Serialized Form


Package org.biojava.bio.structure

Class org.biojava.bio.structure.AminoAcidImpl extends HetatomImpl implements Serializable

serialVersionUID: -6018854413829044230L

Serialized Fields

amino_char

Character amino_char

secstruc

Map<K,V> secstruc

recordType

String recordType

Class org.biojava.bio.structure.AtomImpl extends Object implements Serializable

serialVersionUID: -2258364127420562883L

Serialized Fields

name

String name

fullName

String fullName

element

Element element

coords

double[] coords

pdbline

String pdbline

pdbserial

int pdbserial

occupancy

double occupancy

tempfactor

double tempfactor

altLoc

Character altLoc

parent

Group parent

id

long id

Class org.biojava.bio.structure.Author extends Object implements Serializable

serialVersionUID: 4840370515056666418L

Serialized Fields

surname

String surname

initials

String initials

Class org.biojava.bio.structure.ChainImpl extends Object implements Serializable

serialVersionUID: 1990171805277911840L

Serialized Fields

swissprot_id

String swissprot_id

name

String name

groups

List<E> groups

seqResGroups

List<E> seqResGroups

id

Long id

mol

Compound mol

parent

Structure parent

pdbResnumMap

Map<K,V> pdbResnumMap

Class org.biojava.bio.structure.Compound extends Object implements Serializable

serialVersionUID: 2991897825657586356L

Serialized Fields

chainList

List<E> chainList

chainId

List<E> chainId

refChainId

String refChainId

molId

String molId

molName

String molName

title

String title

synonyms

List<E> synonyms

ecNums

List<E> ecNums

engineered

String engineered

mutation

String mutation

biologicalUnit

String biologicalUnit

details

String details

numRes

String numRes

resNames

String resNames

headerVars

String headerVars

synthetic

String synthetic

fragment

String fragment

organismScientific

String organismScientific

organismTaxId

String organismTaxId

organismCommon

String organismCommon

strain

String strain

variant

String variant

cellLine

String cellLine

atcc

String atcc

organ

String organ

tissue

String tissue

cell

String cell

organelle

String organelle

secretion

String secretion

gene

String gene

cellularLocation

String cellularLocation

expressionSystem

String expressionSystem

expressionSystemTaxId

String expressionSystemTaxId

expressionSystemStrain

String expressionSystemStrain

expressionSystemVariant

String expressionSystemVariant

expressionSystemCellLine

String expressionSystemCellLine

expressionSystemAtccNumber

String expressionSystemAtccNumber

expressionSystemOrgan

String expressionSystemOrgan

expressionSystemTissue

String expressionSystemTissue

expressionSystemCell

String expressionSystemCell

expressionSystemOrganelle

String expressionSystemOrganelle

expressionSystemCellularLocation

String expressionSystemCellularLocation

expressionSystemVectorType

String expressionSystemVectorType

expressionSystemVector

String expressionSystemVector

expressionSystemPlasmid

String expressionSystemPlasmid

expressionSystemGene

String expressionSystemGene

expressionSystemOtherDetails

String expressionSystemOtherDetails

id

Long id

Class org.biojava.bio.structure.DBRef extends Object implements Serializable

serialVersionUID: -1050178577542224379L

Serialized Fields

parent

Structure parent

idCode

String idCode

chainId

Character chainId

seqbegin

int seqbegin

insertBegin

char insertBegin

seqEnd

int seqEnd

insertEnd

char insertEnd

database

String database

dbAccession

String dbAccession

dbIdCode

String dbIdCode

dbSeqBegin

int dbSeqBegin

idbnsBegin

char idbnsBegin

dbSeqEnd

int dbSeqEnd

idbnsEnd

char idbnsEnd

id

Long id

Class org.biojava.bio.structure.HetatomImpl extends Object implements Serializable

serialVersionUID: 4491470432023820382L

Serialized Fields

properties

Map<K,V> properties

id

long id

pdb_flag

boolean pdb_flag

pdb_name

String pdb_name

residueNumber

ResidueNumber residueNumber

atoms

List<E> atoms

parent

Chain parent

atomLookup

Map<K,V> atomLookup

atomSingleCharLookup

Map<K,V> atomSingleCharLookup

chemComp

ChemComp chemComp

altLocs

List<E> altLocs

Class org.biojava.bio.structure.JournalArticle extends Object implements Serializable

serialVersionUID: 5062668226159515468L

Serialized Fields

authorList

List<E> authorList

editorList

List<E> editorList

title

String title

ref

String ref

journalName

String journalName

volume

String volume

startPage

String startPage

publicationDate

int publicationDate

publisher

String publisher

refn

String refn

pmid

String pmid

doi

String doi

published

boolean published

Class org.biojava.bio.structure.NucleotideImpl extends HetatomImpl implements Serializable

serialVersionUID: -7467726932980288712L

Class org.biojava.bio.structure.PDBCrystallographicInfo extends Object implements Serializable

Serialized Fields

a

float a

b

float b

c

float c

alpha

float alpha

beta

float beta

gamma

float gamma

spaceGroup

String spaceGroup

z

int z

Class org.biojava.bio.structure.PDBHeader extends Object implements Serializable

serialVersionUID: -5834326174085429508L

Serialized Fields

method

String method

title

String title

description

String description

idCode

String idCode

classification

String classification

depDate

Date depDate

modDate

Date modDate

technique

String technique

resolution

float resolution

authors

String authors

id

Long id

dateFormat

DateFormat dateFormat

Class org.biojava.bio.structure.ResidueNumber extends Object implements Serializable

serialVersionUID: 1773011704758536083L

Serialized Fields

chainId

String chainId

insCode

Character insCode

seqNum

Integer seqNum

Class org.biojava.bio.structure.Site extends Object implements Serializable

serialVersionUID: -4577047072916341237L

Serialized Fields

siteID

String siteID

groups

List<E> groups

evCode

String evCode

description

String description

Class org.biojava.bio.structure.SSBond extends Object implements Serializable

serialVersionUID: -8663681100691188647L

Serialized Fields

serNum

int serNum

chainID1

String chainID1

chainID2

String chainID2

resnum1

String resnum1

resnum2

String resnum2

insCode1

String insCode1

insCode2

String insCode2

Class org.biojava.bio.structure.StructureException extends Exception implements Serializable

serialVersionUID: 62946250941673093L

Class org.biojava.bio.structure.StructureImpl extends Object implements Serializable

