Serialized Form
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Package edu.sdsc.sirius.ray |
callable
Manager callable
parent
javax.swing.JFrame parent
width
int width
height
int height
sp
javax.swing.JScrollPane sp
imageWidth
int imageWidth
imageHeight
int imageHeight
bufferedImage
java.awt.image.BufferedImage bufferedImage
imageLabel
javax.swing.JLabel imageLabel
tempPanel
ImagePreviewPanel.TempImagePanel tempPanel
imageAvailable
boolean imageAvailable
gray
java.awt.Color gray
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Package edu.sdsc.sirius.dialogs.TableImpl |
dataSet
DataSet dataSet
parentPanel
javax.swing.JPanel parentPanel
scrollPane
javax.swing.JScrollPane scrollPane
scrollBar
javax.swing.JScrollBar scrollBar
vp
javax.swing.JViewport vp
viewOffset
int viewOffset
m_data
BlastResultData m_data
m_table
ResultTable m_table
columnCount
int columnCount
columns
java.util.HashMap columns
columnOrder
java.util.Vector columnOrder
currentColumns
java.util.Vector currentColumns
currentIndices
java.util.Vector currentIndices
searchTypes
java.util.Vector searchTypes
columnWidths
java.util.HashMap columnWidths
columnAlign
java.util.HashMap columnAlign
extraHeight
int extraHeight
tableHeight
int tableHeight
selectedRows
int[] selectedRows
nameField
javax.swing.JTextField nameField
accessionField
javax.swing.JTextField accessionField
descriptionField
javax.swing.JTextField descriptionField
evalueField
javax.swing.JTextField evalueField
tooltips
boolean tooltips
target
java.lang.String target
columnRef
java.util.HashMap columnRef
entryId
java.lang.String entryId
description
java.lang.String description
name
java.lang.String name
source
java.lang.String source
author
java.lang.String author
title
java.lang.String title
journal
java.lang.String journal
year
java.lang.String year
evalue
java.lang.String evalue
accession
java.lang.String accession
selected
boolean selected
id
java.lang.String id
blocks
java.util.HashMap blocks
order
java.util.Vector order
ev
java.lang.String ev
name
java.lang.String name
application
java.lang.String application
acc
java.lang.String acc
start
java.lang.String start
end
java.lang.String end
dataSet
DataSet dataSet
parentPanel
javax.swing.JPanel parentPanel
scrollPane
javax.swing.JScrollPane scrollPane
scrollBar
javax.swing.JScrollBar scrollBar
vp
javax.swing.JViewport vp
viewOffset
int viewOffset
m_data
PubmedResultData m_data
m_table
ResultTable m_table
columnCount
int columnCount
columns
java.util.HashMap columns
columnOrder
java.util.Vector columnOrder
currentColumns
java.util.Vector currentColumns
currentIndices
java.util.Vector currentIndices
searchTypes
java.util.Vector searchTypes
columnWidths
java.util.HashMap columnWidths
columnAlign
java.util.HashMap columnAlign
extraHeight
int extraHeight
tableHeight
int tableHeight
selectedRows
int[] selectedRows
authorField
javax.swing.JTextField authorField
journalField
javax.swing.JTextField journalField
titleField
javax.swing.JTextField titleField
yearField
javax.swing.JTextField yearField
tooltips
boolean tooltips
target
java.lang.String target
columnRef
java.util.HashMap columnRef
tableType
int tableType
dataSet
DataSet dataSet
parentFrame
javax.swing.JFrame parentFrame
parentDialog
javax.swing.JDialog parentDialog
scrollPane
javax.swing.JScrollPane scrollPane
scrollBar
javax.swing.JScrollBar scrollBar
vp
javax.swing.JViewport vp
viewOffset
int viewOffset
filterPanel
javax.swing.JPanel filterPanel
m_data
ResultData m_data
m_table
ResultTable m_table
columnCount
int columnCount
columns
java.util.HashMap columns
columnOrder
java.util.Vector columnOrder
currentColumns
java.util.Vector currentColumns
currentIndices
java.util.Vector currentIndices
searchTypes
java.util.Vector searchTypes
columnWidths
java.util.HashMap columnWidths
columnAlign
java.util.HashMap columnAlign
infoColumn
javax.swing.table.TableColumn infoColumn
checkColumn
javax.swing.table.TableColumn checkColumn
extraHeight
int extraHeight
tableHeight
int tableHeight
selectedRows
int[] selectedRows
parent
Manager parent
filterLabel
javax.swing.JLabel filterLabel
idField
javax.swing.JTextField idField
nameField
javax.swing.JTextField nameField
infoField
javax.swing.JTextField infoField
loadButton
javax.swing.JButton loadButton
book
java.awt.print.Book book
mPageFormat
java.awt.print.PageFormat mPageFormat
tooltips
boolean tooltips
commonSelection
boolean commonSelection
target
java.lang.String target
replacement
java.util.HashMap replacement
columnRef
java.util.HashMap columnRef
contentPane
java.awt.Container contentPane
set
DataSet set
self
javax.swing.JDialog self
menuBar
javax.swing.JMenuBar menuBar
fileMenu
javax.swing.JMenu fileMenu
optionsMenu
javax.swing.JMenu optionsMenu
viewMenu
javax.swing.JMenu viewMenu
contentPanel
ResultPanel contentPanel
workingDir
java.lang.String workingDir
searchTypes
java.util.Vector searchTypes
parent
Manager parent
parentFrame
javax.swing.JFrame parentFrame
base
javax.swing.JPanel base
displayType
int displayType
self
ResultTable self
minimumWidth
int minimumWidth
tableType
int tableType
dataSet
DataSet dataSet
scrollPane
javax.swing.JScrollPane scrollPane
vp
javax.swing.JViewport vp
viewOffset
int viewOffset
filterPanel
javax.swing.JPanel filterPanel
m_data
ResultData m_data
m_table
ResultTable m_table
columnCount
int columnCount
columns
java.util.HashMap columns
columnOrder
java.util.Vector columnOrder
currentColumns
java.util.Vector currentColumns
currentIndices
java.util.Vector currentIndices
searchTypes
java.util.Vector searchTypes
columnWidths
java.util.HashMap columnWidths
columnAlign
java.util.HashMap columnAlign
infoColumn
javax.swing.table.TableColumn infoColumn
checkColumn
javax.swing.table.TableColumn checkColumn
tableHeight
int tableHeight
selectedRows
int[] selectedRows
callable
Manager callable
parent
javax.swing.JPanel parent
book
java.awt.print.Book book
mPageFormat
java.awt.print.PageFormat mPageFormat
tooltips
boolean tooltips
commonSelection
boolean commonSelection
target
java.lang.String target
MIN_WIDTH
int MIN_WIDTH
resultCallable
ResultPanelCallable resultCallable
start
double[] start
end
double[] end
TYPE
int TYPE
color
float[] color
radius
double radius
selected
boolean selected
visible
boolean visible
element
short element
- The element symbol.
For example, "C", "O", "N", "H", etc.
name
java.lang.String name
- The macromolecular ID (element name).
For example, "CA", "CB", "OG1", "N", etc.
number
int number
- The atom serial number.
compound
java.lang.String compound
- Compound 3-letter code.
For example, "VAL", "THR", "ILE", etc.
formalCharge
short formalCharge
chain_id
java.lang.String chain_id
- Chain/Asymetric unit ID.
For example, "A", "B", "C", etc.
residue_id
int residue_id
- Residue/Sequence ID.
Must be a positive integer.
For example, "10", "11", "13", etc.
residue
Residue residue
coordinate
double[] coordinate
- The x,y,z coordinate in angstroms.
For example, (21.023, 30.128, 12.340).
backbone
boolean backbone
- Whether this atom is a part of the protein backbone
partialCharge
float partialCharge
- Partial Charge (-1.0 - 3.0).
For example, "0.3", "1.1", etc.
hybridization
short hybridization
- Atomic orbital hybridization state. Needed for molecular mechanics calculations
forceFieldType
java.lang.String forceFieldType
- Force field type indicates the kind of atom depending on the atoms it's bonded to
render
short render
- Inidcates whether this atom is ionized, hence which radius should be used for rendering
quality
short quality
visible
boolean visible
atoms
Atom[] atoms
order
float order
reference
int reference
render
short render
quality
short quality
visible
boolean visible
residues
java.util.Vector residues
residueToIndexHash
java.util.Hashtable residueToIndexHash
id
java.lang.String id
fragments
RangeMap fragments
- Secondary structure conformation fragments.
This fragment map can be assigned in one of two ways:
1) From the Structure's conformation record assignments
(asigned to each Residue) by calling the resetFragments method.
OR
2) By explictly assigning fragment ranges by calling
the setFragment method to configure ranges.
fragmentObjects
java.util.Vector fragmentObjects
render
short render
quality
short quality
visible
boolean visible
readObject
private void readObject(java.io.ObjectInputStream in)
throws java.io.IOException,
java.lang.ClassNotFoundException
writeObject
private void writeObject(java.io.ObjectOutputStream out)
throws java.io.IOException
readObject
private void readObject(java.io.ObjectInputStream in)
throws java.io.IOException,
java.lang.ClassNotFoundException
writeObject
private void writeObject(java.io.ObjectOutputStream out)
throws java.io.IOException
name
java.lang.String name
- For example, "helix_BA", "turn_1A"
start_compound
java.lang.String start_compound
- For example, "ALA", "GLU", "LYS", etc.
start_chain
java.lang.String start_chain
- This value corresponds to the start Atom.chain_id value.
For example, "A", "B", "D", etc.
start_residue
int start_residue
- This value corresponds to the Atom.residue_id value.
For example, 22, 27, etc.
end_compound
java.lang.String end_compound
- For example, "ALA", "GLU", "LYS", etc.
end_chain
java.lang.String end_chain
- This value corresponds to the end Atom.chain_id value.
For example, "A", "B", "D", etc.
end_residue
int end_residue
- This value corresponds to the end Atom.residue_id value.
For example, 27, 137, etc.
readObject
private void readObject(java.io.ObjectInputStream in)
throws java.io.IOException,
java.lang.ClassNotFoundException
writeObject
private void writeObject(java.io.ObjectOutputStream out)
throws java.io.IOException
chain
Chain chain
startResidueIndex
int startResidueIndex
endResidueIndex
int endResidueIndex
conformationType
java.lang.String conformationType
residues
java.util.Vector residues
readObject
private void readObject(java.io.ObjectInputStream in)
throws java.io.IOException,
java.lang.ClassNotFoundException
writeObject
private void writeObject(java.io.ObjectOutputStream out)
throws java.io.IOException
righthand
boolean righthand
- TRUE=righthanded, FALSE=lefthanded
atom1
Atom atom1
atom2
Atom atom2
label
java.lang.String label
TYPE
int TYPE
color
float[] color
selected
boolean selected
visible
boolean visible
atom
Atom atom
label
java.lang.String label
TYPE
int TYPE
color
float[] color
dataType
int dataType
font
int font
selected
boolean selected
visible
boolean visible
start
double[] start
end
double[] end
atom1
Atom atom1
atom2
Atom atom2
label
java.lang.String label
TYPE
int TYPE
color
float[] color
selected
boolean selected
visible
boolean visible
readObject
private void readObject(java.io.ObjectInputStream in)
throws java.io.IOException,
java.lang.ClassNotFoundException
writeObject
private void writeObject(java.io.ObjectOutputStream out)
throws java.io.IOException
alphaAtomIndex
int alphaAtomIndex
atoms
java.util.Vector atoms
compoundCode
java.lang.String compoundCode
classification
java.lang.String classification
conformationType
java.lang.String conformationType
position
int position
number
int number
parentFragment
Fragment parentFragment
polymerHeadAtom
Atom polymerHeadAtom
polymerTailAtom
Atom polymerTailAtom
centerAtom
Atom centerAtom
render
short render
quality
short quality
visible
boolean visible
ribbon
boolean ribbon
residue
Residue residue
label
java.lang.String label
reference
Atom reference
TYPE
int TYPE
color
float[] color
dataType
int dataType
font
int font
selected
boolean selected
visible
boolean visible
atom1
Atom atom1
atom2
Atom atom2
start
double[] start
end
double[] end
label
java.lang.String label
TYPE
int TYPE
color
float[] color
selected
boolean selected
visible
boolean visible
readObject
private void readObject(java.io.ObjectInputStream in)
throws java.io.IOException,
java.lang.ClassNotFoundException
writeObject
private void writeObject(java.io.ObjectOutputStream out)
throws java.io.IOException
readObject
private void readObject(java.io.ObjectInputStream in)
throws java.io.IOException,
java.lang.ClassNotFoundException
writeObject
private void writeObject(java.io.ObjectOutputStream out)
throws java.io.IOException
structureMap
StructureMap structureMap
- Stores a reference to a StructureMap object for this Structure.
