Overview  Package  Class  Tree  Deprecated  Index  Help 
 PREV   NEXT FRAMES    NO FRAMES    

Serialized Form

Package org.biojava.bio.structure

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

serialVersionUID: -6018854413829044230L

Serialized Fields

amino_char

java.lang.Character amino_char

secstruc

java.util.Map<K,V> secstruc

recordType

java.lang.String recordType

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

serialVersionUID: -2258364127420562883L

Serialized Fields

name

java.lang.String name

fullName

java.lang.String fullName

element

Element element

coords

double[] coords

pdbline

java.lang.String pdbline

pdbserial

int pdbserial

occupancy

double occupancy

tempfactor

double tempfactor

altLoc

java.lang.Character altLoc

parent

Group parent

id

long id

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

serialVersionUID: 4840370515056666418L

Serialized Fields

surname

java.lang.String surname

initials

java.lang.String initials

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

serialVersionUID: 1990171805277911840L

Serialized Fields

swissprot_id

java.lang.String swissprot_id

name

java.lang.String name

groups

java.util.List<E> groups

seqResGroups

java.util.List<E> seqResGroups

id

java.lang.Long id

mol

Compound mol

parent

Structure parent

pdbResnumMap

java.util.Map<K,V> pdbResnumMap

internalChainID

java.lang.String internalChainID

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

serialVersionUID: 2991897825657586356L

Serialized Fields

chainList

java.util.List<E> chainList

chainId

java.util.List<E> chainId

refChainId

java.lang.String refChainId

molId

java.lang.String molId

molName

java.lang.String molName

title

java.lang.String title

synonyms

java.util.List<E> synonyms

ecNums

java.util.List<E> ecNums

engineered

java.lang.String engineered

mutation

java.lang.String mutation

biologicalUnit

java.lang.String biologicalUnit

details

java.lang.String details

numRes

java.lang.String numRes

resNames

java.lang.String resNames

headerVars

java.lang.String headerVars

synthetic

java.lang.String synthetic

fragment

java.lang.String fragment

organismScientific

java.lang.String organismScientific

organismTaxId

java.lang.String organismTaxId

organismCommon

java.lang.String organismCommon

strain

java.lang.String strain

variant

java.lang.String variant

cellLine

java.lang.String cellLine

atcc

java.lang.String atcc

organ

java.lang.String organ

tissue

java.lang.String tissue

cell

java.lang.String cell

organelle

java.lang.String organelle

secretion

java.lang.String secretion

gene

java.lang.String gene

cellularLocation

java.lang.String cellularLocation

expressionSystem

java.lang.String expressionSystem

expressionSystemTaxId

java.lang.String expressionSystemTaxId

expressionSystemStrain

java.lang.String expressionSystemStrain

expressionSystemVariant

java.lang.String expressionSystemVariant

expressionSystemCellLine

java.lang.String expressionSystemCellLine

expressionSystemAtccNumber

java.lang.String expressionSystemAtccNumber

expressionSystemOrgan

java.lang.String expressionSystemOrgan

expressionSystemTissue

java.lang.String expressionSystemTissue

expressionSystemCell

java.lang.String expressionSystemCell

expressionSystemOrganelle

java.lang.String expressionSystemOrganelle

expressionSystemCellularLocation

java.lang.String expressionSystemCellularLocation

expressionSystemVectorType

java.lang.String expressionSystemVectorType

expressionSystemVector

java.lang.String expressionSystemVector

expressionSystemPlasmid

java.lang.String expressionSystemPlasmid

expressionSystemGene

java.lang.String expressionSystemGene

expressionSystemOtherDetails

java.lang.String expressionSystemOtherDetails

id

java.lang.Long id

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

serialVersionUID: -1050178577542224379L

Serialized Fields

parent

Structure parent

idCode

java.lang.String idCode

chainId

java.lang.Character chainId

seqbegin

int seqbegin

insertBegin

char insertBegin

seqEnd

int seqEnd

insertEnd

char insertEnd

database

java.lang.String database

dbAccession

java.lang.String dbAccession

dbIdCode

java.lang.String dbIdCode

dbSeqBegin

int dbSeqBegin

idbnsBegin

char idbnsBegin

dbSeqEnd

int dbSeqEnd

idbnsEnd

char idbnsEnd

id

java.lang.Long id

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

serialVersionUID: 4491470432023820382L

Serialized Fields

properties

java.util.Map<K,V> properties

id

long id

pdb_flag

boolean pdb_flag

pdb_name

java.lang.String pdb_name

residueNumber

ResidueNumber residueNumber

atoms

java.util.List<E> atoms

parent

Chain parent

atomLookup

java.util.Map<K,V> atomLookup

atomSingleCharLookup

java.util.Map<K,V> atomSingleCharLookup

chemComp

ChemComp chemComp

altLocs

java.util.List<E> altLocs

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

serialVersionUID: 5062668226159515468L

Serialized Fields

authorList

java.util.List<E> authorList

editorList

java.util.List<E> editorList

title

java.lang.String title

ref

java.lang.String ref

journalName

java.lang.String journalName

volume

java.lang.String volume

startPage

java.lang.String startPage

publicationDate

int publicationDate

publisher

java.lang.String publisher

refn

java.lang.String refn

pmid

java.lang.String pmid

doi

java.lang.String doi

published

boolean published

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

serialVersionUID: -7467726932980288712L

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

serialVersionUID: -7949886749566087669L

Serialized Fields

a

float a

b

float b

c

float c

alpha

float alpha

beta

float beta

gamma

float gamma

spaceGroup

java.lang.String spaceGroup

z

int z

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

serialVersionUID: -5834326174085429508L

Serialized Fields

method

java.lang.String method

title

java.lang.String title

description

java.lang.String description

idCode

java.lang.String idCode

classification

java.lang.String classification

depDate

java.util.Date depDate

modDate

java.util.Date modDate

technique

java.lang.String technique

resolution

float resolution

authors

java.lang.String authors

nrBioAssemblies

int nrBioAssemblies

id

java.lang.Long id

dateFormat

java.text.DateFormat dateFormat

tranformationMap

java.util.Map<K,V> tranformationMap

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

serialVersionUID: -4577047072916341237L

Serialized Fields

siteID

java.lang.String siteID

groups

java.util.List<E> groups

evCode

java.lang.String evCode

description

java.lang.String description

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

serialVersionUID: -8663681100691188647L

Serialized Fields

serNum

int serNum

chainID1

java.lang.String chainID1

chainID2

java.lang.String chainID2

resnum1

java.lang.String resnum1

resnum2

java.lang.String resnum2

insCode1

java.lang.String insCode1

insCode2

java.lang.String insCode2

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

serialVersionUID: 62946250941673093L

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

serialVersionUID: -8344837138032851347L

Serialized Fields

pdb_id

java.lang.String pdb_id

models

java.util.List<E> models

header

java.util.Map<K,V> header

connections

java.util.List<E> connections