serialVersionUID: -8344837138032851347L

Serialized Fields

pdb_id

String pdb_id

models

List<E> models

header

Map<K,V> header

connections

List<E> connections

compounds

List<E> compounds

dbrefs

List<E> dbrefs

ssbonds

List<E> ssbonds

sites

List<E> sites

hetAtoms

List<E> hetAtoms

name

String name

journalArticle

JournalArticle journalArticle

pdbHeader

PDBHeader pdbHeader

crystallographicInfo

PDBCrystallographicInfo crystallographicInfo

nmrflag

boolean nmrflag

id

Long id

biologicalAssembly

boolean biologicalAssembly

Class org.biojava.bio.structure.UnknownPdbAminoAcidException extends Exception implements Serializable

serialVersionUID: -5571696240026118421L


Package org.biojava.bio.structure.align.client

Class org.biojava.bio.structure.align.client.JobKillException extends Exception implements Serializable

serialVersionUID: 1L

Class org.biojava.bio.structure.align.client.StructureName extends Object implements Serializable

serialVersionUID: 4021229518711762954L

Serialized Fields

name

String name

pdbId

String pdbId

chainId

String chainId

Package org.biojava.bio.structure.align.gui

Class org.biojava.bio.structure.align.gui.AlignmentGui extends JFrame implements Serializable

serialVersionUID: 0L

Serialized Fields

algorithm

StructureAlignment algorithm

abortB

JButton abortB

tab1

SelectPDBPanel tab1

tab2

PDBUploadPanel tab2

tab3

ScopSelectPanel tab3

thread

Thread thread

alicalc

AlignmentCalculationRunnable alicalc

masterPane

JTabbedPane masterPane

tabPane

JTabbedPane tabPane

progress

JProgressBar progress

dbsearch

DBSearchGUI dbsearch

Class org.biojava.bio.structure.align.gui.AlignmentTextPanel extends JPrintPanel implements Serializable

serialVersionUID: 5092386365924879073L

Serialized Fields

tp

JEditorPane tp

Class org.biojava.bio.structure.align.gui.ChooseDirAction extends AbstractAction implements Serializable

serialVersionUID: 0L

Serialized Fields

textField

JTextField textField

config

UserConfiguration config

Class org.biojava.bio.structure.align.gui.ConfigPDBInstallPanel extends JPanel implements Serializable

serialVersionUID: -1055193854675583808L

Serialized Fields

pdbSplit

JCheckBox pdbSplit

fromFtp

JCheckBox fromFtp

fileType

JComboBox fileType

pdbDir

JTextField pdbDir

Class org.biojava.bio.structure.align.gui.DBSearchGUI extends JPanel implements Serializable

serialVersionUID: -5657960663049062301L

Serialized Fields

algorithm

StructureAlignment algorithm

tab1

SelectPDBPanel tab1

tabPane

JTabbedPane tabPane

tab2

PDBUploadPanel tab2

tab3

ScopSelectPanel tab3

listPane

JPanel listPane

abortB

JButton abortB

alicalc

AlignmentCalcDB alicalc

progress

JProgressBar progress

drawer

org.biojava.bio.structure.align.gui.ProgressThreadDrawer drawer

outFileLocation

JTextField outFileLocation

useDomainSplit

Boolean useDomainSplit

Class org.biojava.bio.structure.align.gui.DotPlotPanel extends ScaleableMatrixPanel implements Serializable

serialVersionUID: -7641953255857483895L

Class org.biojava.bio.structure.align.gui.GUIAlignmentProgressListener extends JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

alignmentsProcessed

int alignmentsProcessed

progressBar

JProgressBar progressBar

taskOutput

JTextArea taskOutput

stopButton

JButton stopButton

farmJob

FarmJob farmJob

Class org.biojava.bio.structure.align.gui.JPrintPanel extends JPanel implements Serializable

serialVersionUID: -3337337068138131455L

Class org.biojava.bio.structure.align.gui.ParameterGUI extends JFrame implements Serializable

serialVersionUID: 723386061184110161L

Serialized Fields

params

ConfigStrucAligParams params

textFields

List<E> textFields

Class org.biojava.bio.structure.align.gui.SelectPDBPanel extends JPanel implements Serializable

serialVersionUID: 4002475313717172193L

Serialized Fields

debug

boolean debug

f1

JTextField f1

f2

JTextField f2

c1

JTextField c1

c2

JTextField c2

r1

JTextField r1

r2

JTextField r2

config

UserConfiguration config

configPane

JTabbedPane configPane

Package org.biojava.bio.structure.align.gui.aligpanel

Class org.biojava.bio.structure.align.gui.aligpanel.AligPanel extends JPrintPanel implements Serializable

serialVersionUID: -6892229111166263764L

Serialized Fields

afpChain

AFPChain afpChain

coordManager

AFPChainCoordManager coordManager

seqFont

Font seqFont

eqFont

Font eqFont

jmol

StructureAlignmentJmol jmol

mouseMoLi

AligPanelMouseMotionListener mouseMoLi

selection

BitSet selection

selectionLocked

boolean selectionLocked

ca1

Atom[] ca1

ca2

Atom[] ca2

colorBySimilarity

boolean colorBySimilarity

colorByAlignmentBlock

boolean colorByAlignmentBlock

Class org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay extends JTextField implements Serializable

serialVersionUID: 6939947266417830429L

Serialized Fields

afpChain

AFPChain afpChain

ca1

Atom[] ca1

ca2

Atom[] ca2

Package org.biojava.bio.structure.align.gui.autosuggest

Class org.biojava.bio.structure.align.gui.autosuggest.JAutoSuggest extends JTextField implements Serializable

serialVersionUID: 8591734727984365156L

Serialized Fields

defaultText

String defaultText

dialog

JDialog dialog

location

Point location

list

JList list

suggestions

Vector<E> suggestions

lastWord

String lastWord
last word that was entered by user


autoSuggestProvider

AutoSuggestProvider autoSuggestProvider

regular

Font regular

busy

Font busy

matcher

org.biojava.bio.structure.align.gui.autosuggest.JAutoSuggest.SuggestionFetcher matcher