Only one StructureMap needs to be created for a given Structure,
because no inter-method-call state is kept by the object.
Once a single StructureMap is created, subsequent calls to
the getStructureMap method return the same StructureMap object.
structure
Structure structure
- The Structure to which a StructureComponent instance belongs.
readObject
private void readObject(java.io.ObjectInputStream in)
throws java.io.IOException,
java.lang.ClassNotFoundException
writeObject
private void writeObject(java.io.ObjectOutputStream out)
throws java.io.IOException
structureComponent
StructureComponent structureComponent
cell
Cell cell
structureMap
StructureMap structureMap
batch
boolean batch
changeExtent
int changeExtent
changeType
int changeType
changeAttribute
int changeAttribute
data
java.lang.String data
readObject
private void readObject(java.io.ObjectInputStream in)
throws java.io.IOException,
java.lang.ClassNotFoundException
writeObject
private void writeObject(java.io.ObjectOutputStream out)
throws java.io.IOException
structure
Structure structure
filter
StructureComponentFilter filter
type
java.lang.String type
count
int count
index
int index
foundNext
boolean foundNext
tmpStructureComponent
StructureComponent tmpStructureComponent
readObject
private void readObject(java.io.ObjectInputStream in)
throws java.io.IOException,
java.lang.ClassNotFoundException
writeObject
private void writeObject(java.io.ObjectOutputStream out)
throws java.io.IOException
readObject
private void readObject(java.io.ObjectInputStream in)
throws java.io.IOException,
java.lang.ClassNotFoundException
writeObject
private void writeObject(java.io.ObjectOutputStream out)
throws java.io.IOException
name
java.lang.String name
- The name of this Relation
subject_type
java.lang.String subject_type
object_type
java.lang.String object_type
readObject
private void readObject(java.io.ObjectInputStream in)
throws java.io.IOException,
java.lang.ClassNotFoundException
writeObject
private void writeObject(java.io.ObjectOutputStream out)
throws java.io.IOException
idCode
java.lang.String idCode
- The PDB-ID code by which this entry is registered.
For example, "2CPK", "4HHB", "10MH", etc.
compoundName
java.lang.String compoundName
- The name of this macromolecular structure.
For example, "c-AMP-Dependent Protein Kinase (E.C. 2.7.1.37) (cAPK)
(Catalytic Subunit)".
releaseDate
int[] releaseDate
- The date on which this entry was released.
releaseDate[0] = year.
releaseDate[1] = month.
releaseDate[2] = day.
For example, "1993-1-15".
authors
java.lang.String authors
- The authors of this entry.
For example, "D. R. Knighton, J. Zheng, L. F. Ten Eyck, V. A. Ashford,
N.-H. Xuong, S. S. Taylor, J. M. Sowadski".
primaryReference
java.lang.String primaryReference
- The primary citation reference for this entry.
For example, "Knighton, D. R., Zheng, J. H., Ten Eyck, L. F., Ashford,
V. A., Xuong, N. H., Taylor, S. S., Sowadski, J. M.: Crystal structure of
the catalytic subunit of cyclic adenosine monophosphate-dependent protein
kinase. Science 253 pp. 407 (1991)".
sourceSpecies
java.lang.String sourceSpecies
- The source species of this compound.
For example, "Mus musculus".
determinationMethod
java.lang.String determinationMethod
- The exerimental method used to determine this compound.
For example, "X-ray Diffraction".
readObject
private void readObject(java.io.ObjectInputStream in)
throws java.io.IOException,
java.lang.ClassNotFoundException
writeObject
private void writeObject(java.io.ObjectOutputStream out)
throws java.io.IOException
name
java.lang.String name
- The symmetry space group name.
For example, "C 2", "I 2"
count
int count
- The count of the number of symmetry copies.
For example, 6
matrix
double[][][] matrix
- The symmetry matricies expressed as an array of 4x4 3D transforms.
For example,
[1.0, 0.0, 0.0, 0.0]
[0.0, 1.0, 0.0, 0.0]
[0.0, 0.0, 1.0, 0.0]
[0.0, 0.0, 0.0, 1.0]
The 1st array index is the matrix number.
The 2nd array index is the row number.
The 3rd array index is the column number.
readObject
private void readObject(java.io.ObjectInputStream in)
throws java.io.IOException,
java.lang.ClassNotFoundException
writeObject
private void writeObject(java.io.ObjectOutputStream out)
throws java.io.IOException
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Package edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util |
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Package edu.sdsc.sirius.util |
maxLength
int maxLength
parent_id
java.lang.String parent_id
structureId
java.lang.String structureId
pdbCode
java.lang.String pdbCode
description
java.lang.String description
resolution
java.lang.String resolution
aligned
boolean aligned
m_fm
java.awt.FontMetrics m_fm
m_insets
java.awt.Insets m_insets
m_defaultTab
int m_defaultTab
m_tabs
int[] m_tabs
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Package edu.sdsc.sirius.dialogs |
parent
javax.swing.JFrame parent
parentDialog
javax.swing.JDialog parentDialog
message
java.lang.String message
contentPane
java.awt.Container contentPane
scrollPane
javax.swing.JScrollPane scrollPane
textPane
javax.swing.JEditorPane textPane
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
atoms
Atom[] atoms
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
label1
javax.swing.JLabel label1
field1
javax.swing.JTextField field1
label2
javax.swing.JLabel label2
field2
javax.swing.JTextField field2
label3
javax.swing.JLabel label3
field3
javax.swing.JTextField field3
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
activeField
javax.swing.JTextField activeField
parentFrame
javax.swing.JFrame parentFrame
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
AngleMonitorDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
label
javax.swing.JLabel label
field
javax.swing.JTextField field
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
atoms
Atom[] atoms
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
label
javax.swing.JLabel label
field
javax.swing.JTextField field
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
type
int type
atomDialog
AtomDialog atomDialog
parent
Manager parent
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
atoms
Atom[] atoms
label1
javax.swing.JLabel label1
field1
javax.swing.JTextField field1
label2
javax.swing.JLabel label2
field2
javax.swing.JTextField field2
group
javax.swing.ButtonGroup group
button1
javax.swing.JRadioButton button1
button2
javax.swing.JRadioButton button2
button3
javax.swing.JRadioButton button3
button4
javax.swing.JRadioButton button4
selectedOrder
float selectedOrder
box
javax.swing.JCheckBox box
keepOpen
boolean keepOpen
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
activeField
javax.swing.JTextField activeField
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
atoms
Atom[] atoms
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
label1
javax.swing.JLabel label1
field1
javax.swing.JTextField field1
label2
javax.swing.JLabel label2
field2
javax.swing.JTextField field2
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
activeField
javax.swing.JTextField activeField
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
setPanel1
javax.swing.JPanel setPanel1
setPanel2
javax.swing.JPanel setPanel2
topPanel
javax.swing.JPanel topPanel
overlapPanel
javax.swing.JPanel overlapPanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
interaction
int interaction
group1
javax.swing.ButtonGroup group1
selected1
javax.swing.JRadioButton selected1
structure1
javax.swing.JRadioButton structure1
chain1
javax.swing.JRadioButton chain1
residue1
javax.swing.JRadioButton residue1
group2
javax.swing.ButtonGroup group2
selected2
javax.swing.JRadioButton selected2
structure2
javax.swing.JRadioButton structure2
chain2
javax.swing.JRadioButton chain2
residue2
javax.swing.JRadioButton residue2
group3
javax.swing.ButtonGroup group3
intra
javax.swing.JRadioButton intra
inter
javax.swing.JRadioButton inter
field1
javax.swing.JTextField field1
header1
javax.swing.JLabel header1
label1
javax.swing.JLabel label1
field2
javax.swing.JTextField field2
header2
javax.swing.JLabel header2
label2
javax.swing.JLabel label2
activeField
javax.swing.JTextField activeField
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
overlapLabel
javax.swing.JLabel overlapLabel
overlapText
javax.swing.JTextField overlapText
or1
javax.swing.JLabel or1
combo1
javax.swing.JComboBox combo1
structures1
java.util.Vector structures1
or2
javax.swing.JLabel or2
combo2
javax.swing.JComboBox combo2
structures2
java.util.Vector structures2
event
StericEvent event
atoms
Atom[] atoms
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
label
javax.swing.JLabel label
field
javax.swing.JTextField field
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
atoms
Atom[] atoms
label1
javax.swing.JLabel label1
field1
javax.swing.JTextField field1
label2
javax.swing.JLabel label2
selectedCharge
int selectedCharge
box
javax.swing.JCheckBox box
keepOpen
boolean keepOpen
combo
javax.swing.JComboBox combo
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
setPanel
javax.swing.JPanel setPanel
colorPanel
javax.swing.JPanel colorPanel
cPanel
javax.swing.JPanel cPanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
setGroup
javax.swing.ButtonGroup setGroup
radio1
javax.swing.JRadioButton radio1
radio2
javax.swing.JRadioButton radio2
radio3
javax.swing.JRadioButton radio3
radio4
javax.swing.JRadioButton radio4
radio5
javax.swing.JRadioButton radio5
colorGroup
javax.swing.ButtonGroup colorGroup
radio6
javax.swing.JRadioButton radio6
radio65
javax.swing.JRadioButton radio65
radio67
javax.swing.JRadioButton radio67
radio7
javax.swing.JRadioButton radio7
field
javax.swing.JTextField field
header
javax.swing.JLabel header
label
javax.swing.JLabel label
rgbLabel
javax.swing.JLabel rgbLabel
rgbField
javax.swing.JTextField rgbField
colorButton
javax.swing.JButton colorButton
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
or
javax.swing.JLabel or
combo
javax.swing.JComboBox combo
structures
java.util.Vector structures
m_image
java.awt.image.BufferedImage m_image
colorFlag
boolean colorFlag
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
colorPanel
javax.swing.JPanel colorPanel
cPanel
javax.swing.JPanel cPanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
colorGroup
javax.swing.ButtonGroup colorGroup
radio6
javax.swing.JRadioButton radio6
radio5
javax.swing.JRadioButton radio5
radio7
javax.swing.JRadioButton radio7
rgbLabel
javax.swing.JLabel rgbLabel
rgbField
javax.swing.JTextField rgbField
colorButton
javax.swing.JButton colorButton
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
m_image
java.awt.image.BufferedImage m_image
colorFlag
boolean colorFlag
width
int width
height
int height
ribbon
boolean ribbon
structureComponent
StructureComponent structureComponent
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
stylePanel
javax.swing.JPanel stylePanel
qPanel
javax.swing.JPanel qPanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
styleGroup
javax.swing.ButtonGroup styleGroup
radio6
javax.swing.JRadioButton radio6
radio7
javax.swing.JRadioButton radio7
radio8
javax.swing.JRadioButton radio8
radio9
javax.swing.JRadioButton radio9
qGroup
javax.swing.ButtonGroup qGroup
radio10
javax.swing.JRadioButton radio10
radio11
javax.swing.JRadioButton radio11
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
width
int width
height
int height
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
typePanel
javax.swing.JPanel typePanel
qPanel
javax.swing.JPanel qPanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
typeGroup
javax.swing.ButtonGroup typeGroup
type1
javax.swing.JRadioButton type1
type2
javax.swing.JRadioButton type2
type3
