Serialized Form
Package org.biojava.bio.structure |
serialVersionUID: -6018854413829044230L
amino_char
Character amino_char
secstruc
Map<K,V> secstruc
recordType
String recordType
serialVersionUID: -2258364127420562883L
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
serialVersionUID: 4840370515056666418L
surname
String surname
initials
String initials
serialVersionUID: 1990171805277911840L
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
serialVersionUID: 2991897825657586356L
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
serialVersionUID: -1050178577542224379L
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
serialVersionUID: 4491470432023820382L
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
serialVersionUID: 5062668226159515468L
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
serialVersionUID: -7467726932980288712L
a
float a
b
float b
c
float c
alpha
float alpha
beta
float beta
gamma
float gamma
spaceGroup
String spaceGroup
z
int z
serialVersionUID: -5834326174085429508L
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
serialVersionUID: 1773011704758536083L
chainId
String chainId
insCode
Character insCode
seqNum
Integer seqNum
serialVersionUID: -4577047072916341237L
siteID
String siteID
groups
List<E> groups
evCode
String evCode
description
String description
serialVersionUID: -8663681100691188647L
serNum
int serNum
chainID1
String chainID1
chainID2
String chainID2
resnum1
String resnum1
resnum2
String resnum2
insCode1
String insCode1
insCode2
String insCode2
serialVersionUID: 62946250941673093L
serialVersionUID: -8344837138032851347L
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
serialVersionUID: -5571696240026118421L
Package org.biojava.bio.structure.align.client |
serialVersionUID: 1L
serialVersionUID: 4021229518711762954L
name
String name
pdbId
String pdbId
chainId
String chainId
Package org.biojava.bio.structure.align.gui |
serialVersionUID: 0L
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
serialVersionUID: 5092386365924879073L
tp
JEditorPane tp
serialVersionUID: 0L
textField
JTextField textField
config
UserConfiguration config
serialVersionUID: -1055193854675583808L
pdbSplit
JCheckBox pdbSplit
fromFtp
JCheckBox fromFtp
fileType
JComboBox fileType
pdbDir
JTextField pdbDir
serialVersionUID: -5657960663049062301L
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
serialVersionUID: -7641953255857483895L
serialVersionUID: 1L
alignmentsProcessed
int alignmentsProcessed
progressBar
JProgressBar progressBar
taskOutput
JTextArea taskOutput
stopButton
JButton stopButton
farmJob
FarmJob farmJob
serialVersionUID: -3337337068138131455L
serialVersionUID: 723386061184110161L
params
ConfigStrucAligParams params
textFields
List<E> textFields
serialVersionUID: 4002475313717172193L
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 |
serialVersionUID: -6892229111166263764L
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
serialVersionUID: 6939947266417830429L
afpChain
AFPChain afpChain
ca1
Atom[] ca1
ca2
Atom[] ca2
Package org.biojava.bio.structure.align.gui.autosuggest |
serialVersionUID: 8591734727984365156L
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 |
serialVersionUID: -3661941083797644242L
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 |
serialVersionUID: -4040926588803887471L
value
int value
contig
int contig
serialVersionUID: 1832393751152650420L
row
short row
col
short col
Package org.biojava.bio.structure.align.model |
serialVersionUID: 3901209995477111829L
p1
int p1
p2
int p2
fragLen
int fragLen
rmsd
double rmsd
m
Matrix m
t
double[] t
score
double score
id
long id
serialVersionUID: -4474029015606617947L
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 |
serialVersionUID: -4132105905712445473L
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
serialVersionUID: -6226717654562221241L
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 |
serialVersionUID: -8047100079715000276L
Package org.biojava.bio.structure.domain.pdp |
serialVersionUID: -1293994033102271366L
id
String id
size
int size
nseg
int nseg
score
double score
segments
List<E> segments
serialVersionUID: 1393487067559539657L
from
Integer from
to
Integer to
score
double score
Package org.biojava.bio.structure.gui |
serialVersionUID: -1720879395453257846L
_bufImage
BufferedImage _bufImage
matrix
Matrix matrix
cellColor
ContinuousColorMapper cellColor
scale
float scale
fragmentPairs
FragmentPair[] fragmentPairs
aligs
AlternativeAlignment[] aligs
selectedAlignmentPos
int selectedAlignmentPos
params
StrucAligParameters params
serialVersionUID: -8082261434322968652L
mPanel
JMatrixPanel mPanel
slider
JSlider slider
scroll
JScrollPane scroll
coloring
JComboBox coloring
gradients
Map<K,V> gradients
serialVersionUID: -2000575579184232365L
min
int min
max
int max
title
JLabel title
gradientContainer
JPanel gradientContainer
serialVersionUID: -1829252532712454236L
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 |
