Serialized Form
Class util.AAMap extends java.util.HashMap<java.lang.String,java.lang.Character> implements Serializable |
serialVersionUID: 1L
serialVersionUID: 1L
files
java.io.File[] files
serialVersionUID: 1L
parent
AlignFrame parent
viewProps
AlignViewProps viewProps
method
java.lang.String method
filterDialog
FilterAlignment filterDialog
paramMttf
javax.swing.JTextField paramMttf
paramRttf
javax.swing.JTextField paramRttf
paramFttf
javax.swing.JTextField paramFttf
paramGttf
javax.swing.JCheckBox paramGttf
presetsCombo
javax.swing.JComboBox presetsCombo
presets
java.util.HashMap<K,V> presets
serialVersionUID: 1L
parent
AlignFrame parent
viewProps
AlignViewProps viewProps
method
java.lang.String method
runDialog
RunMethods runDialog
paramsTtf
javax.swing.JTextField paramsTtf
warningsLabel
javax.swing.JLabel warningsLabel
serialVersionUID: 1L
frequencyMatrix
java.util.Vector<E> frequencyMatrix
clusterColors
java.util.Vector<E> clusterColors
currentSelection
java.util.Vector<E> currentSelection
horizontalScrollbar
javax.swing.JScrollBar horizontalScrollbar
verticalScrollbar
javax.swing.JScrollBar verticalScrollbar
logoPanel
javax.swing.JPanel logoPanel
horizontalChange
int horizontalChange
verticalChange
int verticalChange
logoFrame
javax.swing.JFrame logoFrame
startX
int startX
endX
int endX
startY
int startY
endY
int endY
seqOrderer
SequenceOrderer seqOrderer
sequenceLength
int sequenceLength
clusterPanelScale
int clusterPanelScale
logoHeight
int logoHeight
serialVersionUID: 1L
header
java.awt.Image header
fImages
java.util.Vector<E> fImages
imageHeight
int imageHeight
imageWidth
int imageWidth
position
int position
serialVersionUID: 1L
viewProps
AlignViewProps viewProps
alignPanel
AlignPanel alignPanel
methods
Methods methods
loadAlignmentItem
javax.swing.JMenuItem loadAlignmentItem
exitMenuItem
javax.swing.JMenuItem exitMenuItem
alignFrame
AlignFrame alignFrame
exportMenuItem
javax.swing.JMenuItem exportMenuItem
saveAlignmentItem
javax.swing.JMenuItem saveAlignmentItem
alObj
AlignObject alObj
loadMethodItem
javax.swing.JMenuItem loadMethodItem
loadS3DetItem
javax.swing.JMenuItem loadS3DetItem
loadStructureItem
javax.swing.JMenuItem loadStructureItem
loadClusterItem
javax.swing.JMenuItem loadClusterItem
loadXDetItem
javax.swing.JMenuItem loadXDetItem
loadMethodMenu
javax.swing.JMenu loadMethodMenu
saveMethodMenu
javax.swing.JMenu saveMethodMenu
saveS3DetItem
javax.swing.JMenuItem saveS3DetItem
saveXDetItem
javax.swing.JMenuItem saveXDetItem
seqPainter
SequencePainter seqPainter
namePainter
NamePainter namePainter
statusPnl
StatusPanel statusPnl
selectMethodItem
javax.swing.JMenu selectMethodItem
selectEntropyItem
javax.swing.JMenuItem selectEntropyItem
selectXDetItem
javax.swing.JMenuItem selectXDetItem
selectS3Item
javax.swing.JMenuItem selectS3Item
filterAlignment
javax.swing.JMenuItem filterAlignment
runMethodMenu
javax.swing.JMenu runMethodMenu
runXDetItem
javax.swing.JMenuItem runXDetItem
runS3DetItem
javax.swing.JMenuItem runS3DetItem
selectUdm
javax.swing.JMenu selectUdm
selectUdmItems
javax.swing.JMenuItem[] selectUdmItems
unselectResiduesItem
javax.swing.JMenuItem unselectResiduesItem