javax.swing.JRadioButton type3
type4
javax.swing.JRadioButton type4
ribbonSlider
javax.swing.JSlider ribbonSlider
width
int width
height
int height
addRibbon
boolean addRibbon
chain
Chain chain
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
ribbonType
int ribbonType
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
atoms
Atom[] atoms
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
label1
javax.swing.JLabel label1
field1
javax.swing.JTextField field1
label2
javax.swing.JLabel label2
field2
javax.swing.JTextField field2
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
activeField
javax.swing.JTextField activeField
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
label1
javax.swing.JLabel label1
field1
javax.swing.JTextField field1
label2
javax.swing.JLabel label2
pane
javax.swing.JScrollPane pane
area
javax.swing.JTextArea area
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
contentPane
java.awt.Container contentPane
self
javax.swing.JDialog self
width
int width
height
int height
contentPanel
ResultPanel contentPanel
workingDir
java.lang.String workingDir
searchTypes
java.util.Vector searchTypes
parent
Manager parent
parentFrame
javax.swing.JFrame parentFrame
structureDocument
StructureDocument structureDocument
base
javax.swing.JPanel base
buttonPanel
javax.swing.JPanel buttonPanel
loadButton
javax.swing.JButton loadButton
removeButton
javax.swing.JButton removeButton
closeButton
javax.swing.JButton closeButton
initialTitle
java.lang.String initialTitle
replacement
java.util.HashMap replacement
parentId
java.lang.String parentId
set
DataSet set
filename
java.lang.String filename
file
java.io.File file
url
java.net.URL url
data
java.util.Vector data
loader
FileEntryLoader loader
entries
Entry[] entries
contentPane
java.awt.Container contentPane
self
javax.swing.JDialog self
width
int width
height
int height
contentPanel
ResultPanel contentPanel
workingDir
java.lang.String workingDir
searchTypes
java.util.Vector searchTypes
parent
Manager parent
parentFrame
javax.swing.JFrame parentFrame
content
java.lang.String content
structureDocument
StructureDocument structureDocument
base
javax.swing.JPanel base
buttonPanel
javax.swing.JPanel buttonPanel
loadButton
javax.swing.JButton loadButton
removeButton
javax.swing.JButton removeButton
closeButton
javax.swing.JButton closeButton
initialTitle
java.lang.String initialTitle
replacement
java.util.HashMap replacement
parentLabel
java.lang.String parentLabel
set
DataSet set
filename
java.lang.String filename
file
java.io.File file
loader
FileEntryLoader loader
entries
Entry[] entries
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
atoms
Atom[] atoms
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
label1
javax.swing.JLabel label1
field1
javax.swing.JTextField field1
label2
javax.swing.JLabel label2
field2
javax.swing.JTextField field2
label3
javax.swing.JLabel label3
field3
javax.swing.JTextField field3
label4
javax.swing.JLabel label4
field4
javax.swing.JTextField field4
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
activeField
javax.swing.JTextField activeField
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
atoms
Atom[] atoms
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
label1
javax.swing.JLabel label1
field1
javax.swing.JTextField field1
label2
javax.swing.JLabel label2
field2
javax.swing.JTextField field2
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
activeField
javax.swing.JTextField activeField
data
java.util.HashMap data
pane
javax.swing.JTabbedPane pane
imagePanel
javax.swing.JPanel imagePanel
tablePanel
javax.swing.JPanel tablePanel
distributionFrame
javax.swing.JDialog distributionFrame
parent
javax.swing.JFrame parent
aminoacids
java.lang.String[] aminoacids
scales
int[] scales
organismIntColors
java.util.HashMap organismIntColors
total
int total
colors
java.util.HashMap colors
m_image
java.awt.image.BufferedImage m_image
g2
java.awt.Graphics2D g2
m_table
javax.swing.JTable m_table
m_data
DistributionData m_data
sp
javax.swing.JScrollPane sp
v
javax.swing.JViewport v
imageWidth
int imageWidth
imageHeight
int imageHeight
leftMargin
int leftMargin
bottomMargin
int bottomMargin
topMargin
int topMargin
rowHeight
int rowHeight
value
java.lang.Object value
mia1
javax.swing.event.MouseInputAdapter mia1
mia2
javax.swing.event.MouseInputAdapter mia2
imagePopup
javax.swing.JPopupMenu imagePopup
tablePopup
javax.swing.JPopupMenu tablePopup
book
java.awt.print.Book book
mPageFormat
java.awt.print.PageFormat mPageFormat
m_maxNumPage
int m_maxNumPage
callable
Manager callable
parent
javax.swing.JFrame parent
container
java.awt.Container container
basel
javax.swing.JPanel basel
pte
ElementSelectionPanel pte
settable
ElementSettable settable
preferences
ElementPreferences preferences
colors
float[][] colors
dialog
ElementSelectionDialog dialog
element
Element element
atomicNumber
java.lang.String atomicNumber
parent
javax.swing.JFrame parent
callable
Manager callable
container
java.awt.Container container
base
javax.swing.JPanel base
pte
ElementStylesEditor pte
buttonPanel
javax.swing.JPanel buttonPanel
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
defaultButton
javax.swing.JButton defaultButton
preferences
ElementPreferences preferences
colors
float[][] colors
element
Element element
atomicNumber
java.lang.String atomicNumber
dialogType
int dialogType
contentPane
java.awt.Container contentPane
self
javax.swing.JDialog self
contentPanel
TableViewPanel contentPanel
workingDir
java.lang.String workingDir
searchTypes
java.util.Vector searchTypes
parent
Manager parent
parentFrame
javax.swing.JFrame parentFrame
structureDocument
StructureDocument structureDocument
base
javax.swing.JPanel base
buttonPanel
javax.swing.JPanel buttonPanel
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
initialTitle
java.lang.String initialTitle
parentId
java.lang.String parentId
set
DataSet set
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
fSlider
javax.swing.JSlider fSlider
bSlider
javax.swing.JSlider bSlider
oldFogNear
float oldFogNear
oldFogFar
float oldFogFar
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
check
javax.swing.JCheckBox check
initialCheckStatus
boolean initialCheckStatus
near
double near
far
double far
wall
double wall
fogNear
float fogNear
fogFar
float fogFar
fogMin
float fogMin
- See Also:
- Constant Field Values
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
setPanel1
javax.swing.JPanel setPanel1
setPanel2
javax.swing.JPanel setPanel2
topPanel
javax.swing.JPanel topPanel
overlapPanel
javax.swing.JPanel overlapPanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
interaction
int interaction
group1
javax.swing.ButtonGroup group1
selected1
javax.swing.JRadioButton selected1
structure1
javax.swing.JRadioButton structure1
chain1
javax.swing.JRadioButton chain1
residue1
javax.swing.JRadioButton residue1
group2
javax.swing.ButtonGroup group2
selected2
javax.swing.JRadioButton selected2
structure2
javax.swing.JRadioButton structure2
chain2
javax.swing.JRadioButton chain2
residue2
javax.swing.JRadioButton residue2
group3
javax.swing.ButtonGroup group3
intra
javax.swing.JRadioButton intra
inter
javax.swing.JRadioButton inter
field1
javax.swing.JTextField field1
header1
javax.swing.JLabel header1
label1
javax.swing.JLabel label1
field2
javax.swing.JTextField field2
header2
javax.swing.JLabel header2
label2
javax.swing.JLabel label2
activeField
javax.swing.JTextField activeField
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
overlapLabel
javax.swing.JLabel overlapLabel
overlapText
javax.swing.JTextField overlapText
or1
javax.swing.JLabel or1
combo1
javax.swing.JComboBox combo1
structures1
java.util.Vector structures1
or2
javax.swing.JLabel or2
combo2
javax.swing.JComboBox combo2
structures2
java.util.Vector structures2
event
StericEvent event
atoms
Atom[] atoms
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
atoms
Atom[] atoms
label1
javax.swing.JLabel label1
field1
javax.swing.JTextField field1
group
javax.swing.ButtonGroup group
button1
javax.swing.JRadioButton button1
button2
javax.swing.JRadioButton button2
button3
javax.swing.JRadioButton button3
selectedHybridization
short selectedHybridization
box
javax.swing.JCheckBox box
keepOpen
boolean keepOpen
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
setPanel
javax.swing.JPanel setPanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
phFlag
int phFlag
setGroup
javax.swing.ButtonGroup setGroup
radio1
javax.swing.JRadioButton radio1
radio2
javax.swing.JRadioButton radio2
radio3
javax.swing.JRadioButton radio3
radio4
javax.swing.JRadioButton radio4
radio5
javax.swing.JRadioButton radio5
phGroup
javax.swing.ButtonGroup phGroup
radio6
javax.swing.JRadioButton radio6
radio7
javax.swing.JRadioButton radio7
phText
javax.swing.JTextField phText
field
javax.swing.JTextField field
header
javax.swing.JLabel header
label
javax.swing.JLabel label
or
javax.swing.JLabel or
combo
javax.swing.JComboBox combo
structures
java.util.Vector structures
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
event
HydrogenEvent event
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
itself
DisplayDialog itself
thisFrame
javax.swing.JDialog thisFrame
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
parameterPanel
javax.swing.JPanel parameterPanel
filePanel
javax.swing.JPanel filePanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
imageFormatComboBox
javax.swing.JComboBox imageFormatComboBox
resolutionComboBox
javax.swing.JComboBox resolutionComboBox
field
javax.swing.JTextField field
formatLabel
javax.swing.JLabel formatLabel
resLabel
javax.swing.JLabel resLabel
fileButton
javax.swing.JButton fileButton
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
suffix
java.lang.String suffix
file
java.io.File file
chooserFlag
boolean chooserFlag
resolution
int resolution
imageFormatComboBox
javax.swing.JComboBox imageFormatComboBox
parentComponent
java.awt.Component parentComponent
font
java.awt.Font font
fontNames
javax.swing.JList fontNames
fontSizes
javax.swing.JList fontSizes
fontStyles
javax.swing.JList fontStyles
currentSize
javax.swing.JTextField currentSize
okay
javax.swing.JButton okay
cancel
javax.swing.JButton cancel
availableFonts
java.awt.Font[] availableFonts
preview
JFontPreviewPanel preview
dialog
javax.swing.JDialog dialog
returnValue
int returnValue
font
java.awt.Font font
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
setPanel
javax.swing.JPanel setPanel
typePanel
javax.swing.JPanel typePanel
actionPanel
javax.swing.JPanel actionPanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
setFlag
int setFlag
typeFlag
int typeFlag
setGroup
javax.swing.ButtonGroup setGroup
radio1
javax.swing.JRadioButton radio1
radio2
javax.swing.JRadioButton radio2
radio3
javax.swing.JRadioButton radio3
radio4
javax.swing.JRadioButton radio4
radio5
javax.swing.JRadioButton radio5
radio6
javax.swing.JRadioButton radio6
typeGroup
javax.swing.ButtonGroup typeGroup
radio7
javax.swing.JRadioButton radio7
radio8
javax.swing.JRadioButton radio8
radio9
javax.swing.JRadioButton radio9
radio10
javax.swing.JRadioButton radio10
radio11
javax.swing.JRadioButton radio11
actionGroup
javax.swing.ButtonGroup actionGroup
radio12
javax.swing.JRadioButton radio12
radio13
javax.swing.JRadioButton radio13
field
javax.swing.JTextField field
header
javax.swing.JLabel header
label
javax.swing.JLabel label
customField
javax.swing.JTextField customField
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
or
javax.swing.JLabel or
combo
javax.swing.JComboBox combo
structures
java.util.Vector structures
event
LabelEvent event
parent
javax.swing.JFrame parent
parentDialog
javax.swing.JDialog parentDialog
message