compounds

java.util.List<E> compounds

dbrefs

java.util.List<E> dbrefs

ssbonds

java.util.List<E> ssbonds

sites

java.util.List<E> sites

hetAtoms

java.util.List<E> hetAtoms

name

java.lang.String name

journalArticle

JournalArticle journalArticle

pdbHeader

PDBHeader pdbHeader

crystallographicInfo

PDBCrystallographicInfo crystallographicInfo

nmrflag

boolean nmrflag

id

java.lang.Long id

biologicalAssembly

boolean biologicalAssembly

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

serialVersionUID: -5571696240026118421L

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

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

serialVersionUID: 1L

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

serialVersionUID: 4021229518711762954L

Serialized Fields

name

java.lang.String name

pdbId

java.lang.String pdbId

chainId

java.lang.String chainId

cathPattern

java.lang.String cathPattern

mySource

org.biojava.bio.structure.align.client.StructureName.Source mySource
Package org.biojava.bio.structure.align.gui

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

serialVersionUID: 0L

Serialized Fields

algorithm

StructureAlignment algorithm

abortB

javax.swing.JButton abortB

tab1

SelectPDBPanel tab1

tab2

PDBUploadPanel tab2

tab3

ScopSelectPanel tab3

thread

java.lang.Thread thread

alicalc

AlignmentCalculationRunnable alicalc

masterPane

javax.swing.JTabbedPane masterPane

tabPane

javax.swing.JTabbedPane tabPane

progress

javax.swing.JProgressBar progress

dbsearch

DBSearchGUI dbsearch

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

serialVersionUID: 5092386365924879073L

Serialized Fields

tp

javax.swing.JEditorPane tp

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

serialVersionUID: 0L

Serialized Fields

textField

javax.swing.JTextField textField

config

UserConfiguration config

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

serialVersionUID: -1055193854675583808L

Serialized Fields

pdbSplit

javax.swing.JCheckBox pdbSplit

fromFtp

javax.swing.JCheckBox fromFtp

fileType

javax.swing.JComboBox fileType

pdbDir

javax.swing.JTextField pdbDir

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

serialVersionUID: -5657960663049062301L

Serialized Fields

algorithm

StructureAlignment algorithm

tab1

SelectPDBPanel tab1

tabPane

javax.swing.JTabbedPane tabPane

tab2

PDBUploadPanel tab2

tab3

ScopSelectPanel tab3

listPane

javax.swing.JPanel listPane

abortB

javax.swing.JButton abortB

alicalc

AlignmentCalcDB alicalc

progress

javax.swing.JProgressBar progress

drawer

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

outFileLocation

javax.swing.JTextField outFileLocation

useDomainSplit

java.lang.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 javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

alignmentsProcessed

int alignmentsProcessed

progressBar

javax.swing.JProgressBar progressBar

taskOutput

javax.swing.JTextArea taskOutput

stopButton

javax.swing.JButton stopButton

farmJob

FarmJob farmJob

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

serialVersionUID: -3337337068138131455L

Class org.biojava.bio.structure.align.gui.MemoryMonitor extends javax.swing.JPanel implements Serializable

serialVersionUID: 56289234782130L

Serialized Fields

surf

MemoryMonitor.Surface surf

controls

javax.swing.JPanel controls

doControls

boolean doControls

tf

javax.swing.JTextField tf

Class org.biojava.bio.structure.align.gui.MemoryMonitor.Surface extends javax.swing.JPanel implements Serializable

serialVersionUID: 2387409854370432908L

Serialized Fields

thread

java.lang.Thread thread

sleepAmount

long sleepAmount

w

int w

h

int h

bimg

java.awt.image.BufferedImage bimg

big

java.awt.Graphics2D big

font

java.awt.Font font

r

java.lang.Runtime r

columnInc

int columnInc

pts

int[] pts

ptNum

int ptNum

ascent

int ascent

descent

int descent

graphOutlineRect

java.awt.Rectangle graphOutlineRect

mfRect

java.awt.geom.Rectangle2D mfRect

muRect

java.awt.geom.Rectangle2D muRect

graphLine

java.awt.geom.Line2D graphLine

graphColor

java.awt.Color graphColor

mfColor

java.awt.Color mfColor

usedStr

java.lang.String usedStr

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

serialVersionUID: 723386061184110161L

Serialized Fields

params

ConfigStrucAligParams params

textFields

java.util.List<E> textFields

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

serialVersionUID: 4002475313717172193L

Serialized Fields

debug

boolean debug

f1

javax.swing.JTextField f1

f2

javax.swing.JTextField f2

c1

javax.swing.JTextField c1

c2

javax.swing.JTextField c2

r1

javax.swing.JTextField r1

r2

javax.swing.JTextField r2

config

UserConfiguration config

configPane

javax.swing.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

java.awt.Font seqFont

eqFont

java.awt.Font eqFont

jmol

StructureAlignmentJmol jmol

mouseMoLi

AligPanelMouseMotionListener mouseMoLi

selection

java.util.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 javax.swing.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 javax.swing.JTextField implements Serializable

serialVersionUID: 8591734727984365156L

Serialized Fields

defaultText

java.lang.String defaultText

dialog

javax.swing.JDialog dialog

location

java.awt.Point location

list

javax.swing.JList list

suggestions

java.util.Vector<E> suggestions

lastWord

java.lang.String lastWord
last word that was entered by user

autoSuggestProvider

AutoSuggestProvider autoSuggestProvider

regular

java.awt.Font regular

busy

java.awt.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

java.awt.Dimension currentSize

rectClip

java.awt.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 java.lang.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 java.lang.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 java.lang.Object implements Serializable

serialVersionUID: -4474029015606617947L

Serialized Fields

algorithmName

java.lang.String algorithmName

version

java.lang.String version

name1

java.lang.String name1

name2

java.lang.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

java.util.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

java.lang.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

java.lang.Double conn

dvar

java.lang.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

java.lang.String description2
Package org.biojava.bio.structure.align.pairwise

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

serialVersionUID: -4132105905712445473L

Serialized Fields

alignments

AlternativeAlignment[] alignments

pdb1

java.lang.String pdb1

pdb2

java.lang.String pdb2

chain1

java.lang.String chain1

chain2

java.lang.String chain2

length1

int length1

length2

int length2

calculationTime

long calculationTime

ioTime

long ioTime

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

serialVersionUID: -6226717654562221241L

Serialized Fields

idx1

int[] idx1

idx2

int[] idx2

pdbresnum1

java.lang.String[] pdbresnum1

pdbresnum2

java.lang.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 java.lang.Exception implements Serializable

serialVersionUID: -8047100079715000276L

Package org.biojava.bio.structure.cath

Class org.biojava.bio.structure.cath.CathDomain extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