Package org.biojava.bio.structure.align.gui.jmol

Class org.biojava.bio.structure.align.gui.jmol.JmolPanel extends JPrintPanel implements Serializable

serialVersionUID: -3661941083797644242L

Serialized Fields

viewer

JmolViewer viewer

adapter

JmolAdapter adapter

statusListener

JmolStatusListener statusListener

currentSize

Dimension currentSize

rectClip

Rectangle rectClip

structure

Structure structure

Package org.biojava.bio.structure.align.helper

Class org.biojava.bio.structure.align.helper.AligMatEl extends IndexPair implements Serializable

serialVersionUID: -4040926588803887471L

Serialized Fields

value

int value

contig

int contig

Class org.biojava.bio.structure.align.helper.IndexPair extends Object implements Serializable

serialVersionUID: 1832393751152650420L

Serialized Fields

row

short row

col

short col

Package org.biojava.bio.structure.align.model

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

serialVersionUID: 3901209995477111829L

Serialized Fields

p1

int p1

p2

int p2

fragLen

int fragLen

rmsd

double rmsd

m

Matrix m

t

double[] t

score

double score

id

long id

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

serialVersionUID: -4474029015606617947L

Serialized Fields

algorithmName

String algorithmName

version

String version

name1

String name1

name2

String name2

ioTime

long ioTime

calculationTime

long calculationTime

id

long id

alignScore

double alignScore

alignScoreUpdate

double alignScoreUpdate

afpChainTwiNum

int afpChainTwiNum

tmScore

double tmScore

minLen

int minLen

afpSet

List<E> afpSet

afpIndex

int[][] afpIndex

afpAftIndex

int[][] afpAftIndex

afpBefIndex

int[][] afpBefIndex

disTable1

Matrix disTable1

disTable2

Matrix disTable2

twi

int[] twi

afpChainLen

int afpChainLen

afpChainList

int[] afpChainList

afpChainTwiBin

double[] afpChainTwiBin

afpChainTwiList

double[] afpChainTwiList

chainRmsd

double chainRmsd

chainLen

int chainLen

misLen

int misLen

gapLen

int gapLen

blockNum

int blockNum

blockNumIni

int blockNumIni

blockNumClu

int blockNumClu

blockNumSpt

int blockNumSpt

blockRmsd

double[] blockRmsd

block2Afp

int[] block2Afp

blockSize

int[] blockSize

blockScore

double[] blockScore

blockGap

int[] blockGap

blockResSize

int[] blockResSize

blockResList

int[][][] blockResList

blockRotationMatrix

Matrix[] blockRotationMatrix

blockShiftVector

Atom[] blockShiftVector

focusResn

int focusResn

focusRes1

int[] focusRes1

focusRes2

int[] focusRes2

focusAfpn

int focusAfpn

focusAfpList

int[] focusAfpList

shortAlign

boolean shortAlign

pdbAln

String[][][] pdbAln

optAln

int[][][] optAln

optLen

int[] optLen

optRmsd

double[] optRmsd

optLength

int optLength

alnsymb

char[] alnsymb

alnseq1

char[] alnseq1

alnseq2

char[] alnseq2

alnLength

int alnLength

alnbeg1

int alnbeg1

alnbeg2

int alnbeg2

totalLenIni

int totalLenIni

totalLenOpt

int totalLenOpt

totalRmsdIni

double totalRmsdIni

totalRmsdOpt

double totalRmsdOpt

ca1Length

int ca1Length

ca2Length

int ca2Length

maxTra

int maxTra

conn

Double conn

dvar

Double dvar

probability

double probability

identity

double identity

similarity

double similarity

normAlignScore

double normAlignScore

myResultsEQR

int myResultsEQR

myResultsSimilarity1

int myResultsSimilarity1

myResultsSimilarity2

int myResultsSimilarity2

sequentialAlignment

boolean sequentialAlignment

distanceMatrix

Matrix distanceMatrix

description2

String description2

Package org.biojava.bio.structure.align.pairwise

Class org.biojava.bio.structure.align.pairwise.AlignmentResult extends Object implements Serializable

serialVersionUID: -4132105905712445473L

Serialized Fields

alignments

AlternativeAlignment[] alignments

pdb1

String pdb1

pdb2

String pdb2

chain1

String chain1

chain2

String chain2

length1

int length1

length2

int length2

calculationTime

long calculationTime

ioTime

long ioTime

Class org.biojava.bio.structure.align.pairwise.AlternativeAlignment extends Object implements Serializable

serialVersionUID: -6226717654562221241L

Serialized Fields

idx1

int[] idx1

idx2

int[] idx2

pdbresnum1

String[] pdbresnum1

pdbresnum2

String[] pdbresnum2

nfrags

int nfrags

center

Atom center

rot

Matrix rot

tr

Atom tr

gaps0

int gaps0

eqr0

int eqr0

rms0

int rms0

joined

int joined

percId

int percId

cluster

int cluster

score

float score

aligpath

IndexPair[] aligpath

fromia

int fromia

currentRotMatrix

Matrix currentRotMatrix

currentTranMatrix

Atom currentTranMatrix

rms

double rms

distanceMatrix

Matrix distanceMatrix

Package org.biojava.bio.structure.align.util

Class org.biojava.bio.structure.align.util.ConfigurationException extends Exception implements Serializable

serialVersionUID: -8047100079715000276L


Package org.biojava.bio.structure.domain.pdp

Class org.biojava.bio.structure.domain.pdp.Domain extends Object implements Serializable

serialVersionUID: -1293994033102271366L

Serialized Fields

id

String id

size

int size

nseg

int nseg

score

double score

segments

List<E> segments

Class org.biojava.bio.structure.domain.pdp.Segment extends Object implements Serializable

serialVersionUID: 1393487067559539657L

Serialized Fields

from

Integer from

to

Integer to

score

double score

Package org.biojava.bio.structure.gui

Class org.biojava.bio.structure.gui.JMatrixPanel extends JPanel implements Serializable

serialVersionUID: -1720879395453257846L

Serialized Fields

_bufImage

BufferedImage _bufImage

matrix

Matrix matrix

cellColor

ContinuousColorMapper cellColor

scale

float scale

fragmentPairs

FragmentPair[] fragmentPairs

aligs

AlternativeAlignment[] aligs

selectedAlignmentPos

int selectedAlignmentPos

params

StrucAligParameters params

Class org.biojava.bio.structure.gui.ScaleableMatrixPanel extends JPanel implements Serializable

serialVersionUID: -8082261434322968652L

Serialized Fields

mPanel

JMatrixPanel mPanel

slider

JSlider slider

scroll

JScrollPane scroll

coloring

JComboBox coloring

gradients

Map<K,V> gradients

Class org.biojava.bio.structure.gui.ScaleableMatrixPanel.GradientRenderer extends JPanel implements Serializable