java.lang.String message
contentPane
java.awt.Container contentPane
scrollPane
javax.swing.JScrollPane scrollPane
textPane
javax.swing.JTextPane textPane
applicationFrame
javax.swing.JFrame applicationFrame
parent
SequenceViewer parent
entryCount
int entryCount
base
javax.swing.JPanel base
panel1
javax.swing.JPanel panel1
buttonPanel
javax.swing.JPanel buttonPanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
message
javax.swing.JLabel message
field1
javax.swing.JTextField field1
label1
javax.swing.JLabel label1
selectionFlag
int selectionFlag
setFlag
int setFlag
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
setPanel
javax.swing.JPanel setPanel
bumpPanel
javax.swing.JPanel bumpPanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
check
javax.swing.JCheckBox check
group
javax.swing.ButtonGroup group
selected
javax.swing.JRadioButton selected
structure
javax.swing.JRadioButton structure
chain
javax.swing.JRadioButton chain
residue
javax.swing.JRadioButton residue
atom
javax.swing.JRadioButton atom
field1
javax.swing.JTextField field1
header1
javax.swing.JLabel header1
label1
javax.swing.JLabel label1
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
or
javax.swing.JLabel or
combo
javax.swing.JComboBox combo
structures
java.util.Vector structures
event
ViewEvent event
atoms
Atom[] atoms
trackBumps
boolean trackBumps
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
setPanel
javax.swing.JPanel setPanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
pdbText
javax.swing.JTextField pdbText
group
javax.swing.ButtonGroup group
radio1
javax.swing.JRadioButton radio1
radio2
javax.swing.JRadioButton radio2
pdbIdList
javax.swing.JList pdbIdList
idCodes
java.util.Vector idCodes
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
label
javax.swing.JLabel label
field
javax.swing.JTextField field
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
pane
javax.swing.JTabbedPane pane
parent
javax.swing.JFrame parent
preferences
StylesPreferences preferences
base
javax.swing.JPanel base
panel1
javax.swing.JPanel panel1
panel2
javax.swing.JPanel panel2
panel3
javax.swing.JPanel panel3
panel4
javax.swing.JPanel panel4
panel5
javax.swing.JPanel panel5
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
buttons
javax.swing.ButtonGroup buttons
button1
javax.swing.JRadioButton button1
button2
javax.swing.JRadioButton button2
button3
javax.swing.JRadioButton button3
thisDialog
javax.swing.JDialog thisDialog
callable
Manager callable
alignmentButtons
javax.swing.ButtonGroup alignmentButtons
alignmentButton1
javax.swing.JRadioButton alignmentButton1
alignmentButton2
javax.swing.JRadioButton alignmentButton2
svButtons
javax.swing.ButtonGroup svButtons
svButton1
javax.swing.JRadioButton svButton1
svButton2
javax.swing.JRadioButton svButton2
svButton3
javax.swing.JRadioButton svButton3
svButton4
javax.swing.JRadioButton svButton4
svButton5
javax.swing.JRadioButton svButton5
mmButtons
javax.swing.ButtonGroup mmButtons
mmButton1
javax.swing.JRadioButton mmButton1
mmButton2
javax.swing.JRadioButton mmButton2
rrButtons
javax.swing.ButtonGroup rrButtons
rrButton1
javax.swing.JRadioButton rrButton1
rrButton2
javax.swing.JRadioButton rrButton2
sqButtons
javax.swing.ButtonGroup sqButtons
sqButton1
javax.swing.JRadioButton sqButton1
sqButton2
javax.swing.JRadioButton sqButton2
bond1
javax.swing.JCheckBox bond1
water1
javax.swing.JCheckBox water1
bondOrderReset
boolean bondOrderReset
inputRAM
java.lang.String inputRAM
memoryField
javax.swing.JTextField memoryField
buttonPanel
javax.swing.JPanel buttonPanel
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
defaultButton
javax.swing.JButton defaultButton
importButton
javax.swing.JButton importButton
exportButton
javax.swing.JButton exportButton
bkgButton
javax.swing.JButton bkgButton
monitorButton
javax.swing.JButton monitorButton
elementButton
javax.swing.JButton elementButton
helixButton
javax.swing.JButton helixButton
sheetButton
javax.swing.JButton sheetButton
turnButton
javax.swing.JButton turnButton
coilButton
javax.swing.JButton coilButton
ribbonSlider
javax.swing.JSlider ribbonSlider
ballGroup
javax.swing.ButtonGroup ballGroup
ball1
javax.swing.JRadioButton ball1
ball2
javax.swing.JRadioButton ball2
stickRadiusField
javax.swing.JTextField stickRadiusField
ballRadiusField
javax.swing.JTextField ballRadiusField
fastSlider
javax.swing.JSlider fastSlider
bestSlider
javax.swing.JSlider bestSlider
levelGroup
javax.swing.ButtonGroup levelGroup
atomButton
javax.swing.JRadioButton atomButton
residueButton
javax.swing.JRadioButton residueButton
zoomGroup
javax.swing.ButtonGroup zoomGroup
zoomMiddle
javax.swing.JRadioButton zoomMiddle
zoomAlt
javax.swing.JRadioButton zoomAlt
dirField
javax.swing.JTextField dirField
selectionLabel
javax.swing.JLabel selectionLabel
selectionButton
javax.swing.JButton selectionButton
bondlineSlider
javax.swing.JSlider bondlineSlider
mouseSlider
javax.swing.JSlider mouseSlider
sampleStringLength
int sampleStringLength
fontLabel
javax.swing.JLabel fontLabel
cellBackgroundLabel
javax.swing.JLabel cellBackgroundLabel
cellBackgroundButton
javax.swing.JButton cellBackgroundButton
cache
PreferencesCache cache
commonSelection
javax.swing.JCheckBox commonSelection
commonColoring
javax.swing.JCheckBox commonColoring
showTips
javax.swing.JCheckBox showTips
showGrid
javax.swing.JCheckBox showGrid
showSs
javax.swing.JCheckBox showSs
undo
javax.swing.JCheckBox undo
undoDepth
javax.swing.JComboBox undoDepth
toolbar
javax.swing.JCheckBox toolbar
toolbarTips
javax.swing.JCheckBox toolbarTips
i
int i
imported
boolean imported
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
typePanel
javax.swing.JPanel typePanel
qPanel
javax.swing.JPanel qPanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
label1
javax.swing.JLabel label1
field1
javax.swing.JTextField field1
label2
javax.swing.JLabel label2
field2
javax.swing.JTextField field2
maximumDistance
double maximumDistance
fogSlider
javax.swing.JSlider fogSlider
width
int width
height
int height
addRibbon
boolean addRibbon
chain
Chain chain
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
ribbonType
int ribbonType
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
setPanel
javax.swing.JPanel setPanel
stylePanel
javax.swing.JPanel stylePanel
qPanel
javax.swing.JPanel qPanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
setGroup
javax.swing.ButtonGroup setGroup
radio1
javax.swing.JRadioButton radio1
radio2
javax.swing.JRadioButton radio2
radio3
javax.swing.JRadioButton radio3
radio4
javax.swing.JRadioButton radio4
radio5
javax.swing.JRadioButton radio5
styleGroup
javax.swing.ButtonGroup styleGroup
radio6
javax.swing.JRadioButton radio6
radio7
javax.swing.JRadioButton radio7
radio8
javax.swing.JRadioButton radio8
radio9
javax.swing.JRadioButton radio9
qGroup
javax.swing.ButtonGroup qGroup
radio10
javax.swing.JRadioButton radio10
radio11
javax.swing.JRadioButton radio11
field
javax.swing.JTextField field
header
javax.swing.JLabel header
label
javax.swing.JLabel label
or
javax.swing.JLabel or
combo
javax.swing.JComboBox combo
structures
java.util.Vector structures
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
atoms
Atom[] atoms
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
label
javax.swing.JLabel label
field
javax.swing.JTextField field
elementField
javax.swing.JTextField elementField
select
javax.swing.JButton select
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
element
java.lang.String element
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
topPanel
javax.swing.JPanel topPanel
setPanel
javax.swing.JPanel setPanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
selection
int selection
field
javax.swing.JTextField field
label
javax.swing.JLabel label
selectionField
javax.swing.JTextField selectionField
selectionLabel
javax.swing.JLabel selectionLabel
residue
Residue residue
buttons
java.util.Vector buttons
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
setPanel
javax.swing.JPanel setPanel
typePanel
javax.swing.JPanel typePanel
actionPanel
javax.swing.JPanel actionPanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
setFlag
int setFlag
typeFlag
int typeFlag
setGroup
javax.swing.ButtonGroup setGroup
radio1
javax.swing.JRadioButton radio1
radio2
javax.swing.JRadioButton radio2
radio3
javax.swing.JRadioButton radio3
radio4
javax.swing.JRadioButton radio4
radio5
javax.swing.JRadioButton radio5
typeGroup
javax.swing.ButtonGroup typeGroup
radio7
javax.swing.JRadioButton radio7
radio11
javax.swing.JRadioButton radio11
actionGroup
javax.swing.ButtonGroup actionGroup
radio12
javax.swing.JRadioButton radio12
radio13
javax.swing.JRadioButton radio13
field
javax.swing.JTextField field
header
javax.swing.JLabel header
label
javax.swing.JLabel label
customField
javax.swing.JTextField customField
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
or
javax.swing.JLabel or
combo
javax.swing.JComboBox combo
structures
java.util.Vector structures
event
LabelEvent event
parent
Manager parent
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
setPanel
javax.swing.JPanel setPanel
colorPanel
javax.swing.JPanel colorPanel
cPanel
javax.swing.JPanel cPanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
setGroup
javax.swing.ButtonGroup setGroup
radio1
javax.swing.JRadioButton radio1
radio2
javax.swing.JRadioButton radio2
radio3
javax.swing.JRadioButton radio3
radio4
javax.swing.JRadioButton radio4
colorGroup
javax.swing.ButtonGroup colorGroup
radio6
javax.swing.JRadioButton radio6
radio65
javax.swing.JRadioButton radio65
radio7
javax.swing.JRadioButton radio7
field
javax.swing.JTextField field
header
javax.swing.JLabel header
label
javax.swing.JLabel label
rgbLabel
javax.swing.JLabel rgbLabel
rgbField
javax.swing.JTextField rgbField
colorButton
javax.swing.JButton colorButton
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
or
javax.swing.JLabel or
combo
javax.swing.JComboBox combo
structures
java.util.Vector structures
m_image
java.awt.image.BufferedImage m_image
colorFlag
boolean colorFlag
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
switchPanel
javax.swing.JPanel switchPanel
typePanel
javax.swing.JPanel typePanel
qPanel
javax.swing.JPanel qPanel
setPanel
javax.swing.JPanel setPanel
sPanel
javax.swing.JPanel sPanel
setGroup
javax.swing.ButtonGroup setGroup
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
switchGroup
javax.swing.ButtonGroup switchGroup
radio1
javax.swing.JRadioButton radio1
radio2
javax.swing.JRadioButton radio2
typeGroup
javax.swing.ButtonGroup typeGroup
type1
javax.swing.JRadioButton type1
type2
javax.swing.JRadioButton type2
type3
javax.swing.JRadioButton type3
radiusLabel
javax.swing.JLabel radiusLabel
radiusField
javax.swing.JTextField radiusField
helixLabel
javax.swing.JLabel helixLabel
helixCombo
javax.swing.JComboBox helixCombo
dimensionLabel
javax.swing.JLabel dimensionLabel
dimensionField
javax.swing.JTextField dimensionField
setFlag
int setFlag
radio3
javax.swing.JRadioButton radio3
radio4
javax.swing.JRadioButton radio4
radio5
javax.swing.JRadioButton radio5
radio6
javax.swing.JRadioButton radio6
radio7
javax.swing.JRadioButton radio7
ribbonSlider
javax.swing.JSlider ribbonSlider
box
javax.swing.JCheckBox box
ignore
boolean ignore
field
javax.swing.JTextField field
label
javax.swing.JLabel label
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
or
javax.swing.JLabel or
combo
javax.swing.JComboBox combo
typeSet
boolean typeSet
ribbonType
int ribbonType
structures
java.util.Vector structures
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
atoms
Atom[] atoms
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
label1
javax.swing.JLabel label1
field1
javax.swing.JTextField field1
label2