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.

classId

java.lang.Integer classId
The class number of this domain.

architectureId

java.lang.Integer architectureId
The architecture number of this domain.

topologyId

java.lang.Integer topologyId
The topology number of this domain.

homologyId

java.lang.Integer homologyId
The homologous superfamily number of this domain.

sequenceFamilyId

java.lang.Integer sequenceFamilyId
The sequence family (35% identity) number of this domain.

orthologousSequenceFamilyId

java.lang.Integer orthologousSequenceFamilyId
The "orthologous" sequence family (60% identity) number of this domain.

likeSequenceFamilyId

java.lang.Integer likeSequenceFamilyId
The "Like" sequence family (95% identity) number of this domain.

identicalSequenceFamilyId

java.lang.Integer identicalSequenceFamilyId
The identical sequence family (100% identity) number of this domain.

domainCounter

java.lang.Integer domainCounter
The count of this domain among the identical sequence family members.

length

java.lang.Integer length
The domain length..

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.

format

java.lang.String format
The format and version of the CathDomainDescriptionFile.

version

java.lang.String version
The CATH version.

date

java.util.Date date

name

java.lang.String name
The so-called name field holds a potentially long description of the domain.

source

java.lang.String source
Complete source organism listing.

sequenceHeader

java.lang.String sequenceHeader
FASTA header.

sequence

java.lang.String sequence
FASTA sequence.

segments

java.util.List<E> segments
List of all sub-domain segments.

comment

java.lang.String comment
A (potentially long) comment. Usually empty.

Class org.biojava.bio.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.

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).

length

java.lang.Integer length
Number of residues in the segment. This value is parsed, not calculated.

Class org.biojava.bio.structure.cath.CathNode extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

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.

description

java.lang.String description
A name or description.

category

CathCategory category
This node's level within the hierarchy. One of CATH, not CATHSOLID.

Class org.biojava.bio.structure.cath.CathSegment extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

segmentId

java.lang.Integer segmentId
The number of this segment within the domain.

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).

length

java.lang.Integer length
Number of residues in the segment. This value is parsed, not calculated.

sequenceHeader

java.lang.String sequenceHeader
FASTA header.

sequence

java.lang.String sequence
FASTA sequence.

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

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

serialVersionUID: -1293994033102271366L

Serialized Fields

id

java.lang.String id

size

int size

nseg

int nseg

score

double score

segments

java.util.List<E> segments

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

serialVersionUID: 1393487067559539657L

Serialized Fields

from

java.lang.Integer from

to

java.lang.Integer to

score

double score
Package org.biojava.bio.structure.gui

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

serialVersionUID: -1720879395453257846L

Serialized Fields

_bufImage

java.awt.image.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 javax.swing.JPanel implements Serializable

serialVersionUID: -8082261434322968652L

Serialized Fields

mPanel

JMatrixPanel mPanel

slider

javax.swing.JSlider slider

scroll

javax.swing.JScrollPane scroll

coloring

javax.swing.JComboBox coloring

gradients

java.util.Map<K,V> gradients

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

serialVersionUID: -2000575579184232365L

Serialized Fields

min

int min

max

int max

title

javax.swing.JLabel title

gradientContainer

javax.swing.JPanel gradientContainer

Class org.biojava.bio.structure.gui.SequenceDisplay extends javax.swing.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

javax.swing.JSlider residueSizeSlider

percentageDisplay

javax.swing.JLabel percentageDisplay

idx1

int[] idx1

idx2

int[] idx2

logger

java.util.logging.Logger logger

apos

java.util.List<E> apos

scale

float scale

mouseListener1

SequenceMouseListener mouseListener1

mouseListener2

SequenceMouseListener mouseListener2

label1

javax.swing.JLabel label1

label2

javax.swing.JLabel label2
Package org.biojava.bio.structure.gui.util

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

serialVersionUID: -5682120627824627408L

Serialized Fields

debug

boolean debug

pdbDir

javax.swing.JTextField pdbDir

f1

javax.swing.JTextField f1

f2

javax.swing.JTextField f2

c1

javax.swing.JTextField c1

c2

javax.swing.JTextField c2

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

serialVersionUID: -5682120627824627408L

Serialized Fields

debug

boolean debug

pdbDir

javax.swing.JTextField pdbDir

f1

javax.swing.JTextField f1

f2

javax.swing.JTextField f2

c1

javax.swing.JTextField c1

c2

javax.swing.JTextField c2

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

serialVersionUID: 1L

Serialized Fields

fileType

javax.swing.JComboBox fileType

filePath1

javax.swing.JTextField filePath1

filePath2

javax.swing.JTextField filePath2

chain1

javax.swing.JTextField chain1

chain2

javax.swing.JTextField chain2

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

serialVersionUID: 757947454156959178L

Serialized Fields

dom1

JAutoSuggest dom1

dom2

JAutoSuggest dom2

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

serialVersionUID: 7893248902423L

Serialized Fields

logger

java.util.logging.Logger logger

chain

Chain chain

chainLength

int chainLength

scale

float scale

seqArr

java.lang.Character[] seqArr

coordManager

CoordManager coordManager

position

int position

apos

java.util.List<E> apos
Package org.biojava.bio.structure.gui.util.color

Class org.biojava.bio.structure.gui.util.color.GradientPanel extends javax.swing.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 java.awt.color.ColorSpace implements Serializable

serialVersionUID: 8324413992279510075L

Package org.biojava.bio.structure.io

Class org.biojava.bio.structure.io.FileParsingParameters extends java.lang.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

parseBioAssembly

boolean parseBioAssembly
should we parse the biological assembly information from a file?

