Serialized Form (biojava 5.2.0 API)

Package demo
- Class demo.GetColorGradient extends JPanel implements Serializable
  
  serialVersionUID:
  
  -4954397192682351367L
  - Serialized Fields
    - colors
      
      Color[] colors
Package org.biojava.nbio.alignment
- Class org.biojava.nbio.alignment.SimpleGapPenalty extends Object implements Serializable
  
  serialVersionUID:
  
  3945671344135815456L
  - Serialized Fields
    - gep
      
      int gep
    - gop
      
      int gop
    - type
      
      GapPenalty.Type type
Package org.biojava.nbio.alignment.routines
- Class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor.QueryIndexComparator extends Object implements Serializable
  
  serialVersionUID:
  
  1L
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
Package org.biojava.nbio.genome.parsers.cytoband
- Class org.biojava.nbio.genome.parsers.cytoband.Cytoband extends Object implements Serializable
  
  serialVersionUID:
  
  2805976387404499650L
  - Serialized Fields
    - chromosome
      
      String chromosome
    - end
      
      Integer end
    - locus
      
      String locus
    - start
      
      Integer start
    - type
      
      StainType type
Package org.biojava.nbio.genome.parsers.genename
- Class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition extends Object implements Serializable
  
  serialVersionUID:
  
  -6886306238993367835L
  - Serialized Fields
    - cdsEnd
      
      Integer cdsEnd
    - cdsStart
      
      Integer cdsStart
    - chromosome
      
      String chromosome
    - exonCount
      
      int exonCount
    - exonEnds
      
      List<Integer> exonEnds
    - exonStarts
      
      List<Integer> exonStarts
    - genebankId
      
      String genebankId
    - geneName
      
      String geneName
    - orientation
      
      Character orientation
    - transcriptionEnd
      
      Integer transcriptionEnd
    - transcriptionStart
      
      Integer transcriptionStart
- Class org.biojava.nbio.genome.parsers.genename.GeneName extends Object implements Serializable
  
  serialVersionUID:
  
  -7163977639324764020L
  - Serialized Fields
    - accessionNr
      
      String accessionNr
    - approvedName
      
      String approvedName
    - approvedSymbol
      
      String approvedSymbol
    - chromosome
      
      String chromosome
    - ensemblGeneId
      
      String ensemblGeneId
    - hgncId
      
      String hgncId
    - omimId
      
      String omimId
    - previousNames
      
      String previousNames
    - previousSymbols
      
      String previousSymbols
    - refseqIds
      
      String refseqIds
    - status
      
      String status
    - synonyms
      
      String synonyms
    - uniprot
      
      String uniprot
Package org.biojava.nbio.genome.parsers.gff
- Class org.biojava.nbio.genome.parsers.gff.FeatureList extends ArrayList<FeatureI> implements Serializable
  - Serialized Fields
    - featindex
      
      Map<String,Map<String,List<FeatureI>>> featindex
    - mLocation
      
      Location mLocation
Package org.biojava.nbio.ontology
- Class org.biojava.nbio.ontology.AlreadyExistsException extends OntologyException implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.ontology.DefaultOps extends Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.ontology.InvalidTermException extends OntologyException implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.ontology.Ontology.Impl extends Object implements Serializable
  
  serialVersionUID:
  
  -8064461497813727957L
  - Serialized Fields
    - description
      
      String description
    - localRemoteTerms
      
      Set<Term> localRemoteTerms
    - name
      
      String name
    - objectTriples
      
      Map<Term,Set<Triple>> objectTriples
    - ops
      
      OntologyOps ops
    - relationTriples
      
      Map<Term,Set<Triple>> relationTriples
    - remoteTerms
      
      Map<Term,RemoteTerm> remoteTerms
    - subjectTriples
      
      Map<Term,Set<Triple>> subjectTriples
    - terms
      
      Map<String,Term> terms
    - triples
      
      Set<Triple> triples
- Class org.biojava.nbio.ontology.OntologyException extends Exception implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.ontology.OntologyTerm.Impl extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - ontology
      
      Ontology ontology
    - synonyms
      
      Set synonyms
    - target
      
      Ontology target
- Class org.biojava.nbio.ontology.RemoteTerm.Impl extends AbstractTerm implements Serializable
  
  serialVersionUID:
  
  922700041939183676L
  - Serialized Fields
    - name
      
      String name
    - ontology
      
      Ontology ontology
    - remoteTerm
      
      Term remoteTerm
    - synonyms
      
      Set synonyms
- Class org.biojava.nbio.ontology.Term.Impl extends AbstractTerm implements Serializable
  
  serialVersionUID:
  
  6561668917514377417L
  - Serialized Fields
    - annotation
      
      Annotation annotation
    - name
      
      String name
    - ontology
      
      Ontology ontology
    - synonyms
      
      Set<Object> synonyms
- Class org.biojava.nbio.ontology.Triple.Impl extends Object implements Serializable
  
  serialVersionUID:
  
  3807331980372839221L
  - Serialized Fields
    - description
      
      String description
    - name
      
      String name
    - object
      
      Term object
    - predicate
      
      Term predicate
    - subject
      
      Term subject
    - synonyms
      
      Set<Object> synonyms
- Class org.biojava.nbio.ontology.Variable.Impl extends Term.Impl implements Serializable
  
  serialVersionUID:
  
  1L
Package org.biojava.nbio.ontology.utils
- Class org.biojava.nbio.ontology.utils.AbstractAnnotation extends Object implements Serializable
  
  serialVersionUID:
  
  2753449055959952873L
- Class org.biojava.nbio.ontology.utils.AssertionFailure extends AssertionError implements Serializable
- Class org.biojava.nbio.ontology.utils.SmallAnnotation extends AbstractAnnotation implements Serializable
  - Serialized Fields
    - properties
      
      Map properties
- Class org.biojava.nbio.ontology.utils.SmallMap extends AbstractMap implements Serializable
  - Serialized Fields
    - mappings
      
      Object[] mappings
    - numMappings
      
      int numMappings
- Class org.biojava.nbio.ontology.utils.StaticMemberPlaceHolder extends Object implements Serializable
  - Serialization Methods
    - readResolve
      
      public Object readResolve() throws ObjectStreamException
      
      Throws:
      
      ObjectStreamException
  - Serialized Fields
    - className
      
      String className
    - fieldName
      
      String fieldName
Package org.biojava.nbio.protmod.structure
- Class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl extends Object implements Serializable
  
  serialVersionUID:
  
  1656563037849815427L
  - Serialized Fields
    - atomLinkages
      
      Map<Set<StructureGroup>,Set<StructureAtomLinkage>> atomLinkages
    - groups
      
      Set<StructureGroup> groups
    - modification
      
      ProteinModification modification
    - originalModification
      
      ProteinModification originalModification
Package org.biojava.nbio.ronn
- Class org.biojava.nbio.ronn.Jronn extends Object implements Serializable
  
  serialVersionUID:
  
  8104272449130849946L
Package org.biojava.nbio.structure
- Class org.biojava.nbio.structure.AminoAcidImpl extends HetatomImpl implements Serializable
  
  serialVersionUID:
  
  -6018854413829044230L
  - Serialized Fields
    - amino_char
      
      Character amino_char
      
      IUPAC amino acid residue names
    - recordType
      
      String recordType
- Class org.biojava.nbio.structure.AtomImpl extends Object implements Serializable
  
  serialVersionUID:
  
  -2258364127420562883L
  - Serialized Fields
    - altLoc
      
      char altLoc
    - bonds
      
      List<Bond> bonds
    - charge
      
      short charge
    - coords
      
      javax.vecmath.Point3d coords
    - element
      
      Element element
    - name
      
      String name
    - occupancy
      
      float occupancy
    - parent
      
      Group parent
    - pdbserial
      
      int pdbserial
    - tempfactor
      
      float tempfactor
- Class org.biojava.nbio.structure.Author extends Object implements Serializable
  
  serialVersionUID:
  
  4840370515056666418L
  - Serialized Fields
    - initials
      
      String initials
    - surname
      
      String surname
- Class org.biojava.nbio.structure.BioAssemblyIdentifier extends Object implements Serializable
  
  serialVersionUID:
  
  -356206725119993449L
  - Serialized Fields
    - biolNr
      
      int biolNr
    - pdbCode
      
      String pdbCode
- Class org.biojava.nbio.structure.BondImpl extends Object implements Serializable
  
  serialVersionUID:
  
  8836120946858134380L
  - Serialized Fields
    - atomA
      
      Atom atomA
    - atomB
      
      Atom atomB
    - bondOrder
      
      int bondOrder
- Class org.biojava.nbio.structure.ChainImpl extends Object implements Serializable
  
  serialVersionUID:
  
  1990171805277911840L
  - Serialized Fields
    - asymId
      
      String asymId
    - authId
      
      String authId
    - entity
      
      EntityInfo entity
    - groups
      
      List<Group> groups
    - parent
      
      Structure parent
    - pdbResnumMap
      
      Map<String,Integer> pdbResnumMap
    - seqMisMatches
      
      List<SeqMisMatch> seqMisMatches
    - seqResGroups
      
      List<Group> seqResGroups
    - swissprot_id
      
      String swissprot_id
- Class org.biojava.nbio.structure.DBRef extends Object implements Serializable
  
  serialVersionUID:
  
  -1050178577542224379L
  - Serialized Fields
    - chainName
      
      String chainName
    - database
      
      String database
    - dbAccession
      
      String dbAccession
    - dbIdCode
      
      String dbIdCode
    - dbSeqBegin
      
      int dbSeqBegin
    - dbSeqEnd
      
      int dbSeqEnd
    - id
      
      Long id
    - idbnsBegin
      
      char idbnsBegin
    - idbnsEnd
      
      char idbnsEnd
    - idCode
      
      String idCode
    - insertBegin
      
      char insertBegin
    - insertEnd
      
      char insertEnd
    - parent
      
      Structure parent
    - seqbegin
      
      int seqbegin
    - seqEnd
      
      int seqEnd
- Class org.biojava.nbio.structure.EntityInfo extends Object implements Serializable
  
  serialVersionUID:
  
  2991897825657586356L
  - Serialized Fields
    - atcc
      
      String atcc
    - biologicalUnit
      
      String biologicalUnit
    - cell
      
      String cell
    - cellLine
      
      String cellLine
    - cellularLocation
      
      String cellularLocation
    - chains
      
      List<Chain> chains
      
      The list of chains that are described by this EntityInfo
    - chains2pdbResNums2ResSerials
      
