Serialized Form
-
Package org.biojava.nbio.alignment
-
Class org.biojava.nbio.alignment.SimpleGapPenalty extends java.lang.Object implements Serializable
- serialVersionUID:
- 3945671344135815456L
-
Serialized Fields
-
gep
int gep
-
gop
int gop
-
type
GapPenalty.Type type
-
-
-
Package org.biojava.nbio.core.alignment
-
Class org.biojava.nbio.core.alignment.SimpleAlignedSequence extends java.lang.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 java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Class org.biojava.nbio.core.alignment.SimpleProfilePair extends SimpleProfile<S extends Sequence<C>,C extends Compound> implements Serializable
- serialVersionUID:
- 1L
-
Class org.biojava.nbio.core.alignment.SimpleSequencePair extends SimpleProfile<S extends Sequence<C>,C extends Compound> implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
identicals
int identicals
-
similars
int similars
-
-
-
Package org.biojava.nbio.core.alignment.matrices
-
Class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix extends java.lang.Object implements Serializable
- serialVersionUID:
- -2645265638108462479L
-
Class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper extends java.lang.Object implements Serializable
- serialVersionUID:
- 148491724604653225L
-
-
Package org.biojava.nbio.core.exceptions
-
Class org.biojava.nbio.core.exceptions.CompoundNotFoundException extends java.lang.Exception implements Serializable
- serialVersionUID:
- 1L
-
Class org.biojava.nbio.core.exceptions.ParserException extends java.lang.RuntimeException implements Serializable
- serialVersionUID:
- -4101924035353204493L
-
Class org.biojava.nbio.core.exceptions.TranslationException extends java.lang.RuntimeException implements Serializable
- serialVersionUID:
- -3017433758219757440L
-
-
Package org.biojava.nbio.core.sequence.compound
-
Class org.biojava.nbio.core.sequence.compound.AminoAcidCompound extends AbstractCompound implements Serializable
- serialVersionUID:
- -1955116496725902319L
-
Serialized Fields
-
compoundSet
AminoAcidCompoundSet compoundSet
-
-
Class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet extends java.lang.Object implements Serializable
- serialVersionUID:
- 4000344194364133456L
-
Serialized Fields
-
aminoAcidCompoundCache
java.util.Map<java.lang.String,AminoAcidCompound> aminoAcidCompoundCache
-
aminoAcidCompoundCache3Letter
java.util.Map<java.lang.String,AminoAcidCompound> aminoAcidCompoundCache3Letter
-
equivalentsCache
java.util.Map<AminoAcidCompound,java.util.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 java.lang.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 java.lang.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
java.util.List<Location> subLocations
-
-
-
Package org.biojava.nbio.genome.parsers.cytoband
-
Class org.biojava.nbio.genome.parsers.cytoband.Cytoband extends java.lang.Object implements Serializable
- serialVersionUID:
- 2805976387404499650L
-
Serialized Fields
-
chromosome
java.lang.String chromosome
-
end
java.lang.Integer end
-
locus
java.lang.String locus
-
start
java.lang.Integer start
-
type
StainType type
-
-
-
Package org.biojava.nbio.genome.parsers.genename
-
Class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition extends java.lang.Object implements Serializable
- serialVersionUID:
- -6886306238993367835L
-
Serialized Fields
-
cdsEnd
java.lang.Integer cdsEnd
-
cdsStart
java.lang.Integer cdsStart
-
chromosome
java.lang.String chromosome
-
exonCount
int exonCount
-
exonEnds
java.util.List<java.lang.Integer> exonEnds
-
exonStarts
java.util.List<java.lang.Integer> exonStarts
-
genebankId
java.lang.String genebankId
-
geneName
java.lang.String geneName
-
orientation
java.lang.Character orientation
-
transcriptionEnd
java.lang.Integer transcriptionEnd
-
transcriptionStart
java.lang.Integer transcriptionStart
-
-
Class org.biojava.nbio.genome.parsers.genename.GeneName extends java.lang.Object implements Serializable
- serialVersionUID:
- -7163977639324764020L
-
Serialized Fields
-
accessionNr
java.lang.String accessionNr
-
approvedName
java.lang.String approvedName
-
approvedSymbol
java.lang.String approvedSymbol
-
chromosome
java.lang.String chromosome
-
ensemblGeneId
java.lang.String ensemblGeneId
-
hgncId
java.lang.String hgncId
-
omimId
java.lang.String omimId
-
previousNames
java.lang.String previousNames
-
previousSymbols
java.lang.String previousSymbols
-
refseqIds
java.lang.String refseqIds
-
status
java.lang.String status
-
synonyms
java.lang.String synonyms
-
uniprot
java.lang.String uniprot
-
-
-
Package org.biojava.nbio.genome.parsers.gff
-
Class org.biojava.nbio.genome.parsers.gff.FeatureList extends java.util.ArrayList<FeatureI> implements Serializable
-
-
Package org.biojava.nbio.ontology
-
Class org.biojava.nbio.ontology.AlreadyExistsException extends OntologyException implements Serializable
- serialVersionUID:
- 1L
-
Class org.biojava.nbio.ontology.DefaultOps extends java.lang.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 java.lang.Object implements Serializable
- serialVersionUID:
- -8064461497813727957L
-
Serialized Fields
-
description
java.lang.String description
-
localRemoteTerms
java.util.Set<Term> localRemoteTerms
-
name
java.lang.String name
-
objectTriples
java.util.Map<Term,java.util.Set<Triple>> objectTriples
-
ops
OntologyOps ops
-
relationTriples
java.util.Map<Term,java.util.Set<Triple>> relationTriples
-
remoteTerms
java.util.Map<Term,RemoteTerm> remoteTerms
-
subjectTriples
java.util.Map<Term,java.util.Set<Triple>> subjectTriples
-
terms
java.util.Map<java.lang.String,Term> terms
-
triples
java.util.Set<Triple> triples
-
-
Class org.biojava.nbio.ontology.OntologyException extends java.lang.Exception implements Serializable
- serialVersionUID:
- 1L
-
Class org.biojava.nbio.ontology.OntologyTerm.Impl extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Class org.biojava.nbio.ontology.RemoteTerm.Impl extends AbstractTerm implements Serializable
- serialVersionUID:
- 922700041939183676L
-
Class org.biojava.nbio.ontology.Term.Impl extends AbstractTerm implements Serializable
- serialVersionUID:
- 6561668917514377417L
-
Serialized Fields
-
annotation
Annotation annotation
-
name
java.lang.String name
-
ontology
Ontology ontology
-
synonyms
java.util.Set<java.lang.Object> synonyms
-
-
Class org.biojava.nbio.ontology.Triple.Impl extends java.lang.Object implements Serializable
- serialVersionUID:
- 3807331980372839221L
-
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 java.lang.Object implements Serializable
- serialVersionUID:
- 2753449055959952873L
-
Class org.biojava.nbio.ontology.utils.AssertionFailure extends java.lang.AssertionError implements Serializable
-
Class org.biojava.nbio.ontology.utils.SmallAnnotation extends AbstractAnnotation implements Serializable
-
Serialized Fields
-
properties
java.util.Map properties
-
-
-
Class org.biojava.nbio.ontology.utils.SmallMap extends java.util.AbstractMap implements Serializable
-
Serialized Fields
-
mappings
java.lang.Object[] mappings
-
numMappings
int numMappings
-
-
-
Class org.biojava.nbio.ontology.utils.StaticMemberPlaceHolder extends java.lang.Object implements Serializable
-
Serialization Methods
-
readResolve
public java.lang.Object readResolve() throws java.io.ObjectStreamException
- Throws:
java.io.ObjectStreamException
-
-
Serialized Fields
-
className
java.lang.String className
-
fieldName
java.lang.String fieldName
-
-
-
-
Package org.biojava.nbio.protmod.structure
-
Class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl extends java.lang.Object implements Serializable
- serialVersionUID:
- 1656563037849815427L
-
Serialized Fields
-
atomLinkages
java.util.Map<java.util.Set<StructureGroup>,java.util.Set<StructureAtomLinkage>> atomLinkages
-
groups
java.util.Set<StructureGroup> groups
-
modification
ProteinModification modification
-
originalModification
ProteinModification originalModification
-
-
-
Package org.biojava.nbio.structure
-
Class org.biojava.nbio.structure.AminoAcidImpl extends HetatomImpl implements Serializable
- serialVersionUID:
- -6018854413829044230L
-
Serialized Fields
-
amino_char
java.lang.Character amino_char
IUPAC amino acid residue names -
recordType
java.lang.String recordType
-
-
Class org.biojava.nbio.structure.AtomImpl extends java.lang.Object implements Serializable
- serialVersionUID:
- -2258364127420562883L
-
Class org.biojava.nbio.structure.Author extends java.lang.Object implements Serializable
- serialVersionUID:
- 4840370515056666418L
-
Serialized Fields
-
initials
java.lang.String initials
-
surname
java.lang.String surname
-
-
Class org.biojava.nbio.structure.BondImpl extends java.lang.Object implements Serializable
- serialVersionUID:
- 8836120946858134380L
-
Class org.biojava.nbio.structure.ChainImpl extends java.lang.Object implements Serializable
- serialVersionUID:
- 1990171805277911840L
-
Serialized Fields
-
chainID
java.lang.String chainID
-
groups
java.util.List<Group> groups
-
id
java.lang.Long id
-
internalChainID
java.lang.String internalChainID
-
mol
Compound mol
-
parent
Structure parent
-
pdbResnumMap
java.util.Map<java.lang.String,java.lang.Integer> pdbResnumMap
-
seqMisMatches
java.util.List<SeqMisMatch> seqMisMatches
-
seqResGroups
java.util.List<Group> seqResGroups
-
swissprot_id
java.lang.String swissprot_id
-
-
Class org.biojava.nbio.structure.Compound extends java.lang.Object implements Serializable
- serialVersionUID:
- 2991897825657586356L
-
Serialized Fields
-
atcc
java.lang.String atcc
-
biologicalUnit
java.lang.String biologicalUnit
-
cell
java.lang.String cell
-
cellLine
java.lang.String cellLine
-
cellularLocation
java.lang.String cellularLocation
-
chains
java.util.List<Chain> chains
The list of chains that are described by this Compound -
chains2pdbResNums2ResSerials
java.util.Map<java.lang.String,java.util.Map<ResidueNumber,java.lang.Integer>> chains2pdbResNums2ResSerials
A map to cache residue number mapping, between ResidueNumbers and index (1-based) in aligned sequences (SEQRES). Initialised lazily upon call toCompound.getAlignedResIndex(Group, Chain)
-
details
java.lang.String details
-
ecNums
java.util.List<java.lang.String> ecNums
-
engineered
java.lang.String engineered
-
expressionSystem
java.lang.String expressionSystem
-
expressionSystemAtccNumber
java.lang.String expressionSystemAtccNumber
-
expressionSystemCell
java.lang.String expressionSystemCell
-
expressionSystemCellLine
java.lang.String expressionSystemCellLine
-
expressionSystemCellularLocation
java.lang.String expressionSystemCellularLocation
-
expressionSystemGene
java.lang.String expressionSystemGene
-
expressionSystemOrgan
java.lang.String expressionSystemOrgan
-
expressionSystemOrganelle
java.lang.String expressionSystemOrganelle
-
expressionSystemOtherDetails
java.lang.String expressionSystemOtherDetails
-
expressionSystemPlasmid
java.lang.String expressionSystemPlasmid
-
expressionSystemStrain
java.lang.String expressionSystemStrain
-
expressionSystemTaxId
java.lang.String expressionSystemTaxId
-
expressionSystemTissue
java.lang.String expressionSystemTissue
-
expressionSystemVariant
java.lang.String expressionSystemVariant
-
expressionSystemVector
java.lang.String expressionSystemVector
-
expressionSystemVectorType
java.lang.String expressionSystemVectorType
-
fragment
java.lang.String fragment
-
gene
java.lang.String gene
-