maxAtoms

int maxAtoms

fullAtomNames

java.lang.String[] fullAtomNames

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

serialVersionUID: 219047230178423923L

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

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

serialVersionUID: -4736341142030215915L

Serialized Fields

id

java.lang.String id

name

java.lang.String name

type

java.lang.String type

pdbx_type

java.lang.String pdbx_type

formula

java.lang.String formula

mon_nstd_parent_comp_id

java.lang.String mon_nstd_parent_comp_id

pdbx_synonyms

java.lang.String pdbx_synonyms

pdbx_formal_charge

java.lang.String pdbx_formal_charge

pdbx_initial_date

java.lang.String pdbx_initial_date

pdbx_modified_date

java.lang.String pdbx_modified_date

pdbx_ambiguous_flag

java.lang.String pdbx_ambiguous_flag

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

formula_weight

java.lang.String formula_weight

one_letter_code

java.lang.String one_letter_code

three_letter_code

java.lang.String three_letter_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_ideal_coordinates_details

java.lang.String pdbx_ideal_coordinates_details

pdbx_ideal_coordinates_missing_flag

java.lang.String pdbx_ideal_coordinates_missing_flag

pdbx_model_coordinates_db_code

java.lang.String pdbx_model_coordinates_db_code

pdbx_subcomponent_list

java.lang.String pdbx_subcomponent_list

pdbx_processing_site

java.lang.String pdbx_processing_site

mon_nstd_flag

java.lang.String mon_nstd_flag

descriptors

java.util.List<E> descriptors

residueType

ResidueType residueType

polymerType

PolymerType polymerType

standard

boolean standard

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

serialVersionUID: 1078685833800736278L

Serialized Fields

comp_id

java.lang.String comp_id

type

java.lang.String type

program

java.lang.String program

program_version

java.lang.String program_version

descriptor

java.lang.String descriptor

Class org.biojava.bio.structure.io.mmcif.model.PdbxStructAssembly extends java.lang.Object implements Serializable

serialVersionUID: 3104504686693887219L

Serialized Fields

id

java.lang.String id

details

java.lang.String details

method_details

java.lang.String method_details

oligomeric_details

java.lang.String oligomeric_details

oligomeric_count

java.lang.String oligomeric_count

Class org.biojava.bio.structure.io.mmcif.model.PdbxStructAssemblyGen extends java.lang.Object implements Serializable

serialVersionUID: 6739568389242514332L

Serialized Fields

assembly_id

java.lang.String assembly_id

oper_expression

java.lang.String oper_expression

asym_id_list

java.lang.String asym_id_list

Class org.biojava.bio.structure.io.mmcif.model.PdbxStructOperList extends java.lang.Object implements Serializable

serialVersionUID: 8933552854747969787L

Serialized Fields

id

java.lang.String id

type

java.lang.String type

matrix

Matrix matrix

vector

double[] vector
Package org.biojava.bio.structure.io.sifts

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

serialVersionUID: 750353252427491487L

Serialized Fields

type

java.lang.String type

entityId

java.lang.String entityId

segments

java.util.List<E> segments

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

serialVersionUID: 3425769737629800828L

Serialized Fields

pdbResNum

java.lang.String pdbResNum

pdbResName

java.lang.String pdbResName

chainId

java.lang.String chainId

uniProtResName

java.lang.String uniProtResName

uniProtPos

java.lang.Integer uniProtPos

naturalPos

java.lang.Integer naturalPos

seqResName

java.lang.String seqResName

pdbId

java.lang.String pdbId

uniProtAccessionId

java.lang.String uniProtAccessionId

notObserved

java.lang.Boolean notObserved

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

serialVersionUID: -8005129863256307153L

Serialized Fields

segId

java.lang.String segId

start

java.lang.String start

end

java.lang.String end

residues

java.util.List<E> residues
Package org.biojava.bio.structure.jama

Class org.biojava.bio.structure.jama.CholeskyDecomposition extends java.lang.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 java.lang.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 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.

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 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.bio.structure.jama.QRDecomposition extends java.lang.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 java.lang.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 java.lang.Object implements Serializable

serialVersionUID: 8579808155176839161L

Serialized Fields

sunID

int sunID

category

ScopCategory category

classificationId

java.lang.String classificationId

name

java.lang.String name

description

java.lang.String description

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

serialVersionUID: 5890476209571654301L

Serialized Fields

scopId

java.lang.String scopId

pdbId

java.lang.String pdbId

ranges

java.util.List<E> ranges

classificationId

java.lang.String classificationId

sunid

java.lang.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 java.lang.Object implements Serializable

serialVersionUID: 1187083944488580995L

Serialized Fields

sunid

int sunid

parentSunid

int parentSunid

children

java.util.List<E> children
Package org.biojava.bio.structure.scop.server

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

serialVersionUID: 4924350548761431852L

Serialized Fields

scopDescriptions

java.util.List<E> scopDescriptions

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

serialVersionUID: 7693404355005856746L

Serialized Fields

domains

java.util.List<E> domains

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

serialVersionUID: 5327454882500340305L

Serialized Fields

scopNodes

java.util.List<E> scopNodes

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

serialVersionUID: 4193799052494327416L

Serialized Fields

data

java.util.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 java.lang.Error implements Serializable

serialVersionUID: 1L

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

serialVersionUID: 6513440232428438424L

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

serialVersionUID: -8356845980320906455L

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

serialVersionUID: -4101924035353204493L

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

serialVersionUID: -5486504706601790351L

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

serialVersionUID: -3017433758219757440L

Package org.biojava3.genome.parsers.gff

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

Serialized Fields

featindex

java.util.Map<K,V> featindex

mLocation

Location mLocation
Package org.biojava3.protmod.structure

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

serialVersionUID: 1656563037849815427L

Serialized Fields

originalModification

ProteinModification originalModification

modification

ProteinModification modification

groups

java.util.Set<E> groups

atomLinkages

java.util.Map<K,V> atomLinkages
Package org.biojava3.structure.gui

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

Package org.biojava3.ws.alignment
Package org.biojava3.ws.alignment.qblast

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

serialVersionUID: 7158270364392309841L

Serialized Fields

param

java.util.Map<K,V> param

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

serialVersionUID: -9202060390925345163L

Serialized Fields

param

java.util.Map<K,V> param
Package org.biojava3.ws.hmmer

Class org.biojava3.ws.hmmer.HmmerDomain extends java.lang.Object implements Serializable

serialVersionUID: 8004302800150892757L

Serialized Fields

sqFrom

java.lang.Integer sqFrom

sqTo

java.lang.Integer sqTo

aliLenth

java.lang.Integer aliLenth

simCount

java.lang.Integer simCount

hmmFrom

java.lang.Integer hmmFrom

hmmTo

java.lang.Integer hmmTo

hmmName

java.lang.String hmmName

hmmDesc

java.lang.String hmmDesc

hmmAcc

java.lang.String hmmAcc

Class org.biojava3.ws.hmmer.HmmerResult extends java.lang.Object implements Serializable

serialVersionUID: -6016026193090737943L

Serialized Fields

desc

java.lang.String desc

score

java.lang.Float score

evalue

java.lang.Float evalue

pvalue

java.lang.Double pvalue

acc

java.lang.String acc

dcl

java.lang.Integer dcl

name

java.lang.String name

ndom

java.lang.Integer ndom

nreported

java.lang.Integer nreported

domains

java.util.SortedSet<E> domains
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

