strand strand
```
    - subLocations
```
java.util.List<E> subLocations
```
    - circular
```
boolean circular
```
    - betweenCompounds
```
boolean betweenCompounds
```
    - accession
```
AccessionID accession
```
    - partialOn5prime
```
boolean partialOn5prime
```
    - partialOn3prime
```
boolean partialOn3prime
```

Serialized Form

Package org.biojava.nbio.core.alignment

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

Serialized Fields

prev

original

length

numBefore

numAfter

location

numGaps

numGapPositions

alignmentFromSequence

sequenceFromAlignment

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

Serialized Fields

list

originals

length

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 java.lang.Object implements Serializable

Serialized Fields

compoundSet

description

name

matrix

max

min

rows

cols

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

Package org.biojava.nbio.core.exceptions

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

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

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

Package org.biojava.nbio.core.sequence

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

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

Class org.biojava.nbio.core.sequence.SequenceComparator extends java.lang.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 java.lang.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

min

max

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 java.lang.Object implements Serializable

Serialized Fields

position

unknown

uncertain

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

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

Serialized Fields

start

end