      Map<String,Map<ResidueNumber,Integer>> chains2pdbResNums2ResSerials
      
      A map to cache residue number mapping, between ResidueNumbers and index (1-based) in aligned sequences (SEQRES). Initialised lazily upon call to EntityInfo.getAlignedResIndex(Group, Chain) Keys are asym_ids of chains, values maps of residue numbers to indices.
    - description
      
      String description
    - details
      
      String details
    - ecNums
      
      List<String> ecNums
    - engineered
      
      String engineered
    - expressionSystem
      
      String expressionSystem
    - expressionSystemAtccNumber
      
      String expressionSystemAtccNumber
    - expressionSystemCell
      
      String expressionSystemCell
    - expressionSystemCellLine
      
      String expressionSystemCellLine
    - expressionSystemCellularLocation
      
      String expressionSystemCellularLocation
    - expressionSystemGene
      
      String expressionSystemGene
    - expressionSystemOrgan
      
      String expressionSystemOrgan
    - expressionSystemOrganelle
      
      String expressionSystemOrganelle
    - expressionSystemOtherDetails
      
      String expressionSystemOtherDetails
    - expressionSystemPlasmid
      
      String expressionSystemPlasmid
    - expressionSystemStrain
      
      String expressionSystemStrain
    - expressionSystemTaxId
      
      String expressionSystemTaxId
    - expressionSystemTissue
      
      String expressionSystemTissue
    - expressionSystemVariant
      
      String expressionSystemVariant
    - expressionSystemVector
      
      String expressionSystemVector
    - expressionSystemVectorType
      
      String expressionSystemVectorType
    - fragment
      
      String fragment
    - gene
      
      String gene
    - headerVars
      
      String headerVars
    - id
      
      Long id
    - molId
      
      int molId
      
      The Molecule identifier, called entity_id in mmCIF dictionary
    - mutation
      
      String mutation
    - numRes
      
      String numRes
    - organ
      
      String organ
    - organelle
      
      String organelle
    - organismCommon
      
      String organismCommon
    - organismScientific
      
      String organismScientific
    - organismTaxId
      
      String organismTaxId
    - refChainId
      
      String refChainId
    - resNames
      
      String resNames
    - secretion
      
      String secretion
    - strain
      
      String strain
    - synonyms
      
      List<String> synonyms
    - synthetic
      
      String synthetic
    - tissue
      
      String tissue
    - title
      
      String title
    - type
      
      EntityType type
      
      The type of entity (polymer, non-polymer, water)
    - variant
      
      String variant
- Class org.biojava.nbio.structure.HetatomImpl extends Object implements Serializable
  
  serialVersionUID:
  
  4491470432023820382L
  - Serialized Fields
    - altLocs
      
      List<Group> altLocs
    - atomNameLookup
      
      Map<String,Atom> atomNameLookup
    - atoms
      
      List<Atom> atoms
    - chemComp
      
      ChemComp chemComp
    - id
      
      long id
    - isHetAtomInFile
      
      boolean isHetAtomInFile
    - parent
      
      Chain parent
    - pdb_flag
      
      boolean pdb_flag
      
      stores if 3d coordinates are available.
    - pdb_name
      
      String pdb_name
      
      3 letter name of amino acid in pdb file.
    - properties
      
      Map<String,Object> properties
    - residueNumber
      
      ResidueNumber residueNumber
- Class org.biojava.nbio.structure.JournalArticle extends Object implements Serializable
  
  serialVersionUID:
  
  5062668226159515468L
  - Serialized Fields
    - authorList
      
      List<Author> authorList
    - doi
      
      String doi
    - editorList
      
      List<Author> editorList
    - journalName
      
      String journalName
    - pmid
      
      String pmid
    - publicationDate
      
      int publicationDate
    - published
      
      boolean published
    - publisher
      
      String publisher
    - ref
      
      String ref
    - refn
      
      String refn
    - startPage
      
      String startPage
    - title
      
      String title
    - volume
      
      String volume
- Class org.biojava.nbio.structure.Model extends Object implements Serializable
  
  serialVersionUID:
  
  5320613424668781882L
  - Serialized Fields
    - nonPolyChains
      
      List<Chain> nonPolyChains
    - polyChains
      
      List<Chain> polyChains
    - waterChains
      
      List<Chain> waterChains
- Class org.biojava.nbio.structure.NucleotideImpl extends HetatomImpl implements Serializable
  
  serialVersionUID:
  
  -7467726932980288712L
- Class org.biojava.nbio.structure.PassthroughIdentifier extends Object implements Serializable
  
  serialVersionUID:
  
  -2773111624414448950L
  - Serialized Fields
    - identifier
      
      String identifier
- Class org.biojava.nbio.structure.PDBCrystallographicInfo extends Object implements Serializable
  
  serialVersionUID:
  
  -7949886749566087669L
  - Serialized Fields
    - cell
      
      CrystalCell cell
    - ncsOperators
      
      javax.vecmath.Matrix4d[] ncsOperators
      
      Some PDB files contain NCS operators necessary to create the full AU. Usually this happens for viral proteins. See http://www.wwpdb.org/documentation/format33/sect8.html#MTRIXn . Note that the "given" operators (iGiven field =1 in PDB format, "given" string in _struct_ncs_oper.code in mmCIF format) are not stored.
    - nonStandardCoordFrameConvention
      
      boolean nonStandardCoordFrameConvention
      
      Whether this structure is non-standard coordinate frame convention, for which our scale matrix calculation and thus the crystal reconstruction will be incorrect. There's ~ 200 old structures in the PDB affected by the non-standard frame problem, hopefully they will be remediated in the future. For more info see: https://github.com/eppic-team/owl/issues/4
      
      Since:
      
      4.2.5
    - nonStandardSg
      
      boolean nonStandardSg
      
      Whether this structure has a non-standard space group not supported by Biojava. If this is true the sg member will be null.
      
      Since:
      
      4.2.5
    - sg
      
      SpaceGroup sg
- Class org.biojava.nbio.structure.PDBHeader extends Object implements Serializable
  
  serialVersionUID:
  
  -5834326174085429508L
  - Serialized Fields
    - authors
      
      String authors
    - bioAssemblies
      
      Map<Integer,BioAssemblyInfo> bioAssemblies
    - classification
      
      String classification
    - crystallographicInfo
      
      PDBCrystallographicInfo crystallographicInfo
    - dateFormat
      
      DateFormat dateFormat
    - depDate
      
      Date depDate
    - description
      
      String description
    - id
      
      Long id
    - idCode
      
      String idCode
    - journalArticle
      
      JournalArticle journalArticle
    - modDate
      
      Date modDate
    - relDate
      
      Date relDate
    - resolution
      
      float resolution
    - revisionRecords
      
      List<DatabasePdbrevRecord> revisionRecords
    - rFree
      
      float rFree
    - rWork
      
      float rWork
    - techniques
      
      Set<ExperimentalTechnique> techniques
    - title
      
      String title
- Class org.biojava.nbio.structure.ResidueNumber extends Object implements Serializable
  
  serialVersionUID:
  
  1773011704758536083L
  - Serialized Fields
    - chainName
      
      String chainName
    - insCode
      
      Character insCode
    - seqNum
      
      Integer seqNum
- Class org.biojava.nbio.structure.SeqMisMatchImpl extends Object implements Serializable
  
  serialVersionUID:
  
  -3699285122925652562L
  - Serialized Fields
    - details
      
      String details
    - insCode
      
      String insCode
    - origGroup
      
      String origGroup
    - pdbGroup
      
      String pdbGroup
    - pdbResNum
      
      String pdbResNum
    - seqNum
      
      Integer seqNum
    - uniProtId
      
      String uniProtId
- Class org.biojava.nbio.structure.Site extends Object implements Serializable
  
  serialVersionUID:
  
  -4577047072916341237L
  - Serialized Fields
    - description
      
      String description
    - evCode
      
      String evCode
    - groups
      
      List<Group> groups
    - siteID
      
      String siteID
- Class org.biojava.nbio.structure.StructureException extends Exception implements Serializable
  
  serialVersionUID:
  
  62946250941673093L
- Class org.biojava.nbio.structure.StructureImpl extends Object implements Serializable
  
  serialVersionUID:
  
  -8344837138032851348L
  - Serialized Fields
    - biologicalAssembly
      
      boolean biologicalAssembly
    - dbrefs
      
      List<DBRef> dbrefs
    - entityInfos
      
      List<EntityInfo> entityInfos
    - id
      
      Long id
    - models
      
      List<Model> models
    - name
      
      String name
    - pdb_id
      
      String pdb_id
    - pdbHeader
      
      PDBHeader pdbHeader
    - sites
      
      List<Site> sites
    - ssbonds
      
      List<Bond> ssbonds
    - structureIdentifier
      
      StructureIdentifier structureIdentifier
- Class org.biojava.nbio.structure.SubstructureIdentifier extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - pdbId
      
      String pdbId
    - ranges
      
      List<ResidueRange> ranges
- Class org.biojava.nbio.structure.URLIdentifier extends Object implements Serializable
  
  serialVersionUID:
  
  -5161230822868926035L
  - Serialized Fields
    - url
      
      URL url
Package org.biojava.nbio.structure.align.client
- Class org.biojava.nbio.structure.align.client.JobKillException extends Exception implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.structure.align.client.StructureName extends Object implements Serializable
  
  serialVersionUID:
  
  4021229518711762957L
  - Serialized Fields
    - base
      
      StructureIdentifier base
    - chainName
      
      String chainName
    - mySource
      
      StructureName.Source mySource
    - name
      
      String name
    - pdbId
      
      String pdbId
Package org.biojava.nbio.structure.align.gui
- Class org.biojava.nbio.structure.align.gui.AlignmentGui extends JFrame implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - abortB
      
      JButton abortB
    - algorithm
      
      StructureAlignment algorithm
    - alicalc
      
      AlignmentCalculationRunnable alicalc
    - dbsearch
      
      DBSearchGUI dbsearch
    - masterPane
      
      JTabbedPane masterPane
    - progress
      
      JProgressBar progress
    - tab1
      
      SelectPDBPanel tab1
    - tab2
      
      PDBUploadPanel tab2
    - tab3
      
      ScopSelectPanel tab3
    - tabPane
      
      JTabbedPane tabPane
    - thread
      
      Thread thread
- Class org.biojava.nbio.structure.align.gui.AlignmentTextPanel extends JPrintPanel implements Serializable
  
  serialVersionUID:
  