serialVersionUID: -2000575579184232365L

Serialized Fields

min

int min

max

int max

title

JLabel title

gradientContainer

JPanel gradientContainer

Class org.biojava.bio.structure.gui.SequenceDisplay extends JPanel implements Serializable

serialVersionUID: -1829252532712454236L

Serialized Fields

structure1

Structure structure1

structure2

Structure structure2

alig

AlternativeAlignment alig

structurePairAligner

StructurePairAligner structurePairAligner

panel1

SequenceScalePanel panel1

panel2

SequenceScalePanel panel2

residueSizeSlider

JSlider residueSizeSlider

percentageDisplay

JLabel percentageDisplay

idx1

int[] idx1

idx2

int[] idx2

logger

Logger logger

apos

List<E> apos

scale

float scale

mouseListener1

SequenceMouseListener mouseListener1

mouseListener2

SequenceMouseListener mouseListener2

label1

JLabel label1

label2

JLabel label2

Package org.biojava.bio.structure.gui.util

Class org.biojava.bio.structure.gui.util.AlternativeAlignmentFrame extends JFrame implements Serializable

serialVersionUID: 0L

Serialized Fields

aligs

AlternativeAlignment[] aligs

panel

JPanel panel

structure1

Structure structure1

structure2

Structure structure2

structurePairAligner

StructurePairAligner structurePairAligner

Class org.biojava.bio.structure.gui.util.PDBDirPanel extends JPanel implements Serializable

serialVersionUID: -5682120627824627408L

Serialized Fields

debug

boolean debug

pdbDir

JTextField pdbDir

f1

JTextField f1

f2

JTextField f2

c1

JTextField c1

c2

JTextField c2

Class org.biojava.bio.structure.gui.util.PDBServerPanel extends JPanel implements Serializable

serialVersionUID: -5682120627824627408L

Serialized Fields

debug

boolean debug

pdbDir

JTextField pdbDir

f1

JTextField f1

f2

JTextField f2

c1

JTextField c1

c2

JTextField c2

Class org.biojava.bio.structure.gui.util.PDBUploadPanel extends JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

fileType

JComboBox fileType

filePath1

JTextField filePath1

filePath2

JTextField filePath2

chain1

JTextField chain1

chain2

JTextField chain2

Class org.biojava.bio.structure.gui.util.ScopSelectPanel extends JPanel implements Serializable

serialVersionUID: 757947454156959178L

Serialized Fields

dom1

JAutoSuggest dom1

dom2

JAutoSuggest dom2

Class org.biojava.bio.structure.gui.util.SequenceScalePanel extends JPanel implements Serializable

serialVersionUID: 7893248902423L

Serialized Fields

logger

Logger logger

chain

Chain chain

chainLength

int chainLength

scale

float scale

seqArr

Character[] seqArr

coordManager

CoordManager coordManager

position

int position

apos

List<E> apos

Package org.biojava.bio.structure.gui.util.color

Class org.biojava.bio.structure.gui.util.color.GradientPanel extends JPanel implements Serializable

serialVersionUID: -6387922432121206731L

Serialized Fields

mapper

ContinuousColorMapper mapper

min

double min

max

double max

Class org.biojava.bio.structure.gui.util.color.HSVColorSpace extends ColorSpace implements Serializable

serialVersionUID: 8324413992279510075L


Package org.biojava.bio.structure.io

Class org.biojava.bio.structure.io.FileParsingParameters extends Object implements Serializable

serialVersionUID: 5878292315163939027L

Serialized Fields

parseSecStruc

boolean parseSecStruc
flag to detect if the secondary structure info should be read


alignSeqRes

boolean alignSeqRes
Flag to control if SEQRES and ATOM records should be aligned


loadChemCompInfo

boolean loadChemCompInfo
Flag to control if the chemical component info should be downloaded while parsing the files. (files will be cached).


parseCAOnly

boolean parseCAOnly
Set the flag to only read in Ca atoms - this is useful for parsing large structures like 1htq.


headerOnly

boolean headerOnly
Flag to parse header only


updateRemediatedFiles

boolean updateRemediatedFiles
update locally cached files to the latest version of remediated files


storeEmptySeqRes

boolean storeEmptySeqRes

atomCaThreshold

int atomCaThreshold

maxAtoms

int maxAtoms

fullAtomNames

String[] fullAtomNames

Class org.biojava.bio.structure.io.PDBParseException extends Exception implements Serializable

serialVersionUID: 219047230178423923L


Package org.biojava.bio.structure.io.mmcif.model

Class org.biojava.bio.structure.io.mmcif.model.ChemComp extends Object implements Serializable

serialVersionUID: -4736341142030215915L

Serialized Fields

id

String id

name

String name

type

String type

pdbx_type

String pdbx_type

formula

String formula

mon_nstd_parent_comp_id

String mon_nstd_parent_comp_id

pdbx_synonyms

String pdbx_synonyms

pdbx_formal_charge

String pdbx_formal_charge

pdbx_initial_date

String pdbx_initial_date

pdbx_modified_date

String pdbx_modified_date

pdbx_ambiguous_flag

String pdbx_ambiguous_flag

pdbx_release_status

String pdbx_release_status

pdbx_replaced_by

String pdbx_replaced_by

pdbx_replaces

String pdbx_replaces

formula_weight

String formula_weight

one_letter_code

String one_letter_code

three_letter_code

String three_letter_code

pdbx_model_coordinates_details

String pdbx_model_coordinates_details

pdbx_model_coordinates_missing_flag

String pdbx_model_coordinates_missing_flag

pdbx_ideal_coordinates_details

String pdbx_ideal_coordinates_details

pdbx_ideal_coordinates_missing_flag

String pdbx_ideal_coordinates_missing_flag

pdbx_model_coordinates_db_code

String pdbx_model_coordinates_db_code

pdbx_subcomponent_list

String pdbx_subcomponent_list

pdbx_processing_site

String pdbx_processing_site

mon_nstd_flag

String mon_nstd_flag

descriptors

List<E> descriptors

residueType

ResidueType residueType

polymerType

PolymerType polymerType

standard

boolean standard

Class org.biojava.bio.structure.io.mmcif.model.ChemCompDescriptor extends Object implements Serializable

serialVersionUID: 1078685833800736278L

Serialized Fields

comp_id

String comp_id

type

String type

program

String program

program_version

String program_version

descriptor

String descriptor

Package org.biojava.bio.structure.io.sifts

Class org.biojava.bio.structure.io.sifts.SiftsEntity extends Object implements Serializable