javax.swing.JLabel label2
field2
javax.swing.JTextField field2
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
activeField
javax.swing.JTextField activeField
check
javax.swing.JCheckBox check
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
atoms
Atom[] atoms
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
panel1
javax.swing.JPanel panel1
panel2
javax.swing.JPanel panel2
group
javax.swing.ButtonGroup group
radio1
javax.swing.JRadioButton radio1
radio2
javax.swing.JRadioButton radio2
radio3
javax.swing.JRadioButton radio3
radio4
javax.swing.JRadioButton radio4
label1
javax.swing.JLabel label1
field1
javax.swing.JTextField field1
label2
javax.swing.JLabel label2
field2
javax.swing.JTextField field2
field3
javax.swing.JTextField field3
label3
javax.swing.JLabel label3
field4
javax.swing.JTextField field4
check
javax.swing.JCheckBox check
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
topPanel
javax.swing.JPanel topPanel
setPanel
javax.swing.JPanel setPanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
selection
int selection
group
javax.swing.ButtonGroup group
add
javax.swing.JRadioButton add
replace
javax.swing.JRadioButton replace
field
javax.swing.JTextField field
label1
javax.swing.JLabel label1
field2
javax.swing.JTextField field2
label2
javax.swing.JLabel label2
label3
javax.swing.JLabel label3
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
combo1
javax.swing.JComboBox combo1
structures
java.util.Vector structures
combo2
javax.swing.JComboBox combo2
chains
java.util.Vector chains
structure
Structure structure
chain
Chain chain
residues
java.util.Vector residues
event
StericEvent event
atoms
Atom[] atoms
parent
Manager parent
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
StructureAlignmentDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
setPanel1
javax.swing.JPanel setPanel1
setPanel2
javax.swing.JPanel setPanel2
subsetPanel1
javax.swing.JPanel subsetPanel1
subsetPanel2
javax.swing.JPanel subsetPanel2
midPanel
javax.swing.JPanel midPanel
alignButton
javax.swing.JButton alignButton
rmsdPanel
javax.swing.JPanel rmsdPanel
rmsdLabel
javax.swing.JLabel rmsdLabel
rmsdValue
javax.swing.JTextField rmsdValue
namePanel
javax.swing.JPanel namePanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
width
int width
height
int height
group1
javax.swing.ButtonGroup group1
select1
javax.swing.JRadioButton select1
pick1
javax.swing.JRadioButton pick1
group2
javax.swing.ButtonGroup group2
select2
javax.swing.JRadioButton select2
pick2
javax.swing.JRadioButton pick2
sg1
javax.swing.ButtonGroup sg1
sbAll1
javax.swing.JRadioButton sbAll1
sbSelection1
javax.swing.JRadioButton sbSelection1
sbSet1
javax.swing.JRadioButton sbSet1
sbCombo1
javax.swing.JComboBox sbCombo1
setName1
java.lang.String setName1
sets1
java.util.Vector sets1
sg2
javax.swing.ButtonGroup sg2
sbAll2
javax.swing.JRadioButton sbAll2
sbSelection2
javax.swing.JRadioButton sbSelection2
sbSet2
javax.swing.JRadioButton sbSet2
sbCombo2
javax.swing.JComboBox sbCombo2
setName2
java.lang.String setName2
sets2
java.util.Vector sets2
field1
javax.swing.JTextField field1
field2
javax.swing.JTextField field2
atoms
Atom[] atoms
label11
javax.swing.JLabel label11
label12
javax.swing.JLabel label12
label21
javax.swing.JLabel label21
label22
javax.swing.JLabel label22
activeField
javax.swing.JTextField activeField
cancelButton
javax.swing.JButton cancelButton
nameLabel1
javax.swing.JLabel nameLabel1
nameLabel2
javax.swing.JLabel nameLabel2
combo11
javax.swing.JComboBox combo11
structures1
java.util.Vector structures1
combo12
javax.swing.JComboBox combo12
chains1
java.util.Vector chains1
combo21
javax.swing.JComboBox combo21
structures2
java.util.Vector structures2
combo22
javax.swing.JComboBox combo22
chains2
java.util.Vector chains2
structure1
Structure structure1
structure2
Structure structure2
chain1
Chain chain1
chain2
Chain chain2
structureOut1
Structure structureOut1
structureOut2
Structure structureOut2
subset1
int subset1
subset2
int subset2
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
setPanel1
javax.swing.JPanel setPanel1
setPanel2
javax.swing.JPanel setPanel2
topPanel
javax.swing.JPanel topPanel
namePanel
javax.swing.JPanel namePanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
type
int type
group1
javax.swing.ButtonGroup group1
selected1
javax.swing.JRadioButton selected1
structure1
javax.swing.JRadioButton structure1
chain1
javax.swing.JRadioButton chain1
residue1
javax.swing.JRadioButton residue1
group2
javax.swing.ButtonGroup group2
selected2
javax.swing.JRadioButton selected2
structure2
javax.swing.JRadioButton structure2
chain2
javax.swing.JRadioButton chain2
residue2
javax.swing.JRadioButton residue2
group3
javax.swing.ButtonGroup group3
delete
javax.swing.JRadioButton delete
extract
javax.swing.JRadioButton extract
merge
javax.swing.JRadioButton merge
field1
javax.swing.JTextField field1
header1
javax.swing.JLabel header1
label1
javax.swing.JLabel label1
field2
javax.swing.JTextField field2
header2
javax.swing.JLabel header2
label2
javax.swing.JLabel label2
activeField
javax.swing.JTextField activeField
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
nameLabel
javax.swing.JLabel nameLabel
nameText
javax.swing.JTextField nameText
or1
javax.swing.JLabel or1
combo1
javax.swing.JComboBox combo1
structures1
java.util.Vector structures1
or2
javax.swing.JLabel or2
combo2
javax.swing.JComboBox combo2
structures2
java.util.Vector structures2
event
StericEvent event
atoms
Atom[] atoms
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
setPanel
javax.swing.JPanel setPanel
namePanel
javax.swing.JPanel namePanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
field
javax.swing.JTextField field
label1
javax.swing.JLabel label1
field2
javax.swing.JTextField field2
label2
javax.swing.JLabel label2
field3
javax.swing.JTextField field3
label3
javax.swing.JLabel label3
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
combo1
javax.swing.JComboBox combo1
structures
java.util.Vector structures
structure
Structure structure
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
setPanel
javax.swing.JPanel setPanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
field
javax.swing.JTextField field
label1
javax.swing.JLabel label1
field2
javax.swing.JTextField field2
label2
javax.swing.JLabel label2
label3
javax.swing.JLabel label3
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
combo1
javax.swing.JComboBox combo1
structures
java.util.Vector structures
structure
Structure structure
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
topPanel
javax.swing.JPanel topPanel
choicePanel
javax.swing.JPanel choicePanel
setPanel
javax.swing.JPanel setPanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
CREATE_SET
int CREATE_SET
- See Also:
- Constant Field Values
ADD_SET
int ADD_SET
- See Also:
- Constant Field Values
DELETE_SET
int DELETE_SET
- See Also:
- Constant Field Values
setAction
int setAction
useSelection
boolean useSelection
nameField
javax.swing.JTextField nameField
group
javax.swing.ButtonGroup group
newSet
javax.swing.JRadioButton newSet
addSet
javax.swing.JRadioButton addSet
deleteSet
javax.swing.JRadioButton deleteSet
group2
javax.swing.ButtonGroup group2
selectionButton
javax.swing.JRadioButton selectionButton
setButton
javax.swing.JRadioButton setButton
currentSets
javax.swing.JComboBox currentSets
field
javax.swing.JTextField field
label1
javax.swing.JLabel label1
field2
javax.swing.JTextField field2
label2
javax.swing.JLabel label2
label3
javax.swing.JLabel label3
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
combo1
javax.swing.JComboBox combo1
structures
java.util.Vector structures
combo2
javax.swing.JComboBox combo2
chains
java.util.Vector chains
structure
Structure structure
chain
Chain chain
residues
java.util.Vector residues
existingSets
java.util.Vector existingSets
event
StericEvent event
atoms
Atom[] atoms
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
setPanel1
javax.swing.JPanel setPanel1
setPanel2
javax.swing.JPanel setPanel2
namePanel
javax.swing.JPanel namePanel
nameGroup
javax.swing.ButtonGroup nameGroup
alignAll
javax.swing.JRadioButton alignAll
alignSelected
javax.swing.JRadioButton alignSelected
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
group1
javax.swing.ButtonGroup group1
select1
javax.swing.JRadioButton select1
pick1
javax.swing.JRadioButton pick1
group2
javax.swing.ButtonGroup group2
select2
javax.swing.JRadioButton select2
pick2
javax.swing.JRadioButton pick2
field1
javax.swing.JTextField field1
field2
javax.swing.JTextField field2
atoms
Atom[] atoms
label11
javax.swing.JLabel label11
label12
javax.swing.JLabel label12
label21
javax.swing.JLabel label21
label22
javax.swing.JLabel label22
activeField
javax.swing.JTextField activeField
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
combo11
javax.swing.JComboBox combo11
structures1
java.util.Vector structures1
combo12
javax.swing.JComboBox combo12
chains1
java.util.Vector chains1
combo21
javax.swing.JComboBox combo21
structures2
java.util.Vector structures2
combo22
javax.swing.JComboBox combo22
chains2
java.util.Vector chains2
structure1
Structure structure1
structure2
Structure structure2
chain1
Chain chain1
chain2
Chain chain2
structureOut1
Structure structureOut1
structureOut2
Structure structureOut2
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
atoms1
StructureComponent[] atoms1
atoms2
StructureComponent[] atoms2
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
panel1
javax.swing.JPanel panel1
panel2
javax.swing.JPanel panel2
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
activeField
javax.swing.JTextField activeField
atom11
javax.swing.JTextField atom11
atom12
javax.swing.JTextField atom12
atom13
javax.swing.JTextField atom13
atom21
javax.swing.JTextField atom21
atom22
javax.swing.JTextField atom22
atom23
javax.swing.JTextField atom23
label11
javax.swing.JLabel label11
label12
javax.swing.JLabel label12
label13
javax.swing.JLabel label13
label21
javax.swing.JLabel label21
label22
javax.swing.JLabel label22
label23
javax.swing.JLabel label23
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
message
boolean message
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
setPanel
javax.swing.JPanel setPanel
visPanel
javax.swing.JPanel visPanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
setFlag
int setFlag
visFlag
int visFlag
typeFlag
int typeFlag
setGroup
javax.swing.ButtonGroup setGroup
radio1
javax.swing.JRadioButton radio1
radio2
javax.swing.JRadioButton radio2
radio3
javax.swing.JRadioButton radio3
radio4
javax.swing.JRadioButton radio4
radio5
javax.swing.JRadioButton radio5
visGroup
javax.swing.ButtonGroup visGroup
radio6
javax.swing.JRadioButton radio6
radio7
javax.swing.JRadioButton radio7
radio8
javax.swing.JRadioButton radio8
field
javax.swing.JTextField field
header
javax.swing.JLabel header
label
javax.swing.JLabel label
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
or
javax.swing.JLabel or
combo
javax.swing.JComboBox combo
structures
java.util.Vector structures
event
VisibilityEvent event
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
setPanel
javax.swing.JPanel setPanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
setGroup
javax.swing.ButtonGroup setGroup
radio1
javax.swing.JRadioButton radio1
radio2
javax.swing.JRadioButton radio2
radio3
javax.swing.JRadioButton radio3
radio4
javax.swing.JRadioButton radio4
radio5
javax.swing.JRadioButton radio5
field
javax.swing.JTextField field
header
javax.swing.JLabel header
label
javax.swing.JLabel label
or
javax.swing.JLabel or
combo
javax.swing.JComboBox combo
structures
java.util.Vector structures
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