headerVars
java.lang.String headerVars
-
id
java.lang.Long id
-
molId
int molId
The Molecule identifier, called entity_id in mmCIF dictionary -
molName
java.lang.String molName
-
mutation
java.lang.String mutation
-
numRes
java.lang.String numRes
-
organ
java.lang.String organ
-
organelle
java.lang.String organelle
-
organismCommon
java.lang.String organismCommon
-
organismScientific
java.lang.String organismScientific
-
organismTaxId
java.lang.String organismTaxId
-
refChainId
java.lang.String refChainId
-
resNames
java.lang.String resNames
-
secretion
java.lang.String secretion
-
strain
java.lang.String strain
-
synonyms
java.util.List<java.lang.String> synonyms
-
synthetic
java.lang.String synthetic
-
tissue
java.lang.String tissue
-
title
java.lang.String title
-
variant
java.lang.String variant
-
-
Class org.biojava.nbio.structure.DBRef extends java.lang.Object implements Serializable
- serialVersionUID:
- -1050178577542224379L
-
Serialized Fields
-
chainId
java.lang.String chainId
-
database
java.lang.String database
-
dbAccession
java.lang.String dbAccession
-
dbIdCode
java.lang.String dbIdCode
-
dbSeqBegin
int dbSeqBegin
-
dbSeqEnd
int dbSeqEnd
-
id
java.lang.Long id
-
idbnsBegin
char idbnsBegin
-
idbnsEnd
char idbnsEnd
-
idCode
java.lang.String idCode
-
insertBegin
char insertBegin
-
insertEnd
char insertEnd
-
parent
Structure parent
-
seqbegin
int seqbegin
-
seqEnd
int seqEnd
-
-
Class org.biojava.nbio.structure.HetatomImpl extends java.lang.Object implements Serializable
- serialVersionUID:
- 4491470432023820382L
-
Serialized Fields
-
altLocs
java.util.List<Group> altLocs
-
atomNameLookup
java.util.Map<java.lang.String,Atom> atomNameLookup
-
atoms
java.util.List<Atom> atoms
-
chemComp
ChemComp chemComp
-
id
long id
-
parent
Chain parent
-
pdb_flag
boolean pdb_flag
stores if 3d coordinates are available. -
pdb_name
java.lang.String pdb_name
3 letter name of amino acid in pdb file. -
properties
java.util.Map<java.lang.String,java.lang.Object> properties
-
residueNumber
ResidueNumber residueNumber
-
-
Class org.biojava.nbio.structure.JournalArticle extends java.lang.Object implements Serializable
- serialVersionUID:
- 5062668226159515468L
-
Serialized Fields
-
authorList
java.util.List<Author> authorList
-
doi
java.lang.String doi
-
editorList
java.util.List<Author> editorList
-
journalName
java.lang.String journalName
-
pmid
java.lang.String pmid
-
publicationDate
int publicationDate
-
published
boolean published
-
publisher
java.lang.String publisher
-
ref
java.lang.String ref
-
refn
java.lang.String refn
-
startPage
java.lang.String startPage
-
title
java.lang.String title
-
volume
java.lang.String volume
-
-
Class org.biojava.nbio.structure.NucleotideImpl extends HetatomImpl implements Serializable
- serialVersionUID:
- -7467726932980288712L
-
Class org.biojava.nbio.structure.PDBCrystallographicInfo extends java.lang.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 java.lang.Object implements Serializable
- serialVersionUID:
- -5834326174085429508L
-
Serialized Fields
-
authors
java.lang.String authors
-
bioAssemblies
java.util.Map<java.lang.Integer,BioAssemblyInfo> bioAssemblies
-
classification
java.lang.String classification
-
crystallographicInfo
PDBCrystallographicInfo crystallographicInfo
-
dateFormat
java.text.DateFormat dateFormat
-
depDate
java.util.Date depDate
-
description
java.lang.String description
-
id
java.lang.Long id
-
idCode
java.lang.String idCode
-
journalArticle
JournalArticle journalArticle
-
modDate
java.util.Date modDate
-
resolution
float resolution
-
revisionRecords
java.util.List<DatabasePdbrevRecord> revisionRecords
-
rFree
float rFree
-
techniques
java.util.Set<ExperimentalTechnique> techniques
-
title
java.lang.String title
-
-
Class org.biojava.nbio.structure.ResidueNumber extends java.lang.Object implements Serializable
- serialVersionUID:
- 1773011704758536083L
-
Serialized Fields
-
chainId
java.lang.String chainId
-
insCode
java.lang.Character insCode
-
seqNum
java.lang.Integer seqNum
-
-
Class org.biojava.nbio.structure.SeqMisMatchImpl extends java.lang.Object implements Serializable
- serialVersionUID:
- -3699285122925652562L
-
Serialized Fields
-
details
java.lang.String details
-
insCode
java.lang.String insCode
-
origGroup
java.lang.String origGroup
-
pdbGroup
java.lang.String pdbGroup
-
pdbResNum
java.lang.String pdbResNum
-
seqNum
java.lang.Integer seqNum
-
uniProtId
java.lang.String uniProtId
-
-
Class org.biojava.nbio.structure.Site extends java.lang.Object implements Serializable
- serialVersionUID:
- -4577047072916341237L
-
Serialized Fields
-
description
java.lang.String description
-
evCode
java.lang.String evCode
-
groups
java.util.List<Group> groups
-
siteID
java.lang.String siteID
-
-
Class org.biojava.nbio.structure.StructureException extends java.lang.Exception implements Serializable
- serialVersionUID:
- 62946250941673093L
-
Class org.biojava.nbio.structure.StructureImpl extends java.lang.Object implements Serializable
- serialVersionUID:
- -8344837138032851348L
-
Serialized Fields
-
biologicalAssembly
boolean biologicalAssembly
-
compounds
java.util.List<Compound> compounds
-
connections
java.util.List<java.util.Map<java.lang.String,java.lang.Integer>> connections
-
dbrefs
java.util.List<DBRef> dbrefs
-
hetAtoms
java.util.List<Group> hetAtoms
-
id
java.lang.Long id
-
models
java.util.List<java.util.List<Chain>> models
-
name
java.lang.String name
-
pdb_id
java.lang.String pdb_id
-
pdbHeader
PDBHeader pdbHeader
-
sites
java.util.List<Site> sites
-
ssbonds
java.util.List<Bond> ssbonds
-
structureIdentifier
StructureIdentifier structureIdentifier
-
-
Class org.biojava.nbio.structure.SubstructureIdentifier extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
pdbId
java.lang.String pdbId
-
ranges
java.util.List<ResidueRange> ranges
-
-
-
Package org.biojava.nbio.structure.align.client
-
Class org.biojava.nbio.structure.align.client.JobKillException extends java.lang.Exception implements Serializable
- serialVersionUID:
- 1L
-
Class org.biojava.nbio.structure.align.client.StructureName extends java.lang.Object implements Serializable
- serialVersionUID:
- 4021229518711762957L
-
Serialized Fields
-
base
StructureIdentifier base
-
chainId
java.lang.String chainId
-
mySource
StructureName.Source mySource
-
name
java.lang.String name
-
pdbId
java.lang.String pdbId
-
-
-
Package org.biojava.nbio.structure.align.gui
-
Class org.biojava.nbio.structure.align.gui.AlignmentGui extends javax.swing.JFrame implements Serializable
- serialVersionUID:
- 0L
-
Serialized Fields
-
abortB
javax.swing.JButton abortB
-
algorithm
StructureAlignment algorithm
-
alicalc
AlignmentCalculationRunnable alicalc
-
dbsearch
DBSearchGUI dbsearch
-
masterPane
javax.swing.JTabbedPane masterPane
-
progress
javax.swing.JProgressBar progress
-
tab1
SelectPDBPanel tab1
-
tab2
PDBUploadPanel tab2
-
tab3
ScopSelectPanel tab3
-
tabPane
javax.swing.JTabbedPane tabPane
-
thread
java.lang.Thread thread
-
-
Class org.biojava.nbio.structure.align.gui.AlignmentTextPanel extends JPrintPanel implements Serializable
- serialVersionUID:
- 5092386365924879073L
-
Serialized Fields
-
tp
javax.swing.JEditorPane tp
-
-
Class org.biojava.nbio.structure.align.gui.ChooseDirAction extends javax.swing.AbstractAction implements Serializable
- serialVersionUID:
- 0L
-
Serialized Fields
-
config
UserConfiguration config
-
textField
javax.swing.JTextField textField
-
-
Class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel extends javax.swing.JPanel implements Serializable
- serialVersionUID:
- -1055193854675583808L
-
Serialized Fields
-
fileType
javax.swing.JComboBox fileType
-
fromFtp
javax.swing.JCheckBox fromFtp
-
pdbDir
javax.swing.JTextField pdbDir
-
-
Class org.biojava.nbio.structure.align.gui.DBSearchGUI extends javax.swing.JPanel implements Serializable
- serialVersionUID:
- -5657960663049062301L
-
Serialized Fields
-
abortB
javax.swing.JButton abortB
-
algorithm
StructureAlignment algorithm
-
alicalc
AlignmentCalcDB alicalc
-
drawer
org.biojava.nbio.structure.align.gui.ProgressThreadDrawer drawer
-
listPane
javax.swing.JPanel listPane
-
outFileLocation
javax.swing.JTextField outFileLocation
-
progress
javax.swing.JProgressBar progress
-
tab1
SelectPDBPanel tab1
-
tab2
PDBUploadPanel tab2
-
tab3
ScopSelectPanel tab3
-
tabPane
javax.swing.JTabbedPane tabPane
-
useDomainSplit
java.lang.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 javax.swing.JPanel implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
alignmentsProcessed
int alignmentsProcessed
-
farmJob
FarmJob farmJob
-
progressBar
javax.swing.JProgressBar progressBar
-
stopButton
javax.swing.JButton stopButton
-
taskOutput
javax.swing.JTextArea taskOutput
-
-
Class org.biojava.nbio.structure.align.gui.JPrintPanel extends javax.swing.JPanel implements Serializable
- serialVersionUID:
- -3337337068138131455L
-
Class org.biojava.nbio.structure.align.gui.MemoryMonitor extends javax.swing.JPanel implements Serializable
- serialVersionUID:
- 56289234782130L
-
Serialized Fields
-
controls
javax.swing.JPanel controls
-
doControls
boolean doControls
-
surf
MemoryMonitor.Surface surf
-
tf
javax.swing.JTextField tf
-
-
Class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface extends javax.swing.JPanel implements Serializable
- serialVersionUID:
- 2387409854370432908L
-
Serialized Fields
-
ascent
int ascent
-
big
java.awt.Graphics2D big
-
bimg
java.awt.image.BufferedImage bimg
-
columnInc
int columnInc
-
descent
int descent
-
font
java.awt.Font font
-
graphColor
java.awt.Color graphColor
-
graphLine
java.awt.geom.Line2D graphLine
-
graphOutlineRect
java.awt.Rectangle graphOutlineRect
-
h
int h
-
mfColor
java.awt.Color mfColor
-
mfRect
java.awt.geom.Rectangle2D mfRect
-
muRect
java.awt.geom.Rectangle2D muRect
-
ptNum
int ptNum
-
pts
int[] pts
-
r
java.lang.Runtime r
-
sleepAmount
long sleepAmount
-
thread
java.lang.Thread thread
-
usedStr
java.lang.String usedStr
-
w
int w
-
-
Class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI extends javax.swing.JFrame implements Serializable
- serialVersionUID:
- 0L
-
Serialized Fields
-
abortB
javax.swing.JButton abortB
-
alicalc
AlignmentCalculationRunnable alicalc
-
multiple
MultipleStructureAligner multiple
-
pairwise
StructureAlignment pairwise
-
progress
javax.swing.JProgressBar progress
-
tab
SelectMultiplePanel tab
-
tabPane
javax.swing.JTabbedPane tabPane
-
thread
java.lang.Thread thread
-
-
Class org.biojava.nbio.structure.align.gui.ParameterGUI extends javax.swing.JFrame implements Serializable
- serialVersionUID:
- 723386061184110161L
-
Serialized Fields
-
params
ConfigStrucAligParams params
-
textFields
java.util.List<java.awt.Component> textFields
-
-
Class org.biojava.nbio.structure.align.gui.SelectPDBPanel extends javax.swing.JPanel implements Serializable
- serialVersionUID:
- 4002475313717172193L
-
Serialized Fields
-
c1
javax.swing.JTextField c1
-
c2
javax.swing.JTextField c2
-
config
UserConfiguration config
-
configPane
javax.swing.JTabbedPane configPane
-
debug
boolean debug
-
f1
javax.swing.JTextField f1
-
f2
javax.swing.JTextField f2
-
r1
javax.swing.JTextField r1
-
r2
javax.swing.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
java.awt.Font eqFont
-
jmol
AbstractAlignmentJmol jmol
-
mouseMoLi
AligPanelMouseMotionListener mouseMoLi
-
selection
java.util.BitSet selection
-
selectionLocked