serialVersionUID: 0L
aligs
AlternativeAlignment[] aligs
panel
JPanel panel
structure1
Structure structure1
structure2
Structure structure2
structurePairAligner
StructurePairAligner structurePairAligner
serialVersionUID: -5682120627824627408L
debug
boolean debug
pdbDir
JTextField pdbDir
f1
JTextField f1
f2
JTextField f2
c1
JTextField c1
c2
JTextField c2
serialVersionUID: -5682120627824627408L
debug
boolean debug
pdbDir
JTextField pdbDir
f1
JTextField f1
f2
JTextField f2
c1
JTextField c1
c2
JTextField c2
serialVersionUID: 1L
fileType
JComboBox fileType
filePath1
JTextField filePath1
filePath2
JTextField filePath2
chain1
JTextField chain1
chain2
JTextField chain2
serialVersionUID: 757947454156959178L
dom1
JAutoSuggest dom1
dom2
JAutoSuggest dom2
serialVersionUID: 7893248902423L
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 |
serialVersionUID: -6387922432121206731L
mapper
ContinuousColorMapper mapper
min
double min
max
double max
serialVersionUID: 8324413992279510075L
Package org.biojava.bio.structure.io |
serialVersionUID: 5878292315163939027L
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
serialVersionUID: 219047230178423923L
Package org.biojava.bio.structure.io.mmcif.model |
serialVersionUID: -4736341142030215915L
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
serialVersionUID: 1078685833800736278L
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 |
serialVersionUID: 750353252427491487L
type
String type
entityId
String entityId
segments
List<E> segments
serialVersionUID: 3425769737629800828L
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
serialVersionUID: -8005129863256307153L
segId
String segId
start
String start
end
String end
residues
List<E> residues
Package org.biojava.bio.structure.jama |
serialVersionUID: 224348942390823L
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.
serialVersionUID: 93489734879234789L
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.
serialVersionUID: 9271028462937843L
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.
serialVersionUID: 8492558293015348719L
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.
serialVersionUID: 10293720387423L
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.
serialVersionUID: 640239472093534756L
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 |
serialVersionUID: 8579808155176839161L
sunID
int sunID
category
ScopCategory category
classificationId
String classificationId
name
String name
description
String description
serialVersionUID: 5890476209571654301L
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
serialVersionUID: 1187083944488580995L
sunid
int sunid
parentSunid
int parentSunid
children
List<E> children
Package org.biojava.bio.structure.scop.server |
serialVersionUID: 4924350548761431852L
scopDescriptions
List<E> scopDescriptions
serialVersionUID: 7693404355005856746L
domains
List<E> domains
serialVersionUID: 5327454882500340305L
scopNodes
List<E> scopNodes
serialVersionUID: 4193799052494327416L
data
TreeSet<E> data
Package org.biojava.bio.structure.secstruc |
serialVersionUID: 313490286720467714L
N
Atom N
CA
Atom CA
C
Atom C
O
Atom O
H
Atom H
original
Group original
Package org.biojava3.core.exceptions |
serialVersionUID: 1L
serialVersionUID: 6513440232428438424L
serialVersionUID: -8356845980320906455L
serialVersionUID: -4101924035353204493L
serialVersionUID: -5486504706601790351L
serialVersionUID: -3017433758219757440L
Package org.biojava3.genome.parsers.gff |
mLocation
Location mLocation
Package org.biojava3.protmod.structure |
serialVersionUID: 1656563037849815427L
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 |
serialVersionUID: 7158270364392309841L
param
Map<K,V> param
serialVersionUID: -9202060390925345163L
param
Map<K,V> param
Package org.forester.archaeopteryx |
serialVersionUID: 2314899014580484146L
_mainframe_applet
MainFrameApplet _mainframe_applet
_url_string
String _url_string
_message_1
String _message_1
_message_2
String _message_2
serialVersionUID: -1220055577935759443L
_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
serialVersionUID: 62256323L
_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
serialVersionUID: 3655000897845508358L
_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
serialVersionUID: 1941019292746717053L
_applet
ArchaeopteryxA _applet
_radio_group_1
ButtonGroup _radio_group_1
serialVersionUID: -799735726778865234L
_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
serialVersionUID: -2682765312661416435L
_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
serialVersionUID: -978349745916505029L
_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 |
serialVersionUID: -4810333295377881086L
Package org.forester.io.parsers.nexus |
serialVersionUID: -8750474393398183410L
Package org.forester.io.parsers.nhx |
serialVersionUID: 3756209394438250170L
Package org.forester.io.parsers.phyloxml |
serialVersionUID: 3756209394438250170L
serialVersionUID: 3756209394438250170L