serialVersionUID: 750353252427491487L

Serialized Fields

type

String type

entityId

String entityId

segments

List<E> segments

Class org.biojava.bio.structure.io.sifts.SiftsResidue extends Object implements Serializable

serialVersionUID: 3425769737629800828L

Serialized Fields

pdbResNum

String pdbResNum

pdbResName

String pdbResName

chainId

String chainId

uniProtResName

String uniProtResName

uniProtPos

Integer uniProtPos

naturalPos

Integer naturalPos

seqResName

String seqResName

pdbId

String pdbId

uniProtAccessionId

String uniProtAccessionId

notObserved

Boolean notObserved

Class org.biojava.bio.structure.io.sifts.SiftsSegment extends Object implements Serializable

serialVersionUID: -8005129863256307153L

Serialized Fields

segId

String segId

start

String start

end

String end

residues

List<E> residues

Package org.biojava.bio.structure.jama

Class org.biojava.bio.structure.jama.CholeskyDecomposition extends Object implements Serializable

serialVersionUID: 224348942390823L

Serialized Fields

L

double[][] L
Array for internal storage of decomposition.

internal array storage.

n

int n
Row and column dimension (square matrix).

matrix dimension.

isspd

boolean isspd
Symmetric and positive definite flag.

is symmetric and positive definite flag.

Class org.biojava.bio.structure.jama.EigenvalueDecomposition extends Object implements Serializable

serialVersionUID: 93489734879234789L

Serialized Fields

n

int n
Row and column dimension (square matrix).

matrix dimension.

issymmetric

boolean issymmetric
Symmetry flag.

internal symmetry flag.

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.

V

double[][] V
Array for internal storage of eigenvectors.

internal storage of eigenvectors.

H

double[][] H
Array for internal storage of nonsymmetric Hessenberg form.

internal storage of nonsymmetric Hessenberg form.

ort

double[] ort
Working storage for nonsymmetric algorithm.

working storage for nonsymmetric algorithm.

Class org.biojava.bio.structure.jama.LUDecomposition extends Object implements Serializable

serialVersionUID: 9271028462937843L

Serialized Fields

LU

double[][] LU
Array for internal storage of decomposition.

internal array storage.

m

int m
Row and column dimensions, and pivot sign.

column dimension.

n

int n
Row and column dimensions, and pivot sign.

column dimension.

pivsign

int pivsign
Row and column dimensions, and pivot sign.

column dimension.

piv

int[] piv
Internal storage of pivot vector.

pivot vector.

Class org.biojava.bio.structure.jama.Matrix extends Object implements Serializable

serialVersionUID: 8492558293015348719L

Serialized Fields

A

double[][] A
Array for internal storage of elements.

internal array storage.

m

int m
Row and column dimensions.

row dimension.

n

int n
Row and column dimensions.

row dimension.

Class org.biojava.bio.structure.jama.QRDecomposition extends Object implements Serializable

serialVersionUID: 10293720387423L

Serialized Fields

QR

double[][] QR
Array for internal storage of decomposition.

internal array storage.

m

int m
Row and column dimensions.

column dimension.

n

int n
Row and column dimensions.

column dimension.

Rdiag

double[] Rdiag
Array for internal storage of diagonal of R.

diagonal of R.

Class org.biojava.bio.structure.jama.SingularValueDecomposition extends Object implements Serializable

serialVersionUID: 640239472093534756L

Serialized Fields

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.

s

double[] s
Array for internal storage of singular values.

internal storage of singular values.

m

int m
Row and column dimensions.

row dimension.

n

int n
Row and column dimensions.

row dimension.

Package org.biojava.bio.structure.scop

Class org.biojava.bio.structure.scop.ScopDescription extends Object implements Serializable

serialVersionUID: 8579808155176839161L

Serialized Fields

sunID

int sunID

category

ScopCategory category

classificationId

String classificationId

name

String name

description

String description

Class org.biojava.bio.structure.scop.ScopDomain extends Object implements Serializable

serialVersionUID: 5890476209571654301L

Serialized Fields

scopId

String scopId

pdbId

String pdbId

ranges

List<E> ranges

classificationId

String classificationId

sunid

Integer sunid

classId

int classId

foldId

int foldId

superfamilyId

int superfamilyId

familyId

int familyId

domainId

int domainId

speciesId

int speciesId

px

int px

Class org.biojava.bio.structure.scop.ScopNode extends Object implements Serializable

serialVersionUID: 1187083944488580995L

Serialized Fields

sunid

int sunid

parentSunid

int parentSunid

children

List<E> children

Package org.biojava.bio.structure.scop.server

Class org.biojava.bio.structure.scop.server.ScopDescriptions extends Object implements Serializable

serialVersionUID: 4924350548761431852L

Serialized Fields

scopDescriptions

List<E> scopDescriptions

Class org.biojava.bio.structure.scop.server.ScopDomains extends Object implements Serializable

serialVersionUID: 7693404355005856746L

Serialized Fields

domains

List<E> domains

Class org.biojava.bio.structure.scop.server.ScopNodes extends Object implements Serializable

serialVersionUID: 5327454882500340305L

Serialized Fields

scopNodes

List<E> scopNodes

Class org.biojava.bio.structure.scop.server.TreeSetStringWrapper extends Object implements Serializable

serialVersionUID: 4193799052494327416L

Serialized Fields

data

TreeSet<E> data

Package org.biojava.bio.structure.secstruc

Class org.biojava.bio.structure.secstruc.SecStrucGroup extends HetatomImpl implements Serializable

serialVersionUID: 313490286720467714L

Serialized Fields

N

Atom N

CA

Atom CA

C

Atom C

O

Atom O

H

Atom H

original

Group original

Package org.biojava3.core.exceptions

Class org.biojava3.core.exceptions.CompoundNotFoundError extends Error implements Serializable

serialVersionUID: 1L

Class org.biojava3.core.exceptions.FileAccessError extends Error implements Serializable

serialVersionUID: 6513440232428438424L

Class org.biojava3.core.exceptions.HeaderParseException extends Error implements Serializable

serialVersionUID: -8356845980320906455L

Class org.biojava3.core.exceptions.ParserException extends RuntimeException implements Serializable

serialVersionUID: -4101924035353204493L

Class org.biojava3.core.exceptions.SequenceLengthError extends Error implements Serializable

serialVersionUID: -5486504706601790351L

Class org.biojava3.core.exceptions.TranslationException extends RuntimeException implements Serializable

serialVersionUID: -3017433758219757440L


Package org.biojava3.genome.parsers.gff

Class org.biojava3.genome.parsers.gff.FeatureList extends ArrayList<FeatureI> implements Serializable