boolean selectionLocked
-
seqFont
java.awt.Font seqFont
-
-
Class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel extends JPrintPanel implements Serializable
- serialVersionUID:
- -6892229111166263764L
-
Serialized Fields
-
alnSeq
java.util.List<java.lang.String> alnSeq
-
colorByAlignmentBlock
boolean colorByAlignmentBlock
-
colorBySimilarity
boolean colorBySimilarity
-
coordManager
MultipleAlignmentCoordManager coordManager
-
eqFont
java.awt.Font eqFont
-
jmol
AbstractAlignmentJmol jmol
-
length
int length
-
mapSeqToStruct
java.util.List<java.lang.Integer> mapSeqToStruct
-
mouseMoLi
MultipleAligPanelMouseMotionListener mouseMoLi
-
multAln
MultipleAlignment multAln
-
selection
java.util.BitSet selection
-
selectionLocked
boolean selectionLocked
-
seqFont
java.awt.Font seqFont
-
size
int size
-
-
Class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay extends javax.swing.JTextField implements Serializable
- serialVersionUID:
- 6939947266417830429L
-
Serialized Fields
-
panel
MultipleAligPanel panel
-
-
Class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay extends javax.swing.JTextField implements Serializable
- serialVersionUID:
- 6939947266417830429L
-
-
Package org.biojava.nbio.structure.align.gui.autosuggest
-
Class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest extends javax.swing.JTextField implements Serializable
- serialVersionUID:
- 8591734727984365156L
-
Serialized Fields
-
autoSuggestProvider
AutoSuggestProvider autoSuggestProvider
-
busy
java.awt.Font busy
-
defaultText
java.lang.String defaultText
-
dialog
javax.swing.JDialog dialog
-
lastWord
java.lang.String lastWord
last word that was entered by user -
list
javax.swing.JList list
-
location
java.awt.Point location
-
matcher
org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest.SuggestionFetcher matcher
-
regular
java.awt.Font regular
-
suggestions
java.util.Vector<java.lang.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
java.awt.Dimension currentSize
-
rectClip
java.awt.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.IndexPair extends java.lang.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 java.lang.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 java.lang.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
java.util.List<AFP> afpSet
-
algorithmName
java.lang.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
java.lang.Double conn
-
description2
java.lang.String description2
-
disTable1
Matrix disTable1
-
disTable2
Matrix disTable2
-
distanceMatrix
Matrix distanceMatrix
-
dvar
java.lang.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
java.lang.String name1
-
name2
java.lang.String name2
-
normAlignScore
double normAlignScore
-
optAln
int[][][] optAln
-
optLen
int[] optLen
-
optLength
int optLength
-
optRmsd
double[] optRmsd
-
pdbAln
java.lang.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
java.lang.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
java.util.List<java.util.List<java.lang.Integer>> alignRes
-
alignResCounts
java.util.List<java.lang.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
java.util.List<java.lang.Integer> alignResCounts
-
blocks
java.util.List<Block> blocks
-
coreLength
int coreLength
-
length
int length
-
parent
MultipleAlignment parent
-
pose
java.util.List<javax.vecmath.Matrix4d> pose
-
-
Class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl extends AbstractScoresCache implements Serializable
- serialVersionUID:
- -5732485866623431898L
-
Serialized Fields
-
algorithmName
java.lang.String algorithmName
-
atomArrays
java.util.List<Atom[]> atomArrays
-
calculationTime
java.lang.Long calculationTime
-
distanceMatrix
java.util.List<Matrix> distanceMatrix
-
ioTime
java.lang.Long ioTime
-
multipleAlignments
java.util.List<MultipleAlignment> multipleAlignments
-
structureIdentifiers
java.util.List<StructureIdentifier> structureIdentifiers
-
version
java.lang.String version
-
-
Class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl extends AbstractScoresCache implements Serializable
- serialVersionUID:
- 3432043794125805139L
-
Serialized Fields
-
alignResCounts
java.util.List<java.lang.Integer> alignResCounts
-
blockSets
java.util.List<BlockSet> blockSets
-
coreLength
int coreLength
-
coverages
java.util.List<java.lang.Double> coverages
-
length
int length
-
parent
MultipleAlignmentEnsemble parent
-
-
-
Package org.biojava.nbio.structure.align.pairwise
-
Class org.biojava.nbio.structure.align.pairwise.AlignmentResult extends java.lang.Object implements Serializable
- serialVersionUID:
- -4132105905712445473L
-
Serialized Fields
-
alignments
AlternativeAlignment[] alignments
-
calculationTime
long calculationTime
-
chain1
java.lang.String chain1
-
chain2
java.lang.String chain2
-
ioTime
long ioTime
-
length1
int length1
-
length2
int length2
-
pdb1
java.lang.String pdb1
-
pdb2
java.lang.String pdb2
-
-
Class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment extends java.lang.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
java.lang.String[] pdbresnum1
-
pdbresnum2
java.lang.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 java.lang.Exception implements Serializable
- serialVersionUID:
- -8047100079715000276L
-
-
Package org.biojava.nbio.structure.asa
-
Class org.biojava.nbio.structure.asa.GroupAsa extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
asaC
double asaC
ASA of complexed residue -
asaU
double asaU
ASA of uncomplexed residue -
atomAsaCs
java.util.List<java.lang.Double> atomAsaCs
The individual atoms complexed ASAs -
atomAsaUs
java.util.List<java.lang.Double> atomAsaUs
The individual atoms uncomplexed ASAs -
g
Group g
-
-
-
Package org.biojava.nbio.structure.cath
-
Class org.biojava.nbio.structure.cath.CathDomain extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
architectureId
java.lang.Integer architectureId
The architecture number of this domain. -
classId
java.lang.Integer classId
The class number of this domain. -
comment
java.lang.String comment
A (potentially long) comment. Usually empty. -
date
java.util.Date date
-
domainCounter
java.lang.Integer domainCounter
The count of this domain among the identical sequence family members. -
domainName
java.lang.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
java.lang.String format
The format and version of the CathDomainDescriptionFile. -
homologyId
java.lang.Integer homologyId
The homologous superfamily number of this domain. -
identicalSequenceFamilyId
java.lang.Integer identicalSequenceFamilyId
The identical sequence family (100% identity) number of this domain. -
length
java.lang.Integer length
The domain length.. -
likeSequenceFamilyId
java.lang.Integer likeSequenceFamilyId
The "Like" sequence family (95% identity) number of this domain. -
name
java.lang.String name
The so-called name field holds a potentially long description of the domain. -
orthologousSequenceFamilyId
java.lang.Integer orthologousSequenceFamilyId
The "orthologous" sequence family (60% identity) number of this domain. -
resolution
java.lang.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
java.util.List<CathSegment> segments
List of all sub-domain segments. -
sequence
java.lang.String sequence
FASTA sequence. -
sequenceFamilyId
java.lang.Integer sequenceFamilyId
The sequence family (35% identity) number of this domain. -
sequenceHeader
java.lang.String sequenceHeader
FASTA header. -
source
java.lang.String source
Complete source organism listing. -
topologyId
java.lang.Integer topologyId
The topology number of this domain. -
version
java.lang.String version
The CATH version.
-
-
Class org.biojava.nbio.structure.cath.CathFragment extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
fragmentId
java.lang.Integer fragmentId
The number of this segment within the domain. -
length
java.lang.Integer length
Number of residues in the segment. This value is parsed, not calculated. -
start
java.lang.String start
The first residue in the segment. Refers to the complete residue specification (sequence number AND insertion code). -
stop
java.lang.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 java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
category
CathCategory category
This node's level within the hierarchy. One of CATH, not CATHSOLID. -
description
java.lang.String description
A name or description. -
nodeId
java.lang.String nodeId
The CATH code of the node, e.g. "1.10.8.10". -
parentId
java.lang.String parentId
The CATH code of the parent, e.g. "1.10.8". Calculated during parsing. -
representative
java.lang.String representative
The representative domain for this node.
-
-
Class org.biojava.nbio.structure.cath.CathSegment extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
length
java.lang.Integer length
Number of residues in the segment. This value is parsed, not calculated. -
segmentId
java.lang.Integer segmentId
The number of this segment within the domain. -
sequence
java.lang.String sequence
FASTA sequence. -
sequenceHeader
java.lang.String sequenceHeader
FASTA header. -
start
java.lang.String start
The first residue in the segment. Refers to the complete residue specification (sequence number AND insertion code). -
stop
java.lang.String stop
The last residue in the segment. Refers to the complete residue specification (sequence number AND insertion code).
-
-
-
Package org.biojava.nbio.structure.contact
-
Class org.biojava.nbio.structure.contact.AtomContact extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Class org.biojava.nbio.structure.contact.AtomContactSet extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
contacts
java.util.HashMap<Pair<AtomIdentifier>,AtomContact> contacts
-
cutoff
double cutoff
-
-
Class org.biojava.nbio.structure.contact.AtomIdentifier extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
chainId
java.lang.String chainId
-
pdbSerial
int pdbSerial
-
-
Class org.biojava.nbio.structure.contact.BoundingBox extends java.lang.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.GroupContact extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
atomContacts
java.util.List<AtomContact> atomContacts
-
pair
Pair<Group> pair
-
-
Class org.biojava.nbio.structure.contact.GroupContactSet extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
contacts
java.util.HashMap<Pair<org.biojava.nbio.structure.contact.ResidueIdentifier>,GroupContact> contacts
-
-
Class org.biojava.nbio.structure.contact.Pair extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Class org.biojava.nbio.structure.contact.StructureInterface extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
cluster
StructureInterfaceCluster cluster
-
contacts
AtomContactSet contacts
-
groupAsas1
java.util.Map<ResidueNumber,GroupAsa> groupAsas1
-
groupAsas2
java.util.Map<ResidueNumber,GroupAsa> groupAsas2
-
groupContacts
GroupContactSet groupContacts
-
id
int id
-
moleculeIds
Pair<java.lang.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 java.lang.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
java.util.List<StructureInterface> members
-
-
Class org.biojava.nbio.structure.contact.StructureInterfaceList extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
clusters
java.util.List<StructureInterfaceCluster> clusters
-
list
java.util.List<StructureInterface> list
-
-
-
Package org.biojava.nbio.structure.domain.pdp
-