  5092386365924879073L
  - Serialized Fields
    - tp
      
      JEditorPane tp
- Class org.biojava.nbio.structure.align.gui.ChooseDirAction extends AbstractAction implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - config
      
      UserConfiguration config
    - textField
      
      JTextField textField
- Class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  -1055193854675583808L
  - Serialized Fields
    - fileType
      
      JComboBox fileType
    - fromFtp
      
      JCheckBox fromFtp
    - pdbDir
      
      JTextField pdbDir
- Class org.biojava.nbio.structure.align.gui.DBSearchGUI extends JPanel implements Serializable
  
  serialVersionUID:
  
  -5657960663049062301L
  - Serialized Fields
    - abortB
      
      JButton abortB
    - algorithm
      
      StructureAlignment algorithm
    - alicalc
      
      AlignmentCalcDB alicalc
    - drawer
      
      org.biojava.nbio.structure.align.gui.ProgressThreadDrawer drawer
    - listPane
      
      JPanel listPane
    - outFileLocation
      
      JTextField outFileLocation
    - progress
      
      JProgressBar progress
    - tab1
      
      SelectPDBPanel tab1
    - tab2
      
      PDBUploadPanel tab2
    - tab3
      
      ScopSelectPanel tab3
    - tabPane
      
      JTabbedPane tabPane
    - useDomainSplit
      
      Boolean useDomainSplit
- Class org.biojava.nbio.structure.align.gui.DotPlotPanel extends ScaleableMatrixPanel implements Serializable
  
  serialVersionUID:
  
  -7641953255857483895L
- Class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener extends JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - alignmentsProcessed
      
      int alignmentsProcessed
    - farmJob
      
      FarmJob farmJob
    - progressBar
      
      JProgressBar progressBar
    - stopButton
      
      JButton stopButton
    - taskOutput
      
      JTextArea taskOutput
- Class org.biojava.nbio.structure.align.gui.JPrintPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  -3337337068138131455L
- Class org.biojava.nbio.structure.align.gui.MemoryMonitor extends JPanel implements Serializable
  
  serialVersionUID:
  
  56289234782130L
  - Serialized Fields
    - controls
      
      JPanel controls
    - doControls
      
      boolean doControls
    - surf
      
      MemoryMonitor.Surface surf
    - tf
      
      JTextField tf
- Class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface extends JPanel implements Serializable
  
  serialVersionUID:
  
  2387409854370432908L
  - Serialized Fields
    - ascent
      
      int ascent
    - big
      
      Graphics2D big
    - bimg
      
      BufferedImage bimg
    - columnInc
      
      int columnInc
    - descent
      
      int descent
    - font
      
      Font font
    - graphColor
      
      Color graphColor
    - graphLine
      
      Line2D graphLine
    - graphOutlineRect
      
      Rectangle graphOutlineRect
    - h
      
      int h
    - mfColor
      
      Color mfColor
    - mfRect
      
      Rectangle2D mfRect
    - muRect
      
      Rectangle2D muRect
    - ptNum
      
      int ptNum
    - pts
      
      int[] pts
    - r
      
      Runtime r
    - sleepAmount
      
      long sleepAmount
    - thread
      
      Thread thread
    - usedStr
      
      String usedStr
    - w
      
      int w
- Class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI extends JFrame implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - abortB
      
      JButton abortB
    - alicalc
      
      AlignmentCalculationRunnable alicalc
    - multiple
      
      MultipleStructureAligner multiple
    - pairwise
      
      StructureAlignment pairwise
    - progress
      
      JProgressBar progress
    - tab
      
      SelectMultiplePanel tab
    - tabPane
      
      JTabbedPane tabPane
    - thread
      
      Thread thread
- Class org.biojava.nbio.structure.align.gui.ParameterGUI extends JFrame implements Serializable
  
  serialVersionUID:
  
  723386061184110161L
  - Serialized Fields
    - params
      
      ConfigStrucAligParams params
    - textFields
      
      List<Component> textFields
- Class org.biojava.nbio.structure.align.gui.SelectPDBPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  4002475313717172193L
  - Serialized Fields
    - c1
      
      JTextField c1
    - c2
      
      JTextField c2
    - config
      
      UserConfiguration config
    - configPane
      
      JTabbedPane configPane
    - debug
      
      boolean debug
    - f1
      
      JTextField f1
    - f2
      
      JTextField f2
    - r1
      
      JTextField r1
    - r2
      
      JTextField r2
Package org.biojava.nbio.structure.align.gui.aligpanel
- Class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel extends JPrintPanel implements Serializable
  
  serialVersionUID:
  
  -6892229111166263764L
  - Serialized Fields
    - afpChain
      
      AFPChain afpChain
    - ca1
      
      Atom[] ca1
    - ca2
      
      Atom[] ca2
    - colorByAlignmentBlock
      
      boolean colorByAlignmentBlock
    - colorBySimilarity
      
      boolean colorBySimilarity
    - coordManager
      
      AFPChainCoordManager coordManager
    - eqFont
      
      Font eqFont
    - jmol
      
      AbstractAlignmentJmol jmol
    - mouseMoLi
      
      AligPanelMouseMotionListener mouseMoLi
    - selection
      
      BitSet selection
    - selectionLocked
      
      boolean selectionLocked
    - seqFont
      
      Font seqFont
- Class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel extends JPrintPanel implements Serializable
  
  serialVersionUID:
  
  -6892229111166263764L
  - Serialized Fields
    - alnSeq
      
      List<String> alnSeq
    - colorByAlignmentBlock
      
      boolean colorByAlignmentBlock
    - colorBySimilarity
      
      boolean colorBySimilarity
    - coordManager
      
      MultipleAlignmentCoordManager coordManager
    - eqFont
      
      Font eqFont
    - jmol
      
      AbstractAlignmentJmol jmol
    - length
      
      int length
    - mapSeqToStruct
      
      List<Integer> mapSeqToStruct
    - mouseMoLi
      
      MultipleAligPanelMouseMotionListener mouseMoLi
    - multAln
      
      MultipleAlignment multAln
    - selection
      
      BitSet selection
    - selectionLocked
      
      boolean selectionLocked
    - seqFont
      
      Font seqFont
    - size
      
      int size
- Class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay extends JTextField implements Serializable
  
  serialVersionUID:
  
  6939947266417830429L
  - Serialized Fields
    - panel
      
      MultipleAligPanel panel
- Class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay extends JTextField implements Serializable
  
  serialVersionUID:
  
  6939947266417830429L
  - Serialized Fields
    - afpChain
      
      AFPChain afpChain
    - ca1
      
      Atom[] ca1
    - ca2
      
      Atom[] ca2
Package org.biojava.nbio.structure.align.gui.autosuggest
- Class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest extends JTextField implements Serializable
  
  serialVersionUID:
  
  8591734727984365156L
  - Serialized Fields
    - autoSuggestProvider
      
      AutoSuggestProvider autoSuggestProvider
    - busy
      
      Font busy
    - defaultText
      
      String defaultText
    - dialog
      
      JDialog dialog
    - lastWord
      
      String lastWord
      
      last word that was entered by user
    - list
      
      JList list
    - location
      
      Point location
    - matcher
      
      org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest.SuggestionFetcher matcher
    - regular
      
      Font regular
    - suggestions
      
      Vector<String> suggestions
Package org.biojava.nbio.structure.align.gui.jmol
- Class org.biojava.nbio.structure.align.gui.jmol.JmolPanel extends JPrintPanel implements Serializable
  
  serialVersionUID:
  
  -3661941083797644242L
  - Serialized Fields
    - adapter
      
      org.jmol.api.JmolAdapter adapter
    - currentSize
      
      Dimension currentSize
    - rectClip
      
      Rectangle rectClip
    - statusListener
      
      org.jmol.api.JmolStatusListener statusListener
    - structure
      
      Structure structure
    - viewer
      
      org.jmol.api.JmolViewer viewer
Package org.biojava.nbio.structure.align.helper
- Class org.biojava.nbio.structure.align.helper.AligMatEl extends IndexPair implements Serializable
  
  serialVersionUID:
  
  -4040926588803887471L
  - Serialized Fields
    - contig
      
      int contig
    - value
      
      int value
- Class org.biojava.nbio.structure.align.helper.IdxComparator extends Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.structure.align.helper.IndexPair extends Object implements Serializable
  
  serialVersionUID:
  
  1832393751152650420L
  - Serialized Fields
    - col
      
      short col
    - row
      
      short row

Package org.biojava.nbio.structure.align.model

Class org.biojava.nbio.structure.align.model.AFP extends Object implements Serializable

serialVersionUID:

3901209995477111829L
- Serialized Fields
  - fragLen
```
int fragLen
```
  - id
```
long id
```
  - m
```
Matrix m
```
  - p1
```
int p1
```
  - p2
```
int p2
```
  - rmsd
```
double rmsd
```
  - score
```
double score
```
  - t
```
double[] t
```

Class org.biojava.nbio.structure.align.model.AFPChain extends Object implements Serializable