Serialized Fields

mLocation

Location mLocation

Package org.biojava3.protmod.structure

Class org.biojava3.protmod.structure.ModifiedCompoundImpl extends Object implements Serializable

serialVersionUID: 1656563037849815427L

Serialized Fields

originalModification

ProteinModification originalModification

modification

ProteinModification modification

groups

Set<E> groups

atomLinkages

Map<K,V> atomLinkages

Package org.biojava3.structure.gui

Class org.biojava3.structure.gui.OpenAstexViewerImpl extends Object implements Serializable


Package org.biojava3.ws.alignment

Package org.biojava3.ws.alignment.qblast

Class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties extends Object implements Serializable

serialVersionUID: 7158270364392309841L

Serialized Fields

param

Map<K,V> param

Class org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties extends Object implements Serializable

serialVersionUID: -9202060390925345163L

Serialized Fields

param

Map<K,V> param

Package org.forester.archaeopteryx

Class org.forester.archaeopteryx.ArchaeopteryxA extends JApplet implements Serializable

serialVersionUID: 2314899014580484146L

Serialized Fields

_mainframe_applet

MainFrameApplet _mainframe_applet

_url_string

String _url_string

_message_1

String _message_1

_message_2

String _message_2

Class org.forester.archaeopteryx.ArchaeopteryxE extends JApplet implements Serializable

serialVersionUID: -1220055577935759443L

Serialized Fields

_configuration

org.forester.archaeopteryx.Configuration _configuration

_main_panel

org.forester.archaeopteryx.MainPanelApplets _main_panel

_jmenubar

JMenuBar _jmenubar

_options_jmenu

JMenu _options_jmenu

_font_size_menu

JMenu _font_size_menu

_super_tiny_fonts_mi

JMenuItem _super_tiny_fonts_mi

_tiny_fonts_mi

JMenuItem _tiny_fonts_mi

_small_fonts_mi

JMenuItem _small_fonts_mi

_medium_fonts_mi

JMenuItem _medium_fonts_mi

_large_fonts_mi

JMenuItem _large_fonts_mi

_textframe

org.forester.archaeopteryx.TextFrame _textframe

_tools_menu

JMenu _tools_menu

_taxcolor_item

JMenuItem _taxcolor_item

_confcolor_item

JMenuItem _confcolor_item

_midpoint_root_item

JMenuItem _midpoint_root_item

_view_jmenu

JMenu _view_jmenu

_view_as_XML_item

JMenuItem _view_as_XML_item

_view_as_NH_item

JMenuItem _view_as_NH_item

_view_as_NHX_item

JMenuItem _view_as_NHX_item

_view_as_nexus_item

JMenuItem _view_as_nexus_item

_type_menu

JMenu _type_menu

_rectangular_type_cbmi

JCheckBoxMenuItem _rectangular_type_cbmi

_triangular_type_cbmi

JCheckBoxMenuItem _triangular_type_cbmi

_curved_type_cbmi

JCheckBoxMenuItem _curved_type_cbmi

_convex_type_cbmi

JCheckBoxMenuItem _convex_type_cbmi

_euro_type_cbmi

JCheckBoxMenuItem _euro_type_cbmi

_rounded_type_cbmi

JCheckBoxMenuItem _rounded_type_cbmi

_unrooted_type_cbmi

JCheckBoxMenuItem _unrooted_type_cbmi

_circular_type_cbmi

JCheckBoxMenuItem _circular_type_cbmi

_help_item

JMenuItem _help_item

_about_item

JMenuItem _about_item

_help_jmenu

JMenu _help_jmenu

_website_item

JMenuItem _website_item

_phyloxml_website_item

JMenuItem _phyloxml_website_item

_phyloxml_ref_item

JMenuItem _phyloxml_ref_item

_aptx_ref_item

JMenuItem _aptx_ref_item

_remove_branch_color_item

JMenuItem _remove_branch_color_item

_infer_common_sn_names_item

JMenuItem _infer_common_sn_names_item

_screen_antialias_cbmi

JCheckBoxMenuItem _screen_antialias_cbmi

_background_gradient_cbmi

JCheckBoxMenuItem _background_gradient_cbmi

_non_lined_up_cladograms_rbmi

JRadioButtonMenuItem _non_lined_up_cladograms_rbmi

_uniform_cladograms_rbmi

JRadioButtonMenuItem _uniform_cladograms_rbmi

_ext_node_dependent_cladogram_rbmi

JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi

_options

org.forester.archaeopteryx.Options _options

_choose_font_mi

JMenuItem _choose_font_mi

_switch_colors_mi

JMenuItem _switch_colors_mi

_label_direction_cbmi

JCheckBoxMenuItem _label_direction_cbmi

_show_node_boxes_cbmi

JCheckBoxMenuItem _show_node_boxes_cbmi

_show_scale_cbmi

JCheckBoxMenuItem _show_scale_cbmi

_search_case_senstive_cbmi

JCheckBoxMenuItem _search_case_senstive_cbmi

_search_whole_words_only_cbmi

JCheckBoxMenuItem _search_whole_words_only_cbmi

_inverse_search_result_cbmi

JCheckBoxMenuItem _inverse_search_result_cbmi

_show_overview_cbmi

JCheckBoxMenuItem _show_overview_cbmi

_choose_minimal_confidence_mi

JMenuItem _choose_minimal_confidence_mi

_show_branch_length_values_cbmi

JCheckBoxMenuItem _show_branch_length_values_cbmi

_collapse_species_specific_subtrees

JMenuItem _collapse_species_specific_subtrees

_overview_placment_mi

JMenuItem _overview_placment_mi

_collapse_below_threshold

JMenuItem _collapse_below_threshold

_radio_group_1

ButtonGroup _radio_group_1

Class org.forester.archaeopteryx.FontChooser extends JDialog implements Serializable

serialVersionUID: 62256323L

Serialized Fields

_font

Font _font

_option

int _option

_type

String _type

_style

int _style

_size

int _size

_font_list

JList _font_list

_style_list

JList _style_list

_size_list

JList _size_list

_fonts_tf

JTextField _fonts_tf

_style_tf

JTextField _style_tf

_size_tf

JTextField _size_tf

_fonts_label

JLabel _fonts_label

_style_label

JLabel _style_label

_size_label

JLabel _size_label

_font_jsp

JScrollPane _font_jsp

_style_jsp

JScrollPane _style_jsp

_size_jsp

JScrollPane _size_jsp

_ok_button

JButton _ok_button

_cancel_button

JButton _cancel_button

_test_tf

JTextField _test_tf

Class org.forester.archaeopteryx.MainFrame extends JFrame implements Serializable