_url_string

java.lang.String _url_string

_message_1

java.lang.String _message_1

_message_2

java.lang.String _message_2

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

serialVersionUID: -1220055577935759443L

Serialized Fields

_configuration

Configuration _configuration

_main_panel

org.forester.archaeopteryx.MainPanelApplets _main_panel

_jmenubar

javax.swing.JMenuBar _jmenubar

_options_jmenu

javax.swing.JMenu _options_jmenu

_font_size_menu

javax.swing.JMenu _font_size_menu

_super_tiny_fonts_mi

javax.swing.JMenuItem _super_tiny_fonts_mi

_tiny_fonts_mi

javax.swing.JMenuItem _tiny_fonts_mi

_small_fonts_mi

javax.swing.JMenuItem _small_fonts_mi

_medium_fonts_mi

javax.swing.JMenuItem _medium_fonts_mi

_large_fonts_mi

javax.swing.JMenuItem _large_fonts_mi

_textframe

org.forester.archaeopteryx.TextFrame _textframe

_tools_menu

javax.swing.JMenu _tools_menu

_taxcolor_item

javax.swing.JMenuItem _taxcolor_item

_confcolor_item

javax.swing.JMenuItem _confcolor_item

_midpoint_root_item

javax.swing.JMenuItem _midpoint_root_item

_view_jmenu

javax.swing.JMenu _view_jmenu

_view_as_XML_item

javax.swing.JMenuItem _view_as_XML_item

_view_as_NH_item

javax.swing.JMenuItem _view_as_NH_item

_view_as_NHX_item

javax.swing.JMenuItem _view_as_NHX_item

_view_as_nexus_item

javax.swing.JMenuItem _view_as_nexus_item

_type_menu

javax.swing.JMenu _type_menu

_rectangular_type_cbmi

javax.swing.JCheckBoxMenuItem _rectangular_type_cbmi

_triangular_type_cbmi

javax.swing.JCheckBoxMenuItem _triangular_type_cbmi

_curved_type_cbmi

javax.swing.JCheckBoxMenuItem _curved_type_cbmi

_convex_type_cbmi

javax.swing.JCheckBoxMenuItem _convex_type_cbmi

_euro_type_cbmi

javax.swing.JCheckBoxMenuItem _euro_type_cbmi

_rounded_type_cbmi

javax.swing.JCheckBoxMenuItem _rounded_type_cbmi

_unrooted_type_cbmi

javax.swing.JCheckBoxMenuItem _unrooted_type_cbmi

_circular_type_cbmi

javax.swing.JCheckBoxMenuItem _circular_type_cbmi

_help_item

javax.swing.JMenuItem _help_item

_about_item

javax.swing.JMenuItem _about_item

_help_jmenu

javax.swing.JMenu _help_jmenu

_website_item

javax.swing.JMenuItem _website_item

_phyloxml_website_item

javax.swing.JMenuItem _phyloxml_website_item

_phyloxml_ref_item

javax.swing.JMenuItem _phyloxml_ref_item

_aptx_ref_item

javax.swing.JMenuItem _aptx_ref_item

_remove_branch_color_item

javax.swing.JMenuItem _remove_branch_color_item

_infer_common_sn_names_item

javax.swing.JMenuItem _infer_common_sn_names_item

_show_domain_labels

javax.swing.JCheckBoxMenuItem _show_domain_labels

_color_labels_same_as_parent_branch

javax.swing.JCheckBoxMenuItem _color_labels_same_as_parent_branch

_abbreviate_scientific_names

javax.swing.JCheckBoxMenuItem _abbreviate_scientific_names

_screen_antialias_cbmi

javax.swing.JCheckBoxMenuItem _screen_antialias_cbmi

_background_gradient_cbmi

javax.swing.JCheckBoxMenuItem _background_gradient_cbmi

_non_lined_up_cladograms_rbmi

javax.swing.JRadioButtonMenuItem _non_lined_up_cladograms_rbmi

_uniform_cladograms_rbmi

javax.swing.JRadioButtonMenuItem _uniform_cladograms_rbmi

_ext_node_dependent_cladogram_rbmi

javax.swing.JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi

_options

Options _options

_choose_font_mi

javax.swing.JMenuItem _choose_font_mi

_switch_colors_mi

javax.swing.JMenuItem _switch_colors_mi

_label_direction_cbmi

javax.swing.JCheckBoxMenuItem _label_direction_cbmi

_show_scale_cbmi

javax.swing.JCheckBoxMenuItem _show_scale_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