Class org.biojava.nbio.structure.domain.pdp.Domain extends java.lang.Object implements Serializable
- serialVersionUID:
- -1293994033102271366L
-
Serialized Fields
-
id
java.lang.String id
-
nseg
int nseg
-
score
double score
-
segments
java.util.List<Segment> segments
-
size
int size
-
-
Class org.biojava.nbio.structure.domain.pdp.Segment extends java.lang.Object implements Serializable
- serialVersionUID:
- 1393487067559539657L
-
Serialized Fields
-
from
java.lang.Integer from
-
score
double score
-
to
java.lang.Integer to
-
-
-
Package org.biojava.nbio.structure.ecod
-
Class org.biojava.nbio.structure.ecod.EcodDomain extends java.lang.Object implements Serializable
- serialVersionUID:
- -7760082165560332048L
-
Serialized Fields
-
architectureName
java.lang.String architectureName
-
assemblyId
java.lang.Long assemblyId
-
chainId
java.lang.String chainId
-
domainId
java.lang.String domainId
-
fGroup
java.lang.Integer fGroup
-
fGroupName
java.lang.String fGroupName
-
hGroup
java.lang.Integer hGroup
-
hGroupName
java.lang.String hGroupName
-
ligands
java.util.Set<java.lang.String> ligands
-
manual
java.lang.Boolean manual
-
pdbId
java.lang.String pdbId
-
range
java.lang.String range
-
seqIdRange
java.lang.String seqIdRange
-
tGroup
java.lang.Integer tGroup
-
tGroupName
java.lang.String tGroupName
-
uid
java.lang.Long uid
-
xGroup
java.lang.Integer xGroup
-
xGroupName
java.lang.String xGroupName
-
-
-
Package org.biojava.nbio.structure.gui
-
Class org.biojava.nbio.structure.gui.JMatrixPanel extends javax.swing.JPanel implements Serializable
- serialVersionUID:
- -1720879395453257846L
-
Serialized Fields
-
_bufImage
java.awt.image.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 javax.swing.JPanel implements Serializable
- serialVersionUID:
- -8082261434322968652L
-
Serialized Fields
-
coloring
javax.swing.JComboBox coloring
-
gradients
java.util.Map<java.lang.String,ContinuousColorMapper> gradients
-
mPanel
JMatrixPanel mPanel
-
scroll
javax.swing.JScrollPane scroll
-
slider
javax.swing.JSlider slider
-
-
Class org.biojava.nbio.structure.gui.ScaleableMatrixPanel.GradientRenderer extends javax.swing.JPanel implements Serializable
- serialVersionUID:
- -2000575579184232365L
-
Serialized Fields
-
gradientContainer
javax.swing.JPanel gradientContainer
-
max
int max
-
min
int min
-
title
javax.swing.JLabel title
-
-
Class org.biojava.nbio.structure.gui.SequenceDisplay extends javax.swing.JPanel implements Serializable
- serialVersionUID:
- -1829252532712454236L
-
Serialized Fields
-
alig
AlternativeAlignment alig
-
apos
java.util.List<AlignedPosition> apos
-
idx1
int[] idx1
-
idx2
int[] idx2
-
label1
javax.swing.JLabel label1
-
label2
javax.swing.JLabel label2
-
mouseListener1
SequenceMouseListener mouseListener1
-
mouseListener2
SequenceMouseListener mouseListener2
-
panel1
SequenceScalePanel panel1
-
panel2
SequenceScalePanel panel2
-
percentageDisplay
javax.swing.JLabel percentageDisplay
-
residueSizeSlider
javax.swing.JSlider residueSizeSlider
-
scale
float scale
-
structure1
Structure structure1
-
structure2
Structure structure2
-
structurePairAligner
StructurePairAligner structurePairAligner
-
-
Class org.biojava.nbio.structure.gui.WrapLayout extends java.awt.FlowLayout implements Serializable
-
Serialized Fields
-
preferredLayoutSize
java.awt.Dimension preferredLayoutSize
-
-
-
-
Package org.biojava.nbio.structure.gui.util
-
Class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame extends javax.swing.JFrame implements Serializable
- serialVersionUID:
- 0L
-
Serialized Fields
-
aligs
AlternativeAlignment[] aligs
-
panel
javax.swing.JPanel panel
-
structure1
Structure structure1
-
structure2
Structure structure2
-
structurePairAligner
StructurePairAligner structurePairAligner
-
-
Class org.biojava.nbio.structure.gui.util.PDBDirPanel extends javax.swing.JPanel implements Serializable
- serialVersionUID:
- -5682120627824627408L
-
Serialized Fields
-
c1
javax.swing.JTextField c1
-
c2
javax.swing.JTextField c2
-
debug
boolean debug
-
f1
javax.swing.JTextField f1
-
f2
javax.swing.JTextField f2
-
pdbDir
javax.swing.JTextField pdbDir
-
-
Class org.biojava.nbio.structure.gui.util.PDBServerPanel extends javax.swing.JPanel implements Serializable
- serialVersionUID:
- -5682120627824627408L
-
Serialized Fields
-
c1
javax.swing.JTextField c1
-
c2
javax.swing.JTextField c2
-
debug
boolean debug
-
f1
javax.swing.JTextField f1
-
f2
javax.swing.JTextField f2
-
pdbDir
javax.swing.JTextField pdbDir
-
-
Class org.biojava.nbio.structure.gui.util.PDBUploadPanel extends javax.swing.JPanel implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
chain1
javax.swing.JTextField chain1
-
chain2
javax.swing.JTextField chain2
-
filePath1
javax.swing.JTextField filePath1
-
filePath2
javax.swing.JTextField filePath2
-
fileType
javax.swing.JComboBox fileType
-
-
Class org.biojava.nbio.structure.gui.util.ScopSelectPanel extends javax.swing.JPanel implements Serializable
- serialVersionUID:
- 757947454156959178L
-
Serialized Fields
-
dom1
JAutoSuggest dom1
-
dom2
JAutoSuggest dom2
-
-
Class org.biojava.nbio.structure.gui.util.SelectMultiplePanel extends javax.swing.JPanel implements Serializable
- serialVersionUID:
- 757947454156959178L
-
Serialized Fields
-
input
javax.swing.JTextField input
-
-
Class org.biojava.nbio.structure.gui.util.SequenceScalePanel extends javax.swing.JPanel implements Serializable
- serialVersionUID:
- 7893248902423L
-
Serialized Fields
-
apos
java.util.List<AlignedPosition> apos
-
chain
Chain chain
-
chainLength
int chainLength
-
coordManager
CoordManager coordManager
-
position
int position
-
scale
float scale
-
seqArr
java.lang.Character[] seqArr
-
-
-
Package org.biojava.nbio.structure.gui.util.color
-
Class org.biojava.nbio.structure.gui.util.color.GradientPanel extends javax.swing.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 java.awt.color.ColorSpace implements Serializable
- serialVersionUID:
- 8324413992279510075L
-
-
Package org.biojava.nbio.structure.io
-
Class org.biojava.nbio.structure.io.FileParsingParameters extends java.lang.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
java.lang.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 -
updateRemediatedFiles
boolean updateRemediatedFiles
Update locally cached files to the latest version of remediated files -
useInternalChainId
boolean useInternalChainId
Should we use internal (asym_id) or public facing (author) chain ids
-
-
Class org.biojava.nbio.structure.io.PDBParseException extends java.lang.Exception implements Serializable
- serialVersionUID:
- 219047230178423923L
-
Class org.biojava.nbio.structure.io.SSBondImpl extends java.lang.Object implements Serializable
- serialVersionUID:
- -8663681100691188647L
-
Serialized Fields
-
chainID1
java.lang.String chainID1
-
chainID2
java.lang.String chainID2
-
insCode1
java.lang.String insCode1
-
insCode2
java.lang.String insCode2
-
resnum1
java.lang.String resnum1
-
resnum2
java.lang.String resnum2
-
serNum
int serNum
-
-
-
Package org.biojava.nbio.structure.io.mmcif.model
-
Class org.biojava.nbio.structure.io.mmcif.model.ChemComp extends java.lang.Object implements Serializable
- serialVersionUID:
- -4736341142030215915L
-
Serialized Fields
-
atoms
java.util.List<ChemCompAtom> atoms
-
bonds
java.util.List<ChemCompBond> bonds
-
descriptors
java.util.List<ChemCompDescriptor> descriptors
-
formula
java.lang.String formula
-
formula_weight
java.lang.String formula_weight
-
id
java.lang.String id
-
mon_nstd_flag
java.lang.String mon_nstd_flag
-
mon_nstd_parent_comp_id
java.lang.String mon_nstd_parent_comp_id
-
name
java.lang.String name
-
one_letter_code
java.lang.String one_letter_code
-
pdbx_ambiguous_flag
java.lang.String pdbx_ambiguous_flag
-
pdbx_formal_charge
java.lang.String pdbx_formal_charge
-
pdbx_ideal_coordinates_details
java.lang.String pdbx_ideal_coordinates_details
-
pdbx_ideal_coordinates_missing_flag
java.lang.String pdbx_ideal_coordinates_missing_flag
-
pdbx_initial_date
java.lang.String pdbx_initial_date
-
pdbx_model_coordinates_db_code
java.lang.String pdbx_model_coordinates_db_code
-
pdbx_model_coordinates_details
java.lang.String pdbx_model_coordinates_details
-
pdbx_model_coordinates_missing_flag
java.lang.String pdbx_model_coordinates_missing_flag
-
pdbx_modified_date
java.lang.String pdbx_modified_date
-
pdbx_processing_site
java.lang.String pdbx_processing_site
-
pdbx_release_status
java.lang.String pdbx_release_status
-
pdbx_replaced_by
java.lang.String pdbx_replaced_by
-
pdbx_replaces
java.lang.String pdbx_replaces
-
pdbx_subcomponent_list
java.lang.String pdbx_subcomponent_list
-
pdbx_synonyms
java.lang.String pdbx_synonyms
-
pdbx_type
java.lang.String pdbx_type
-
polymerType
PolymerType polymerType
-
residueType
ResidueType residueType
-
standard
boolean standard
-
three_letter_code
java.lang.String three_letter_code
-
type
java.lang.String type
-
-
Class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom extends java.lang.Object implements Serializable
- serialVersionUID:
- 4070599340294758941L
-
Serialized Fields
-
alt_atom_id
java.lang.String alt_atom_id
-
atom_id
java.lang.String atom_id
-
charge
java.lang.String charge
-
comp_id
java.lang.String comp_id
-
model_Cartn_x
java.lang.String model_Cartn_x
-
model_Cartn_y
java.lang.String model_Cartn_y
-
model_Cartn_z
java.lang.String model_Cartn_z
-
pdbx_align
java.lang.String pdbx_align
-
pdbx_aromatic_flag
java.lang.String pdbx_aromatic_flag
-
pdbx_component_atom_id
java.lang.String pdbx_component_atom_id
-
pdbx_component_comp_id
java.lang.String pdbx_component_comp_id
-
pdbx_component_id
java.lang.String pdbx_component_id
-
pdbx_leaving_atom_flag
java.lang.String pdbx_leaving_atom_flag
-
pdbx_model_Cartn_x_ideal
java.lang.String pdbx_model_Cartn_x_ideal
-
pdbx_model_Cartn_y_ideal
java.lang.String pdbx_model_Cartn_y_ideal
-
pdbx_model_Cartn_z_ideal
java.lang.String pdbx_model_Cartn_z_ideal
-
pdbx_ordinal
java.lang.String pdbx_ordinal
-
pdbx_polymer_type
java.lang.String pdbx_polymer_type
-
pdbx_ref_id
java.lang.String pdbx_ref_id
-
pdbx_residue_numbering
java.lang.String pdbx_residue_numbering
-
pdbx_stereo_config
java.lang.String pdbx_stereo_config
-
type_symbol
java.lang.String type_symbol
-
-
Class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond extends java.lang.Object implements Serializable
- serialVersionUID:
- 5905371029161975421L
-
Serialized Fields
-
atom_id_1
java.lang.String atom_id_1
-
atom_id_2
java.lang.String atom_id_2
-
comp_id
java.lang.String comp_id
-
pdbx_aromatic_flag
java.lang.String pdbx_aromatic_flag
-
pdbx_ordinal
java.lang.String pdbx_ordinal
-
pdbx_stereo_config
java.lang.String pdbx_stereo_config
-
value_order
java.lang.String value_order
-
-
Class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor extends java.lang.Object implements Serializable
- serialVersionUID:
- 1078685833800736278L
-
Serialized Fields
-
comp_id
java.lang.String comp_id
-
descriptor
java.lang.String descriptor
-
program
java.lang.String program
-
program_version
java.lang.String program_version
-
type
java.lang.String type
-
-
Class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
details
java.lang.String details
-
rev_num
java.lang.String rev_num
-
type
java.lang.String type
-
-
Class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly extends java.lang.Object implements Serializable
- serialVersionUID:
- 3104504686693887219L
-
Serialized Fields
-
details