unselectProteinsItem
javax.swing.JMenuItem unselectProteinsItem
exportFastaItem
javax.swing.JMenuItem exportFastaItem
showSelectionItem
javax.swing.JMenuItem showSelectionItem
sequenceLogoItem
javax.swing.JMenuItem sequenceLogoItem
dualLogoItem
javax.swing.JMenuItem dualLogoItem
clusterLogoItem
javax.swing.JMenuItem clusterLogoItem
manualMenuItem
javax.swing.JMenuItem manualMenuItem
tutorialMenuItem
javax.swing.JMenuItem tutorialMenuItem
aboutMenuItem
javax.swing.JMenuItem aboutMenuItem
defaultColorItem
javax.swing.JCheckBoxMenuItem defaultColorItem
mwColorItem
javax.swing.JCheckBoxMenuItem mwColorItem
polgColorItem
javax.swing.JCheckBoxMenuItem polgColorItem
hdfColorItem
javax.swing.JCheckBoxMenuItem hdfColorItem
userDefColorItem
javax.swing.JCheckBoxMenuItem userDefColorItem
paletteRgbItem
javax.swing.JCheckBoxMenuItem paletteRgbItem
paletteRbItem
javax.swing.JCheckBoxMenuItem paletteRbItem
colorSchemeItems
java.util.Vector<E> colorSchemeItems
colorPaletteItems
java.util.Vector<E> colorPaletteItems
buttonBar
javax.swing.JPanel buttonBar
addGapButton
javax.swing.JButton addGapButton
removeGapButton
javax.swing.JButton removeGapButton
gapId
int gapId
serialVersionUID: 1L
viewProps
AlignViewProps viewProps
indexPanel
IndexPanel indexPanel
namePanel
NamePanel namePanel
seqPanel
SequencePanel seqPanel
alignFrame
AlignFrame alignFrame
wholeSequencePnl
javax.swing.JPanel wholeSequencePnl
horizontalScrollbar
javax.swing.JScrollBar horizontalScrollbar
verticalScrollbar
javax.swing.JScrollBar verticalScrollbar
descriptionPnl
javax.swing.JPanel descriptionPnl
textLabel
javax.swing.JLabel textLabel
descBoxPanel
javax.swing.JPanel descBoxPanel
upperPanel
javax.swing.JPanel upperPanel
methodPanel
MethodPanel methodPanel
upperDescPnl
javax.swing.JPanel upperDescPnl
imageExporter
ImageExporter imageExporter
sliderPanel
SliderPanel sliderPanel
horizontalChange
int horizontalChange
verticalChange
int verticalChange
s3detobj
S3DetObject s3detobj
serialVersionUID: 1L
selProteinColor
Color3f selProteinColor
selResidueColor
Color3f selResidueColor
highestValue
float highestValue
scaleFactor
float scaleFactor
min_x
float min_x
min_y
float min_y
min_z
float min_z
max_x
float max_x
max_y
float max_y
max_z
float max_z
boxValues
int[] boxValues
s3detobj
S3DetObject s3detobj
clusterPanel
javax.swing.JPanel clusterPanel
optionPanel
javax.swing.JPanel optionPanel
axesBox1
java.awt.Choice axesBox1
axesBox2
java.awt.Choice axesBox2
axesBox3
java.awt.Choice axesBox3
label1
javax.swing.JLabel label1
label2
javax.swing.JLabel label2
label3
javax.swing.JLabel label3
defaultBtn
javax.swing.JButton defaultBtn
canvas3D
Canvas3D canvas3D
simpleUni
SimpleUniverse simpleUni
legendPanel
javax.swing.JPanel legendPanel
subFamiliesLbl
javax.swing.JLabel subFamiliesLbl
residuesLbl
javax.swing.JLabel residuesLbl
clusterCentersLbl
javax.swing.JLabel clusterCentersLbl
branchGroup
BranchGroup branchGroup
seqOrderer
SequenceOrderer seqOrderer
name2ClusterIndex
java.util.HashMap<K,V> name2ClusterIndex
serialVersionUID: 1L
minValue
double minValue
maxValue
double maxValue
paletteName
java.lang.String paletteName
serialVersionUID: 1L
viewProps
AlignViewProps viewProps