serialVersionUID:: -4474029015606617947L

Serialized Fields

afpAftIndex
```
int[][] afpAftIndex
```
afpBefIndex
```
int[][] afpBefIndex
```
afpChainLen
```
int afpChainLen
```
afpChainList
```
int[] afpChainList
```
afpChainTwiBin
```
double[] afpChainTwiBin
```
afpChainTwiList
```
double[] afpChainTwiList
```
afpChainTwiNum
```
int afpChainTwiNum
```
afpIndex
```
int[][] afpIndex
```
afpSet
```
List<AFP> afpSet
```
algorithmName
```
String algorithmName
```
alignScore
```
double alignScore
```
alignScoreUpdate
```
double alignScoreUpdate
```
alnbeg1
```
int alnbeg1
```
alnbeg2
```
int alnbeg2
```
alnLength
```
int alnLength
```
alnseq1
```
char[] alnseq1
```
alnseq2
```
char[] alnseq2
```
alnsymb
```
char[] alnsymb
```
block2Afp
```
int[] block2Afp
```
blockGap
```
int[] blockGap
```
blockNum
```
int blockNum
```
blockNumClu
```
int blockNumClu
```
blockNumIni
```
int blockNumIni
```
blockNumSpt
```
int blockNumSpt
```
blockResList
```
int[][][] blockResList
```
blockResSize
```
int[] blockResSize
```
blockRmsd
```
double[] blockRmsd
```
blockRotationMatrix
```
Matrix[] blockRotationMatrix
```
blockScore
```
double[] blockScore
```
blockShiftVector
```
Atom[] blockShiftVector
```
blockSize
```
int[] blockSize
```
ca1Length
```
int ca1Length
```
ca2Length
```
int ca2Length
```
calculationTime
```
long calculationTime
```
chainLen
```
int chainLen
```
chainRmsd
```
double chainRmsd
```
conn
```
Double conn
```
description2
```
String description2
```
disTable1
```
Matrix disTable1
```
disTable2
```
Matrix disTable2
```
distanceMatrix
```
Matrix distanceMatrix
```
dvar
```
Double dvar
```
focusAfpList
```
int[] focusAfpList
```
focusAfpn
```
int focusAfpn
```
focusRes1
```
int[] focusRes1
```
focusRes2
```
int[] focusRes2
```
focusResn
```
int focusResn
```
gapLen
```
int gapLen
```
id
```
long id
```
identity
```
double identity
```
ioTime
```
long ioTime
```
maxTra
```
int maxTra
```
minLen
```
int minLen
```
misLen
```
int misLen
```
myResultsEQR
```
int myResultsEQR
```
myResultsSimilarity1
```
int myResultsSimilarity1
```
myResultsSimilarity2
```
int myResultsSimilarity2
```
name1
```
String name1
```
name2
```
String name2
```
normAlignScore
```
double normAlignScore
```
optAln
```
int[][][] optAln
```
optLen
```
int[] optLen
```
optLength
```
int optLength
```
optRmsd
```
double[] optRmsd
```
pdbAln
```
String[][][] pdbAln
```
probability
```
double probability
```
sequentialAlignment
```
boolean sequentialAlignment
```
shortAlign
```
boolean shortAlign
```
similarity
```
double similarity
```
tmScore
```
double tmScore
```
totalLenIni
```
int totalLenIni
```
totalLenOpt
```
int totalLenOpt
```
totalRmsdIni
```
double totalRmsdIni
```
totalRmsdOpt
```
double totalRmsdOpt
```
twi
```
int[] twi
```
version
```
String version
```

Package org.biojava.nbio.structure.align.multiple
- Class org.biojava.nbio.structure.align.multiple.BlockImpl extends AbstractScoresCache implements Serializable
  
  serialVersionUID:
  
  -5804042669466177641L
  - Serialized Fields
    - alignRes
      
      List<List<Integer>> alignRes
    - alignResCounts
      
      List<Integer> alignResCounts
    - coreLength
      
      int coreLength
    - parent
      
      BlockSet parent
- Class org.biojava.nbio.structure.align.multiple.BlockSetImpl extends AbstractScoresCache implements Serializable
  
  serialVersionUID:
  
  -1015791986000076089L
  - Serialized Fields
    - alignResCounts
      
      List<Integer> alignResCounts
    - blocks
      
      List<Block> blocks
    - coreLength
      
      int coreLength
    - length
      
      int length
    - parent
      
      MultipleAlignment parent
    - pose
      
      List<javax.vecmath.Matrix4d> pose
- Class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl extends AbstractScoresCache implements Serializable
  
  serialVersionUID:
  
  -5732485866623431898L
  - Serialized Fields
    - algorithmName
      
      String algorithmName
    - atomArrays
      
      List<Atom[]> atomArrays
    - calculationTime
      
      Long calculationTime
    - distanceMatrix
      
      List<Matrix> distanceMatrix
    - ioTime
      
      Long ioTime
    - multipleAlignments
      
      List<MultipleAlignment> multipleAlignments
    - structureIdentifiers
      
      List<StructureIdentifier> structureIdentifiers
    - version
      
      String version
- Class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl extends AbstractScoresCache implements Serializable
  
  serialVersionUID:
  
  3432043794125805139L
  - Serialized Fields
    - alignResCounts
      
      List<Integer> alignResCounts
    - blockSets
      
      List<BlockSet> blockSets
    - coreLength
      
      int coreLength
    - coverages
      
      List<Double> coverages
    - length
      
      int length
    - parent
      
      MultipleAlignmentEnsemble parent
Package org.biojava.nbio.structure.align.pairwise
- Class org.biojava.nbio.structure.align.pairwise.AlignmentResult extends Object implements Serializable
  
  serialVersionUID:
  
  -4132105905712445473L
  - Serialized Fields
    - alignments
      
      AlternativeAlignment[] alignments
    - calculationTime
      
      long calculationTime
    - chain1
      
      String chain1
    - chain2
      
      String chain2
    - ioTime
      
      long ioTime
    - length1
      
      int length1
    - length2
      
      int length2
    - pdb1
      
      String pdb1
    - pdb2
      
      String pdb2
- Class org.biojava.nbio.structure.align.pairwise.AltAligComparator extends Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment extends Object implements Serializable
  
  serialVersionUID:
  
  -6226717654562221241L
  - Serialized Fields
    - aligpath
      
      IndexPair[] aligpath
    - center
      
      Atom center
    - cluster
      
      int cluster
    - currentRotMatrix
      
      Matrix currentRotMatrix
    - currentTranMatrix
      
      Atom currentTranMatrix
    - distanceMatrix
      
      Matrix distanceMatrix
    - eqr0
      
      int eqr0
    - fromia
      
      int fromia
    - gaps0
      
      int gaps0
    - idx1
      
      int[] idx1
    - idx2
      
      int[] idx2
    - joined
      
      int joined
    - nfrags
      
      int nfrags
    - pdbresnum1
      
      String[] pdbresnum1
    - pdbresnum2
      
      String[] pdbresnum2
    - percId
      
      int percId
    - rms
      
      double rms
    - rms0
      
      int rms0
    - rot
      
      Matrix rot
    - score
      
      float score
    - tr
      
      Atom tr
Package org.biojava.nbio.structure.align.util
- Class org.biojava.nbio.structure.align.util.ConfigurationException extends Exception implements Serializable
  
  serialVersionUID:
  
  -8047100079715000276L
Package org.biojava.nbio.structure.asa
- Class org.biojava.nbio.structure.asa.GroupAsa extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - asaC
      
      double asaC
      
      ASA of complexed residue
    - asaU
      
      double asaU
      
      ASA of uncomplexed residue
    - atomAsaCs
      
      List<Double> atomAsaCs
      
      The individual atoms complexed ASAs
    - atomAsaUs
      
      List<Double> atomAsaUs
      
      The individual atoms uncomplexed ASAs
    - g
      
      Group g
Package org.biojava.nbio.structure.basepairs
- Class org.biojava.nbio.structure.basepairs.BasePairParameters extends Object implements Serializable
  
  serialVersionUID:
  
  6214502385L
  - Serialized Fields
    - canonical
      
      boolean canonical
    - nonredundant
      
      boolean nonredundant
    - pairingNames
      
      List<String> pairingNames
    - pairingParameters
      
      double[][] pairingParameters
    - pairParameters
      
      double[] pairParameters
    - pairSequence
      
      String pairSequence
    - referenceFrames
      
      List<javax.vecmath.Matrix4d> referenceFrames
    - stepParameters
      
      double[][] stepParameters
    - structure
      
      Structure structure
    - useRNA
      
      boolean useRNA
- Class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters extends BasePairParameters implements Serializable
  
  serialVersionUID:
  
  2837124340169886674L
  - Serialized Fields
    - maxPropeller
      
      double maxPropeller
    - maxShear
      
      double maxShear
    - maxStagger
      
      double maxStagger
    - maxStretch
      
      double maxStretch
- Class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters extends BasePairParameters implements Serializable
  
  serialVersionUID:
  
  2556427111533466577L
  - Serialized Fields
    - maxPropeller
      
      double maxPropeller
    - maxStagger
      
      double maxStagger
Package org.biojava.nbio.structure.cath
- Class org.biojava.nbio.structure.cath.CathDomain extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - architectureId
      
      Integer architectureId
      
      The architecture number of this domain.
    - classId
      
      Integer classId
      
      The class number of this domain.
    - comment
      
      String comment
      
      A (potentially long) comment. Usually empty.
    - date
      
      Date date
    - domainCounter
      
      Integer domainCounter
      
      The count of this domain among the identical sequence family members.
    - domainName
      
      String domainName
      
      The CATH domain code. Always 7 characters in length, combining the PDB and chain letter with the number of the domain within CATH. Example: 1aoiA00 If the chain letter '0', domain refers to an entire PDB entry.
    - format
      
      String format
      
      The format and version of the CathDomainDescriptionFile.
    - homologyId
      
      Integer homologyId
      
      The homologous superfamily number of this domain.
    - identicalSequenceFamilyId
      
      Integer identicalSequenceFamilyId
      
      The identical sequence family (100% identity) number of this domain.
    - length
      
      Integer length
      
      The domain length..
    - likeSequenceFamilyId
      
      Integer likeSequenceFamilyId
      
      The "Like" sequence family (95% identity) number of this domain.
    - name
      
      String name
      
      The so-called name field holds a potentially long description of the domain.
    - orthologousSequenceFamilyId
      
      Integer orthologousSequenceFamilyId
      
      The "orthologous" sequence family (60% identity) number of this domain.
    - resolution
      
      Double resolution
      
      The resolution of the domain structure. Nominally in Angstroms, the values 999.000 and 1000.000 signify NMR structures and obsolete structures, respectively.
    - segments
      
      List<CathSegment> segments
      
      List of all sub-domain segments.
    - sequence
      
      String sequence
      
      FASTA sequence.
    - sequenceFamilyId
      
      Integer sequenceFamilyId
      
      The sequence family (35% identity) number of this domain.
    - sequenceHeader
      
      String sequenceHeader
      
      FASTA header.
    - source
      
      String source
      
      Complete source organism listing.
    - topologyId
      
      Integer topologyId
      
      The topology number of this domain.
    - version
      
      String version
      
      The CATH version.
- Class org.biojava.nbio.structure.cath.CathFragment extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - fragmentId
      
      Integer fragmentId
      
      The number of this segment within the domain.
    - length
      
      Integer length
      
      Number of residues in the segment. This value is parsed, not calculated.
    - start
      
      String start
      
      The first residue in the segment. Refers to the complete residue specification (sequence number AND insertion code).
    - stop
      
      String stop
      
      The last residue in the segment. Refers to the complete residue specification (sequence number AND insertion code).
- Class org.biojava.nbio.structure.cath.CathNode extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - category
      
      CathCategory category
      
      This node's level within the hierarchy. One of CATH, not CATHSOLID.
    - description
      
      String description
      
      A name or description.
    - nodeId
      
      String nodeId
      
      The CATH code of the node, e.g. "1.10.8.10".
    - parentId
      
      String parentId
      
      The CATH code of the parent, e.g. "1.10.8". Calculated during parsing.
    - representative
      