_inverse_search_result_cbmi

javax.swing.JCheckBoxMenuItem _inverse_search_result_cbmi

_show_overview_cbmi

javax.swing.JCheckBoxMenuItem _show_overview_cbmi

_choose_minimal_confidence_mi

javax.swing.JMenuItem _choose_minimal_confidence_mi

_show_branch_length_values_cbmi

javax.swing.JCheckBoxMenuItem _show_branch_length_values_cbmi

_collapse_species_specific_subtrees

javax.swing.JMenuItem _collapse_species_specific_subtrees

_overview_placment_mi

javax.swing.JMenuItem _overview_placment_mi

_radio_group_1

javax.swing.ButtonGroup _radio_group_1

_show_default_node_shapes_cbmi

javax.swing.JCheckBoxMenuItem _show_default_node_shapes_cbmi

_cycle_node_shape_mi

javax.swing.JMenuItem _cycle_node_shape_mi

_cycle_node_fill_mi

javax.swing.JMenuItem _cycle_node_fill_mi

_choose_node_size_mi

javax.swing.JMenuItem _choose_node_size_mi

_taxonomy_colorize_node_shapes_cbmi

javax.swing.JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi

_show_confidence_stddev_cbmi

javax.swing.JCheckBoxMenuItem _show_confidence_stddev_cbmi

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

serialVersionUID: 62256323L

Serialized Fields

_font

java.awt.Font _font

_option

int _option

_type

java.lang.String _type

_style

int _style

_size

int _size

_font_list

javax.swing.JList _font_list

_style_list

javax.swing.JList _style_list

_size_list

javax.swing.JList _size_list

_fonts_tf

javax.swing.JTextField _fonts_tf

_style_tf

javax.swing.JTextField _style_tf

_size_tf

javax.swing.JTextField _size_tf

_fonts_label

javax.swing.JLabel _fonts_label

_style_label

javax.swing.JLabel _style_label

_size_label

javax.swing.JLabel _size_label

_font_jsp

javax.swing.JScrollPane _font_jsp

_style_jsp

javax.swing.JScrollPane _style_jsp

_size_jsp

javax.swing.JScrollPane _size_jsp

_ok_button

javax.swing.JButton _ok_button

_cancel_button

javax.swing.JButton _cancel_button

_test_tf

javax.swing.JTextField _test_tf

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

serialVersionUID: 3655000897845508358L

Serialized Fields

_jmenubar

javax.swing.JMenuBar _jmenubar

_file_jmenu

javax.swing.JMenu _file_jmenu

_tools_menu

javax.swing.JMenu _tools_menu

_view_jmenu

javax.swing.JMenu _view_jmenu

_options_jmenu

javax.swing.JMenu _options_jmenu

_font_size_menu

javax.swing.JMenu _font_size_menu

_help_jmenu

javax.swing.JMenu _help_jmenu

_load_phylogeny_from_webservice_menu_items

javax.swing.JMenuItem[] _load_phylogeny_from_webservice_menu_items

_open_item

javax.swing.JMenuItem _open_item

_open_url_item

javax.swing.JMenuItem _open_url_item

_save_item

javax.swing.JMenuItem _save_item

_save_all_item

javax.swing.JMenuItem _save_all_item

_close_item

javax.swing.JMenuItem _close_item

_exit_item

javax.swing.JMenuItem _exit_item

_new_item

javax.swing.JMenuItem _new_item

_midpoint_root_item

javax.swing.JMenuItem _midpoint_root_item

_taxcolor_item

javax.swing.JMenuItem _taxcolor_item

_confcolor_item

javax.swing.JMenuItem _confcolor_item

_color_rank_jmi

javax.swing.JMenuItem _color_rank_jmi

_infer_common_sn_names_item

javax.swing.JMenuItem _infer_common_sn_names_item

_collapse_species_specific_subtrees

javax.swing.JMenuItem _collapse_species_specific_subtrees

_collapse_below_threshold

javax.swing.JMenuItem _collapse_below_threshold

_obtain_detailed_taxonomic_information_jmi

javax.swing.JMenuItem _obtain_detailed_taxonomic_information_jmi

_obtain_detailed_taxonomic_information_deleting_jmi

javax.swing.JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi

_obtain_uniprot_seq_information_jmi

javax.swing.JMenuItem _obtain_uniprot_seq_information_jmi

_move_node_names_to_tax_sn_jmi

javax.swing.JMenuItem _move_node_names_to_tax_sn_jmi

_move_node_names_to_seq_names_jmi

javax.swing.JMenuItem _move_node_names_to_seq_names_jmi

_extract_tax_code_from_node_names_jmi

javax.swing.JMenuItem _extract_tax_code_from_node_names_jmi

_super_tiny_fonts_item

javax.swing.JMenuItem _super_tiny_fonts_item

_tiny_fonts_item

javax.swing.JMenuItem _tiny_fonts_item

_small_fonts_item

javax.swing.JMenuItem _small_fonts_item

_medium_fonts_item

javax.swing.JMenuItem _medium_fonts_item

_large_fonts_item

javax.swing.JMenuItem _large_fonts_item

_choose_font_mi

javax.swing.JMenuItem _choose_font_mi

_switch_colors_mi

javax.swing.JMenuItem _switch_colors_mi

_label_direction_cbmi

javax.swing.JCheckBoxMenuItem _label_direction_cbmi

_screen_antialias_cbmi

javax.swing.JCheckBoxMenuItem _screen_antialias_cbmi

_background_gradient_cbmi

javax.swing.JCheckBoxMenuItem _background_gradient_cbmi

_non_lined_up_cladograms_rbmi

javax.swing.JRadioButtonMenuItem _non_lined_up_cladograms_rbmi

_uniform_cladograms_rbmi

javax.swing.JRadioButtonMenuItem _uniform_cladograms_rbmi

_ext_node_dependent_cladogram_rbmi

javax.swing.JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi

_show_branch_length_values_cbmi

javax.swing.JCheckBoxMenuItem _show_branch_length_values_cbmi

_show_scale_cbmi

javax.swing.JCheckBoxMenuItem _show_scale_cbmi

_show_overview_cbmi

javax.swing.JCheckBoxMenuItem _show_overview_cbmi

_show_domain_labels

javax.swing.JCheckBoxMenuItem _show_domain_labels

_abbreviate_scientific_names

javax.swing.JCheckBoxMenuItem _abbreviate_scientific_names

_color_labels_same_as_parent_branch

javax.swing.JCheckBoxMenuItem _color_labels_same_as_parent_branch

_overview_placment_mi

javax.swing.JMenuItem _overview_placment_mi

_choose_minimal_confidence_mi

javax.swing.JMenuItem _choose_minimal_confidence_mi

_show_default_node_shapes_cbmi

javax.swing.JCheckBoxMenuItem _show_default_node_shapes_cbmi

_cycle_node_shape_mi

javax.swing.JMenuItem _cycle_node_shape_mi

_cycle_node_fill_mi

javax.swing.JMenuItem _cycle_node_fill_mi

_choose_node_size_mi

javax.swing.JMenuItem _choose_node_size_mi

_taxonomy_colorize_node_shapes_cbmi

javax.swing.JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi

_show_confidence_stddev_cbmi

javax.swing.JCheckBoxMenuItem _show_confidence_stddev_cbmi

_graphics_export_visible_only_cbmi

javax.swing.JCheckBoxMenuItem _graphics_export_visible_only_cbmi

_antialias_print_cbmi

javax.swing.JCheckBoxMenuItem _antialias_print_cbmi

_print_black_and_white_cbmi

javax.swing.JCheckBoxMenuItem _print_black_and_white_cbmi

_print_using_actual_size_cbmi

javax.swing.JCheckBoxMenuItem _print_using_actual_size_cbmi

_graphics_export_using_actual_size_cbmi

javax.swing.JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi

_print_size_mi

javax.swing.JMenuItem _print_size_mi

_choose_pdf_width_mi

javax.swing.JMenuItem _choose_pdf_width_mi

_internal_number_are_confidence_for_nh_parsing_cbmi

javax.swing.JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi

_extract_pfam_style_tax_codes_cbmi

javax.swing.JCheckBoxMenuItem _extract_pfam_style_tax_codes_cbmi

_replace_underscores_cbmi

javax.swing.JCheckBoxMenuItem _replace_underscores_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