java.lang.String details
-
id
java.lang.String id
-
method_details
java.lang.String method_details
-
oligomeric_count
java.lang.String oligomeric_count
-
oligomeric_details
java.lang.String oligomeric_details
-
-
Class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen extends java.lang.Object implements Serializable
- serialVersionUID:
- 6739568389242514332L
-
Serialized Fields
-
assembly_id
java.lang.String assembly_id
-
asym_id_list
java.lang.String asym_id_list
-
oper_expression
java.lang.String oper_expression
-
-
Class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList extends java.lang.Object implements Serializable
- serialVersionUID:
- 8933552854747969787L
-
Serialized Fields
-
id
java.lang.String id
-
matrix
Matrix matrix
-
matrix11
java.lang.String matrix11
-
matrix12
java.lang.String matrix12
-
matrix13
java.lang.String matrix13
-
matrix21
java.lang.String matrix21
-
matrix22
java.lang.String matrix22
-
matrix23
java.lang.String matrix23
-
matrix31
java.lang.String matrix31
-
matrix32
java.lang.String matrix32
-
matrix33
java.lang.String matrix33
-
name
java.lang.String name
-
symmetry_operation
java.lang.String symmetry_operation
-
type
java.lang.String type
-
vector
double[] vector
-
vector1
java.lang.String vector1
-
vector2
java.lang.String vector2
-
vector3
java.lang.String vector3
-
-
-
Package org.biojava.nbio.structure.io.sifts
-
Class org.biojava.nbio.structure.io.sifts.SiftsEntity extends java.lang.Object implements Serializable
- serialVersionUID:
- 750353252427491487L
-
Serialized Fields
-
entityId
java.lang.String entityId
-
segments
java.util.List<SiftsSegment> segments
-
type
java.lang.String type
-
-
Class org.biojava.nbio.structure.io.sifts.SiftsResidue extends java.lang.Object implements Serializable
- serialVersionUID:
- 3425769737629800828L
-
Serialized Fields
-
chainId
java.lang.String chainId
-
naturalPos
java.lang.Integer naturalPos
-
notObserved
java.lang.Boolean notObserved
-
pdbId
java.lang.String pdbId
-
pdbResName
java.lang.String pdbResName
-
pdbResNum
java.lang.String pdbResNum
-
seqResName
java.lang.String seqResName
-
uniProtAccessionId
java.lang.String uniProtAccessionId
-
uniProtPos
java.lang.Integer uniProtPos
-
uniProtResName
java.lang.String uniProtResName
-
-
Class org.biojava.nbio.structure.io.sifts.SiftsSegment extends java.lang.Object implements Serializable
- serialVersionUID:
- -8005129863256307153L
-
Serialized Fields
-
end
java.lang.String end
-
residues
java.util.List<SiftsResidue> residues
-
segId
java.lang.String segId
-
start
java.lang.String start
-
-
-
Package org.biojava.nbio.structure.jama
-
Class org.biojava.nbio.structure.jama.CholeskyDecomposition extends java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.lang.Object implements Serializable
- serialVersionUID:
- -5217767192992868955L
-
Serialized Fields
-
N
int N
-
rows
SparseVector[] rows
-
-
Class org.biojava.nbio.structure.math.SparseVector extends java.lang.Object implements Serializable
- serialVersionUID:
- 1174668523213431927L
-
Serialized Fields
-
N
int N
-
symbolTable
SymbolTable<java.lang.Integer,java.lang.Double> symbolTable
-
-
Class org.biojava.nbio.structure.math.SymbolTable extends java.lang.Object implements Serializable
- serialVersionUID:
- -4417561575046471931L
-
-
Package org.biojava.nbio.structure.quaternary
-
Class org.biojava.nbio.structure.quaternary.BioAssemblyInfo extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
id
int id
-
macromolecularSize
int macromolecularSize
-
transforms
java.util.List<BiologicalAssemblyTransformation> transforms
-
-
Class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation extends java.lang.Object implements Serializable
- serialVersionUID:
- -6388503076022480391L
-
Serialized Fields
-
chainId
java.lang.String chainId
-
id
java.lang.String id
-
transformation
javax.vecmath.Matrix4d transformation
-
-
-
Package org.biojava.nbio.structure.scop
-
Class org.biojava.nbio.structure.scop.ScopDescription extends java.lang.Object implements Serializable
- serialVersionUID:
- 8579808155176839161L
-
Serialized Fields
-
category
ScopCategory category
-
classificationId
java.lang.String classificationId
-
description
java.lang.String description
-
name
java.lang.String name
-
sunID
int sunID
-
-
Class org.biojava.nbio.structure.scop.ScopDomain extends java.lang.Object implements Serializable
- serialVersionUID:
- 5890476209571654301L
-
Serialized Fields
-
classId
int classId
-
classificationId
java.lang.String classificationId
-
domainId
int domainId
-
familyId
int familyId
-
foldId
int foldId
-
pdbId
java.lang.String pdbId
-
px
int px
-
ranges
java.util.List<java.lang.String> ranges
-
scopId
java.lang.String scopId
-
speciesId
int speciesId
-
sunid
java.lang.Integer sunid
-
superfamilyId
int superfamilyId
-
-
Class org.biojava.nbio.structure.scop.ScopIOException extends java.lang.RuntimeException implements Serializable
- serialVersionUID:
- 1L
-
Class org.biojava.nbio.structure.scop.ScopNode extends java.lang.Object implements Serializable
- serialVersionUID:
- 1187083944488580995L
-
Serialized Fields
-
children
java.util.List<java.lang.Integer> children
-
parentSunid
int parentSunid
-
sunid
int sunid
-
-
-
Package org.biojava.nbio.structure.scop.server
-
Class org.biojava.nbio.structure.scop.server.ListStringWrapper extends java.lang.Object implements Serializable
- serialVersionUID:
- 4193799052494327416L
-
Serialized Fields
-
data
java.util.List<java.lang.String> data
-
-
Class org.biojava.nbio.structure.scop.server.ScopDescriptions extends java.lang.Object implements Serializable
- serialVersionUID:
- 4924350548761431852L
-
Serialized Fields
-
scopDescriptions
java.util.List<ScopDescription> scopDescriptions
-
-
Class org.biojava.nbio.structure.scop.server.ScopDomains extends java.lang.Object implements Serializable
- serialVersionUID:
- 7693404355005856746L
-
Serialized Fields
-
domains
java.util.List<ScopDomain> domains
-
-
Class org.biojava.nbio.structure.scop.server.ScopNodes extends java.lang.Object implements Serializable
- serialVersionUID:
- 5327454882500340305L
-
Serialized Fields
-
scopNodes
java.util.List<ScopNode> scopNodes
-
-
Class org.biojava.nbio.structure.scop.server.TreeSetStringWrapper extends java.lang.Object implements Serializable
- serialVersionUID:
- 4193799052494327416L
-
Serialized Fields
-
data
java.util.TreeSet<java.lang.String> data
-
-
-
Package org.biojava.nbio.structure.symmetry.core
-
Class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
absoluteMinimumSequenceLength
int absoluteMinimumSequenceLength
-
alignmentFractionThreshold
double alignmentFractionThreshold
-
angleThreshold
double angleThreshold
-
helixRmsdThreshold
double helixRmsdThreshold
-
helixRmsdToRiseRatio
double helixRmsdToRiseRatio
-
localSymmetry
boolean localSymmetry
-
localTimeLimit
double localTimeLimit
-
maximumLocalCombinations
int maximumLocalCombinations
-
maximumLocalResults
int maximumLocalResults
-
maximumLocalSubunits
int maximumLocalSubunits
-
minimumHelixAngle
double minimumHelixAngle
-
minimumHelixRise
double minimumHelixRise
-
minimumSequenceLength
int minimumSequenceLength
-
minimumSequenceLengthFraction
double minimumSequenceLengthFraction
-
onTheFly
boolean onTheFly
-
rmsdThreshold
double rmsdThreshold
-
sequenceIdentityThresholds
double[] sequenceIdentityThresholds
-
sequencePseudoSymmetryThreshold
double sequencePseudoSymmetryThreshold
-
verbose
boolean verbose
-
-
-
Package org.biojava.nbio.structure.symmetry.gui
-
Class org.biojava.nbio.structure.symmetry.gui.SymmetryGui extends javax.swing.JFrame implements Serializable
- serialVersionUID:
- 0L
-
Serialized Fields
-
abortB
javax.swing.JButton abortB
-
alicalc
AlignmentCalculationRunnable alicalc
-
masterPane
javax.swing.JTabbedPane masterPane
-
params
CESymmParameters params
-
progress
javax.swing.JProgressBar progress
-
tab1
SelectPDBPanel tab1
-
tab2
PDBUploadPanel tab2
-
tab3
ScopSelectPanel tab3
-
tabPane
javax.swing.JTabbedPane tabPane
-
thread
java.lang.Thread thread
-
-
-
Package org.biojava.nbio.structure.symmetry.internal
-
Class org.biojava.nbio.structure.symmetry.internal.RefinerFailedException extends java.lang.Exception implements Serializable
- serialVersionUID:
- -3592155787060329421L
-
-
Package org.biojava.nbio.structure.symmetry.utils
-
Class org.biojava.nbio.structure.symmetry.utils.BlastClustReader extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
clusters
java.util.List<java.util.List<java.lang.String>> clusters
-
sequenceIdentity
int sequenceIdentity
-
-
-
Package org.biojava.nbio.structure.validation
-
Class org.biojava.nbio.structure.validation.WwPDBValidationInformation extends java.lang.Object implements Serializable
- serialVersionUID:
- -996804963717482650L
-
Serialized Fields
-
entry
Entry entry
-
modelledSubgroup
java.util.List<ModelledSubgroup> modelledSubgroup
-
programs
Programs programs
-
-
-
Package org.biojava.nbio.structure.xtal
-
Class org.biojava.nbio.structure.xtal.CrystalCell extends java.lang.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 java.lang.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 java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
altShortSymbol
java.lang.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
java.lang.String shortSymbol
-
transfAlgebraic
java.util.List<java.lang.String> transfAlgebraic
-
transformations
java.util.List<javax.vecmath.Matrix4d> transformations
-
-
-
Package org.biojava.nbio.structure.xtal.io
-
Class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper extends java.lang.Object implements Serializable
- serialVersionUID:
- 4193799052494327416L
-
Serialized Fields
-
data
java.util.TreeMap<java.lang.Integer,SpaceGroup> data
-
-
-
Package org.biojava.nbio.survival.data
-
Class org.biojava.nbio.survival.data.CompactCharSequence extends java.lang.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 javax.swing.JPanel implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
bottom
int bottom
-
df
java.text.DecimalFormat df
-
fileName
java.lang.String fileName
-
fm
java.awt.FontMetrics fm
-
kmfi
KMFigureInfo kmfi
-
labelWidth
int labelWidth
-
left
int left
-
lineInfoList
java.util.ArrayList<java.lang.String> lineInfoList
-
maxTime
java.lang.Double maxTime
-
maxX
java.lang.Double maxX
-
maxY
java.lang.Double maxY
-
mean
java.lang.Double mean
-
minX
java.lang.Double minX
-
minY
java.lang.Double minY
-
right
int right
-
siList
java.util.ArrayList<SurvivalInfo> siList
-
title
java.util.ArrayList<java.lang.String> title
-
titleHeight
int titleHeight
-
top
int top
-
variable
java.lang.String variable
-
xAxisLabelHeight
int xAxisLabelHeight
-
-
Class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure extends javax.swing.JPanel implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
adjustedPercentIncrement
java.lang.Double adjustedPercentIncrement
-
bottom
int bottom
-
df
java.text.DecimalFormat df
-
fileName
java.lang.String fileName
-
fm
java.awt.FontMetrics fm
-
kmfi
KMFigureInfo kmfi
-
labelWidth
int labelWidth
-
left
int left
-
lineInfoList
java.util.ArrayList<java.lang.String> lineInfoList
-
maxPercentage
double maxPercentage
-
maxTime
double maxTime
-
minPercentage
double minPercentage
-
minTime
double minTime
-
right
int right
-
sfi
SurvFitInfo sfi
-
survivalData
java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<CensorStatus>> survivalData
-
title