seqPainter
SequencePainter seqPainter
isInteractive
boolean isInteractive
serialVersionUID: 1L
multAlignTtf
javax.swing.JTextField multAlignTtf
browseAlignFileBtn
JXButton browseAlignFileBtn
filename
java.lang.String filename
loadBtn
JXButton loadBtn
closeBtn
JXButton closeBtn
parent
javax.swing.JFrame parent
loadFrame
LoadAlignFrame loadFrame
serialVersionUID: 1L
frame
javax.swing.JDialog frame
chooser
javax.swing.JFileChooser chooser
file
java.io.File file
name
java.lang.String name
serialVersionUID: 1L
filename
java.lang.String filename
otherTtf
javax.swing.JTextField otherTtf
browseOtherFileBtn
JXButton browseOtherFileBtn
loadBtn
JXButton loadBtn
closeBtn
JXButton closeBtn
parent
AlignFrame parent
loadMethodFrame
LoadMethodFrame loadMethodFrame
methods
Methods methods
alignObject
AlignObject alignObject
scorePnl
javax.swing.JPanel scorePnl
scoreCutoffLbl
javax.swing.JLabel scoreCutoffLbl
scoreCutoffTtf
javax.swing.JTextField scoreCutoffTtf
increasingScoreCB
javax.swing.JCheckBox increasingScoreCB
serialVersionUID: 1L
frame
javax.swing.JDialog frame
chooser
javax.swing.JFileChooser chooser
file
java.io.File file
name
java.lang.String name
type
java.lang.String type
filter
javax.swing.filechooser.FileFilter filter
serialVersionUID: 1L
filename
java.lang.String filename
loadBtn
JXButton loadBtn
closeBtn
JXButton closeBtn
parent
AlignFrame parent
frame
LoadS3DetFrame frame
methods
Methods methods
alignObject
AlignObject alignObject
s3detTtf
javax.swing.JTextField s3detTtf
browseS3DetFileBtn
JXButton browseS3DetFileBtn
avRankPnl
javax.swing.JPanel avRankPnl
avRankCutoffLbl
javax.swing.JLabel avRankCutoffLbl
avRankCutoffTtf
javax.swing.JTextField avRankCutoffTtf
serialVersionUID: 1L
frame
javax.swing.JDialog frame
chooser
javax.swing.JFileChooser chooser
file
java.io.File file
name
java.lang.String name
type
java.lang.String type
filter
javax.swing.filechooser.FileFilter filter
serialVersionUID: 1L
pdbFileTtf
javax.swing.JTextField pdbFileTtf
frame
LoadStructureFrame frame
filename
java.lang.String filename
browspdbFileBtn
javax.swing.JButton browspdbFileBtn
loadBtn
javax.swing.JButton loadBtn
cancelBtn
javax.swing.JButton cancelBtn
chooseFileLbl
javax.swing.JLabel chooseFileLbl
pdbCodeTtf
javax.swing.JTextField pdbCodeTtf
loadpdbonlineBtn
javax.swing.JButton loadpdbonlineBtn
pdbCodeLbl
javax.swing.JLabel pdbCodeLbl
pdbfileOpener
PdbFileOpener pdbfileOpener
downloadInfoArea
javax.swing.JTextArea downloadInfoArea
pdbCode
java.lang.String pdbCode
statusLbl
javax.swing.JLabel statusLbl
centerPnl
javax.swing.JPanel centerPnl
statusPnl
javax.swing.JPanel statusPnl
chainLbl
javax.swing.JLabel chainLbl
chainTtf
javax.swing.JTextField chainTtf
viewprops
AlignViewProps viewprops
comboBox
javax.swing.JComboBox comboBox
blastPdbOnlineBtn
javax.swing.JButton blastPdbOnlineBtn
pdbFilePnl
javax.swing.JPanel pdbFilePnl
seqPainter
SequencePainter seqPainter
namePainter
NamePainter namePainter
alignPanel
AlignPanel alignPanel
parent
AlignFrame parent
serialVersionUID: 1L
frame
javax.swing.JDialog frame
chooser
javax.swing.JFileChooser chooser
filter
view.LoadStructureFrame.InnerPdbFileFilter filter
file
java.io.File file