event
WeightEvent event
|
Package edu.sdsc.mbt.viewers.GLViewerImpl |
printFps
boolean printFps
glJPanel
javax.media.opengl.GLJPanel glJPanel
glCanvas
javax.media.opengl.GLCanvas glCanvas
glut
com.sun.opengl.util.GLUT glut
glu
javax.media.opengl.glu.GLU glu
renderables
java.util.Vector renderables
prevMouseX
int prevMouseX
prevMouseY
int prevMouseY
prevDragDif
int prevDragDif
pickBuffer
java.nio.IntBuffer pickBuffer
PICK_BUFFER_SIZE
int PICK_BUFFER_SIZE
pickSize
double[] pickSize
pickEvent
GvPickEvent pickEvent
viewEye
double[] viewEye
viewCenter
double[] viewCenter
viewUp
double[] viewUp
rotationCenter
double[] rotationCenter
viewport
int[] viewport
aspect
float aspect
virtualSphere
VirtualSphere2 virtualSphere
localVirtualSphere
VirtualSphere2 localVirtualSphere
radiusChanged
boolean radiusChanged
lightSources
java.util.Vector lightSources
black
float[] black
white
float[] white
gray
float[] gray
red
float[] red
green
float[] green
blue
float[] blue
lastTime
long lastTime
frameCount
int frameCount
fps
float fps
fovy
double fovy
backgroundColor
float[] backgroundColor
nearDistance
double nearDistance
farDistance
double farDistance
near
float near
far
float far
enableFog
boolean enableFog
updateBkg
boolean updateBkg
updateFog
boolean updateFog
ROTATION_MODE
boolean ROTATION_MODE
currentRotationPixels
int currentRotationPixels
imageRequested
boolean imageRequested
myDrawable
javax.media.opengl.GLAutoDrawable myDrawable
moveEvent
MoveEvent moveEvent
screenshotWidth
int screenshotWidth
screenshotHeight
int screenshotHeight
tileWidth
int tileWidth
tileHeight
int tileHeight
image
java.awt.image.BufferedImage image
screenshotX
int screenshotX
screenshotY
int screenshotY
imageResolution
int imageResolution
jpanel
boolean jpanel
mouseFactor
int mouseFactor
independent
boolean independent
independentSetupCompleted
boolean independentSetupCompleted
independentCenter
double[] independentCenter
independentRadius
double independentRadius
viewportWidth
int viewportWidth
viewportHeight
int viewportHeight
hold
boolean hold
mouseDownLoc
int[] mouseDownLoc
mouseUpLoc
int[] mouseUpLoc
pickMouseEvent
java.awt.event.MouseEvent pickMouseEvent
pickListeners
java.util.Vector pickListeners
moveListeners
java.util.Vector moveListeners
|
Package edu.sdsc.sirius.viewers.SequenceViewerImpl |
thisPanel
SequencePanel thisPanel
sequences
java.util.Vector sequences
sequenceObjects
java.util.Vector sequenceObjects
viewer
SequenceViewer viewer
backupSequences
java.util.Vector backupSequences
backupSequenceObjects
java.util.Vector backupSequenceObjects
startResidue
int startResidue
startSequence
int startSequence
pane
javax.swing.JLayeredPane pane
gridPanel
SequencePanel.GridPanel gridPanel
textPanel
SequencePanel.TextPanel textPanel
parameters
DisplayParameters parameters
popupMenu
javax.swing.JPopupMenu popupMenu
currentSequence
Sequence currentSequence
currentIndex
int currentIndex
currentKeyboardNumber
int currentKeyboardNumber
editMenu
javax.swing.JPopupMenu editMenu
editUndo
javax.swing.JMenuItem editUndo
selectedPanel
int selectedPanel
selectedColumns
java.util.Vector selectedColumns
selectedSequences
java.util.Vector selectedSequences
selectedCells
java.util.Vector selectedCells
hiddenSequences
java.util.Vector hiddenSequences
matchedSequences
java.util.Vector matchedSequences
clipboard
java.util.Vector clipboard
editPaste
javax.swing.JMenuItem editPaste
editCut
javax.swing.JMenuItem editCut
editCopy
javax.swing.JMenuItem editCopy
toolTipManager
javax.swing.ToolTipManager toolTipManager
toolTipPoint
java.awt.Point toolTipPoint
font
java.awt.Font font
fontSize
int fontSize
cellMargin
int cellMargin
cellWidth
int cellWidth
cellHeight
int cellHeight
fontAscent
int fontAscent
visibleColumns
int visibleColumns
startResidue
int startResidue
stopResidue
int stopResidue
displayRows
int displayRows
structure
Structure structure
residueCount
int residueCount
rgbColor
float[] rgbColor
buttonWidthCells
int buttonWidthCells
buttonSelected
boolean buttonSelected
defaultPanelHeight
int defaultPanelHeight
viewer
SequenceViewer viewer
thisPanel
javax.swing.JPanel thisPanel
panelHeight
int panelHeight
scaleHeight
int scaleHeight
selectionHeight
int selectionHeight
selectedSequence
Sequence selectedSequence
selectedColumns
java.util.Vector selectedColumns
mia
javax.swing.event.MouseInputAdapter mia
popupMenu
javax.swing.JPopupMenu popupMenu
popupNames
javax.swing.JCheckBoxMenuItem popupNames
popupShow
javax.swing.JMenuItem popupShow
popupSort
javax.swing.JMenuItem popupSort
popupHide
javax.swing.JMenuItem popupHide
popupHideSelected
javax.swing.JMenuItem popupHideSelected
popupSave
javax.swing.JMenuItem popupSave
activeSequence
Cell[] activeSequence
sequenceStylesEvent
SequenceStylesEvent sequenceStylesEvent
defaultStyle
java.util.Hashtable defaultStyle
sequence
Sequence sequence
listeners
java.util.Vector listeners
componentListeners
java.util.Vector componentListeners
defaultCellColor
java.awt.Color defaultCellColor
selectedResidues
java.util.Vector selectedResidues
thisObject
SequenceStyles thisObject
cells
Cell[] cells
structureComponentEvent
StructureComponentEvent structureComponentEvent
value
java.lang.Object value
|
Package edu.sdsc.sirius.export |
styleMap
java.util.Vector styleMap
structures
java.util.Vector structures
sequences
java.util.Vector sequences
sequenceOrder
java.util.Vector sequenceOrder
view
ViewerParameters view
cellColors
float[][][] cellColors
atomSetNames
java.util.Vector atomSetNames
independentStructureIndex
int independentStructureIndex
independentResidues
int[] independentResidues
independentAtoms
int[] independentAtoms
trackBumps
boolean trackBumps
ramaViewers
int[] ramaViewers
distanceMonitors
int[][] distanceMonitors
bumps
int[][] bumps
hBonds
int[][] hBonds
atomSelection
boolean[] atomSelection
atomVisibility
boolean[] atomVisibility
atomRenderingStyle
short[] atomRenderingStyle
atomRenderingQuality
short[] atomRenderingQuality
atomColors
float[][] atomColors
residueColors
float[][] residueColors
ribbonColors
float[][] ribbonColors
atomSetAssignment
int[] atomSetAssignment
residueSetAssignment
int[] residueSetAssignment
labeledResidueIndices
int[] labeledResidueIndices
labels
int[] labels
labelText
java.lang.String[] labelText
labelSize
int[] labelSize
labelSelection
boolean[] labelSelection
labelColor
float[][] labelColor
residueLabels
int[] residueLabels
residueLabelText
java.lang.String[] residueLabelText
residueLabelSize
int[] residueLabelSize
residueLabelSelection
boolean[] residueLabelSelection
residueLabelColor
float[][] residueLabelColor
ribbons
int[] ribbons
ribbonQuality
float[] ribbonQuality
ribbonVis
boolean[] ribbonVis
sequenceIndex
int sequenceIndex
- Indicates order in which the given sequence appears in the sequence viewer
sequenceSelected
boolean sequenceSelected
- Indicates whether the sequence is selected in the sequence viewer
cameraPosition
double[] cameraPosition
lookAt
double[] lookAt
up
double[] up
rotationCenter
double[] rotationCenter
bkgColor
float[] bkgColor
fogNear
float fogNear
fogFar
float fogFar
cameraFOV
double cameraFOV
|
Package edu.sdsc.sirius.builder |
builderPanel
BuilderPanel builderPanel
callable
Manager callable
parent
javax.swing.JFrame parent
width
int width
height
int height
parent
Manager parent
basePane
javax.swing.JTabbedPane basePane
panels
java.util.ArrayList panels
- ArrayList of ServicePanels
NAME
java.lang.String NAME
- See Also:
- Constant Field Values
parent
Manager parent
builderPanel
BuilderPanel builderPanel
buttons
java.util.Vector buttons
main
javax.swing.JPanel main
bondPanel
javax.swing.JPanel bondPanel
fragmentRecord
FragmentRecord fragmentRecord
number
java.lang.String number
label
java.lang.String label
tip
java.lang.String tip
border1
javax.swing.border.Border border1
border2
javax.swing.border.Border border2
border
javax.swing.border.CompoundBorder border
buttonLabel
javax.swing.JLabel buttonLabel
parent
FragmentGroupPanel parent
dialog
ReplaceResidueDialog dialog
pressed
boolean pressed
thisButton
FragmentButton thisButton
popupMenu
javax.swing.JPopupMenu popupMenu
NAME
java.lang.String NAME
- See Also:
- Constant Field Values
parent
Manager parent
builderPanel
BuilderPanel builderPanel
buttons
java.util.Vector buttons
main
javax.swing.JPanel main
bondPanel
javax.swing.JPanel bondPanel
NAME
java.lang.String NAME
- See Also:
- Constant Field Values
parent
Manager parent
builderPanel
BuilderPanel builderPanel
buttons
java.util.Vector buttons
main
javax.swing.JPanel main
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
sv
StructureViewer sv
structureComponent
StructureComponent structureComponent
itself
DisplayDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
topPanel
javax.swing.JPanel topPanel
namePanel
javax.swing.JPanel namePanel
attachPanel
javax.swing.JPanel attachPanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
objectField
javax.swing.JTextField objectField
objectLabel
javax.swing.JLabel objectLabel
nameField
javax.swing.JTextField nameField
nameLabel
javax.swing.JLabel nameLabel
attach1
javax.swing.JTextField attach1
attach2
javax.swing.JTextField attach2
attach3
javax.swing.JTextField attach3
attach4
javax.swing.JTextField attach4
attach5
javax.swing.JTextField attach5
attachments
StructureComponent[] attachments
currentField
javax.swing.JTextField currentField
attachLabel1
javax.swing.JLabel attachLabel1
attachLabel2
javax.swing.JLabel attachLabel2
attachLabel3
javax.swing.JLabel attachLabel3
attachLabel4
javax.swing.JLabel attachLabel4
attachLabel5
javax.swing.JLabel attachLabel5
okButton
javax.swing.JButton okButton
cancelButton
javax.swing.JButton cancelButton
|
Package edu.sdsc.mbt.filters |
relation
StructureComponentRelation relation
subject
StructureComponent subject
|
Package edu.sdsc.mbt.util |
start
double start
end
double end
readObject
private void readObject(java.io.ObjectInputStream in)
throws java.io.IOException,
java.lang.ClassNotFoundException
writeObject
private void writeObject(java.io.ObjectOutputStream out)
throws java.io.IOException
start
int start
end
int end
|
Package edu.sdsc.sirius.rasmol |
parent
Manager parent
frame
javax.swing.JFrame frame
width
int width
height
int height
thisObject
CommandPanel thisObject
scrollPane
javax.swing.JScrollPane scrollPane
editorPane
javax.swing.JEditorPane editorPane
text
javax.swing.JTextField text
execButton
javax.swing.JButton execButton
reader
RasmolReader reader
buffer
java.lang.StringBuffer buffer
font
java.awt.Font font
letterWidth
int letterWidth
rasmol
boolean rasmol
menuDataRasmol
javax.swing.JCheckBoxMenuItem menuDataRasmol
|
Package edu.sdsc.sirius.viewers.RamachandranViewerImpl |
viewer
RamachandranViewer viewer
parent
javax.swing.JFrame parent
width
int width
height
int height
basePanel
javax.swing.JPanel basePanel
|
Package edu.sdsc.sirius.io |
structure
Structure structure
id
java.lang.String id
lookAt
double[] lookAt
up
double[] up
center
double[] center
urlString
java.lang.String urlString
expectedInputBytes
long expectedInputBytes
DATA_TYPE
int DATA_TYPE
- See Also:
- Constant Field Values
passComponents
java.util.Hashtable passComponents
urlString
java.lang.String urlString
expectedInputBytes
long expectedInputBytes
currentName
java.lang.String currentName
chainIdList
java.lang.String[] chainIdList
DATA_TYPE
int DATA_TYPE
- See Also:
- Constant Field Values
passComponents
java.util.Hashtable passComponents
sequences
java.util.Vector sequences
structure
Structure structure
structureId
java.lang.String structureId
chiral
boolean chiral
|
Package com.jgoodies.uif_lite.component |
dividerBorderVisible
boolean dividerBorderVisible
- Determines whether the divider border shall be removed when
the UI is updated.