serialVersionUID: 3655000897845508358L

Serialized Fields

_jmenubar

JMenuBar _jmenubar

_file_jmenu

JMenu _file_jmenu

_tools_menu

JMenu _tools_menu

_view_jmenu

JMenu _view_jmenu

_options_jmenu

JMenu _options_jmenu

_font_size_menu

JMenu _font_size_menu

_help_jmenu

JMenu _help_jmenu

_load_phylogeny_from_webservice_menu_items

JMenuItem[] _load_phylogeny_from_webservice_menu_items

_open_item

JMenuItem _open_item

_open_url_item

JMenuItem _open_url_item

_save_item

JMenuItem _save_item

_save_all_item

JMenuItem _save_all_item

_close_item

JMenuItem _close_item

_exit_item

JMenuItem _exit_item

_new_item

JMenuItem _new_item

_midpoint_root_item

JMenuItem _midpoint_root_item

_taxcolor_item

JMenuItem _taxcolor_item

_confcolor_item

JMenuItem _confcolor_item

_infer_common_sn_names_item

JMenuItem _infer_common_sn_names_item

_collapse_species_specific_subtrees

JMenuItem _collapse_species_specific_subtrees

_collapse_below_threshold

JMenuItem _collapse_below_threshold

_super_tiny_fonts_item

JMenuItem _super_tiny_fonts_item

_tiny_fonts_item

JMenuItem _tiny_fonts_item

_small_fonts_item

JMenuItem _small_fonts_item

_medium_fonts_item

JMenuItem _medium_fonts_item

_large_fonts_item

JMenuItem _large_fonts_item

_choose_font_mi

JMenuItem _choose_font_mi

_switch_colors_mi

JMenuItem _switch_colors_mi

_label_direction_cbmi

JCheckBoxMenuItem _label_direction_cbmi

_screen_antialias_cbmi

JCheckBoxMenuItem _screen_antialias_cbmi

_background_gradient_cbmi

JCheckBoxMenuItem _background_gradient_cbmi

_show_node_boxes_cbmi

JCheckBoxMenuItem _show_node_boxes_cbmi

_non_lined_up_cladograms_rbmi

JRadioButtonMenuItem _non_lined_up_cladograms_rbmi

_uniform_cladograms_rbmi

JRadioButtonMenuItem _uniform_cladograms_rbmi

_ext_node_dependent_cladogram_rbmi

JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi

_show_branch_length_values_cbmi

JCheckBoxMenuItem _show_branch_length_values_cbmi

_show_scale_cbmi

JCheckBoxMenuItem _show_scale_cbmi

_show_overview_cbmi

JCheckBoxMenuItem _show_overview_cbmi

_overview_placment_mi

JMenuItem _overview_placment_mi

_choose_minimal_confidence_mi

JMenuItem _choose_minimal_confidence_mi

_graphics_export_visible_only_cbmi

JCheckBoxMenuItem _graphics_export_visible_only_cbmi

_antialias_print_cbmi

JCheckBoxMenuItem _antialias_print_cbmi

_print_black_and_white_cbmi

JCheckBoxMenuItem _print_black_and_white_cbmi

_print_using_actual_size_cbmi

JCheckBoxMenuItem _print_using_actual_size_cbmi

_graphics_export_using_actual_size_cbmi

JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi

_print_size_mi

JMenuItem _print_size_mi

_choose_pdf_width_mi

JMenuItem _choose_pdf_width_mi

_internal_number_are_confidence_for_nh_parsing_cbmi

JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi

_extract_pfam_style_tax_codes_cbmi

JCheckBoxMenuItem _extract_pfam_style_tax_codes_cbmi

_replace_underscores_cbmi

JCheckBoxMenuItem _replace_underscores_cbmi

_ignore_quotes_in_nh_parsing_cbmi

JCheckBoxMenuItem _ignore_quotes_in_nh_parsing_cbmi

_search_case_senstive_cbmi

JCheckBoxMenuItem _search_case_senstive_cbmi

_search_whole_words_only_cbmi

JCheckBoxMenuItem _search_whole_words_only_cbmi

_inverse_search_result_cbmi

JCheckBoxMenuItem _inverse_search_result_cbmi

_type_menu

JMenu _type_menu

_rectangular_type_cbmi

JCheckBoxMenuItem _rectangular_type_cbmi

_triangular_type_cbmi

JCheckBoxMenuItem _triangular_type_cbmi

_curved_type_cbmi

JCheckBoxMenuItem _curved_type_cbmi

_convex_type_cbmi

JCheckBoxMenuItem _convex_type_cbmi

_euro_type_cbmi

JCheckBoxMenuItem _euro_type_cbmi

_rounded_type_cbmi

JCheckBoxMenuItem _rounded_type_cbmi

_unrooted_type_cbmi

JCheckBoxMenuItem _unrooted_type_cbmi

_circular_type_cbmi

JCheckBoxMenuItem _circular_type_cbmi

_view_as_NH_item

JMenuItem _view_as_NH_item

_view_as_NHX_item

JMenuItem _view_as_NHX_item

_view_as_XML_item

JMenuItem _view_as_XML_item

_view_as_nexus_item

JMenuItem _view_as_nexus_item

_about_item

JMenuItem _about_item

_help_item

JMenuItem _help_item

_website_item

JMenuItem _website_item

_phyloxml_website_item

JMenuItem _phyloxml_website_item

_phyloxml_ref_item

JMenuItem _phyloxml_ref_item

_aptx_ref_item

JMenuItem _aptx_ref_item

_mainpanel

MainPanel _mainpanel

_contentpane

Container _contentpane

_textframe

org.forester.archaeopteryx.TextFrame _textframe

_configuration

org.forester.archaeopteryx.Configuration _configuration

_remove_branch_color_item

JMenuItem _remove_branch_color_item

_options

org.forester.archaeopteryx.Options _options

Class org.forester.archaeopteryx.MainFrameApplet extends MainFrame implements Serializable

serialVersionUID: 1941019292746717053L

Serialized Fields

_applet

ArchaeopteryxA _applet

_radio_group_1

ButtonGroup _radio_group_1

Class org.forester.archaeopteryx.MainFrameApplication extends MainFrame implements Serializable