name
java.lang.String name
serialVersionUID: 1L
filename
java.lang.String filename
xDetTtf
javax.swing.JTextField xDetTtf
browseXDetFileBtn
JXButton browseXDetFileBtn
loadBtn
JXButton loadBtn
closeBtn
JXButton closeBtn
parent
AlignFrame parent
frame
LoadXDetFrame frame
methods
Methods methods
alignObject
AlignObject alignObject
correlationPnl
javax.swing.JPanel correlationPnl
entropyPnl
javax.swing.JPanel entropyPnl
entropyCutoffLbl
javax.swing.JLabel entropyCutoffLbl
corrCutoffLbl
javax.swing.JLabel corrCutoffLbl
corrCutoffTtf
javax.swing.JTextField corrCutoffTtf
entropyCutoffTtf
javax.swing.JTextField entropyCutoffTtf
serialVersionUID: 1L
frame
javax.swing.JDialog frame
chooser
javax.swing.JFileChooser chooser
file
java.io.File file
name
java.lang.String name
type
java.lang.String type
filter
javax.swing.filechooser.FileFilter filter
serialVersionUID: 1L
xdetObj
XDetObject xdetObj
s3detObj
S3DetObject s3detObj
udmObjs
UDMObject[] udmObjs
viewProps
AlignViewProps viewProps
pos2funcRes
java.util.HashMap<K,V> pos2funcRes
pos2predPos
java.util.HashMap<K,V> pos2predPos
pos2res
java.util.HashMap<K,V> pos2res
xdetThreshold
double xdetThreshold
entropyThreshold
double entropyThreshold
s3detThreshold
double s3detThreshold
scoreThreshold
double[] scoreThreshold
methods
Methods methods
YINDEX_XDET
int YINDEX_XDET
YINDEX_ENTROPY
int YINDEX_ENTROPY
YINDEX_S3DET
int YINDEX_S3DET
YINDEX_UDM
int[] YINDEX_UDM
firstSequence
java.lang.String firstSequence
seqPainter
SequencePainter seqPainter
height
int height
serialVersionUID: 1L
viewProps
AlignViewProps viewProps
- Alignment view properties.
graphics2d
java.awt.Graphics2D graphics2d
- Graphics2D object.
s3detobj
S3DetObject s3detobj
- S3Det object for the cluster groups.
seqPainter
SequencePainter seqPainter
- SequencePanel for registering and update.
iWidth
int iWidth
- Image width.
iHeight
int iHeight
- Image height
isInteractive
boolean isInteractive
- Is interactive flag.
startSelection
int startSelection
- Marks selection start for multiple sequence selections.
Class view.NamePanel extends javax.swing.JPanel implements Serializable |
serialVersionUID: 1L
nameRenderer
NamePainter nameRenderer
s3detObj
S3DetObject s3detObj
serialVersionUID: 1L
viewProps
AlignViewProps viewProps
- Alignment view properties.
seqPanel
SequencePanel seqPanel
- Sequence panel
s3detobj
S3DetObject s3detobj
- S3Det object for the cluster groups.
indexPanel
IndexPanel indexPanel
namePanel
NamePanel namePanel
wholeSequencePnl
javax.swing.JPanel wholeSequencePnl
descriptionPnl
javax.swing.JPanel descriptionPnl
textLabel
javax.swing.JLabel textLabel
descBoxPanel
javax.swing.JPanel descBoxPanel
upperPanel
javax.swing.JPanel upperPanel
upperDescPnl
javax.swing.JPanel upperDescPnl
horizontalScrollbar
javax.swing.JScrollBar horizontalScrollbar
verticalScrollbar
javax.swing.JScrollBar verticalScrollbar
horizontalChange
int horizontalChange
verticalChange
int verticalChange
serialVersionUID: 1L
leftColor
java.awt.Color leftColor
rightColor
java.awt.Color rightColor
serialVersionUID: 1L
graphics2d
java.awt.Graphics2D graphics2d
- Graphics2D object.
graphics
java.awt.Graphics graphics
- Graphics object.