      String representative
      
      The representative domain for this node.
- Class org.biojava.nbio.structure.cath.CathSegment extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - length
      
      Integer length
      
      Number of residues in the segment. This value is parsed, not calculated.
    - segmentId
      
      Integer segmentId
      
      The number of this segment within the domain.
    - sequence
      
      String sequence
      
      FASTA sequence.
    - sequenceHeader
      
      String sequenceHeader
      
      FASTA header.
    - start
      
      String start
      
      The first residue in the segment. Refers to the complete residue specification (sequence number AND insertion code).
    - stop
      
      String stop
      
      The last residue in the segment. Refers to the complete residue specification (sequence number AND insertion code).
Package org.biojava.nbio.structure.cluster
- Class org.biojava.nbio.structure.cluster.SubunitClustererParameters extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - absoluteMinimumSequenceLength
      
      int absoluteMinimumSequenceLength
    - clustererMethod
      
      SubunitClustererMethod clustererMethod
    - internalSymmetry
      
      boolean internalSymmetry
    - minimumSequenceLength
      
      int minimumSequenceLength
    - minimumSequenceLengthFraction
      
      double minimumSequenceLengthFraction
    - optimizeAlignment
      
      boolean optimizeAlignment
    - rmsdThreshold
      
      double rmsdThreshold
    - sequenceCoverageThreshold
      
      double sequenceCoverageThreshold
    - sequenceIdentityThreshold
      
      double sequenceIdentityThreshold
    - structureCoverageThreshold
      
      double structureCoverageThreshold
    - superpositionAlgorithm
      
      String superpositionAlgorithm
    - tmThreshold
      
      double tmThreshold
    - useGlobalMetrics
      
      boolean useGlobalMetrics
    - useRMSD
      
      boolean useRMSD
    - useSequenceCoverage
      
      boolean useSequenceCoverage
    - useStructureCoverage
      
      boolean useStructureCoverage
    - useTMScore
      
      boolean useTMScore
Package org.biojava.nbio.structure.contact
- Class org.biojava.nbio.structure.contact.AtomContact extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - distance
      
      double distance
    - pair
      
      Pair<Atom> pair
- Class org.biojava.nbio.structure.contact.AtomContactSet extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - contacts
      
      HashMap<Pair<AtomIdentifier>,AtomContact> contacts
    - cutoff
      
      double cutoff
- Class org.biojava.nbio.structure.contact.AtomIdentifier extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - chainId
      
      String chainId
    - pdbSerial
      
      int pdbSerial
- Class org.biojava.nbio.structure.contact.BoundingBox extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - xmax
      
      double xmax
    - xmin
      
      double xmin
    - ymax
      
      double ymax
    - ymin
      
      double ymin
    - zmax
      
      double zmax
    - zmin
      
      double zmin
- Class org.biojava.nbio.structure.contact.Contact extends Object implements Serializable
  
  serialVersionUID:
  
  5059569852079048728L
  - Serialized Fields
    - distance
      
      double distance
    - i
      
      int i
    - j
      
      int j
- Class org.biojava.nbio.structure.contact.GroupContact extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - atomContacts
      
      List<AtomContact> atomContacts
    - pair
      
      Pair<Group> pair
- Class org.biojava.nbio.structure.contact.GroupContactSet extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - contacts
      
      HashMap<Pair<org.biojava.nbio.structure.contact.ResidueIdentifier>,GroupContact> contacts
- Class org.biojava.nbio.structure.contact.Pair extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - first
      
      T first
    - second
      
      T second
- Class org.biojava.nbio.structure.contact.StructureInterface extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - cluster
      
      StructureInterfaceCluster cluster
    - contacts
      
      AtomContactSet contacts
    - groupAsas1
      
      Map<ResidueNumber,GroupAsa> groupAsas1
    - groupAsas2
      
      Map<ResidueNumber,GroupAsa> groupAsas2
    - groupContacts
      
      GroupContactSet groupContacts
    - id
      
      int id
    - moleculeIds
      
      Pair<String> moleculeIds
      
      The identifier for each of the atom arrays (usually a chain identifier, i.e. a single capital letter) Serves to identify the molecules within the Asymmetric Unit of the crystal
    - molecules
      
      Pair<Atom[]> molecules
    - totalArea
      
      double totalArea
    - transforms
      
      Pair<CrystalTransform> transforms
      
      The transformations (crystal operators) applied to each molecule (if applicable)
- Class org.biojava.nbio.structure.contact.StructureInterfaceCluster extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - averageScore
      
      double averageScore
      
      The average similarity score between all pairs of members in the cluster.
    - id
      
      int id
    - members
      
      List<StructureInterface> members
- Class org.biojava.nbio.structure.contact.StructureInterfaceList extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - clusters
      
      List<StructureInterfaceCluster> clusters
    - clustersNcs
      
      List<StructureInterfaceCluster> clustersNcs
    - list
      
      List<StructureInterface> list
Package org.biojava.nbio.structure.domain
- Class org.biojava.nbio.structure.domain.PDPDomain extends Object implements Serializable
  
  serialVersionUID:
  
  6894463080739943026L
  - Serialized Fields
    - canonical
      
      SubstructureIdentifier canonical
    - identifier
      
      String identifier
Package org.biojava.nbio.structure.domain.pdp
- Class org.biojava.nbio.structure.domain.pdp.Domain extends Object implements Serializable
  
  serialVersionUID:
  
  -1293994033102271366L
  - Serialized Fields
    - id
      
      String id
    - nseg
      
      int nseg
    - score
      
      double score
    - segments
      
      List<Segment> segments
    - size
      
      int size
- Class org.biojava.nbio.structure.domain.pdp.Segment extends Object implements Serializable
  
  serialVersionUID:
  
  1393487067559539657L
  - Serialized Fields
    - from
      
      Integer from
    - score
      
      double score
    - to
      
      Integer to
- Class org.biojava.nbio.structure.domain.pdp.SegmentComparator extends Object implements Serializable
  
  serialVersionUID:
  
  1L
Package org.biojava.nbio.structure.ecod
- Class org.biojava.nbio.structure.ecod.EcodDomain extends Object implements Serializable
  
  serialVersionUID:
  
  -7760082165560332048L
  - Serialized Fields
    - architectureName
      
      String architectureName
    - assemblyId
      
      Long assemblyId
    - chainId
      
      String chainId
    - domainId
      
      String domainId
    - fGroup
      
      Integer fGroup
    - fGroupName
      
      String fGroupName
    - hGroup
      
      Integer hGroup
    - hGroupName
      
      String hGroupName
    - ligands
      
      Set<String> ligands
    - manual
      
      Boolean manual
    - pdbId
      
      String pdbId
    - range
      
      String range
    - seqIdRange
      
      String seqIdRange
    - tGroup
      
      Integer tGroup
    - tGroupName
      
      String tGroupName
    - uid
      
      Long uid
    - xGroup
      
      Integer xGroup
    - xGroupName
      
      String xGroupName
Package org.biojava.nbio.structure.gui
- Class org.biojava.nbio.structure.gui.JMatrixPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  -1720879395453257846L
  - Serialized Fields
    - _bufImage
      
      BufferedImage _bufImage
    - aligs
      
      AlternativeAlignment[] aligs
    - cellColor
      
      ContinuousColorMapper cellColor
    - fragmentPairs
      
      FragmentPair[] fragmentPairs
    - matrix
      
      Matrix matrix
    - params
      
      StrucAligParameters params
    - scale
      
      float scale
    - selectedAlignmentPos
      
      int selectedAlignmentPos
- Class org.biojava.nbio.structure.gui.ScaleableMatrixPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  -8082261434322968652L
  - Serialized Fields
    - coloring
      
      JComboBox coloring
    - gradients
      
      Map<String,ContinuousColorMapper> gradients
    - mPanel
      
      JMatrixPanel mPanel
    - scroll
      
      JScrollPane scroll
    - slider
      
      JSlider slider
- Class org.biojava.nbio.structure.gui.ScaleableMatrixPanel.GradientRenderer extends JPanel implements Serializable
  
  serialVersionUID:
  
  -2000575579184232365L
  - Serialized Fields
    - gradientContainer
      
      JPanel gradientContainer
    - max
      
      int max
    - min
      
      int min
    - title
      
      JLabel title
- Class org.biojava.nbio.structure.gui.SequenceDisplay extends JPanel implements Serializable
  
  serialVersionUID:
  
  -1829252532712454236L
  - Serialized Fields
    - alig
      
      AlternativeAlignment alig
    - apos
      
      List<AlignedPosition> apos
    - idx1
      
      int[] idx1
    - idx2
      
      int[] idx2
    - label1
      
      JLabel label1
    - label2
      
      JLabel label2
    - mouseListener1
      
      SequenceMouseListener mouseListener1
    - mouseListener2
      
      SequenceMouseListener mouseListener2
    - panel1
      
      SequenceScalePanel panel1
    - panel2
      
      SequenceScalePanel panel2
    - percentageDisplay
      
      JLabel percentageDisplay
    - residueSizeSlider
      
      JSlider residueSizeSlider
    - scale
      
      float scale
    - structure1
      
      Structure structure1
    - structure2
      
      Structure structure2
    - structurePairAligner
      
      StructurePairAligner structurePairAligner
- Class org.biojava.nbio.structure.gui.WrapLayout extends FlowLayout implements Serializable
  - Serialized Fields
    - preferredLayoutSize
      
      Dimension preferredLayoutSize
Package org.biojava.nbio.structure.gui.util
- Class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame extends JFrame implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - aligs
      
      AlternativeAlignment[] aligs
    - panel
      
      JPanel panel
    - structure1
      
      Structure structure1
    - structure2
      
      Structure structure2
    - structurePairAligner
      
      StructurePairAligner structurePairAligner
- Class org.biojava.nbio.structure.gui.util.PDBDirPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  -5682120627824627408L
  - Serialized Fields
    - c1
      
      JTextField c1
    - c2
      
      JTextField c2
    - debug
      
      boolean debug
    - f1
      
      JTextField f1
    - f2
      
      JTextField f2
    - pdbDir
      
      JTextField pdbDir
- Class org.biojava.nbio.structure.gui.util.PDBServerPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  -5682120627824627408L
  - Serialized Fields
    - c1
      
      JTextField c1
    - c2
      
      JTextField c2
    - debug
      
      boolean debug
    - f1
      
      JTextField f1
    - f2
      
      JTextField f2
    - pdbDir
      
      JTextField pdbDir
- Class org.biojava.nbio.structure.gui.util.PDBUploadPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - chain1
      