_search_case_senstive_cbmi

javax.swing.JCheckBoxMenuItem _search_case_senstive_cbmi

_search_whole_words_only_cbmi

javax.swing.JCheckBoxMenuItem _search_whole_words_only_cbmi

_inverse_search_result_cbmi

javax.swing.JCheckBoxMenuItem _inverse_search_result_cbmi

_type_menu

javax.swing.JMenu _type_menu

_rectangular_type_cbmi

javax.swing.JCheckBoxMenuItem _rectangular_type_cbmi

_triangular_type_cbmi

javax.swing.JCheckBoxMenuItem _triangular_type_cbmi

_curved_type_cbmi

javax.swing.JCheckBoxMenuItem _curved_type_cbmi

_convex_type_cbmi

javax.swing.JCheckBoxMenuItem _convex_type_cbmi

_euro_type_cbmi

javax.swing.JCheckBoxMenuItem _euro_type_cbmi

_rounded_type_cbmi

javax.swing.JCheckBoxMenuItem _rounded_type_cbmi

_unrooted_type_cbmi

javax.swing.JCheckBoxMenuItem _unrooted_type_cbmi

_circular_type_cbmi

javax.swing.JCheckBoxMenuItem _circular_type_cbmi

_view_as_NH_item

javax.swing.JMenuItem _view_as_NH_item

_view_as_NHX_item

javax.swing.JMenuItem _view_as_NHX_item

_view_as_XML_item

javax.swing.JMenuItem _view_as_XML_item

_view_as_nexus_item

javax.swing.JMenuItem _view_as_nexus_item

_display_basic_information_item

javax.swing.JMenuItem _display_basic_information_item

_about_item

javax.swing.JMenuItem _about_item

_help_item

javax.swing.JMenuItem _help_item

_website_item

javax.swing.JMenuItem _website_item

_phyloxml_website_item

javax.swing.JMenuItem _phyloxml_website_item

_phyloxml_ref_item

javax.swing.JMenuItem _phyloxml_ref_item

_aptx_ref_item

javax.swing.JMenuItem _aptx_ref_item

_process_menu

javax.swing.JMenu _process_menu

_mainpanel

MainPanel _mainpanel

_contentpane

java.awt.Container _contentpane

_textframe

org.forester.archaeopteryx.TextFrame _textframe

_configuration

Configuration _configuration

_remove_branch_color_item

javax.swing.JMenuItem _remove_branch_color_item

_options

Options _options

_process_pool

ProcessPool _process_pool

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

_values_filechooser

javax.swing.JFileChooser _values_filechooser

_open_filechooser

javax.swing.JFileChooser _open_filechooser

_msa_filechooser

javax.swing.JFileChooser _msa_filechooser

_seqs_filechooser

javax.swing.JFileChooser _seqs_filechooser

_open_filechooser_for_species_tree

javax.swing.JFileChooser _open_filechooser_for_species_tree

_save_filechooser

javax.swing.JFileChooser _save_filechooser

_writetopdf_filechooser

javax.swing.JFileChooser _writetopdf_filechooser

_writetographics_filechooser

javax.swing.JFileChooser _writetographics_filechooser

_analysis_menu

javax.swing.JMenu _analysis_menu

_load_species_tree_item

javax.swing.JMenuItem _load_species_tree_item

_gsdi_item

javax.swing.JMenuItem _gsdi_item

_root_min_dups_item

javax.swing.JMenuItem _root_min_dups_item

_root_min_cost_l_item

javax.swing.JMenuItem _root_min_cost_l_item

_lineage_inference

javax.swing.JMenuItem _lineage_inference

_function_analysis

javax.swing.JMenuItem _function_analysis

_print_item

javax.swing.JMenuItem _print_item

_write_to_pdf_item

javax.swing.JMenuItem _write_to_pdf_item

_write_to_jpg_item

javax.swing.JMenuItem _write_to_jpg_item

_write_to_gif_item

javax.swing.JMenuItem _write_to_gif_item

_write_to_tif_item

javax.swing.JMenuItem _write_to_tif_item

_write_to_png_item

javax.swing.JMenuItem _write_to_png_item

_write_to_bmp_item

javax.swing.JMenuItem _write_to_bmp_item

_species_tree

Phylogeny _species_tree

_current_dir

java.io.File _current_dir

_radio_group_1

javax.swing.ButtonGroup _radio_group_1

_min_not_collapse

double _min_not_collapse

_inference_menu

javax.swing.JMenu _inference_menu

_inference_from_msa_item

javax.swing.JMenuItem _inference_from_msa_item

_inference_from_seqs_item

javax.swing.JMenuItem _inference_from_seqs_item

_phylogenetic_inference_options

PhylogeneticInferenceOptions _phylogenetic_inference_options

_msa

Msa _msa

_msa_file

java.io.File _msa_file

_seqs

java.util.List<E> _seqs

_seqs_file

java.io.File _seqs_file

_read_values_jmi

javax.swing.JMenuItem _read_values_jmi

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

serialVersionUID: -2682765312661416435L

Serialized Fields

_mainframe

MainFrame _mainframe

_treepanels

java.util.List<E> _treepanels

_control_panel

org.forester.archaeopteryx.ControlPanel _control_panel

_treegraphic_scroll_panes

java.util.List<E> _treegraphic_scroll_panes

_treegraphic_scroll_pane_panels

java.util.List<E> _treegraphic_scroll_pane_panels

_configuration

Configuration _configuration

_tabbed_pane

javax.swing.JTabbedPane _tabbed_pane

_colorset

TreeColorSet _colorset

_fontset

TreeFontSet _fontset

_cut_or_copied_tree

Phylogeny _cut_or_copied_tree

_copied_and_pasted_nodes

java.util.Set<E> _copied_and_pasted_nodes

_image_map

java.util.Hashtable<K,V> _image_map

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

serialVersionUID: -978349745916505029L

Serialized Fields

_rendering_hints

java.awt.RenderingHints _rendering_hints

_treefile

java.io.File _treefile

_configuration

Configuration _configuration

_node_frames

org.forester.archaeopteryx.NodeFrame[] _node_frames

_node_frame_index

int _node_frame_index

_phylogeny

Phylogeny _phylogeny

_sub_phylogenies

Phylogeny[] _sub_phylogenies

_sub_phylogenies_temp_roots

PhylogenyNode[] _sub_phylogenies_temp_roots

_subtree_index

int _subtree_index

_main_panel

MainPanel _main_panel

_found_nodes

java.util.Set<E> _found_nodes

_highlight_node

PhylogenyNode _highlight_node