- See Also:
UIFSplitPane.isDividerBorderVisible(),
UIFSplitPane.setDividerBorderVisible(boolean)
|
Package edu.sdsc.sirius.workbench |
wbPanel
WBListPanel wbPanel
callable
Manager callable
parent
javax.swing.JFrame parent
width
int width
height
int height
callable
Manager callable
items
java.util.Vector items
folders
java.util.Vector folders
tree
javax.swing.JTree tree
model
javax.swing.tree.DefaultTreeModel model
selectedNodes
java.util.Vector selectedNodes
dialog
WBListDialog dialog
nodes
java.lang.Object[] nodes
data
java.util.HashMap data
disabled
java.awt.Color disabled
sp
javax.swing.JScrollPane sp
panel
javax.swing.JPanel panel
buttonLoad
javax.swing.JButton buttonLoad
buttonDelete
javax.swing.JButton buttonDelete
buttonCancel
javax.swing.JButton buttonCancel
nodeVisible
javax.swing.ImageIcon nodeVisible
nodeInvisible
javax.swing.ImageIcon nodeInvisible
PARENT_OPEN
javax.swing.ImageIcon PARENT_OPEN
PARENT_CLOSED
javax.swing.ImageIcon PARENT_CLOSED
STRUCTURES_OPEN
javax.swing.ImageIcon STRUCTURES_OPEN
STRUCTURES_CLOSED
javax.swing.ImageIcon STRUCTURES_CLOSED
SEQUENCES_OPEN
javax.swing.ImageIcon SEQUENCES_OPEN
SEQUENCES_CLOSED
javax.swing.ImageIcon SEQUENCES_CLOSED
VIEWS_OPEN
javax.swing.ImageIcon VIEWS_OPEN
VIEWS_CLOSED
javax.swing.ImageIcon VIEWS_CLOSED
LEAF
javax.swing.ImageIcon LEAF
rootNode
javax.swing.tree.DefaultMutableTreeNode rootNode
expanded
boolean[] expanded
parentFrame
javax.swing.JFrame parentFrame
parent
Manager parent
structureDocument
StructureDocument structureDocument
itself
WBSaveDialog itself
contentPane
java.awt.Container contentPane
base
javax.swing.JPanel base
setPanel
javax.swing.JPanel setPanel
namePanel
javax.swing.JPanel namePanel
folderPanel
javax.swing.JPanel folderPanel
entityPanel
javax.swing.JPanel entityPanel
border1
javax.swing.border.Border border1
border2
javax.swing.border.TitledBorder border2
border
javax.swing.border.Border border
width
int width
height
int height
group
javax.swing.ButtonGroup group
saveLoaded
javax.swing.JRadioButton saveLoaded
saveView
javax.swing.JRadioButton saveView
label
javax.swing.JLabel label
combo
javax.swing.JComboBox combo
folderCombo
javax.swing.JComboBox folderCombo
entityCombo
javax.swing.JComboBox entityCombo
nameField
javax.swing.JTextField nameField
nameLabel
javax.swing.JLabel nameLabel
cancelButton
javax.swing.JButton cancelButton
saveButton
javax.swing.JButton saveButton
entries
java.util.Vector entries
|
Package edu.sdsc.sirius.monitors |
monitorPanel
MonitorPanel monitorPanel
callable
Manager callable
parent
javax.swing.JFrame parent
width
int width
height
int height
callable
Manager callable
structureViewer
StructureViewer structureViewer
monitors
java.util.HashMap monitors
hbonds
java.util.HashMap hbonds
bumps
java.util.HashMap bumps
labels
java.util.HashMap labels
tree
javax.swing.JTree tree
model
javax.swing.tree.DefaultTreeModel model
selectedNodes
java.util.Vector selectedNodes
nodeMap
java.util.HashMap nodeMap
nodes
java.lang.Object[] nodes
sp
javax.swing.JScrollPane sp
panel
javax.swing.JPanel panel
buttonShow
javax.swing.JButton buttonShow
buttonHide
javax.swing.JButton buttonHide
buttonDelete
javax.swing.JButton buttonDelete
listener
MonitorPanel.MonitorNodeSelectionListener listener
nodeVisible
javax.swing.ImageIcon nodeVisible
nodeInvisible
javax.swing.ImageIcon nodeInvisible
PARENT_OPEN
javax.swing.ImageIcon PARENT_OPEN
PARENT_CLOSED
javax.swing.ImageIcon PARENT_CLOSED
DISTANCE_OPEN
javax.swing.ImageIcon DISTANCE_OPEN
DISTANCE_CLOSED
javax.swing.ImageIcon DISTANCE_CLOSED
HB_OPEN
javax.swing.ImageIcon HB_OPEN
HB_CLOSED
javax.swing.ImageIcon HB_CLOSED
BUMPS_OPEN
javax.swing.ImageIcon BUMPS_OPEN
BUMPS_CLOSED
javax.swing.ImageIcon BUMPS_CLOSED
LABELS_OPEN
javax.swing.ImageIcon LABELS_OPEN
LABELS_CLOSED
javax.swing.ImageIcon LABELS_CLOSED
DISTANCE_VISIBLE
javax.swing.ImageIcon DISTANCE_VISIBLE
DISTANCE_INVISIBLE
javax.swing.ImageIcon DISTANCE_INVISIBLE
HB_VISIBLE
javax.swing.ImageIcon HB_VISIBLE
HB_INVISIBLE
javax.swing.ImageIcon HB_INVISIBLE
BUMPS_VISIBLE
javax.swing.ImageIcon BUMPS_VISIBLE
BUMPS_INVISIBLE
javax.swing.ImageIcon BUMPS_INVISIBLE
LABELS_VISIBLE
javax.swing.ImageIcon LABELS_VISIBLE
LABELS_INVISIBLE
javax.swing.ImageIcon LABELS_INVISIBLE
menuBar
javax.swing.JMenuBar menuBar
distanceNode
javax.swing.tree.DefaultMutableTreeNode distanceNode
hbNode
javax.swing.tree.DefaultMutableTreeNode hbNode
bumpNode
javax.swing.tree.DefaultMutableTreeNode bumpNode
labelNode
javax.swing.tree.DefaultMutableTreeNode labelNode
rootNode
javax.swing.tree.DefaultMutableTreeNode rootNode
expanded
boolean[] expanded
|
Package edu.sdsc.sirius.viewers |
percent
float percent
structure
Structure structure
parent
Manager parent
structureDocument
StructureDocument structureDocument
pane
javax.swing.JLayeredPane pane
imagePanel
javax.swing.JPanel imagePanel
gridPanel
javax.swing.JPanel gridPanel
graphPanel
RamachandranViewer.GraphPanel graphPanel
coordinates
java.util.HashMap coordinates
positions
java.util.HashMap positions
points
java.util.HashMap points
residueIndices
java.util.HashMap residueIndices
structureIndex
int structureIndex
styles
StructureStyles styles
map
StructureMap map
statsPanel
javax.swing.JPanel statsPanel
menuBar
javax.swing.JMenuBar menuBar
results
java.lang.String[] results
statsList
javax.swing.JList statsList
scroll
javax.swing.JScrollPane scroll
ramaImage
java.awt.Image ramaImage
ramaGrid
java.awt.Image ramaGrid
menuViewDock
javax.swing.JCheckBoxMenuItem menuViewDock
elementSize
int elementSize
glycineCount
int glycineCount
prolineCount
int prolineCount
totalCount
int totalCount
rest
int rest
aCount
int aCount
bCount
int bCount
cCount
int cCount
dCount
int dCount
dialog
RamachandranViewerDialog dialog
structureDocument
StructureDocument structureDocument
parent
Manager parent
thisViewer
SequenceViewer thisViewer
sequences
java.util.Vector sequences
backupSequences
java.util.Vector backupSequences
entries
java.util.HashMap entries
sequenceObjects
java.util.Vector sequenceObjects
styleMap
java.util.HashMap styleMap
residueCellMapping
java.util.HashMap residueCellMapping
cellResidueMapping
java.util.HashMap cellResidueMapping
hiddenSequences
java.util.Vector hiddenSequences
base
javax.swing.JPanel base
scalePanel
SequenceScalePanel scalePanel
sequencePanel
SequencePanel sequencePanel
undoMode
boolean undoMode
styleManager
StyleManager styleManager
scrollPane
javax.swing.JScrollPane scrollPane
scrollBarH
javax.swing.JScrollBar scrollBarH
scrollBarV
javax.swing.JScrollBar scrollBarV
scrollBarPanel
javax.swing.JPanel scrollBarPanel
scrollBarFiller
javax.swing.JPanel scrollBarFiller
messageLabel
javax.swing.JLabel messageLabel
selectedColumns
java.util.Vector selectedColumns
selectedCells
java.util.Vector selectedCells
alignmentData
java.lang.String alignmentData
menuBar
javax.swing.JMenuBar menuBar
residueMax
int residueMax
file
java.io.File file
buttonWidthCells
int buttonWidthCells
- See Also:
- Constant Field Values
editMode
boolean editMode
menuEditMode
javax.swing.JCheckBoxMenuItem menuEditMode
menuEditReset
javax.swing.JMenuItem menuEditReset
parameters
DisplayParameters parameters
alignmentOutput
java.lang.String alignmentOutput
menuOptionsSs
javax.swing.JCheckBoxMenuItem menuOptionsSs
menuSequenceAlignmentDownload
javax.swing.JMenuItem menuSequenceAlignmentDownload
replacedResidue
java.lang.String replacedResidue
mPageFormat
java.awt.print.PageFormat mPageFormat
book
java.awt.print.Book book
showSs
boolean showSs
textArea
javax.swing.JTextArea textArea
jScrollPane
javax.swing.JScrollPane jScrollPane
progressPanel
ProgressPanel progressPanel
progressVisible
boolean progressVisible
geometryViewer
GlGeometryViewer geometryViewer
objectHash
java.util.Hashtable objectHash
renderablesList
java.util.Vector renderablesList
ribbonHash
java.util.HashMap ribbonHash
residueToFragment
java.util.HashMap residueToFragment
structureDocument
StructureDocument structureDocument
- The StructureDocument to which we are currently added/viewing.
selectedChains
java.util.Vector selectedChains
componentListeners
java.util.Vector componentListeners
thisViewer
StructureViewer thisViewer
updateViewOnRemove
boolean updateViewOnRemove
- Indicates whether the geometry viewer should refresh once a structure is removed. Needs to be set to false when an
undo is performed, to avoid useless display refresh with a blank screen.
structures
java.util.HashMap structures
- Holds references to all entries with their associated Structure objects
entries
java.util.HashMap entries
structureList
java.util.Vector structureList
dummyAtoms
java.util.ArrayList dummyAtoms
selection
java.util.HashMap selection
- Stores all Residues affected by Residue, Atom and Bond selections. Values of the hash are boolean flags indicating selection states.
value
java.lang.Object value
undoBuffer
java.util.Vector undoBuffer
- Stores Objects that are serialized states of the display identical to those used for state saving
hiddenComponents
java.util.HashMap hiddenComponents
- Stores references to StructureComponent instances that are hidden from the display.
renderables
java.util.HashMap renderables
rotationGroup
TransformGroupRenderable rotationGroup
init
boolean init
motionCenter
double[] motionCenter
fogBackDistance
double fogBackDistance
fogFrontDistance
double fogFrontDistance
fogDefaultDistance
double fogDefaultDistance
minZ
double minZ
maxZ
double maxZ
rotationMode
boolean rotationMode
angleDialog
AngleMonitorDialog angleDialog
rotatedAtoms
java.util.Vector rotatedAtoms
rotationAxis
double[] rotationAxis
rotationRootAtom
Atom rotationRootAtom
currentRotationAngle
double currentRotationAngle
toOrigin
double[] toOrigin
fromOrigin
double[] fromOrigin
xCoord
double[] xCoord
yCoord
double[] yCoord
zCoord
double[] zCoord
standardCoordinates
double[][] standardCoordinates
atomSets
java.util.HashMap atomSets
atomSetNames
java.util.Vector atomSetNames
globalResidues
java.util.Vector globalResidues
renderHidden
boolean renderHidden
- Flag that indicates whether hidden structure components should be included in rendering
atomToBumps
java.util.HashMap atomToBumps
atomToHBonds
java.util.HashMap atomToHBonds
atomToMonitors
java.util.HashMap atomToMonitors
atomToLabels
java.util.HashMap atomToLabels
atomToResidueLabels
java.util.HashMap atomToResidueLabels
repaintMonitors
boolean repaintMonitors
trackGeometry
boolean trackGeometry
rotatedResidue
Residue rotatedResidue
colorHidden
boolean colorHidden
- Flag that indicates whether hidden structure components should be included in coloring
trackBumps
boolean trackBumps
transformedCoordinates
java.util.HashMap transformedCoordinates
coordinateMatrix
double[] coordinateMatrix
fragmentLocation
double[] fragmentLocation
updatedMonitors
java.util.Vector updatedMonitors
monitors
java.util.HashMap monitors
- Stores references to currently existing monitors.