      JTextField chain1
    - chain2
      
      JTextField chain2
    - filePath1
      
      JTextField filePath1
    - filePath2
      
      JTextField filePath2
    - fileType
      
      JComboBox fileType
- Class org.biojava.nbio.structure.gui.util.ScopSelectPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  757947454156959178L
  - Serialized Fields
    - dom1
      
      JAutoSuggest dom1
    - dom2
      
      JAutoSuggest dom2
- Class org.biojava.nbio.structure.gui.util.SelectMultiplePanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  757947454156959178L
  - Serialized Fields
    - input
      
      JTextField input
- Class org.biojava.nbio.structure.gui.util.SequenceScalePanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  7893248902423L
  - Serialized Fields
    - apos
      
      List<AlignedPosition> apos
    - chain
      
      Chain chain
    - chainLength
      
      int chainLength
    - coordManager
      
      CoordManager coordManager
    - position
      
      int position
    - scale
      
      float scale
    - seqArr
      
      Character[] seqArr
Package org.biojava.nbio.structure.gui.util.color
- Class org.biojava.nbio.structure.gui.util.color.GradientPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  -6387922432121206731L
  - Serialized Fields
    - mapper
      
      ContinuousColorMapper mapper
    - max
      
      double max
    - min
      
      double min
- Class org.biojava.nbio.structure.gui.util.color.HSVColorSpace extends ColorSpace implements Serializable
  
  serialVersionUID:
  
  8324413992279510075L
Package org.biojava.nbio.structure.io
- Class org.biojava.nbio.structure.io.FileParsingParameters extends Object implements Serializable
  
  serialVersionUID:
  
  5878292315163939027L
  - Serialized Fields
    - alignSeqRes
      
      boolean alignSeqRes
      
      Flag to control if SEQRES and ATOM records should be aligned
    - atomCaThreshold
      
      int atomCaThreshold
    - createAtomBonds
      
      boolean createAtomBonds
      
      Should we create bonds between atoms when parsing a file?
    - createAtomCharges
      
      boolean createAtomCharges
      
      Should we create charges on atoms when parsing a file?
    - fullAtomNames
      
      String[] fullAtomNames
    - headerOnly
      
      boolean headerOnly
      
      Flag to parse header only
    - maxAtoms
      
      int maxAtoms
    - parseBioAssembly
      
      boolean parseBioAssembly
      
      Should we parse the biological assembly information from a file?
    - parseCAOnly
      
      boolean parseCAOnly
      
      Flag to control reading in only Calpha atoms - this is useful for parsing large structures like 1htq.
    - parseSecStruc
      
      boolean parseSecStruc
      
      Flag to detect if the secondary structure info should be read
- Class org.biojava.nbio.structure.io.PDBParseException extends Exception implements Serializable
  
  serialVersionUID:
  
  219047230178423923L
- Class org.biojava.nbio.structure.io.SSBondImpl extends Object implements Serializable
  
  serialVersionUID:
  
  -8663681100691188647L
  - Serialized Fields
    - chainID1
      
      String chainID1
    - chainID2
      
      String chainID2
    - insCode1
      
      String insCode1
    - insCode2
      
      String insCode2
    - resnum1
      
      String resnum1
    - resnum2
      
      String resnum2
    - serNum
      
      int serNum
Package org.biojava.nbio.structure.io.mmcif.model
- Class org.biojava.nbio.structure.io.mmcif.model.ChemComp extends Object implements Serializable
  
  serialVersionUID:
  
  -4736341142030215915L
  - Serialized Fields
    - atoms
      
      List<ChemCompAtom> atoms
    - bonds
      
      List<ChemCompBond> bonds
    - descriptors
      
      List<ChemCompDescriptor> descriptors
    - formula
      
      String formula
    - formula_weight
      
      String formula_weight
    - id
      
      String id
    - mon_nstd_flag
      
      String mon_nstd_flag
    - mon_nstd_parent_comp_id
      
      String mon_nstd_parent_comp_id
    - name
      
      String name
    - one_letter_code
      
      String one_letter_code
    - pdbx_ambiguous_flag
      
      String pdbx_ambiguous_flag
    - pdbx_formal_charge
      
      String pdbx_formal_charge
    - pdbx_ideal_coordinates_details
      
      String pdbx_ideal_coordinates_details
    - pdbx_ideal_coordinates_missing_flag
      
      String pdbx_ideal_coordinates_missing_flag
    - pdbx_initial_date
      
      String pdbx_initial_date
    - pdbx_model_coordinates_db_code
      
      String pdbx_model_coordinates_db_code
    - pdbx_model_coordinates_details
      
      String pdbx_model_coordinates_details
    - pdbx_model_coordinates_missing_flag
      
      String pdbx_model_coordinates_missing_flag
    - pdbx_modified_date
      
      String pdbx_modified_date
    - pdbx_processing_site
      
      String pdbx_processing_site
    - pdbx_release_status
      
      String pdbx_release_status
    - pdbx_replaced_by
      
      String pdbx_replaced_by
    - pdbx_replaces
      
      String pdbx_replaces
    - pdbx_subcomponent_list
      
      String pdbx_subcomponent_list
    - pdbx_synonyms
      
      String pdbx_synonyms
    - pdbx_type
      
      String pdbx_type
    - polymerType
      
      PolymerType polymerType
    - residueType
      
      ResidueType residueType
    - standard
      
      boolean standard
    - three_letter_code
      
      String three_letter_code
    - type
      
      String type
- Class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom extends Object implements Serializable
  
  serialVersionUID:
  
  4070599340294758941L
  - Serialized Fields
    - alt_atom_id
      
      String alt_atom_id
    - atom_id
      
      String atom_id
    - charge
      
      String charge
    - comp_id
      
      String comp_id
    - model_Cartn_x
      
      String model_Cartn_x
    - model_Cartn_y
      
      String model_Cartn_y
    - model_Cartn_z
      
      String model_Cartn_z
    - pdbx_align
      
      String pdbx_align
    - pdbx_aromatic_flag
      
      String pdbx_aromatic_flag
    - pdbx_component_atom_id
      
      String pdbx_component_atom_id
    - pdbx_component_comp_id
      
      String pdbx_component_comp_id
    - pdbx_component_id
      
      String pdbx_component_id
    - pdbx_leaving_atom_flag
      
      String pdbx_leaving_atom_flag
    - pdbx_model_Cartn_x_ideal
      
      String pdbx_model_Cartn_x_ideal
    - pdbx_model_Cartn_y_ideal
      
      String pdbx_model_Cartn_y_ideal
    - pdbx_model_Cartn_z_ideal
      
      String pdbx_model_Cartn_z_ideal
    - pdbx_ordinal
      
      String pdbx_ordinal
    - pdbx_polymer_type
      
      String pdbx_polymer_type
    - pdbx_ref_id
      
      String pdbx_ref_id
    - pdbx_residue_numbering
      
      String pdbx_residue_numbering
    - pdbx_stereo_config
      
      String pdbx_stereo_config
    - type_symbol
      
      String type_symbol
- Class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond extends Object implements Serializable
  
  serialVersionUID:
  
  5905371029161975421L
  - Serialized Fields
    - atom_id_1
      
      String atom_id_1
    - atom_id_2
      
      String atom_id_2
    - comp_id
      
      String comp_id
    - pdbx_aromatic_flag
      
      String pdbx_aromatic_flag
    - pdbx_ordinal
      
      String pdbx_ordinal
    - pdbx_stereo_config
      
      String pdbx_stereo_config
    - value_order
      
      String value_order
- Class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor extends Object implements Serializable
  
  serialVersionUID:
  
  1078685833800736278L
  - Serialized Fields
    - comp_id
      
      String comp_id
    - descriptor
      
      String descriptor
    - program
      
      String program
    - program_version
      
      String program_version
    - type
      
      String type
- Class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - details
      
      String details
    - rev_num
      
      String rev_num
    - type
      
      String type
- Class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly extends Object implements Serializable
  
  serialVersionUID:
  
  3104504686693887219L
  - Serialized Fields
    - details
      
      String details
    - id
      
      String id
    - method_details
      
      String method_details
    - oligomeric_count
      
      String oligomeric_count
    - oligomeric_details
      
      String oligomeric_details
- Class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen extends Object implements Serializable
  
  serialVersionUID:
  
  6739568389242514332L
  - Serialized Fields
    - assembly_id
      
      String assembly_id
    - asym_id_list
      
      String asym_id_list
    - oper_expression
      
      String oper_expression
- Class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList extends Object implements Serializable
  
  serialVersionUID:
  
  8933552854747969787L
  - Serialized Fields
    - id
      
      String id
    - matrix11
      
      String matrix11
    - matrix12
      
      String matrix12
    - matrix13
      
      String matrix13
    - matrix21
      
      String matrix21
    - matrix22
      
      String matrix22
    - matrix23
      
      String matrix23
    - matrix31
      
      String matrix31
    - matrix32
      
      String matrix32
    - matrix33
      
      String matrix33
    - name
      
      String name
    - symmetry_operation
      
      String symmetry_operation
    - type
      
      String type
    - vector1
      
      String vector1
    - vector2
      
      String vector2
    - vector3
      
      String vector3
Package org.biojava.nbio.structure.io.mmtf
- Class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader extends Object implements Serializable
  
  serialVersionUID:
  
  6772030485225130853L
  - Serialized Fields
    - allAtoms
      
      Atom[] allAtoms
      
      All the atoms.
    - atomCounter
      
      int atomCounter
    - atomsInGroup
      
      List<Atom> atomsInGroup
      
      The atoms in a group.
    - bioassIndex
      
      int bioassIndex
    - chain
      
      Chain chain
      
      The chain.
    - chainList
      
      List<Chain> chainList
      
      All the chains
    - chainMap
      
      List<Map<String,Chain>> chainMap
      
      All the chains as a list of maps
    - chainSequenceMap
      
      Map<String,String> chainSequenceMap
    - entityInfoList
      
      List<EntityInfo> entityInfoList
      
      The list of EntityInformation
    - group
      
      Group group
      
      The group.
    - modelNumber
      
      int modelNumber
      
      The model number.
    - structure
      
      Structure structure
      
      The structure.
    - transformList
      
      List<double[]> transformList
Package org.biojava.nbio.structure.io.sifts
- Class org.biojava.nbio.structure.io.sifts.SiftsEntity extends Object implements Serializable
  
  serialVersionUID:
  