java.util.ArrayList<java.lang.String> title
-
titleHeight
int titleHeight
-
top
int top
-
xAxisLabelHeight
int xAxisLabelHeight
-
xAxisTimeCoordinates
java.util.ArrayList<java.lang.Integer> xAxisTimeCoordinates
-
xAxisTimeValues
java.util.ArrayList<java.lang.Double> xAxisTimeValues
-
yaxisLabel
int yaxisLabel
-
-
Class org.biojava.nbio.survival.kaplanmeier.figure.NumbersAtRiskPanel extends javax.swing.JPanel implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
kmf
KaplanMeierFigure kmf
-
timePercentage
java.lang.Double timePercentage
-
-
-
Package org.biojava.nbio.ws.alignment
-
Package org.biojava.nbio.ws.alignment.qblast
-
Class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties extends java.lang.Object implements Serializable
- serialVersionUID:
- 7158270364392309841L
-
Serialized Fields
-
param
java.util.Map<BlastAlignmentParameterEnum,java.lang.String> param
-
-
Class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties extends java.lang.Object implements Serializable
- serialVersionUID:
- -9202060390925345163L
-
Serialized Fields
-
param
java.util.Map<BlastOutputParameterEnum,java.lang.String> param
-
-
-
Package org.biojava.nbio.ws.hmmer
-
Class org.biojava.nbio.ws.hmmer.HmmerDomain extends java.lang.Object implements Serializable
- serialVersionUID:
- 8004302800150892757L
-
Serialized Fields
-
aliLenth
java.lang.Integer aliLenth
-
evalue
java.lang.Float evalue
-
hmmAcc
java.lang.String hmmAcc
-
hmmDesc
java.lang.String hmmDesc
-
hmmFrom
java.lang.Integer hmmFrom
-
hmmName
java.lang.String hmmName
-
hmmTo
java.lang.Integer hmmTo
-
simCount
java.lang.Integer simCount
-
sqFrom
java.lang.Integer sqFrom
-
sqTo
java.lang.Integer sqTo
-
-
Class org.biojava.nbio.ws.hmmer.HmmerResult extends java.lang.Object implements Serializable
- serialVersionUID:
- -6016026193090737943L
-
Serialized Fields
-
acc
java.lang.String acc
-
dcl
java.lang.Integer dcl
-
desc
java.lang.String desc
-
domains
java.util.SortedSet<HmmerDomain> domains
-
evalue
java.lang.Float evalue
-
name
java.lang.String name
-
ndom
java.lang.Integer ndom
-
nreported
java.lang.Integer nreported
-
pvalue
java.lang.Double pvalue
-
score
java.lang.Float score
-
-
-
Package org.forester.analysis
-
Class org.forester.analysis.AncestralTaxonomyInferenceException extends java.lang.Exception implements Serializable
- serialVersionUID:
- 1L
-
-
Package org.forester.archaeopteryx
-
Class org.forester.archaeopteryx.ArchaeopteryxA extends javax.swing.JApplet implements Serializable
- serialVersionUID:
- 2314899014580484146L
-
Serialized Fields
-
_mainframe_applet
MainFrameApplet _mainframe_applet
-
_message_1
java.lang.String _message_1
-
_message_2
java.lang.String _message_2
-
_species_tree_url_str
java.lang.String _species_tree_url_str
-
_tree_url_str
java.lang.String _tree_url_str
-
-
Class org.forester.archaeopteryx.ArchaeopteryxE extends javax.swing.JApplet implements Serializable
- serialVersionUID:
- -1220055577935759443L
-
Serialized Fields
-
_abbreviate_scientific_names
javax.swing.JCheckBoxMenuItem _abbreviate_scientific_names
-
_about_item
javax.swing.JMenuItem _about_item
-
_analysis_menu
javax.swing.JMenu _analysis_menu
-
_antialias_print_cbmi
javax.swing.JCheckBoxMenuItem _antialias_print_cbmi
-
_aptx_ref_item
javax.swing.JMenuItem _aptx_ref_item
-
_background_gradient_cbmi
javax.swing.JCheckBoxMenuItem _background_gradient_cbmi
-
_choose_font_mi
javax.swing.JMenuItem _choose_font_mi
-
_choose_minimal_confidence_mi
javax.swing.JMenuItem _choose_minimal_confidence_mi
-
_choose_node_size_mi
javax.swing.JMenuItem _choose_node_size_mi
-
_choose_pdf_width_mi
javax.swing.JMenuItem _choose_pdf_width_mi
-
_circular_type_cbmi
javax.swing.JCheckBoxMenuItem _circular_type_cbmi
-
_collapse_species_specific_subtrees
javax.swing.JMenuItem _collapse_species_specific_subtrees
-
_color_by_taxonomic_group_cbmi
javax.swing.JCheckBoxMenuItem _color_by_taxonomic_group_cbmi
-
_color_labels_same_as_parent_branch
javax.swing.JCheckBoxMenuItem _color_labels_same_as_parent_branch
-
_confcolor_item
javax.swing.JMenuItem _confcolor_item
-
_configuration
Configuration _configuration
-
_convex_type_cbmi
javax.swing.JCheckBoxMenuItem _convex_type_cbmi
-
_current_dir
java.io.File _current_dir
-
_curved_type_cbmi
javax.swing.JCheckBoxMenuItem _curved_type_cbmi
-
_cycle_node_fill_mi
javax.swing.JMenuItem _cycle_node_fill_mi
-
_cycle_node_shape_mi
javax.swing.JMenuItem _cycle_node_shape_mi
-
_display_basic_information_item
javax.swing.JMenuItem _display_basic_information_item
-
_euro_type_cbmi
javax.swing.JCheckBoxMenuItem _euro_type_cbmi
-
_ext_node_dependent_cladogram_rbmi
javax.swing.JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi
-
_file_jmenu
javax.swing.JMenu _file_jmenu
-
_font_size_menu
javax.swing.JMenu _font_size_menu
-
_graphics_export_using_actual_size_cbmi
javax.swing.JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi
-
_graphics_export_visible_only_cbmi
javax.swing.JCheckBoxMenuItem _graphics_export_visible_only_cbmi
-
_gsdi_item
javax.swing.JMenuItem _gsdi_item
-
_gsdir_item
javax.swing.JMenuItem _gsdir_item
-
_help_item
javax.swing.JMenuItem _help_item
-
_help_jmenu
javax.swing.JMenu _help_jmenu
-
_inverse_search_result_cbmi
javax.swing.JCheckBoxMenuItem _inverse_search_result_cbmi
-
_jmenubar
javax.swing.JMenuBar _jmenubar
-
_label_direction_cbmi
javax.swing.JCheckBoxMenuItem _label_direction_cbmi
-
_large_fonts_mi
javax.swing.JMenuItem _large_fonts_mi
-
_line_up_renderable_data_cbmi
javax.swing.JCheckBoxMenuItem _line_up_renderable_data_cbmi
-
_mainpanel
MainPanel _mainpanel
-
_medium_fonts_mi
javax.swing.JMenuItem _medium_fonts_mi
-
_midpoint_root_item
javax.swing.JMenuItem _midpoint_root_item
-
_non_lined_up_cladograms_rbmi
javax.swing.JRadioButtonMenuItem _non_lined_up_cladograms_rbmi
-
_options
Options _options
-
_options_jmenu
javax.swing.JMenu _options_jmenu
-
_overview_placment_mi
javax.swing.JMenuItem _overview_placment_mi
-
_phyloxml_ref_item
javax.swing.JMenuItem _phyloxml_ref_item
-
_phyloxml_website_item
javax.swing.JMenuItem _phyloxml_website_item
-
_print_black_and_white_cbmi
javax.swing.JCheckBoxMenuItem _print_black_and_white_cbmi
-
_print_item
javax.swing.JMenuItem _print_item
-
_print_size_mi
javax.swing.JMenuItem _print_size_mi
-
_print_using_actual_size_cbmi
javax.swing.JCheckBoxMenuItem _print_using_actual_size_cbmi
-
_radio_group_1
javax.swing.ButtonGroup _radio_group_1
-
_rectangular_type_cbmi
javax.swing.JCheckBoxMenuItem _rectangular_type_cbmi
-
_remove_branch_color_item
javax.swing.JMenuItem _remove_branch_color_item
-
_remove_visual_styles_item
javax.swing.JMenuItem _remove_visual_styles_item
-
_right_line_up_domains_cbmi
javax.swing.JCheckBoxMenuItem _right_line_up_domains_cbmi
-
_rounded_type_cbmi
javax.swing.JCheckBoxMenuItem _rounded_type_cbmi
-
_save_filechooser
javax.swing.JFileChooser _save_filechooser
-
_save_item
javax.swing.JMenuItem _save_item
-
_screen_antialias_cbmi
javax.swing.JCheckBoxMenuItem _screen_antialias_cbmi
-
_search_case_senstive_cbmi
javax.swing.JCheckBoxMenuItem _search_case_senstive_cbmi
-
_search_whole_words_only_cbmi
javax.swing.JCheckBoxMenuItem _search_whole_words_only_cbmi
-
_search_with_regex_cbmi
javax.swing.JCheckBoxMenuItem _search_with_regex_cbmi
-
_show_annotation_ref_source
javax.swing.JCheckBoxMenuItem _show_annotation_ref_source
-
_show_confidence_stddev_cbmi
javax.swing.JCheckBoxMenuItem _show_confidence_stddev_cbmi
-
_show_default_node_shapes_external_cbmi
javax.swing.JCheckBoxMenuItem _show_default_node_shapes_external_cbmi
-
_show_default_node_shapes_for_marked_cbmi
javax.swing.JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi
-
_show_default_node_shapes_internal_cbmi
javax.swing.JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi
-
_show_domain_labels
javax.swing.JCheckBoxMenuItem _show_domain_labels
-
_show_overview_cbmi
javax.swing.JCheckBoxMenuItem _show_overview_cbmi
-
_show_scale_cbmi
javax.swing.JCheckBoxMenuItem _show_scale_cbmi
-
_small_fonts_mi
javax.swing.JMenuItem _small_fonts_mi
-
_species_tree
Phylogeny _species_tree
-
_super_tiny_fonts_mi
javax.swing.JMenuItem _super_tiny_fonts_mi
-
_switch_colors_mi
javax.swing.JMenuItem _switch_colors_mi
-
_taxcolor_item
javax.swing.JMenuItem _taxcolor_item
-
_textframes
java.util.LinkedList<org.forester.archaeopteryx.TextFrame> _textframes
-
_tiny_fonts_mi
javax.swing.JMenuItem _tiny_fonts_mi
-
_tools_menu
javax.swing.JMenu _tools_menu
-
_triangular_type_cbmi
javax.swing.JCheckBoxMenuItem _triangular_type_cbmi
-
_type_menu
javax.swing.JMenu _type_menu
-
_uniform_cladograms_rbmi
javax.swing.JRadioButtonMenuItem _uniform_cladograms_rbmi
-
_unrooted_type_cbmi
javax.swing.JCheckBoxMenuItem _unrooted_type_cbmi
-
_view_as_nexus_item
javax.swing.JMenuItem _view_as_nexus_item
-
_view_as_NH_item
javax.swing.JMenuItem _view_as_NH_item
-
_view_as_XML_item
javax.swing.JMenuItem _view_as_XML_item
-
_view_jmenu
javax.swing.JMenu _view_jmenu
-
_website_item
javax.swing.JMenuItem _website_item
-
_write_to_bmp_item
javax.swing.JMenuItem _write_to_bmp_item
-
_write_to_gif_item
javax.swing.JMenuItem _write_to_gif_item
-
_write_to_jpg_item
javax.swing.JMenuItem _write_to_jpg_item
-
_write_to_pdf_item
javax.swing.JMenuItem _write_to_pdf_item
-
_write_to_png_item
javax.swing.JMenuItem _write_to_png_item
-
_write_to_tif_item
javax.swing.JMenuItem _write_to_tif_item
-
_writetographics_filechooser
javax.swing.JFileChooser _writetographics_filechooser
-
_writetopdf_filechooser
javax.swing.JFileChooser _writetopdf_filechooser
-
-
Class org.forester.archaeopteryx.FontChooser extends javax.swing.JDialog implements Serializable
- serialVersionUID:
- 62256323L
-
Serialized Fields
-
_cancel_button
javax.swing.JButton _cancel_button
-
_font
java.awt.Font _font
-
_font_jsp
javax.swing.JScrollPane _font_jsp
-
_font_list
javax.swing.JList<java.lang.String> _font_list
-
_fonts_label
javax.swing.JLabel _fonts_label
-
_fonts_tf
javax.swing.JTextField _fonts_tf
-
_ok_button
javax.swing.JButton _ok_button
-
_option
int _option
-
_size
int _size
-
_size_jsp
javax.swing.JScrollPane _size_jsp
-
_size_label
javax.swing.JLabel _size_label
-
_size_list
javax.swing.JList<java.lang.String> _size_list
-
_size_tf
javax.swing.JTextField _size_tf
-
_style
int _style
-
_style_jsp
javax.swing.JScrollPane _style_jsp
-
_style_label
javax.swing.JLabel _style_label
-
_style_list
javax.swing.JList<java.lang.String> _style_list
-
_style_tf
javax.swing.JTextField _style_tf
-
_test_tf
javax.swing.JTextField _test_tf
-
_type
java.lang.String _type
-
-
Class org.forester.archaeopteryx.MainFrame extends javax.swing.JFrame implements Serializable
- serialVersionUID:
- 3655000897845508358L
-
Serialized Fields
-
_abbreviate_scientific_names
javax.swing.JCheckBoxMenuItem _abbreviate_scientific_names
-
_about_item
javax.swing.JMenuItem _about_item
-
_allow_errors_in_distance_to_parent_cbmi
javax.swing.JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi
-
_analysis_menu
javax.swing.JMenu _analysis_menu
-
_annotate_item
javax.swing.JMenuItem _annotate_item
-
_antialias_print_cbmi
javax.swing.JCheckBoxMenuItem _antialias_print_cbmi
-
_aptx_ref_item
javax.swing.JMenuItem _aptx_ref_item
-
_background_gradient_cbmi
javax.swing.JCheckBoxMenuItem _background_gradient_cbmi
-
_choose_font_mi
javax.swing.JMenuItem _choose_font_mi
-
_choose_minimal_confidence_mi
javax.swing.JMenuItem _choose_minimal_confidence_mi