hBonds
java.util.HashMap hBonds
bumps
java.util.HashMap bumps
labels
java.util.HashMap labels
arrows
java.util.HashMap arrows
rotationArrow
java.util.HashMap rotationArrow
rotationAxisBond
Bond rotationAxisBond
rotatedSet
java.util.Vector rotatedSet
structureNames
java.util.HashMap structureNames
independentSet
java.util.Vector independentSet
independentComponents
java.util.Vector independentComponents
independentGroup
TransformGroupRenderable independentGroup
independentStructure
Structure independentStructure
initialMotionCenter
double[] initialMotionCenter
fogEnabled
boolean fogEnabled
stopCheckDummyAtoms
boolean stopCheckDummyAtoms
fragmentDistanceFromCamera
int fragmentDistanceFromCamera
initialCoordinates
java.util.HashMap initialCoordinates
|
Package edu.sdsc.sirius.viewers.TreeViewer |
structureComponent
StructureComponent structureComponent
contentPanel
TableViewPanel contentPanel
data
DataSet data
callable
Manager callable
searchTypes
java.util.Vector searchTypes
componentName
java.lang.String componentName
callable
Manager callable
structureViewer
StructureViewer structureViewer
sequenceViewer
SequenceViewer sequenceViewer
width
int width
height
int height
structureDocument
StructureDocument structureDocument
scrollToSelection
boolean scrollToSelection
tree
javax.swing.JTree tree
model
javax.swing.tree.DefaultTreeModel model
selectedChainNodes
java.util.Vector selectedChainNodes
selectedResidueNodes
java.util.Vector selectedResidueNodes
selectedAtomNodes
java.util.Vector selectedAtomNodes
nodeMap
java.util.HashMap nodeMap
nodes
java.lang.Object[] nodes
structureNodes
java.util.Vector structureNodes
sp
javax.swing.JScrollPane sp
panel
javax.swing.JPanel panel
buttonVisibility
javax.swing.JButton buttonVisibility
buttonRendering
javax.swing.JButton buttonRendering
buttonColor
javax.swing.JButton buttonColor
nodeVisible
javax.swing.ImageIcon nodeVisible
nodeInvisible
javax.swing.ImageIcon nodeInvisible
PARENT_OPEN
javax.swing.ImageIcon PARENT_OPEN
PARENT_CLOSED
javax.swing.ImageIcon PARENT_CLOSED
STRUCTURE_OPEN
javax.swing.ImageIcon STRUCTURE_OPEN
STRUCTURE_CLOSED
javax.swing.ImageIcon STRUCTURE_CLOSED
CHAIN_OPEN
javax.swing.ImageIcon CHAIN_OPEN
CHAIN_CLOSED
javax.swing.ImageIcon CHAIN_CLOSED
RESIDUE_OPEN
javax.swing.ImageIcon RESIDUE_OPEN
RESIDUE_CLOSED
javax.swing.ImageIcon RESIDUE_CLOSED
ATOM_LABEL
javax.swing.ImageIcon ATOM_LABEL
LABELS_INVISIBLE
javax.swing.ImageIcon LABELS_INVISIBLE
menuBar
javax.swing.JMenuBar menuBar
rootNode
javax.swing.tree.DefaultMutableTreeNode rootNode
atomPopup
javax.swing.JPopupMenu atomPopup
residuePopup
javax.swing.JPopupMenu residuePopup
chainPopup
javax.swing.JPopupMenu chainPopup
popupActive
boolean popupActive
activeAtom
Atom activeAtom
activeResidue
Residue activeResidue
activeChain
Chain activeChain
chainPopupRibbon
javax.swing.JMenuItem chainPopupRibbon
viewInfo
javax.swing.JCheckBoxMenuItem viewInfo
optionsScroll
javax.swing.JCheckBoxMenuItem optionsScroll
splitPane
javax.swing.JSplitPane splitPane
infoViewer
InfoViewer infoViewer
internalSelection
boolean internalSelection
processSelectionEvent
boolean processSelectionEvent
|
Package com.jgoodies.uif_lite.panel |
titleLabel
javax.swing.JLabel titleLabel
gradientPanel
com.jgoodies.uif_lite.panel.SimpleInternalFrame.GradientPanel gradientPanel
headerPanel
javax.swing.JPanel headerPanel
selected
boolean selected
|
Package edu.sdsc.mbt.viewables |
color
float[] color
color
float[] color
color
float[] color
bcolor
float[] bcolor
values
java.util.HashMap values
color
float[] color
color
float[] color
color
float[] color
entries
java.util.ArrayList entries
- List of Entry objects currently contained in the StructureDocument
viewers
java.util.ArrayList viewers
- The repository of Viewers viewing this StructureDocument.
parent
Manager parent
structureDocument
StructureDocument structureDocument
- The StructureDocument object for which the state changed
(once a Viewer is added to a StructureDocument this value shouldn't
change since each Viewer instance only views one document at a time).
entry
Entry entry
- The Structure object that was effected in the StructureDocument.
(for a TYPE_VIEWER add/remove event, this may be null since a Viewer
should examine ALL structures in a StructureDocument).
viewer
Viewer viewer
- The Viewer object that was effected in the StructureDocument.
type
int type
- The type of object that was added/removed in the StructureDocument.
change
int change
- The kind of change that occured in the StructureDocument.
structureStylesEvent
StructureStylesEvent structureStylesEvent
ribbonTypes
java.util.HashMap ribbonTypes
ribbonQuality
java.util.HashMap ribbonQuality
ribbonDiameters
java.util.HashMap ribbonDiameters
ribbonVisible
java.util.Vector ribbonVisible
ribbonInvisible
java.util.Vector ribbonInvisible
selection
java.util.Hashtable selection
selectionFlag
int selectionFlag
selectedChains
java.util.Vector selectedChains
zero
short zero
ribbonDiameter
float ribbonDiameter
defaultStyle
java.util.Hashtable defaultStyle
styleReference
java.util.HashMap styleReference
atomRadiusStyles
java.util.HashMap atomRadiusStyles
atomRadiusStyleReference
java.util.HashMap atomRadiusStyleReference
bondRadiusStyles
java.util.HashMap bondRadiusStyles
bondRadiusStyleReference
java.util.HashMap bondRadiusStyleReference
atomColorStyles
java.util.HashMap atomColorStyles
atomColorStyleReference
java.util.HashMap atomColorStyleReference
bondColorStyles
java.util.HashMap bondColorStyles
bondColorStyleReference
java.util.HashMap bondColorStyleReference
residueColorStyles
java.util.HashMap residueColorStyles
residueColorStyleReference
java.util.HashMap residueColorStyleReference
ribbonColorStyles
java.util.HashMap ribbonColorStyles
ribbonColorStyleReference
java.util.HashMap ribbonColorStyleReference
structureMap
StructureMap structureMap
listeners
java.util.Vector listeners
componentListeners
java.util.Vector componentListeners
defaultAtomRadius
AtomRadius defaultAtomRadius
defaultBondRadius
BondRadius defaultBondRadius
defaultAtomColor
AtomColor defaultAtomColor
defaultBondColor
BondColor defaultBondColor
defaultResidueColor
ResidueColor defaultResidueColor
defaultRibbonColor
RibbonColor defaultRibbonColor
selectedAtoms
java.util.Vector selectedAtoms
selectedResidues
java.util.Vector selectedResidues
thisObject
StructureStyles thisObject
structureComponentEvent
StructureComponentEvent structureComponentEvent
value
java.lang.Object value
chainRibbonDrawing
java.util.HashMap chainRibbonDrawing
- This hash contains pairs Chain -> Boolean, which are entered once chain drawing is attempted.
If it's a protein and a chain can be drawn, the value is true.
nativeLibInfo
AppletLauncher3D.NativeLibInfo nativeLibInfo
nativeLibNames
java.lang.String[] nativeLibNames
driHackPresent
boolean driHackPresent
subApplet
java.applet.Applet subApplet
- The applet we have to start
subAppletClassName
java.lang.String subAppletClassName
subAppletDisplayName
java.lang.String subAppletDisplayName
subAppletImageName
java.lang.String subAppletImageName
- URL string to an image used while installing
installDirectory
java.lang.String installDirectory
loaderPanel
javax.swing.JPanel loaderPanel
progressBar
javax.swing.JProgressBar progressBar
isInitOk
boolean isInitOk
firstStart
boolean firstStart
- false once start() has been invoked
joglStarted
boolean joglStarted
- true if start() has passed successfully
nativeLibInfo
SiriusAppletLauncher.NativeLibInfo nativeLibInfo
nativeLibNames
java.lang.String[] nativeLibNames
subApplet
java.applet.Applet subApplet
- The applet we have to start
subAppletClassName
java.lang.String subAppletClassName
subAppletDisplayName
java.lang.String subAppletDisplayName
subAppletImageName
java.lang.String subAppletImageName
- URL string to an image used while installing
installDirectory
java.lang.String installDirectory
loaderPanel
javax.swing.JPanel loaderPanel
progressBar
javax.swing.JProgressBar progressBar
isInitOk
boolean isInitOk
firstStart
boolean firstStart
- false once start() has been invoked
joglStarted
boolean joglStarted
- true if start() has passed successfully
haveJOAL
boolean haveJOAL
- Indicates whether JOAL is present
|
Class Viewer extends java.applet.Applet implements Serializable |
settings
Settings settings
checkInputParameters
boolean checkInputParameters
applicationFrame
javax.swing.JFrame applicationFrame
structurePanel
javax.swing.JPanel structurePanel
statusPanel
javax.swing.JPanel statusPanel
sequenceViewer
SequenceViewer sequenceViewer
parent
Viewer parent
jFileChooser
javax.swing.JFileChooser jFileChooser
searchOpen
boolean searchOpen
sequenceOpen
boolean sequenceOpen
dataListerDialog
ListerDialog dataListerDialog
imagePreviewPanel
ImagePreviewPanel imagePreviewPanel
viewers
java.util.Vector viewers
structureDocument
StructureDocument structureDocument
structureViewer
StructureViewer structureViewer
idCodes
java.util.Vector idCodes
pdbId
java.lang.String pdbId
w
SplashWindow w
displayDialog
DisplayDialog displayDialog
displayDialogStatus
boolean displayDialogStatus
menuViewSelectionAtom
javax.swing.JCheckBoxMenuItem menuViewSelectionAtom
menuViewSelectionResidue
javax.swing.JCheckBoxMenuItem menuViewSelectionResidue
menuViewModeMove
javax.swing.JCheckBoxMenuItem menuViewModeMove
menuViewModeZoom
javax.swing.JCheckBoxMenuItem menuViewModeZoom
menuOptionsOpenBuilder
javax.swing.JCheckBoxMenuItem menuOptionsOpenBuilder
menuGeometryOpenMonitors
javax.swing.JCheckBoxMenuItem menuGeometryOpenMonitors
menuComponentsStructureBrowser
javax.swing.JCheckBoxMenuItem menuComponentsStructureBrowser
menuComponentsOpenSequence
javax.swing.JCheckBoxMenuItem menuComponentsOpenSequence
menuComponentsStructure
javax.swing.JCheckBoxMenuItem menuComponentsStructure
menuViewResetOnLoad
javax.swing.JCheckBoxMenuItem menuViewResetOnLoad
menuViewAntialiasing
javax.swing.JCheckBoxMenuItem menuViewAntialiasing
installationHome
java.lang.String installationHome
rasmolReader
RasmolReader rasmolReader
menuViewUndo
javax.swing.JMenuItem menuViewUndo
commonSelection
javax.swing.JCheckBoxMenuItem commonSelection
commonColoring
javax.swing.JCheckBoxMenuItem commonColoring
properties
java.util.Properties properties
node
java.util.prefs.Preferences node
structureViewerComponent
javax.swing.JComponent structureViewerComponent
sequenceViewerComponent
javax.swing.JComponent sequenceViewerComponent
structureBrowserComponent
javax.swing.JComponent structureBrowserComponent
splitDesktop
javax.swing.JComponent splitDesktop
upperSplitDesktop
javax.swing.JComponent upperSplitDesktop
prefs
StylesPreferences prefs
basePanel
javax.swing.JPanel basePanel
about
AboutDialog about
builderDialog
BuilderDialog builderDialog
monitorDialog
MonitorDialog monitorDialog
structureBrowser
StructureBrowser structureBrowser
menuViewMotionCommon
javax.swing.JCheckBoxMenuItem menuViewMotionCommon
menuViewMotionSeparate
javax.swing.JCheckBoxMenuItem menuViewMotionSeparate
menuComponentsCommand
javax.swing.JCheckBoxMenuItem menuComponentsCommand
toolBar
javax.swing.JToolBar toolBar
toolHolder
javax.swing.JScrollPane toolHolder
toolbarAdded
boolean toolbarAdded
tipManager
javax.swing.ToolTipManager tipManager
openButton
javax.swing.JButton openButton
pdbButton
javax.swing.JButton pdbButton
saveButton
javax.swing.JButton saveButton
clearButton
javax.swing.JButton clearButton
displayButton
javax.swing.JButton displayButton
renderButton
javax.swing.JButton renderButton
colorButton
javax.swing.JButton colorButton
labelsButton
javax.swing.JButton labelsButton
centerButton
javax.swing.JButton centerButton
separateButton
javax.swing.JButton separateButton
commonButton
javax.swing.JButton commonButton
fogButton
javax.swing.JButton fogButton
undoButton
javax.swing.JButton undoButton
distanceButton
javax.swing.JButton distanceButton
angleButton
javax.swing.JButton angleButton
dihedralButton
javax.swing.JButton dihedralButton
preferencesButton
javax.swing.JButton preferencesButton
resetButton
javax.swing.JButton resetButton
closeMenu
javax.swing.JMenu closeMenu
startup
java.lang.String startup
menuBar
javax.swing.JMenuBar menuBar
loaded
boolean loaded
closeListeners
java.util.Vector closeListeners
superimpose
boolean superimpose
lastWorkingDirectory
java.lang.String lastWorkingDirectory
commandPanel
CommandPanel commandPanel
wbManager
WBManager wbManager
wbListDialog
WBListDialog wbListDialog
ramaReference
java.util.HashMap ramaReference
applet
Viewer applet
innerFilename
java.lang.String innerFilename
loadedFile
boolean loadedFile
username
java.lang.String username
password
java.lang.String password
input
java.lang.String input
server
java.lang.String server
inputType
java.lang.String inputType