  750353252427491487L
  - Serialized Fields
    - entityId
      
      String entityId
    - segments
      
      List<SiftsSegment> segments
    - type
      
      String type
- Class org.biojava.nbio.structure.io.sifts.SiftsResidue extends Object implements Serializable
  
  serialVersionUID:
  
  3425769737629800828L
  - Serialized Fields
    - chainId
      
      String chainId
    - naturalPos
      
      Integer naturalPos
    - notObserved
      
      Boolean notObserved
    - pdbId
      
      String pdbId
    - pdbResName
      
      String pdbResName
    - pdbResNum
      
      String pdbResNum
    - seqResName
      
      String seqResName
    - uniProtAccessionId
      
      String uniProtAccessionId
    - uniProtPos
      
      Integer uniProtPos
    - uniProtResName
      
      String uniProtResName
- Class org.biojava.nbio.structure.io.sifts.SiftsSegment extends Object implements Serializable
  
  serialVersionUID:
  
  -8005129863256307153L
  - Serialized Fields
    - end
      
      String end
    - residues
      
      List<SiftsResidue> residues
    - segId
      
      String segId
    - start
      
      String start
Package org.biojava.nbio.structure.jama
- Class org.biojava.nbio.structure.jama.CholeskyDecomposition extends Object implements Serializable
  
  serialVersionUID:
  
  224348942390823L
  - Serialized Fields
    - isspd
      
      boolean isspd
      
      Symmetric and positive definite flag.
      
      is symmetric and positive definite flag.
    - L
      
      double[][] L
      
      Array for internal storage of decomposition.
      
      internal array storage.
    - n
      
      int n
      
      Row and column dimension (square matrix).
      
      matrix dimension.
- Class org.biojava.nbio.structure.jama.EigenvalueDecomposition extends Object implements Serializable
  
  serialVersionUID:
  
  3557806515310435894L
  - Serialized Fields
    - d
      
      double[] d
      
      Arrays for internal storage of eigenvalues.
      
      internal storage of eigenvalues.
    - e
      
      double[] e
      
      Arrays for internal storage of eigenvalues.
      
      internal storage of eigenvalues.
    - H
      
      double[][] H
      
      Array for internal storage of nonsymmetric Hessenberg form.
      
      internal storage of nonsymmetric Hessenberg form.
    - issymmetric
      
      boolean issymmetric
      
      Symmetry flag.
      
      internal symmetry flag.
    - n
      
      int n
      
      Row and column dimension (square matrix).
      
      matrix dimension.
    - ort
      
      double[] ort
      
      Working storage for nonsymmetric algorithm.
      
      working storage for nonsymmetric algorithm.
    - V
      
      double[][] V
      
      Array for internal storage of eigenvectors.
      
      internal storage of eigenvectors.
- Class org.biojava.nbio.structure.jama.LUDecomposition extends Object implements Serializable
  
  serialVersionUID:
  
  9271028462937843L
  - Serialized Fields
    - LU
      
      double[][] LU
      
      Array for internal storage of decomposition.
      
      internal array storage.
    - m
      
      int m
      
      Row and column dimensions, and pivot sign.
      
      column dimension.
    - n
      
      int n
      
      Row and column dimensions, and pivot sign.
      
      column dimension.
    - piv
      
      int[] piv
      
      Internal storage of pivot vector.
      
      pivot vector.
    - pivsign
      
      int pivsign
      
      Row and column dimensions, and pivot sign.
      
      column dimension.
- Class org.biojava.nbio.structure.jama.Matrix extends Object implements Serializable
  
  serialVersionUID:
  
  8492558293015348719L
  - Serialized Fields
    - A
      
      double[][] A
      
      Array for internal storage of elements.
      
      internal array storage.
    - m
      
      int m
      
      Row and column dimensions.
      
      row dimension.
    - n
      
      int n
      
      Row and column dimensions.
      
      row dimension.
- Class org.biojava.nbio.structure.jama.QRDecomposition extends Object implements Serializable
  
  serialVersionUID:
  
  10293720387423L
  - Serialized Fields
    - m
      
      int m
      
      Row and column dimensions.
      
      column dimension.
    - n
      
      int n
      
      Row and column dimensions.
      
      column dimension.
    - QR
      
      double[][] QR
      
      Array for internal storage of decomposition.
      
      internal array storage.
    - Rdiag
      
      double[] Rdiag
      
      Array for internal storage of diagonal of R.
      
      diagonal of R.
- Class org.biojava.nbio.structure.jama.SingularValueDecomposition extends Object implements Serializable
  
  serialVersionUID:
  
  640239472093534756L
  - Serialized Fields
    - m
      
      int m
      
      Row and column dimensions.
      
      row dimension.
    - n
      
      int n
      
      Row and column dimensions.
      
      row dimension.
    - s
      
      double[] s
      
      Array for internal storage of singular values.
      
      internal storage of singular values.
    - U
      
      double[][] U
      
      Arrays for internal storage of U and V.
      
      internal storage of U.
    - V
      
      double[][] V
      
      Arrays for internal storage of U and V.
      
      internal storage of U.
Package org.biojava.nbio.structure.math
- Class org.biojava.nbio.structure.math.SparseSquareMatrix extends Object implements Serializable
  
  serialVersionUID:
  
  -5217767192992868955L
  - Serialized Fields
    - N
      
      int N
    - rows
      
      SparseVector[] rows
- Class org.biojava.nbio.structure.math.SparseVector extends Object implements Serializable
  
  serialVersionUID:
  
  1174668523213431927L
  - Serialized Fields
    - N
      
      int N
    - symbolTable
      
      SymbolTable<Integer,Double> symbolTable
- Class org.biojava.nbio.structure.math.SymbolTable extends Object implements Serializable
  
  serialVersionUID:
  
  -4417561575046471931L
  - Serialized Fields
    - st
      
      TreeMap<Key extends Comparable<Key>,Value> st
Package org.biojava.nbio.structure.quaternary
- Class org.biojava.nbio.structure.quaternary.BioAssemblyInfo extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - id
      
      int id
    - macromolecularSize
      
      int macromolecularSize
    - transforms
      
      List<BiologicalAssemblyTransformation> transforms
- Class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation extends Object implements Serializable
  
  serialVersionUID:
  
  -6388503076022480391L
  - Serialized Fields
    - chainId
      
      String chainId
    - id
      
      String id
    - transformation
      
      javax.vecmath.Matrix4d transformation
Package org.biojava.nbio.structure.scop
- Class org.biojava.nbio.structure.scop.ScopDescription extends Object implements Serializable
  
  serialVersionUID:
  
  8579808155176839161L
  - Serialized Fields
    - category
      
      ScopCategory category
    - classificationId
      
      String classificationId
    - description
      
      String description
    - name
      
      String name
    - sunID
      
      int sunID
- Class org.biojava.nbio.structure.scop.ScopDomain extends Object implements Serializable
  
  serialVersionUID:
  
  5890476209571654301L
  - Serialized Fields
    - classId
      
      int classId
    - classificationId
      
      String classificationId
    - domainId
      
      int domainId
    - familyId
      
      int familyId
    - foldId
      
      int foldId
    - pdbId
      
      String pdbId
    - px
      
      int px
    - ranges
      
      List<String> ranges
    - scopId
      
      String scopId
    - speciesId
      
      int speciesId
    - sunid
      
      Integer sunid
    - superfamilyId
      
      int superfamilyId
- Class org.biojava.nbio.structure.scop.ScopIOException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.structure.scop.ScopNode extends Object implements Serializable
  
  serialVersionUID:
  
  1187083944488580995L
  - Serialized Fields
    - children
      
      List<Integer> children
    - parentSunid
      
      int parentSunid
    - sunid
      
      int sunid
Package org.biojava.nbio.structure.scop.server
- Class org.biojava.nbio.structure.scop.server.ListStringWrapper extends Object implements Serializable
  
  serialVersionUID:
  
  4193799052494327416L
  - Serialized Fields
    - data
      
      List<String> data
- Class org.biojava.nbio.structure.scop.server.ScopDescriptions extends Object implements Serializable
  
  serialVersionUID:
  
  4924350548761431852L
  - Serialized Fields
    - scopDescriptions
      
      List<ScopDescription> scopDescriptions
- Class org.biojava.nbio.structure.scop.server.ScopDomains extends Object implements Serializable
  
  serialVersionUID:
  
  7693404355005856746L
  - Serialized Fields
    - domains
      
      List<ScopDomain> domains
- Class org.biojava.nbio.structure.scop.server.ScopNodes extends Object implements Serializable
  
  serialVersionUID:
  
  5327454882500340305L
  - Serialized Fields
    - scopNodes
      
      List<ScopNode> scopNodes
- Class org.biojava.nbio.structure.scop.server.TreeSetStringWrapper extends Object implements Serializable
  
  serialVersionUID:
  
  4193799052494327416L
  - Serialized Fields
    - data
      
      TreeSet<String> data
Package org.biojava.nbio.structure.secstruc
- Class org.biojava.nbio.structure.secstruc.BetaBridge extends Object implements Serializable
  
  serialVersionUID:
  
  -5097435425455958487L
  - Serialized Fields
    - partner1
      
      int partner1
    - partner2
      
      int partner2
    - type
      
      BridgeType type
- Class org.biojava.nbio.structure.secstruc.HBond extends Object implements Serializable
  
  serialVersionUID:
  
  8246764841329431337L
  - Serialized Fields
    - energy
      
      double energy
    - partner
      
      int partner
- Class org.biojava.nbio.structure.secstruc.Ladder extends Object implements Serializable
  
  serialVersionUID:
  
  -1658305503250364409L
  - Serialized Fields
    - btype
      
      BridgeType btype
    - connectedFrom
      
      int connectedFrom
    - connectedTo
      
      int connectedTo
    - from
      
      int from
    - lfrom
      
      int lfrom
    - lto
      
      int lto
    - to
      
      int to
- Class org.biojava.nbio.structure.secstruc.SecStrucElement extends Object implements Serializable
  
  serialVersionUID:
  
  -8485685793171396131L
  - Serialized Fields
    - index
      
      int index
    - range
      
      ResidueRangeAndLength range
    - type
      
      SecStrucType type
- Class org.biojava.nbio.structure.secstruc.SecStrucInfo extends Object implements Serializable
  
  serialVersionUID:
  
  4516925175715607227L
  - Serialized Fields
    - assignment
      
      String assignment
    - parent
      
      Group parent
    - type
      
      SecStrucType type
- Class org.biojava.nbio.structure.secstruc.SecStrucState extends SecStrucInfo implements Serializable
  
  serialVersionUID:
  