-
_choose_node_size_mi
javax.swing.JMenuItem _choose_node_size_mi
-
_choose_pdf_width_mi
javax.swing.JMenuItem _choose_pdf_width_mi
-
_circular_type_cbmi
javax.swing.JCheckBoxMenuItem _circular_type_cbmi
-
_close_item
javax.swing.JMenuItem _close_item
-
_collapse_species_specific_subtrees
javax.swing.JMenuItem _collapse_species_specific_subtrees
-
_color_by_taxonomic_group_cbmi
javax.swing.JCheckBoxMenuItem _color_by_taxonomic_group_cbmi
-
_color_labels_same_as_parent_branch
javax.swing.JCheckBoxMenuItem _color_labels_same_as_parent_branch
-
_color_rank_jmi
javax.swing.JMenuItem _color_rank_jmi
-
_confcolor_item
javax.swing.JMenuItem _confcolor_item
-
_configuration
Configuration _configuration
-
_contentpane
java.awt.Container _contentpane
-
_convex_type_cbmi
javax.swing.JCheckBoxMenuItem _convex_type_cbmi
-
_current_dir
java.io.File _current_dir
-
_curved_type_cbmi
javax.swing.JCheckBoxMenuItem _curved_type_cbmi
-
_cycle_data_return
javax.swing.JMenuItem _cycle_data_return
-
_cycle_node_fill_mi
javax.swing.JMenuItem _cycle_node_fill_mi
-
_cycle_node_shape_mi
javax.swing.JMenuItem _cycle_node_shape_mi
-
_delete_not_selected_nodes_item
javax.swing.JMenuItem _delete_not_selected_nodes_item
-
_delete_selected_nodes_item
javax.swing.JMenuItem _delete_selected_nodes_item
-
_display_basic_information_item
javax.swing.JMenuItem _display_basic_information_item
-
_euro_type_cbmi
javax.swing.JCheckBoxMenuItem _euro_type_cbmi
-
_exit_item
javax.swing.JMenuItem _exit_item
-
_ext_node_dependent_cladogram_rbmi
javax.swing.JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi
-
_extract_tax_code_from_node_names_jmi
javax.swing.JMenuItem _extract_tax_code_from_node_names_jmi
-
_extract_taxonomy_agressive_rbmi
javax.swing.JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi
-
_extract_taxonomy_no_rbmi
javax.swing.JRadioButtonMenuItem _extract_taxonomy_no_rbmi
-
_extract_taxonomy_pfam_relaxed_rbmi
javax.swing.JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi
-
_extract_taxonomy_pfam_strict_rbmi
javax.swing.JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi
-
_file_jmenu
javax.swing.JMenu _file_jmenu
-
_font_size_menu
javax.swing.JMenu _font_size_menu
-
_graphics_export_using_actual_size_cbmi
javax.swing.JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi
-
_graphics_export_visible_only_cbmi
javax.swing.JCheckBoxMenuItem _graphics_export_visible_only_cbmi
-
_gsdi_item
javax.swing.JMenuItem _gsdi_item
-
_gsdir_item
javax.swing.JMenuItem _gsdir_item
-
_help_item
javax.swing.JMenuItem _help_item
-
_help_jmenu
javax.swing.JMenu _help_jmenu
-
_inference_manager
InferenceManager _inference_manager
-
_internal_number_are_confidence_for_nh_parsing_cbmi
javax.swing.JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi
-
_inverse_search_result_cbmi
javax.swing.JCheckBoxMenuItem _inverse_search_result_cbmi
-
_jmenubar
javax.swing.JMenuBar _jmenubar
-
_label_direction_cbmi
javax.swing.JCheckBoxMenuItem _label_direction_cbmi
-
_large_fonts_item
javax.swing.JMenuItem _large_fonts_item
-
_line_up_renderable_data_cbmi
javax.swing.JCheckBoxMenuItem _line_up_renderable_data_cbmi
-
_lineage_inference
javax.swing.JMenuItem _lineage_inference
-
_load_phylogeny_from_webservice_menu_items
javax.swing.JMenuItem[] _load_phylogeny_from_webservice_menu_items
-
_load_species_tree_item
javax.swing.JMenuItem _load_species_tree_item
-
_mainpanel
MainPanel _mainpanel
-
_medium_fonts_item
javax.swing.JMenuItem _medium_fonts_item
-
_midpoint_root_item
javax.swing.JMenuItem _midpoint_root_item
-
_move_node_names_to_seq_names_jmi
javax.swing.JMenuItem _move_node_names_to_seq_names_jmi
-
_move_node_names_to_tax_sn_jmi
javax.swing.JMenuItem _move_node_names_to_tax_sn_jmi
-
_new_item
javax.swing.JMenuItem _new_item
-
_non_lined_up_cladograms_rbmi
javax.swing.JRadioButtonMenuItem _non_lined_up_cladograms_rbmi
-
_obtain_detailed_taxonomic_information_deleting_jmi
javax.swing.JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi
-
_obtain_detailed_taxonomic_information_jmi
javax.swing.JMenuItem _obtain_detailed_taxonomic_information_jmi
-
_obtain_seq_information_jmi
javax.swing.JMenuItem _obtain_seq_information_jmi
-
_open_item
javax.swing.JMenuItem _open_item
-
_open_url_item
javax.swing.JMenuItem _open_url_item
-
_options
Options _options
-
_options_jmenu
javax.swing.JMenu _options_jmenu
-
_overview_placment_mi
javax.swing.JMenuItem _overview_placment_mi
-
_phyloxml_ref_item
javax.swing.JMenuItem _phyloxml_ref_item
-
_phyloxml_website_item
javax.swing.JMenuItem _phyloxml_website_item
-
_previous_node_annotation_ref
java.lang.String _previous_node_annotation_ref
-
_print_black_and_white_cbmi
javax.swing.JCheckBoxMenuItem _print_black_and_white_cbmi
-
_print_item
javax.swing.JMenuItem _print_item
-
_print_size_mi
javax.swing.JMenuItem _print_size_mi
-
_print_using_actual_size_cbmi
javax.swing.JCheckBoxMenuItem _print_using_actual_size_cbmi
-
_process_menu
javax.swing.JMenu _process_menu
-
_process_pool
ProcessPool _process_pool
-
_rectangular_type_cbmi
javax.swing.JCheckBoxMenuItem _rectangular_type_cbmi
-
_remove_branch_color_item
javax.swing.JMenuItem _remove_branch_color_item
-
_remove_visual_styles_item
javax.swing.JMenuItem _remove_visual_styles_item
-
_replace_underscores_cbmi
javax.swing.JCheckBoxMenuItem _replace_underscores_cbmi
-
_right_line_up_domains_cbmi
javax.swing.JCheckBoxMenuItem _right_line_up_domains_cbmi
-
_rounded_type_cbmi
javax.swing.JCheckBoxMenuItem _rounded_type_cbmi
-
_save_all_item
javax.swing.JMenuItem _save_all_item
-
_save_filechooser
javax.swing.JFileChooser _save_filechooser
-
_save_item
javax.swing.JMenuItem _save_item
-
_screen_antialias_cbmi
javax.swing.JCheckBoxMenuItem _screen_antialias_cbmi
-
_search_case_senstive_cbmi
javax.swing.JCheckBoxMenuItem _search_case_senstive_cbmi
-
_search_whole_words_only_cbmi
javax.swing.JCheckBoxMenuItem _search_whole_words_only_cbmi
-
_search_with_regex_cbmi
javax.swing.JCheckBoxMenuItem _search_with_regex_cbmi
-
_show_annotation_ref_source
javax.swing.JCheckBoxMenuItem _show_annotation_ref_source
-
_show_confidence_stddev_cbmi
javax.swing.JCheckBoxMenuItem _show_confidence_stddev_cbmi
-
_show_default_node_shapes_external_cbmi
javax.swing.JCheckBoxMenuItem _show_default_node_shapes_external_cbmi
-
_show_default_node_shapes_for_marked_cbmi
javax.swing.JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi
-
_show_default_node_shapes_internal_cbmi
javax.swing.JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi
-
_show_domain_labels
javax.swing.JCheckBoxMenuItem _show_domain_labels
-
_show_overview_cbmi
javax.swing.JCheckBoxMenuItem _show_overview_cbmi
-
_show_scale_cbmi
javax.swing.JCheckBoxMenuItem _show_scale_cbmi
-
_small_fonts_item
javax.swing.JMenuItem _small_fonts_item
-
_species_tree
Phylogeny _species_tree
-
_super_tiny_fonts_item
javax.swing.JMenuItem _super_tiny_fonts_item
-
_switch_colors_mi
javax.swing.JMenuItem _switch_colors_mi
-
_taxcolor_item
javax.swing.JMenuItem _taxcolor_item
-
_textframes
java.util.LinkedList<org.forester.archaeopteryx.TextFrame> _textframes
-
_tiny_fonts_item
javax.swing.JMenuItem _tiny_fonts_item
-
_tools_menu
javax.swing.JMenu _tools_menu
-
_triangular_type_cbmi
javax.swing.JCheckBoxMenuItem _triangular_type_cbmi
-
_type_menu
javax.swing.JMenu _type_menu
-
_uniform_cladograms_rbmi
javax.swing.JRadioButtonMenuItem _uniform_cladograms_rbmi
-
_unrooted_type_cbmi
javax.swing.JCheckBoxMenuItem _unrooted_type_cbmi
-
_use_brackets_for_conf_in_nh_export_cbmi
javax.swing.JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi
-
_use_internal_names_for_conf_in_nh_export_cbmi
javax.swing.JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi
-
_view_as_nexus_item
javax.swing.JMenuItem _view_as_nexus_item
-
_view_as_NH_item
javax.swing.JMenuItem _view_as_NH_item
-
_view_as_XML_item
javax.swing.JMenuItem _view_as_XML_item
-
_view_jmenu
javax.swing.JMenu _view_jmenu
-
_website_item
javax.swing.JMenuItem _website_item
-
_write_to_bmp_item
javax.swing.JMenuItem _write_to_bmp_item
-
_write_to_gif_item
javax.swing.JMenuItem _write_to_gif_item
-
_write_to_jpg_item
javax.swing.JMenuItem _write_to_jpg_item
-
_write_to_pdf_item
javax.swing.JMenuItem _write_to_pdf_item
-
_write_to_png_item
javax.swing.JMenuItem _write_to_png_item
-
_write_to_tif_item
javax.swing.JMenuItem _write_to_tif_item
-
_writetographics_filechooser
javax.swing.JFileChooser _writetographics_filechooser
-
_writetopdf_filechooser
javax.swing.JFileChooser _writetopdf_filechooser
-
-
Class org.forester.archaeopteryx.MainFrameApplet extends MainFrame implements Serializable
- serialVersionUID:
- 1941019292746717053L
-
Serialized Fields
-
_applet
ArchaeopteryxA _applet
-
_radio_group_1
javax.swing.ButtonGroup _radio_group_1
-
-
Class org.forester.archaeopteryx.MainFrameApplication extends MainFrame implements Serializable
- serialVersionUID:
- -799735726778865234L
-
Serialized Fields
-
_collapse_below_branch_length
javax.swing.JMenuItem _collapse_below_branch_length
-
_collapse_below_threshold
javax.swing.JMenuItem _collapse_below_threshold
-
_inference_from_msa_item
javax.swing.JMenuItem _inference_from_msa_item
-
_inference_from_seqs_item
javax.swing.JMenuItem _inference_from_seqs_item
-
_inference_menu
javax.swing.JMenu _inference_menu
-
_min_not_collapse
double _min_not_collapse
-
_min_not_collapse_bl
double _min_not_collapse_bl
-
_msa
Msa _msa
-
_msa_file
java.io.File _msa_file
-
_msa_filechooser
javax.swing.JFileChooser _msa_filechooser
-
_open_filechooser
javax.swing.JFileChooser _open_filechooser
-
_open_filechooser_for_species_tree
javax.swing.JFileChooser _open_filechooser_for_species_tree
-
_phylogenetic_inference_options
PhylogeneticInferenceOptions _phylogenetic_inference_options
-
_radio_group_1
javax.swing.ButtonGroup _radio_group_1
-
_radio_group_2
javax.swing.ButtonGroup _radio_group_2
-
_read_seqs_jmi
javax.swing.JMenuItem _read_seqs_jmi
-
_read_values_jmi
javax.swing.JMenuItem _read_values_jmi
-
_seqs
java.util.List<MolecularSequence> _seqs
-
_seqs_file
java.io.File _seqs_file
-
_seqs_pi_filechooser
javax.swing.JFileChooser _seqs_pi_filechooser
-
_sequences_filechooser
javax.swing.JFileChooser _sequences_filechooser
-
_values_filechooser
javax.swing.JFileChooser _values_filechooser
-
-
Class org.forester.archaeopteryx.MainPanel extends javax.swing.JPanel implements Serializable
- serialVersionUID:
- -2682765312661416435L
-
Serialized Fields
-
_colorset
TreeColorSet _colorset
-
_configuration
Configuration _configuration
-
_control_panel
org.forester.archaeopteryx.ControlPanel _control_panel
-
_copied_and_pasted_nodes
java.util.Set<java.lang.Long> _copied_and_pasted_nodes
-
_cut_or_copied_tree
Phylogeny _cut_or_copied_tree
-
_fontset
TreeFontSet _fontset
-
_image_map
java.util.Hashtable<java.lang.String,java.awt.image.BufferedImage> _image_map
-
_mainframe
MainFrame _mainframe
-
_tabbed_pane
javax.swing.JTabbedPane _tabbed_pane
-
_treegraphic_scroll_pane_panels
java.util.List<javax.swing.JPanel> _treegraphic_scroll_pane_panels
-
_treegraphic_scroll_panes
java.util.List<javax.swing.JScrollPane> _treegraphic_scroll_panes
-
_treepanels
java.util.List<TreePanel> _treepanels
-
-
Class org.forester.archaeopteryx.TreePanel extends javax.swing.JPanel implements Serializable
- serialVersionUID:
- -978349745916505029L
-
Serialized Fields
-
_arc
java.awt.geom.Arc2D _arc
-
_at
java.awt.geom.AffineTransform _at