serialVersionUID: -799735726778865234L

Serialized Fields

_open_filechooser

JFileChooser _open_filechooser

_open_filechooser_for_species_tree

JFileChooser _open_filechooser_for_species_tree

_save_filechooser

JFileChooser _save_filechooser

_writetopdf_filechooser

JFileChooser _writetopdf_filechooser

_writetographics_filechooser

JFileChooser _writetographics_filechooser

_analysis_menu

JMenu _analysis_menu

_load_species_tree_item

JMenuItem _load_species_tree_item

_sdi_item

JMenuItem _sdi_item

_gsdi_item

JMenuItem _gsdi_item

_root_min_dups_item

JMenuItem _root_min_dups_item

_root_min_cost_l_item

JMenuItem _root_min_cost_l_item

_print_item

JMenuItem _print_item

_write_to_pdf_item

JMenuItem _write_to_pdf_item

_write_to_jpg_item

JMenuItem _write_to_jpg_item

_write_to_gif_item

JMenuItem _write_to_gif_item

_write_to_tif_item

JMenuItem _write_to_tif_item

_write_to_png_item

JMenuItem _write_to_png_item

_write_to_bmp_item

JMenuItem _write_to_bmp_item

_species_tree

Phylogeny _species_tree

_current_dir

File _current_dir

_radio_group_1

ButtonGroup _radio_group_1

Class org.forester.archaeopteryx.MainPanel extends JPanel implements Serializable

serialVersionUID: -2682765312661416435L

Serialized Fields

_mainframe

MainFrame _mainframe

_treepanels

List<E> _treepanels

_control_panel

org.forester.archaeopteryx.ControlPanel _control_panel

_treegraphic_scroll_panes

List<E> _treegraphic_scroll_panes

_treegraphic_scroll_pane_panels

List<E> _treegraphic_scroll_pane_panels

_configuration

org.forester.archaeopteryx.Configuration _configuration

_tabbed_pane

JTabbedPane _tabbed_pane

_colorset

org.forester.archaeopteryx.TreeColorSet _colorset

_fontset

TreeFontSet _fontset

_cut_or_copied_tree

Phylogeny _cut_or_copied_tree

_copied_and_pasted_nodes

Set<E> _copied_and_pasted_nodes

Class org.forester.archaeopteryx.TreePanel extends JPanel implements Serializable

serialVersionUID: -978349745916505029L

Serialized Fields

_rendering_hints

RenderingHints _rendering_hints

_treefile

File _treefile

_configuration

org.forester.archaeopteryx.Configuration _configuration

_node_frames

org.forester.archaeopteryx.NodeFrame[] _node_frames

_node_frame_index

int _node_frame_index

_phylogeny

Phylogeny _phylogeny

_phylogenies

Phylogeny[] _phylogenies

_subtree_index

int _subtree_index

_main_panel

MainPanel _main_panel

_found_nodes

Set<E> _found_nodes

_highlight_node

PhylogenyNode _highlight_node

_node_popup_menu

JPopupMenu _node_popup_menu

_node_popup_menu_items

JMenuItem[] _node_popup_menu_items

_longest_ext_node_info

int _longest_ext_node_info

_x_correction_factor

float _x_correction_factor

_ov_x_correction_factor

float _ov_x_correction_factor

_x_distance

float _x_distance

_y_distance

float _y_distance

_graphics_type

org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE _graphics_type

_domain_structure_width

double _domain_structure_width

_domain_structure_e_value_thr_exp

int _domain_structure_e_value_thr_exp

_last_drag_point_x

float _last_drag_point_x

_last_drag_point_y

float _last_drag_point_y

_control_panel

org.forester.archaeopteryx.ControlPanel _control_panel

_external_node_index

int _external_node_index

_polygon

Polygon _polygon

_sb

StringBuilder _sb

_color_chooser

JColorChooser _color_chooser

_scale_distance

double _scale_distance

_scale_label

String _scale_label

_cubic_curve

CubicCurve2D _cubic_curve

_quad_curve

QuadCurve2D _quad_curve

_line

Line2D _line

_ellipse

Ellipse2D _ellipse

_rectangle

Rectangle2D _rectangle

_options

org.forester.archaeopteryx.Options _options

_ov_max_width

float _ov_max_width

_ov_max_height

float _ov_max_height

_ov_x_position

int _ov_x_position

_ov_y_position

int _ov_y_position

_ov_y_start

int _ov_y_start

_ov_y_distance

float _ov_y_distance

_ov_x_distance

float _ov_x_distance

_ov_on

boolean _ov_on

_urt_starting_angle

double _urt_starting_angle

_urt_factor

float _urt_factor

_urt_factor_ov

float _urt_factor_ov

_phy_has_branch_lengths

boolean _phy_has_branch_lengths

_ov_rectangle

Rectangle2D _ov_rectangle

_in_ov_rect

boolean _in_ov_rect

_in_ov

boolean _in_ov

_ov_virtual_rectangle

Rectangle _ov_virtual_rectangle

_circ_max_depth

int _circ_max_depth

_circ_num_ext_nodes

int _circ_num_ext_nodes

_root

PhylogenyNode _root

_arc

Arc2D _arc

_urt_nodeid_angle_map

HashMap<K,V> _urt_nodeid_angle_map

_urt_nodeid_index_map

HashMap<K,V> _urt_nodeid_index_map

_nodeid_dist_to_leaf

HashMap<K,V> _nodeid_dist_to_leaf

_at

AffineTransform _at

_max_distance_to_root

double _max_distance_to_root

_dynamic_hiding_factor

int _dynamic_hiding_factor

_edited

boolean _edited

_node_desc_popup

Popup _node_desc_popup

_rollover_popup

JTextArea _rollover_popup

_popup_buffer

StringBuffer _popup_buffer

Package org.forester.io.parsers

Class org.forester.io.parsers.PhylogenyParserException extends IOException implements Serializable

serialVersionUID: -4810333295377881086L


Package org.forester.io.parsers.nexus

Class org.forester.io.parsers.nexus.NexusFormatException extends IOException implements Serializable

serialVersionUID: -8750474393398183410L


Package org.forester.io.parsers.nhx

Class org.forester.io.parsers.nhx.NHXFormatException extends IOException implements Serializable

serialVersionUID: 3756209394438250170L


Package org.forester.io.parsers.phyloxml

Class org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException extends PhyloXmlException implements Serializable

serialVersionUID: 3756209394438250170L

Class org.forester.io.parsers.phyloxml.PhyloXmlException extends RuntimeException implements Serializable

serialVersionUID: 3756209394438250170L