viewProps
AlignViewProps viewProps
- Alignment view properties.
fontMetrics
java.awt.FontMetrics fontMetrics
- Font Metrics
alignPanel
AlignPanel alignPanel
- Alignment panel
colColorMap
java.util.HashMap<K,V> colColorMap
- Integer to color hash map
iWidth
int iWidth
- Image width.
iHeight
int iHeight
- Image height.
s3detobj
S3DetObject s3detobj
- s3det object
observersList
java.util.Vector<E> observersList
- List of observers.
currentPosition
int currentPosition
- Current position in the sequence.
selectedSequence
SequenceImpl selectedSequence
- Selected sequence
sumScrollX
int sumScrollX
- Sum of the scroll x values.
jmolPanel
view.Structure3DFrame.JmolPanel jmolPanel
- The JmolPanel.
isExport
boolean isExport
- Is export flag.
isInteractive
boolean isInteractive
- Is interactive flag.
serialVersionUID: 1L
seqPainter
SequencePainter seqPainter
s3detObj
S3DetObject s3detObj
serialVersionUID: 1L
alignFrame
AlignFrame alignFrame
xDetSlider
javax.swing.JSlider xDetSlider
xDetTtf
javax.swing.JTextField xDetTtf
entropySlider
javax.swing.JSlider entropySlider
entropyTtf
javax.swing.JTextField entropyTtf
s3DetTtf
javax.swing.JTextField s3DetTtf
s3DetSlider
javax.swing.JSlider s3DetSlider
otherTtf
javax.swing.JTextField[] otherTtf
otherSlider
javax.swing.JSlider[] otherSlider
methods
Methods methods
xDetLbl
javax.swing.JLabel xDetLbl
entropyLbl
javax.swing.JLabel entropyLbl
s3DetLbl
javax.swing.JLabel s3DetLbl
otherLbl
javax.swing.JLabel[] otherLbl
udmNumber
int udmNumber
index
int index
xDetCutoff
int xDetCutoff
entropyCutoff
int entropyCutoff
s3DetCutoff
int s3DetCutoff
scoreCutoff
int scoreCutoff
xDetSelectOr
javax.swing.JButton xDetSelectOr
entropySelectOr
javax.swing.JButton entropySelectOr
s3DetSelectOr
javax.swing.JButton s3DetSelectOr
otherSelectOr
javax.swing.JButton[] otherSelectOr
xDetSelectAnd
javax.swing.JButton xDetSelectAnd
entropySelectAnd
javax.swing.JButton entropySelectAnd
s3DetSelectAnd
javax.swing.JButton s3DetSelectAnd
otherSelectAnd
javax.swing.JButton[] otherSelectAnd
serialVersionUID: 1L
alObj
AlignObject alObj
seqNumberLabel
javax.swing.JLabel seqNumberLabel
alignLengthLabel
javax.swing.JLabel alignLengthLabel
filenameLabel
javax.swing.JLabel filenameLabel
filenameLabel2
javax.swing.JLabel filenameLabel2
alignLengthLabel2
javax.swing.JLabel alignLengthLabel2
seqNumberLabel2
javax.swing.JLabel seqNumberLabel2
contentPanel
javax.swing.JPanel contentPanel
colorLabel
javax.swing.JLabel colorLabel
colorPalette
ColorSchemeInfo colorPalette
serialVersionUID: 1L
jmolPanel
view.Structure3DFrame.JmolPanel jmolPanel
frame
javax.swing.JFrame frame
ribbonMenuItem
javax.swing.JMenuItem ribbonMenuItem
cartoonMenuItem
javax.swing.JMenuItem cartoonMenuItem
spacefillMenuItem
javax.swing.JMenuItem spacefillMenuItem
selectedChain
java.lang.String selectedChain
zoomOutMenuItem
javax.swing.JMenuItem zoomOutMenuItem
zoomInMenuItem
javax.swing.JMenuItem zoomInMenuItem
alignment
Alignment alignment
commandsPanel
javax.swing.JPanel commandsPanel
commandsBox
javax.swing.JTextField commandsBox
execCommand
javax.swing.JButton execCommand