-
_circ_max_depth
int _circ_max_depth
-
_collapsed_external_nodeid_set
java.util.Set<java.lang.Long> _collapsed_external_nodeid_set
-
_color_chooser
javax.swing.JColorChooser _color_chooser
-
_configuration
Configuration _configuration
-
_control_panel
org.forester.archaeopteryx.ControlPanel _control_panel
-
_cubic_curve
java.awt.geom.CubicCurve2D _cubic_curve
-
_current_external_nodes
java.util.Set<java.lang.Long> _current_external_nodes
-
_current_external_nodes_data_buffer
java.lang.StringBuilder _current_external_nodes_data_buffer
-
_current_external_nodes_data_buffer_change_counter
int _current_external_nodes_data_buffer_change_counter
-
_domain_structure_e_value_thr_exp
int _domain_structure_e_value_thr_exp
-
_domain_structure_width
double _domain_structure_width
-
_dynamic_hiding_factor
int _dynamic_hiding_factor
-
_edited
boolean _edited
-
_ellipse
java.awt.geom.Ellipse2D _ellipse
-
_ext_node_with_longest_txt_info
PhylogenyNode _ext_node_with_longest_txt_info
-
_external_node_index
int _external_node_index
-
_found_nodes_0
java.util.Set<java.lang.Long> _found_nodes_0
-
_found_nodes_1
java.util.Set<java.lang.Long> _found_nodes_1
-
_frc
java.awt.font.FontRenderContext _frc
-
_graphics_type
Options.PHYLOGENY_GRAPHICS_TYPE _graphics_type
-
_highlight_node
PhylogenyNode _highlight_node
-
_in_ov
boolean _in_ov
-
_in_ov_rect
boolean _in_ov_rect
-
_last_drag_point_x
float _last_drag_point_x
-
_last_drag_point_y
float _last_drag_point_y
-
_length_of_longest_text
int _length_of_longest_text
-
_line
java.awt.geom.Line2D _line
-
_longest_domain
int _longest_domain
-
_longest_ext_node_info
int _longest_ext_node_info
-
_main_panel
MainPanel _main_panel
-
_max_distance_to_root
double _max_distance_to_root
-
_node_desc_popup
javax.swing.Popup _node_desc_popup
-
_node_frame_index
int _node_frame_index
-
_node_frames
org.forester.archaeopteryx.NodeFrame[] _node_frames
-
_node_popup_menu
javax.swing.JPopupMenu _node_popup_menu
-
_node_popup_menu_items
javax.swing.JMenuItem[] _node_popup_menu_items
-
_nodeid_dist_to_leaf
java.util.HashMap<java.lang.Long,java.lang.Short> _nodeid_dist_to_leaf
-
_nodes_in_preorder
PhylogenyNode[] _nodes_in_preorder
-
_options
Options _options
-
_ov_max_height
float _ov_max_height
-
_ov_max_width
float _ov_max_width
-
_ov_on
boolean _ov_on
-
_ov_rectangle
java.awt.geom.Rectangle2D _ov_rectangle
-
_ov_virtual_rectangle
java.awt.Rectangle _ov_virtual_rectangle
-
_ov_x_correction_factor
float _ov_x_correction_factor
-
_ov_x_distance
float _ov_x_distance
-
_ov_x_position
int _ov_x_position
-
_ov_y_distance
float _ov_y_distance
-
_ov_y_position
int _ov_y_position
-
_ov_y_start
int _ov_y_start
-
_phy_has_branch_lengths
boolean _phy_has_branch_lengths
-
_phylogeny
Phylogeny _phylogeny
-
_polygon
java.awt.geom.Path2D.Float _polygon
-
_popup_buffer
java.lang.StringBuffer _popup_buffer
-
_quad_curve
java.awt.geom.QuadCurve2D _quad_curve
-
_query_sequence
Sequence _query_sequence
-
_rectangle
java.awt.geom.Rectangle2D _rectangle
-
_rendering_hints
java.awt.RenderingHints _rendering_hints
-
_rollover_popup
javax.swing.JTextArea _rollover_popup
-
_root
PhylogenyNode _root
-
_sb
java.lang.StringBuilder _sb
-
_scale_distance
double _scale_distance
-
_scale_label
java.lang.String _scale_label
-
_statistics_for_vector_data
DescriptiveStatistics _statistics_for_vector_data
-
_sub_phylogenies
Phylogeny[] _sub_phylogenies
-
_sub_phylogenies_temp_roots
PhylogenyNode[] _sub_phylogenies_temp_roots
-
_subtree_index
int _subtree_index
-
_treefile
java.io.File _treefile
-
_urt_factor
float _urt_factor
-
_urt_factor_ov
float _urt_factor_ov
-
_urt_nodeid_angle_map
java.util.HashMap<java.lang.Long,java.lang.Double> _urt_nodeid_angle_map
-
_urt_nodeid_index_map
java.util.HashMap<java.lang.Long,java.lang.Integer> _urt_nodeid_index_map
-
_urt_starting_angle
double _urt_starting_angle
-
_x_correction_factor
float _x_correction_factor
-
_x_distance
float _x_distance
-
_y_distance
float _y_distance
-
-
-
Package org.forester.archaeopteryx.tools
-
Class org.forester.archaeopteryx.tools.PhyloInferenceDialog extends javax.swing.JDialog implements Serializable
- serialVersionUID:
- 8337543508238133614L
-
Serialized Fields
-
_bootstrap_cb
javax.swing.JCheckBox _bootstrap_cb
-
_bootstrap_tf
javax.swing.JFormattedTextField _bootstrap_tf
-
_cancel_btn
javax.swing.JButton _cancel_btn
-
_distance_calc_fract_dissimilarity_rb
javax.swing.JRadioButton _distance_calc_fract_dissimilarity_rb
-
_distance_calc_kimura_rb
javax.swing.JRadioButton _distance_calc_kimura_rb
-
_distance_calc_poisson_rb
javax.swing.JRadioButton _distance_calc_poisson_rb
-
_execute_msa_processing_cb
javax.swing.JCheckBox _execute_msa_processing_cb
-
_input_msa_file_tf
javax.swing.JTextField _input_msa_file_tf
-
_input_seqs_max_length_tf
javax.swing.JTextField _input_seqs_max_length_tf
-
_input_seqs_median_length_tf
javax.swing.JTextField _input_seqs_median_length_tf
-
_input_seqs_min_length_tf
javax.swing.JTextField _input_seqs_min_length_tf
-
_input_seqs_number_tf
javax.swing.JTextField _input_seqs_number_tf
-
_input_seqs_tf
javax.swing.JTextField _input_seqs_tf
-
_input_seqs_type_tf
javax.swing.JTextField _input_seqs_type_tf
-
_launch_btn
javax.swing.JButton _launch_btn
-
_mafft_cb
javax.swing.JCheckBox _mafft_cb
-
_mafft_paramenters_tf
javax.swing.JTextField _mafft_paramenters_tf
-
_msa_length_tf
javax.swing.JTextField _msa_length_tf
-
_msa_processing_max_allowed_gap_ratio_tf
javax.swing.JTextField _msa_processing_max_allowed_gap_ratio_tf
-
_msa_processing_min_allowed_length_tf
javax.swing.JTextField _msa_processing_min_allowed_length_tf
-
_msa_processing_remove_all_gap_columns_cb
javax.swing.JCheckBox _msa_processing_remove_all_gap_columns_cb
-
_msa_size_tf
javax.swing.JTextField _msa_size_tf
-
_msa_type_tf
javax.swing.JTextField _msa_type_tf
-
_opts
PhylogeneticInferenceOptions _opts
-
_original_msa_outfile_tf
javax.swing.JTextField _original_msa_outfile_tf
-
_parent_frame
MainFrameApplication _parent_frame
-
_pnl
javax.swing.JPanel _pnl
-
_processed_msa_outfile_tf
javax.swing.JTextField _processed_msa_outfile_tf
-
_pwd_outfile_tf
javax.swing.JTextField _pwd_outfile_tf
-
_random_seed_tf
javax.swing.JTextField _random_seed_tf
-
_save_original_msa_cb
javax.swing.JCheckBox _save_original_msa_cb
-
_save_processed_msa_cb
javax.swing.JCheckBox _save_processed_msa_cb
-
_save_pwd_file_cb
javax.swing.JCheckBox _save_pwd_file_cb
-
_select_input_msa_btn
javax.swing.JButton _select_input_msa_btn
-
_select_input_seqs_btn
javax.swing.JButton _select_input_seqs_btn
-
_value
int _value
-
-
-
Package org.forester.development
-
Class org.forester.development.AbstractRenderer extends javax.swing.JComponent implements Serializable
- serialVersionUID:
- 7236434322552764776L
-
Serialized Fields
-
_status
byte _status
-
_well_size
int _well_size
-
_x
int _x
-
_y
int _y
-
-
Class org.forester.development.MsaRenderer extends javax.swing.JComponent implements Serializable
- serialVersionUID:
- -68078011081748093L
-
Serialized Fields
-
_columns
int _columns
-
_max
double _max
-
_maxColor
java.awt.Color _maxColor
-
_mean
double _mean
-
_meanColor
java.awt.Color _meanColor
-
_min
double _min
-
_minColor
java.awt.Color _minColor
-
_msa
Msa _msa
-
_parent
javax.swing.JComponent _parent
-
_rows
int _rows
-
_useMean
boolean _useMean
-
_wells
AbstractRenderer[][] _wells
-
_wellSize
int _wellSize
-
-
Class org.forester.development.ResidueRenderer extends AbstractRenderer implements Serializable
- serialVersionUID:
- -2331160296913478874L
-
Serialized Fields
-
_isMarked
boolean _isMarked
-
_isSelected
boolean _isSelected
-
_parentPlateRenderer
MsaRenderer _parentPlateRenderer
-
_value
char _value
-
_wellColor
java.awt.Color _wellColor
-
-
-
Package org.forester.io.parsers.nexus
-
Class org.forester.io.parsers.nexus.NexusFormatException extends java.io.IOException implements Serializable
- serialVersionUID:
- -8750474393398183410L
-
-
Package org.forester.io.parsers.nhx
-
Class org.forester.io.parsers.nhx.NHXFormatException extends java.io.IOException implements Serializable
- serialVersionUID:
- 3756209394438250170L
-
-
Package org.forester.io.parsers.phyloxml
-
Class org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException extends java.io.IOException implements Serializable
- serialVersionUID:
- 3756209394438250170L
-
Class org.forester.io.parsers.phyloxml.PhyloXmlException extends java.lang.RuntimeException implements Serializable
- serialVersionUID:
- 3756209394438250170L
-
-
Package org.forester.io.parsers.util
-
Class org.forester.io.parsers.util.PhylogenyParserException extends java.io.IOException implements Serializable
- serialVersionUID:
- -4810333295377881086L
-
-
Package org.forester.msa
-
Class org.forester.msa.MsaFormatException extends java.io.IOException implements Serializable
- serialVersionUID:
- 690079849050106491L
-
-
Package org.forester.msa_compactor
-
Class org.forester.msa_compactor.Chart extends javax.swing.JDialog implements Serializable
- serialVersionUID:
- -5292420246132943515L
-
Serialized Fields
-
_initial_number_of_seqs
int _initial_number_of_seqs
-
_m_exit
javax.swing.JMenuItem _m_exit
-
_msa_props
java.util.List<MsaProperties> _msa_props
-
_show_msa_qual
boolean _show_msa_qual
-
_title
java.lang.String _title
-
-
-
Package org.forester.rio
-
Class org.forester.rio.RIOException extends java.lang.Exception implements Serializable
- serialVersionUID:
- 4691098852783522097L
-
-
Package org.forester.sdi
-
Class org.forester.sdi.SDIException extends java.lang.Exception implements Serializable
- serialVersionUID:
- 5154733429066500435L
-
-
Package org.forester.util
-
Class org.forester.util.FailedConditionCheckException extends java.lang.RuntimeException implements Serializable
- serialVersionUID:
- -860013990231493438L
-
Class org.forester.util.IllegalFormatUseException extends java.lang.IllegalArgumentException implements Serializable
- serialVersionUID:
- -1126329548396073983L
-
-
Package org.jcolorbrewer.ui
-
Class org.jcolorbrewer.ui.ColorPaletteChooserDialog extends javax.swing.JDialog implements Serializable
- serialVersionUID:
- -5953604049348574107L
-
Serialized Fields
-
colorChooser
javax.swing.JColorChooser colorChooser
The style editor panel. -
innerPanel
javax.swing.JPanel innerPanel
The inner panel containing everything. -
okWasPressed
boolean okWasPressed
True if OK was pressed; false otherwise. -
parent
java.awt.Window parent
The parent window. -
startingColor
java.awt.Color startingColor
Starting color, set by setColor, and the color we return to on a reset. -
startingColorBrewer
ColorBrewer startingColorBrewer
Starting color, set by setColor, and the color we return to on a reset.
-
-
Class org.jcolorbrewer.ui.ColorPanelSelectionModel extends javax.swing.colorchooser.DefaultColorSelectionModel implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
brewer
ColorBrewer brewer
-
-
Class org.jcolorbrewer.ui.DivergingColorPalettePanel extends javax.swing.colorchooser.AbstractColorChooserPanel implements Serializable
- serialVersionUID:
- 1L
-
Class org.jcolorbrewer.ui.QualitativeColorPalettePanel extends javax.swing.colorchooser.AbstractColorChooserPanel implements Serializable
- serialVersionUID:
- 1L
-
Class org.jcolorbrewer.ui.SequentialColorPalettePanel extends javax.swing.colorchooser.AbstractColorChooserPanel implements Serializable
- serialVersionUID:
- 1L
-