  -5549430890272724340L
  - Serialized Fields
    - accept1
      
      HBond accept1
    - accept2
      
      HBond accept2
    - bend
      
      boolean bend
    - bridge1
      
      BetaBridge bridge1
    - bridge2
      
      BetaBridge bridge2
    - donor1
      
      HBond donor1
    - donor2
      
      HBond donor2
    - kappa
      
      float kappa
    - omega
      
      double omega
    - phi
      
      double phi
    - psi
      
      double psi
    - turn
      
      char[] turn
Package org.biojava.nbio.structure.symmetry.core
- Class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - angleThreshold
      
      double angleThreshold
    - helixRmsdThreshold
      
      double helixRmsdThreshold
    - helixRmsdToRiseRatio
      
      double helixRmsdToRiseRatio
    - localTimeLimit
      
      double localTimeLimit
    - localTimeStart
      
      double localTimeStart
    - maximumLocalCombinations
      
      int maximumLocalCombinations
    - minimumHelixAngle
      
      double minimumHelixAngle
    - minimumHelixRise
      
      double minimumHelixRise
    - onTheFly
      
      boolean onTheFly
    - rmsdThreshold
      
      double rmsdThreshold
Package org.biojava.nbio.structure.symmetry.gui
- Class org.biojava.nbio.structure.symmetry.gui.SymmetryGui extends JFrame implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - abortB
      
      JButton abortB
    - alicalc
      
      AlignmentCalculationRunnable alicalc
    - masterPane
      
      JTabbedPane masterPane
    - params
      
      CESymmParameters params
    - progress
      
      JProgressBar progress
    - tab1
      
      SelectPDBPanel tab1
    - tab2
      
      PDBUploadPanel tab2
    - tab3
      
      ScopSelectPanel tab3
    - tabPane
      
      JTabbedPane tabPane
    - thread
      
      Thread thread
Package org.biojava.nbio.structure.symmetry.internal
- Class org.biojava.nbio.structure.symmetry.internal.RefinerFailedException extends Exception implements Serializable
  
  serialVersionUID:
  
  -3592155787060329421L
Package org.biojava.nbio.structure.symmetry.utils
- Class org.biojava.nbio.structure.symmetry.utils.BlastClustReader extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - clusters
      
      List<List<String>> clusters
    - sequenceIdentity
      
      int sequenceIdentity
Package org.biojava.nbio.structure.validation
- Class org.biojava.nbio.structure.validation.WwPDBValidationInformation extends Object implements Serializable
  
  serialVersionUID:
  
  -996804963717482650L
  - Serialized Fields
    - entry
      
      Entry entry
    - modelledSubgroup
      
      List<ModelledSubgroup> modelledSubgroup
    - programs
      
      Programs programs
Package org.biojava.nbio.structure.xtal
- Class org.biojava.nbio.structure.xtal.CrystalCell extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - a
      
      double a
    - alpha
      
      double alpha
    - alphaRad
      
      double alphaRad
    - b
      
      double b
    - beta
      
      double beta
    - betaRad
      
      double betaRad
    - c
      
      double c
    - gamma
      
      double gamma
    - gammaRad
      
      double gammaRad
    - M
      
      javax.vecmath.Matrix3d M
    - maxDimension
      
      double maxDimension
    - Minv
      
      javax.vecmath.Matrix3d Minv
    - Mtransp
      
      javax.vecmath.Matrix3d Mtransp
    - MtranspInv
      
      javax.vecmath.Matrix3d MtranspInv
    - volume
      
      double volume
- Class org.biojava.nbio.structure.xtal.CrystalTransform extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - crystalTranslation
      
      javax.vecmath.Point3i crystalTranslation
      
      The crystal translation (always integer)
    - matTransform
      
      javax.vecmath.Matrix4d matTransform
      
      The 4-dimensional matrix transformation in crystal basis. Note that the translational component of this matrix is not necessarily identical to crystalTranslation since some operators have fractional translations within the cell
    - sg
      
      SpaceGroup sg
      
      The space group to which this transform belongs
    - transformId
      
      int transformId
      
      The transform id corresponding to the SpaceGroup's transform indices. From 0 (identity) to m (m=number of symmetry operations of the space group) It is unique within the unit cell but equivalent units of different crystal unit cells will have same id
- Class org.biojava.nbio.structure.xtal.SpaceGroup extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - altShortSymbol
      
      String altShortSymbol
    - axisAngles
      
      javax.vecmath.AxisAngle4d[] axisAngles
    - axisTypes
      
      int[] axisTypes
    - bravLattice
      
      BravaisLattice bravLattice
    - cellTranslations
      
      javax.vecmath.Vector3d[] cellTranslations
    - id
      
      int id
    - multiplicity
      
      int multiplicity
    - primitiveMultiplicity
      
      int primitiveMultiplicity
    - shortSymbol
      
      String shortSymbol
    - transfAlgebraic
      
      List<String> transfAlgebraic
    - transformations
      
      List<javax.vecmath.Matrix4d> transformations
Package org.biojava.nbio.structure.xtal.io
- Class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper extends Object implements Serializable
  
  serialVersionUID:
  
  4193799052494327416L
  - Serialized Fields
    - data
      
      TreeMap<Integer,SpaceGroup> data
Package org.biojava.nbio.survival.cox.comparators
- Class org.biojava.nbio.survival.cox.comparators.CoxVariablesOverallModelFitComparator extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - variables
      
      String variables
- Class org.biojava.nbio.survival.cox.comparators.MeanModelComparator extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - variable
      
      String variable
- Class org.biojava.nbio.survival.cox.comparators.SurvivalInfoComparator extends Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.survival.cox.comparators.SurvivalInfoValueComparator extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - variable
      
      String variable
Package org.biojava.nbio.survival.data
- Class org.biojava.nbio.survival.data.CompactCharSequence extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - data
      
      byte[] data
    - end
      
      int end
    - nullstring
      
      boolean nullstring
    - offset
      
      int offset

Package org.biojava.nbio.survival.kaplanmeier.figure

Class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure extends JPanel implements Serializable

serialVersionUID:: 1L

Serialized Fields

bottom
```
int bottom
```
df
```
DecimalFormat df
```
fileName
```
String fileName
```
fm
```
FontMetrics fm
```
kmfi
```
KMFigureInfo kmfi
```
labelWidth
```
int labelWidth
```
left
```
int left
```
lineInfoList
```
ArrayList<String> lineInfoList
```
maxTime
```
Double maxTime
```
maxX
```
Double maxX
```
maxY
```
Double maxY
```
mean
```
Double mean
```
minX
```
Double minX
```
minY
```
Double minY
```
right
```
int right
```
siList
```
ArrayList<SurvivalInfo> siList
```
title
```
ArrayList<String> title
```
titleHeight
```
int titleHeight
```
top
```
int top
```
variable
```
String variable
```
xAxisLabelHeight
```
int xAxisLabelHeight
```

Class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure extends JPanel implements Serializable

serialVersionUID:: 1L

Serialized Fields

adjustedPercentIncrement
```
Double adjustedPercentIncrement
```
bottom
```
int bottom
```
df
```
DecimalFormat df
```
fileName
```
String fileName
```
fm
```
FontMetrics fm
```
kmfi
```
KMFigureInfo kmfi
```
labelWidth
```
int labelWidth
```
left
```
int left
```
lineInfoList
```
ArrayList<String> lineInfoList
```
maxPercentage
```
double maxPercentage
```
maxTime
```
double maxTime
```
minPercentage
```
double minPercentage
```
minTime
```
double minTime
```
right
```
int right
```
sfi
```
SurvFitInfo sfi
```

survivalData

LinkedHashMap<String,ArrayList<CensorStatus>> survivalData

title
```
ArrayList<String> title
```
titleHeight
```
int titleHeight
```
top
```
int top
```
xAxisLabelHeight
```
int xAxisLabelHeight
```
xAxisTimeCoordinates
```
ArrayList<Integer> xAxisTimeCoordinates
```
xAxisTimeValues
```
ArrayList<Double> xAxisTimeValues
```
yaxisLabel
```
int yaxisLabel
```

Class org.biojava.nbio.survival.kaplanmeier.figure.NumbersAtRiskPanel extends JPanel implements Serializable

serialVersionUID:

1L
- Serialized Fields
  - kmf
```
KaplanMeierFigure kmf
```
  - timePercentage
```
Double timePercentage
```

Package org.biojava.nbio.ws.alignment
Package org.biojava.nbio.ws.alignment.qblast
- Class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties extends Object implements Serializable
  
  serialVersionUID:
  
  7158270364392309841L
  - Serialized Fields
    - param
      
      Map<BlastAlignmentParameterEnum,String> param
- Class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties extends Object implements Serializable
  
  serialVersionUID:
  
  -9202060390925345163L
  - Serialized Fields
    - param
      
      Map<BlastOutputParameterEnum,String> param
Package org.biojava.nbio.ws.hmmer
- Class org.biojava.nbio.ws.hmmer.HmmerDomain extends Object implements Serializable
  
  serialVersionUID:
  
  8004302800150892757L
  - Serialized Fields
    - aliLenth
      
      Integer aliLenth
    - evalue
      
      Float evalue
    - hmmAcc
      
      String hmmAcc
    - hmmDesc
      
      String hmmDesc
    - hmmFrom
      
      Integer hmmFrom
    - hmmName
      
      String hmmName
    - hmmTo
      
      Integer hmmTo
    - simCount
      
      Integer simCount
    - sqFrom
      
      Integer sqFrom
    - sqTo
      
      Integer sqTo
- Class org.biojava.nbio.ws.hmmer.HmmerResult extends Object implements Serializable
  
  serialVersionUID:
  
  -6016026193090737943L
  - Serialized Fields
    - acc
      
      String acc
    - dcl
      
      Integer dcl
    - desc
      
      String desc
    - domains
      
      SortedSet<HmmerDomain> domains
    - evalue
      
      Float evalue
    - name
      
      String name
    - ndom
      
      Integer ndom
    - nreported
      
      Integer nreported
    - pvalue
      
      Double pvalue
    - score
      
      Float score

Serialized Form

Package demo

Class demo.GetColorGradient extends JPanel implements Serializable

Serialized Fields

colors

Package org.biojava.nbio.alignment

Class org.biojava.nbio.alignment.SimpleGapPenalty extends Object implements Serializable

Serialized Fields

gep

gop

type

Package org.biojava.nbio.alignment.routines

Class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor.QueryIndexComparator extends Object implements Serializable

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

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