Serialized Form

Package demo

Class demo.GetColorGradient

class GetColorGradient extends JPanel implements Serializable

serialVersionUID:

-4954397192682351367L

Serialized Fields

colors

Color[] colors

Package org.biojava.nbio.alignment

Class org.biojava.nbio.alignment.SimpleGapPenalty

class 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

class QueryIndexComparator extends Object implements Serializable

serialVersionUID:

1L

Package org.biojava.nbio.core.alignment

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

class SimpleAlignedSequence extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

alignmentFromSequence

int[] alignmentFromSequence

length

int length

location

Location location

numAfter

int numAfter

numBefore

int numBefore

numGapPositions

int numGapPositions

numGaps

int numGaps

original

S extends Sequence<C> original

prev

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

sequenceFromAlignment

int[] sequenceFromAlignment

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

class SimpleProfile extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

length

int length

list

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

originals

List<S extends Sequence<C>> originals

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

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

serialVersionUID:

1L

Serialized Fields

query

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

target

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

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

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

serialVersionUID:

1L

Serialized Fields

identicals

int identicals

similars

int similars

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

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

class SimpleSubstitutionMatrix extends Object implements Serializable

serialVersionUID:

-2645265638108462479L

Serialized Fields

cols

List<C extends Compound> cols

compoundSet

CompoundSet<C extends Compound> compoundSet

description

String description

matrix

short[][] matrix

max

short max

min

short min

name

String name

rows

List<C extends Compound> rows

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

class SubstitutionMatrixHelper extends Object implements Serializable

serialVersionUID:

148491724604653225L

Package org.biojava.nbio.core.exceptions

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

class CompoundNotFoundException extends Exception implements Serializable

serialVersionUID:

1L

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

class ParserException extends RuntimeException implements Serializable

serialVersionUID:

-4101924035353204493L

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

class TranslationException extends RuntimeException implements Serializable

serialVersionUID:

-3017433758219757440L

Package org.biojava.nbio.core.sequence

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

class CDSComparator extends Object implements Serializable

serialVersionUID:

1L

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

class ExonComparator extends Object implements Serializable

serialVersionUID:

1L

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

class SequenceComparator extends Object implements Serializable

serialVersionUID:

1L

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

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

class AminoAcidCompound extends AbstractCompound implements Serializable

serialVersionUID:

-1955116496725902319L

Serialized Fields

compoundSet

AminoAcidCompoundSet compoundSet

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

class AminoAcidCompoundSet extends Object implements Serializable

serialVersionUID:

4000344194364133456L

Serialized Fields

aminoAcidCompoundCache

Map<String,AminoAcidCompound> aminoAcidCompoundCache

aminoAcidCompoundCache3Letter

Map<String,AminoAcidCompound> aminoAcidCompoundCache3Letter

equivalentsCache

Map<AminoAcidCompound,Set<AminoAcidCompound>> equivalentsCache

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

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

class FuzzyPoint extends SimplePoint implements Serializable

Serialized Fields

max

int max

min

int min

resolver

Point.Resolver<FuzzyPoint> resolver

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

class BondLocation extends AbstractLocation implements Serializable

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

class GroupLocation extends SimpleLocation implements Serializable

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

class OneOfLocation extends AbstractLocation implements Serializable

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

class OrderLocation extends SimpleLocation implements Serializable

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

class SequenceLocation extends SimpleLocation implements Serializable

Serialized Fields

sequence

S extends AbstractSequence<C> sequence

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

class SimpleLocation extends AbstractLocation implements Serializable

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

class SimplePoint extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

position

int position

uncertain

boolean uncertain

unknown

boolean unknown

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

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

class AbstractLocation extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

accession

AccessionID accession

betweenCompounds

boolean betweenCompounds

circular

boolean circular

end

Point end

partialOn3prime

boolean partialOn3prime

partialOn5prime

boolean partialOn5prime

start

Point start

strand

Strand strand

subLocations

List<Location> subLocations

Package org.biojava.nbio.genome.parsers.cytoband

Class org.biojava.nbio.genome.parsers.cytoband.Cytoband

class 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

class 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

class 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

class FeatureList extends ArrayList<FeatureI> implements Serializable

Serialized Fields

featindex

Map<String,Map<String,List<FeatureI>>> featindex

mLocation

Location mLocation

Package org.biojava.nbio.ontology

Exception Class org.biojava.nbio.ontology.AlreadyExistsException

class AlreadyExistsException extends OntologyException implements Serializable

serialVersionUID:

1L

Class org.biojava.nbio.ontology.DefaultOps

class DefaultOps extends Object implements Serializable

serialVersionUID:

1L

Exception Class org.biojava.nbio.ontology.InvalidTermException

class InvalidTermException extends OntologyException implements Serializable

serialVersionUID:

1L

Class org.biojava.nbio.ontology.Ontology.Impl

class 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

Exception Class org.biojava.nbio.ontology.OntologyException

class OntologyException extends Exception implements Serializable

serialVersionUID:

1L

Class org.biojava.nbio.ontology.OntologyTerm.Impl

class 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

class 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

class 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

class 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

class Impl extends Term.Impl implements Serializable

serialVersionUID:

1L

Package org.biojava.nbio.ontology.utils

Class org.biojava.nbio.ontology.utils.AbstractAnnotation

class AbstractAnnotation extends Object implements Serializable

serialVersionUID:

2753449055959952873L

Exception Class org.biojava.nbio.ontology.utils.AssertionFailure

class AssertionFailure extends AssertionError implements Serializable

Class org.biojava.nbio.ontology.utils.SmallAnnotation

class SmallAnnotation extends AbstractAnnotation implements Serializable

Serialized Fields

properties

Map properties

Class org.biojava.nbio.ontology.utils.SmallMap

class SmallMap extends AbstractMap implements Serializable

Serialized Fields

mappings

Object[] mappings

numMappings

int numMappings

Class org.biojava.nbio.ontology.utils.StaticMemberPlaceHolder

class 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

class 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

class Jronn extends Object implements Serializable

serialVersionUID:

8104272449130849946L

Package org.biojava.nbio.structure

Class org.biojava.nbio.structure.AminoAcidImpl

class 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

class 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

class Author extends Object implements Serializable

serialVersionUID:

4840370515056666418L

Serialized Fields

initials

String initials

surname

String surname

Class org.biojava.nbio.structure.BioAssemblyIdentifier

class BioAssemblyIdentifier extends Object implements Serializable

serialVersionUID:

-356206725119993449L

Serialized Fields

biolNr

int biolNr

pdbId

PdbId pdbId

Class org.biojava.nbio.structure.BondImpl

class BondImpl extends Object implements Serializable

serialVersionUID:

8836120946858134380L

Serialized Fields

atomA

Atom atomA

atomB

Atom atomB

bondOrder

int bondOrder

Class org.biojava.nbio.structure.ChainImpl

class 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

Class org.biojava.nbio.structure.DatabasePDBRevRecord

class DatabasePDBRevRecord extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

details

String details

revNum

String revNum

type

String type

Class org.biojava.nbio.structure.DBRef

class 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

class 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

class 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

class 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

class 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

class NucleotideImpl extends HetatomImpl implements Serializable

serialVersionUID:

-7467726932980288712L

Class org.biojava.nbio.structure.PassthroughIdentifier

class PassthroughIdentifier extends Object implements Serializable

serialVersionUID:

-2773111624414448950L

Serialized Fields

identifier

String identifier

Class org.biojava.nbio.structure.PDBCrystallographicInfo

class 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

class 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

Deprecated.

This field should not be used. It will be removed later. Use PDBHeader.getKeywords() instead.

id

Long id

journalArticle

JournalArticle journalArticle

keywords

List<String> keywords

modDate

Date modDate

pdbId

PdbId pdbId

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.PdbId

class PdbId extends Object implements Serializable

serialVersionUID:

-7740865530486255113L

Serialized Fields

idCode

String idCode

Keeps the ID in UPPER CASE, in a reduced form (without the PDB_ prefix).

Class org.biojava.nbio.structure.ResidueNumber

class ResidueNumber extends Object implements Serializable

serialVersionUID:

1773011704758536083L

Serialized Fields

chainName

String chainName

insCode

Character insCode

seqNum

Integer seqNum

Class org.biojava.nbio.structure.SeqMisMatchImpl

class 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

class Site extends Object implements Serializable

serialVersionUID:

-4577047072916341237L

Serialized Fields

description

String description

evCode

String evCode

groups

List<Group> groups

siteID

String siteID

Exception Class org.biojava.nbio.structure.StructureException

class StructureException extends Exception implements Serializable

serialVersionUID:

62946250941673093L

Class org.biojava.nbio.structure.StructureImpl

class StructureImpl extends Object implements Serializable

serialVersionUID:

-8344837138032851348L

Serialized Fields

biologicalAssembly

boolean biologicalAssembly

dbrefs

List<DBRef> dbrefs

entityInfos

List<EntityInfo> entityInfos

models

List<Model> models

name

String name

pdbHeader

PDBHeader pdbHeader

pdbId

PdbId pdbId

sites

List<Site> sites

ssbonds

List<Bond> ssbonds

structureIdentifier

StructureIdentifier structureIdentifier

Class org.biojava.nbio.structure.SubstructureIdentifier

class SubstructureIdentifier extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

pdbId

PdbId pdbId

ranges

List<ResidueRange> ranges

Class org.biojava.nbio.structure.URLIdentifier

class 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.StructureName

class StructureName extends Object implements Serializable

serialVersionUID:

4021229518711762957L

Serialized Fields

base

StructureIdentifier base

chainName

String chainName

mySource

StructureName.Source mySource

name

String name

pdbId

PdbId pdbId

Package org.biojava.nbio.structure.align.gui

Class org.biojava.nbio.structure.align.gui.AlignmentGui

class AlignmentGui extends JFrame implements Serializable

serialVersionUID:

0L

Serialized Fields

abortB

JButton abortB

algorithm

StructureAlignment algorithm

alicalc

AlignmentCalculationRunnable alicalc

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

class AlignmentTextPanel extends JPrintPanel implements Serializable

serialVersionUID:

5092386365924879073L

Serialized Fields

tp

JEditorPane tp

Class org.biojava.nbio.structure.align.gui.ChooseDirAction

class ChooseDirAction extends AbstractAction implements Serializable

serialVersionUID:

0L

Serialized Fields

config

UserConfiguration config

textField

JTextField textField

Class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel

class 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.DotPlotPanel

class DotPlotPanel extends ScaleableMatrixPanel implements Serializable

serialVersionUID:

-7641953255857483895L

Class org.biojava.nbio.structure.align.gui.JPrintPanel

class JPrintPanel extends JPanel implements Serializable

serialVersionUID:

-3337337068138131455L

Class org.biojava.nbio.structure.align.gui.MemoryMonitor

class 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

class 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

class 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

class ParameterGUI extends JFrame implements Serializable

serialVersionUID:

723386061184110161L

Serialized Fields

params

ConfigStrucAligParams params

textFields

List<Component> textFields

Class org.biojava.nbio.structure.align.gui.SelectPDBPanel

class 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

class 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

class 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

class MultipleStatusDisplay extends JTextField implements Serializable

serialVersionUID:

6939947266417830429L

Serialized Fields

panel

MultipleAligPanel panel

Class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay

class 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

class 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

class 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

class AligMatEl extends IndexPair implements Serializable

serialVersionUID:

-4040926588803887471L

Serialized Fields

contig

int contig

value

int value

Class org.biojava.nbio.structure.align.helper.IdxComparator

class IdxComparator extends Object implements Serializable

serialVersionUID:

1L

Class org.biojava.nbio.structure.align.helper.IndexPair

class 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

class 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

class 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

class 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

class 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

class 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

class 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

class 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.AlternativeAlignment

class 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

Exception Class org.biojava.nbio.structure.align.util.ConfigurationException

class ConfigurationException extends Exception implements Serializable

serialVersionUID:

-8047100079715000276L

Package org.biojava.nbio.structure.asa

Class org.biojava.nbio.structure.asa.GroupAsa

class 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

class 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

class 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

class 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

class 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

class 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

class 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

class 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.chem

Class org.biojava.nbio.structure.chem.ChemComp

class ChemComp extends Object implements Serializable

serialVersionUID:

-4736341142030215915L

Serialized Fields

atoms

List<ChemCompAtom> atoms

bonds

List<ChemCompBond> bonds

descriptors

List<ChemCompDescriptor> descriptors

formula

String formula

formulaWeight

double formulaWeight

id

String id

monNstdFlag

String monNstdFlag

monNstdParentCompId

String monNstdParentCompId

name

String name

oneLetterCode

String oneLetterCode

pdbxAmbiguousFlag

String pdbxAmbiguousFlag

pdbxFormalCharge

int pdbxFormalCharge

pdbxIdealCoordinatesDetails

String pdbxIdealCoordinatesDetails

pdbxIdealCoordinatesMissingFlag

String pdbxIdealCoordinatesMissingFlag

pdbxInitialDate

String pdbxInitialDate

pdbxModelCoordinatesDbCode

String pdbxModelCoordinatesDbCode

pdbxModelCoordinatesDetails

String pdbxModelCoordinatesDetails

pdbxModelCoordinatesMissingFlag

String pdbxModelCoordinatesMissingFlag

pdbxModifiedDate

String pdbxModifiedDate

pdbxProcessingSite

String pdbxProcessingSite

pdbxReleaseStatus

String pdbxReleaseStatus

pdbxReplacedBy

String pdbxReplacedBy

pdbxReplaces

String pdbxReplaces

pdbxSubcomponentList

String pdbxSubcomponentList

pdbxSynonyms

String pdbxSynonyms

pdbxType

String pdbxType

polymerType

PolymerType polymerType

residueType

ResidueType residueType

standard

boolean standard

threeLetterCode

String threeLetterCode

type

String type

Class org.biojava.nbio.structure.chem.ChemCompAtom

class ChemCompAtom extends Object implements Serializable

serialVersionUID:

4070599340294758941L

Serialized Fields

altAtomId

String altAtomId

atomId

String atomId

charge

int charge

compId

String compId

modelCartnX

double modelCartnX

modelCartnY

double modelCartnY

modelCartnZ

double modelCartnZ

pdbxAlign

int pdbxAlign

pdbxAromaticFlag

String pdbxAromaticFlag

pdbxComponentAtomId

String pdbxComponentAtomId

pdbxComponentCompId

String pdbxComponentCompId

pdbxComponentId

String pdbxComponentId

pdbxLeavingAtomFlag

String pdbxLeavingAtomFlag

pdbxModelCartnXIdeal

double pdbxModelCartnXIdeal

pdbxModelCartnYIdeal

double pdbxModelCartnYIdeal

pdbxModelCartnZIdeal

double pdbxModelCartnZIdeal

pdbxOrdinal

int pdbxOrdinal

pdbxPolymerType

String pdbxPolymerType

pdbxRefId

String pdbxRefId

pdbxResidueNumbering

String pdbxResidueNumbering

pdbxStereoConfig

String pdbxStereoConfig

typeSymbol

String typeSymbol

Class org.biojava.nbio.structure.chem.ChemCompBond

class ChemCompBond extends Object implements Serializable

serialVersionUID:

5905371029161975421L

Serialized Fields

atomId1

String atomId1

atomId2

String atomId2

compId

String compId

pdbxAromaticFlag

String pdbxAromaticFlag

pdbxOrdinal

int pdbxOrdinal

pdbxStereoConfig

String pdbxStereoConfig

valueOrder

String valueOrder

Class org.biojava.nbio.structure.chem.ChemCompDescriptor

class ChemCompDescriptor extends Object implements Serializable

serialVersionUID:

1078685833800736278L

Serialized Fields

compId

String compId

descriptor

String descriptor

program

String program

programVersion

String programVersion

type

String type

Package org.biojava.nbio.structure.cluster

Class org.biojava.nbio.structure.cluster.SubunitClustererParameters

class 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

useEntityIdForSeqIdentityDetermination

boolean useEntityIdForSeqIdentityDetermination

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

class AtomContact extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

distance

double distance

pair

Pair<Atom> pair

Class org.biojava.nbio.structure.contact.AtomContactSet

class 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

class AtomIdentifier extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

chainId

String chainId

pdbSerial

int pdbSerial

Class org.biojava.nbio.structure.contact.BoundingBox

class 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

class 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

class GroupContact extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

atomContacts

List<AtomContact> atomContacts

pair

Pair<Group> pair

Class org.biojava.nbio.structure.contact.GroupContactSet

class 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

class Pair extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

first

T first

second

T second

Class org.biojava.nbio.structure.contact.StructureInterface

class 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

class 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

class StructureInterfaceList extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

chainOrigNamesMap

Map<String,String> chainOrigNamesMap

clusters

List<StructureInterfaceCluster> clusters

clustersNcs

List<StructureInterfaceCluster> clustersNcs

list

List<StructureInterface> list

Package org.biojava.nbio.structure.domain.pdp

Class org.biojava.nbio.structure.domain.pdp.Domain

class 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

class 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

class SegmentComparator extends Object implements Serializable

serialVersionUID:

1L

Package org.biojava.nbio.structure.ecod

Class org.biojava.nbio.structure.ecod.EcodDomain

class 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

PdbId 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

class 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

class 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

class 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

class 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

class 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

class 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

class 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

class 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

class PDBUploadPanel extends JPanel implements Serializable

serialVersionUID:

1L

Serialized Fields

chain1

JTextField chain1

chain2

JTextField chain2

filePath1

JTextField filePath1

filePath2

JTextField filePath2

fileType

JComboBox<String> fileType

Class org.biojava.nbio.structure.gui.util.ScopSelectPanel

class ScopSelectPanel extends JPanel implements Serializable

serialVersionUID:

757947454156959178L

Serialized Fields

dom1

JAutoSuggest dom1

dom2

JAutoSuggest dom2

Class org.biojava.nbio.structure.gui.util.SelectMultiplePanel

class SelectMultiplePanel extends JPanel implements Serializable

serialVersionUID:

757947454156959178L

Serialized Fields

input

JTextField input

Class org.biojava.nbio.structure.gui.util.SequenceScalePanel

class 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

class 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

class HSVColorSpace extends ColorSpace implements Serializable

serialVersionUID:

8324413992279510075L

Package org.biojava.nbio.structure.io

Class org.biojava.nbio.structure.io.FileParsingParameters

class 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

Exception Class org.biojava.nbio.structure.io.PDBParseException

class PDBParseException extends Exception implements Serializable

serialVersionUID:

219047230178423923L

Class org.biojava.nbio.structure.io.SSBondImpl

class 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.cif

Package org.biojava.nbio.structure.io.mmtf

Class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

class 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

class 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

class 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

class 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

class 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

class 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

class 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

class 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

class 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

class 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

class SparseSquareMatrix extends Object implements Serializable

serialVersionUID:

-5217767192992868955L

Serialized Fields

N

int N

rows

SparseVector[] rows

Class org.biojava.nbio.structure.math.SparseVector

class SparseVector extends Object implements Serializable

serialVersionUID:

1174668523213431927L

Serialized Fields

N

int N

symbolTable

SymbolTable<Integer,Double> symbolTable

Class org.biojava.nbio.structure.math.SymbolTable

class 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

class 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

class 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

class 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

class 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

PdbId pdbId

px

int px

ranges

List<String> ranges

scopId

String scopId

speciesId

int speciesId

sunid

Integer sunid

superfamilyId

int superfamilyId

Exception Class org.biojava.nbio.structure.scop.ScopIOException

class ScopIOException extends RuntimeException implements Serializable

serialVersionUID:

1L

Class org.biojava.nbio.structure.scop.ScopNode

class ScopNode extends Object implements Serializable

serialVersionUID:

1187083944488580995L

Serialized Fields

children

List<Integer> children

parentSunid

int parentSunid

sunid

int sunid

Package org.biojava.nbio.structure.secstruc

Class org.biojava.nbio.structure.secstruc.BetaBridge

class 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

class HBond extends Object implements Serializable

serialVersionUID:

8246764841329431337L

Serialized Fields

energy

double energy

partner

int partner

Class org.biojava.nbio.structure.secstruc.Ladder

class 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

class 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

class 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

class 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

class 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

class 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

Exception Class org.biojava.nbio.structure.symmetry.internal.RefinerFailedException

class RefinerFailedException extends Exception implements Serializable

serialVersionUID:

-3592155787060329421L

Package org.biojava.nbio.structure.symmetry.utils

Class org.biojava.nbio.structure.symmetry.utils.BlastClustReader

class BlastClustReader extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

clusters

List<List<String>> clusters

sequenceIdentity

int sequenceIdentity

Package org.biojava.nbio.structure.xtal

Class org.biojava.nbio.structure.xtal.CrystalCell

class 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

class 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

class 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

class 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

class CoxVariablesOverallModelFitComparator extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

variables

String variables

Class org.biojava.nbio.survival.cox.comparators.MeanModelComparator

class MeanModelComparator extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

variable

String variable

Class org.biojava.nbio.survival.cox.comparators.SurvivalInfoComparator

class SurvivalInfoComparator extends Object implements Serializable

serialVersionUID:

1L

Class org.biojava.nbio.survival.cox.comparators.SurvivalInfoValueComparator

class 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

class 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

class 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

class 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

class 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

class NCBIQBlastAlignmentProperties extends Object implements Serializable

serialVersionUID:

7158270364392309841L

Serialized Fields

param

Map<BlastAlignmentParameterEnum,String> param

Class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties

class 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

class 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

class 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