_node_popup_menu

javax.swing.JPopupMenu _node_popup_menu

_node_popup_menu_items

javax.swing.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

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

java.awt.Polygon _polygon

_sb

java.lang.StringBuilder _sb

_color_chooser

javax.swing.JColorChooser _color_chooser

_scale_distance

double _scale_distance

_scale_label

java.lang.String _scale_label

_cubic_curve

java.awt.geom.CubicCurve2D _cubic_curve

_quad_curve

java.awt.geom.QuadCurve2D _quad_curve

_line

java.awt.geom.Line2D _line

_ellipse

java.awt.geom.Ellipse2D _ellipse

_rectangle

java.awt.geom.Rectangle2D _rectangle

_options

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

java.awt.geom.Rectangle2D _ov_rectangle

_in_ov_rect

boolean _in_ov_rect

_in_ov

boolean _in_ov

_ov_virtual_rectangle

java.awt.Rectangle _ov_virtual_rectangle

_circ_max_depth

int _circ_max_depth

_root

PhylogenyNode _root

_arc

java.awt.geom.Arc2D _arc

_urt_nodeid_angle_map

java.util.HashMap<K,V> _urt_nodeid_angle_map

_urt_nodeid_index_map

java.util.HashMap<K,V> _urt_nodeid_index_map

_collapsed_external_nodeid_set

java.util.Set<E> _collapsed_external_nodeid_set

_nodeid_dist_to_leaf

java.util.HashMap<K,V> _nodeid_dist_to_leaf

_at

java.awt.geom.AffineTransform _at

_max_distance_to_root

double _max_distance_to_root

_dynamic_hiding_factor

int _dynamic_hiding_factor

_edited

boolean _edited

_node_desc_popup

javax.swing.Popup _node_desc_popup

_rollover_popup

javax.swing.JTextArea _rollover_popup

_popup_buffer

java.lang.StringBuffer _popup_buffer

_query_sequence

Sequence _query_sequence

_frc

java.awt.font.FontRenderContext _frc

_statistics_for_vector_data

DescriptiveStatistics _statistics_for_vector_data

_nodes_in_preorder

PhylogenyNode[] _nodes_in_preorder
Package org.forester.archaeopteryx.tools

Class org.forester.archaeopteryx.tools.PhyloInferenceDialog extends javax.swing.JDialog implements Serializable

serialVersionUID: 8337543508238133614L

Serialized Fields

_pnl

javax.swing.JPanel _pnl

_launch_btn

javax.swing.JButton _launch_btn

_cancel_btn

javax.swing.JButton _cancel_btn

_bootstrap_tf

javax.swing.JFormattedTextField _bootstrap_tf

_bootstrap_cb

javax.swing.JCheckBox _bootstrap_cb

_opts

PhylogeneticInferenceOptions _opts

_input_msa_file_tf

javax.swing.JTextField _input_msa_file_tf

_select_input_msa_btn

javax.swing.JButton _select_input_msa_btn

_parent_frame

MainFrameApplication _parent_frame

_msa_length_tf

javax.swing.JTextField _msa_length_tf

_msa_size_tf

javax.swing.JTextField _msa_size_tf

_msa_type_tf

javax.swing.JTextField _msa_type_tf

_distance_calc_kimura_rb

javax.swing.JRadioButton _distance_calc_kimura_rb

_distance_calc_poisson_rb

javax.swing.JRadioButton _distance_calc_poisson_rb

_distance_calc_fract_dissimilarity_rb

javax.swing.JRadioButton _distance_calc_fract_dissimilarity_rb

_value

int _value

_input_seqs_tf

javax.swing.JTextField _input_seqs_tf

_select_input_seqs_btn

javax.swing.JButton _select_input_seqs_btn

_input_seqs_number_tf

javax.swing.JTextField _input_seqs_number_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_max_length_tf

javax.swing.JTextField _input_seqs_max_length_tf

_input_seqs_type_tf

javax.swing.JTextField _input_seqs_type_tf

_input_seqs_msa_program_name_tf

javax.swing.JTextField _input_seqs_msa_program_name_tf

_input_seqs_msa_paramenters_tf

javax.swing.JTextField _input_seqs_msa_paramenters_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

_random_seed_tf

javax.swing.JTextField _random_seed_tf

_execute_msa_processing_cb

javax.swing.JCheckBox _execute_msa_processing_cb

_msa_processing_remove_all_gap_columns_cb

javax.swing.JCheckBox _msa_processing_remove_all_gap_columns_cb

_save_pwd_file_cb

javax.swing.JCheckBox _save_pwd_file_cb

_save_processed_msa_cb

javax.swing.JCheckBox _save_processed_msa_cb

_save_original_msa_cb

javax.swing.JCheckBox _save_original_msa_cb

_pwd_outfile_tf

javax.swing.JTextField _pwd_outfile_tf

_processed_msa_outfile_tf

javax.swing.JTextField _processed_msa_outfile_tf

_original_msa_outfile_tf

javax.swing.JTextField _original_msa_outfile_tf
Package org.forester.development

Class org.forester.development.AbstractRenderer extends javax.swing.JComponent implements Serializable

serialVersionUID: 7236434322552764776L

Serialized Fields

_x

int _x

_y

int _y

_well_size

int _well_size

_status

byte _status

Class org.forester.development.MsaRenderer extends javax.swing.JComponent implements Serializable

serialVersionUID: -68078011081748093L

Serialized Fields

_rows

int _rows

_columns

int _columns

_wellSize

int _wellSize

_wells

AbstractRenderer[][] _wells

_min

double _min

_max

double _max

_mean

double _mean

_minColor

java.awt.Color _minColor

_maxColor

java.awt.Color _maxColor

_meanColor

java.awt.Color _meanColor

_useMean

boolean _useMean

_msa

Msa _msa

_parent

javax.swing.JComponent _parent

Class org.forester.development.ResidueRenderer extends AbstractRenderer implements Serializable

serialVersionUID: -2331160296913478874L

Serialized Fields

_value

char _value

_wellColor

java.awt.Color _wellColor

_isMarked

boolean _isMarked

_isSelected

boolean _isSelected

_parentPlateRenderer

MsaRenderer _parentPlateRenderer
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.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

Overview  Package  Class  Tree  Deprecated  Index  Help 
 PREV   NEXT FRAMES    NO FRAMES