Serialized Form (biojava-structure-gui 5.4.0 API)

Package demo
- Class demo.GetColorGradient extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  -4954397192682351367L
  - Serialized Fields
    - colors
```
java.awt.Color[] colors
```
Package org.biojava.nbio.structure.align.gui
- Class org.biojava.nbio.structure.align.gui.AlignmentGui extends javax.swing.JFrame implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - algorithm
```
StructureAlignment algorithm
```
    - abortB
```
javax.swing.JButton abortB
```
    - tab1
```
SelectPDBPanel tab1
```
    - tab2
```
PDBUploadPanel tab2
```
    - tab3
```
ScopSelectPanel tab3
```
    - thread
```
java.lang.Thread thread
```
    - alicalc
```
AlignmentCalculationRunnable alicalc
```
    - masterPane
```
javax.swing.JTabbedPane masterPane
```
    - tabPane
```
javax.swing.JTabbedPane tabPane
```
    - progress
```
javax.swing.JProgressBar progress
```
    - dbsearch
```
DBSearchGUI dbsearch
```
- Class org.biojava.nbio.structure.align.gui.AlignmentTextPanel extends JPrintPanel implements Serializable
  
  serialVersionUID:
  
  5092386365924879073L
  - Serialized Fields
    - tp
```
javax.swing.JEditorPane tp
```
- Class org.biojava.nbio.structure.align.gui.ChooseDirAction extends javax.swing.AbstractAction implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - textField
```
javax.swing.JTextField textField
```
    - config
```
UserConfiguration config
```
- Class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  -1055193854675583808L
  - Serialized Fields
    - fromFtp
```
javax.swing.JCheckBox fromFtp
```
    - fileType
```
javax.swing.JComboBox<E> fileType
```
    - pdbDir
```
javax.swing.JTextField pdbDir
```
- Class org.biojava.nbio.structure.align.gui.DBSearchGUI extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  -5657960663049062301L
  - Serialized Fields
    - algorithm
```
StructureAlignment algorithm
```
    - tab1
```
SelectPDBPanel tab1
```
    - tabPane
```
javax.swing.JTabbedPane tabPane
```
    - tab2
```
PDBUploadPanel tab2
```
    - tab3
```
ScopSelectPanel tab3
```
    - listPane
```
javax.swing.JPanel listPane
```
    - abortB
```
javax.swing.JButton abortB
```
    - alicalc
```
AlignmentCalcDB alicalc
```
    - progress
```
javax.swing.JProgressBar progress
```
    - drawer
```
org.biojava.nbio.structure.align.gui.ProgressThreadDrawer drawer
```
    - outFileLocation
```
javax.swing.JTextField outFileLocation
```
    - useDomainSplit
```
java.lang.Boolean useDomainSplit
```
- Class org.biojava.nbio.structure.align.gui.DotPlotPanel extends ScaleableMatrixPanel implements Serializable
  
  serialVersionUID:
  
  -7641953255857483895L
- Class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - alignmentsProcessed
```
int alignmentsProcessed
```
    - progressBar
```
javax.swing.JProgressBar progressBar
```
    - taskOutput
```
javax.swing.JTextArea taskOutput
```
    - stopButton
```
javax.swing.JButton stopButton
```
    - farmJob
```
FarmJob farmJob
```
- Class org.biojava.nbio.structure.align.gui.JPrintPanel extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  -3337337068138131455L
- Class org.biojava.nbio.structure.align.gui.MemoryMonitor extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  56289234782130L
  - Serialized Fields
    - surf
```
MemoryMonitor.Surface surf
```
    - controls
```
javax.swing.JPanel controls
```
    - doControls
```
boolean doControls
```
    - tf
```
javax.swing.JTextField tf
```
- Class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  2387409854370432908L
  - Serialized Fields
    - thread
```
java.lang.Thread thread
```
    - sleepAmount
```
long sleepAmount
```
    - w
```
int w
```
    - h
```
int h
```
    - bimg
```
java.awt.image.BufferedImage bimg
```
    - big
```
java.awt.Graphics2D big
```
    - font
```
java.awt.Font font
```
    - r
```
java.lang.Runtime r
```
    - columnInc
```
int columnInc
```
    - pts
```
int[] pts
```
    - ptNum
```
int ptNum
```
    - ascent
```
int ascent
```
    - descent
```
int descent
```
    - graphOutlineRect
```
java.awt.Rectangle graphOutlineRect
```
    - mfRect
```
java.awt.geom.Rectangle2D mfRect
```
    - muRect
```
java.awt.geom.Rectangle2D muRect
```
    - graphLine
```
java.awt.geom.Line2D graphLine
```
    - graphColor
```
java.awt.Color graphColor
```
    - mfColor
```
java.awt.Color mfColor
```
    - usedStr
```
java.lang.String usedStr
```
- Class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI extends javax.swing.JFrame implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - multiple
```
MultipleStructureAligner multiple
```
    - pairwise
```
StructureAlignment pairwise
```
    - tab
```
SelectMultiplePanel tab
```
    - tabPane
```
javax.swing.JTabbedPane tabPane
```
    - thread
```
java.lang.Thread thread
```
    - alicalc
```
AlignmentCalculationRunnable alicalc
```
    - progress
```
javax.swing.JProgressBar progress
```
    - abortB
```
javax.swing.JButton abortB
```
- Class org.biojava.nbio.structure.align.gui.ParameterGUI extends javax.swing.JFrame implements Serializable
  
  serialVersionUID:
  
  723386061184110161L
  - Serialized Fields
    - params
```
ConfigStrucAligParams params
```
    - textFields
```
java.util.List<E> textFields
```
- Class org.biojava.nbio.structure.align.gui.SelectPDBPanel extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  4002475313717172193L
  - Serialized Fields
    - debug
```
boolean debug
```
    - f1
```
javax.swing.JTextField f1
```
    - f2
```
javax.swing.JTextField f2
```
    - c1
```
javax.swing.JTextField c1
```
    - c2
```
javax.swing.JTextField c2
```
    - r1
```
javax.swing.JTextField r1
```
    - r2
```
javax.swing.JTextField r2
```
    - config
```
UserConfiguration config
```
    - configPane
```
javax.swing.JTabbedPane configPane
```
Package org.biojava.nbio.structure.align.gui.aligpanel
- Class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel extends JPrintPanel implements Serializable
  
  serialVersionUID:
  
  -6892229111166263764L
  - Serialized Fields
    - afpChain
```
AFPChain afpChain
```
    - coordManager
```
AFPChainCoordManager coordManager
```
    - seqFont
```
java.awt.Font seqFont
```
    - eqFont
```
java.awt.Font eqFont
```
    - jmol
```
AbstractAlignmentJmol jmol
```
    - mouseMoLi
```
AligPanelMouseMotionListener mouseMoLi
```
    - selection
```
java.util.BitSet selection
```
    - selectionLocked
```
boolean selectionLocked
```
    - ca1
```
Atom[] ca1
```
    - ca2
```
Atom[] ca2
```
    - colorBySimilarity
```
boolean colorBySimilarity
```
    - colorByAlignmentBlock
```
boolean colorByAlignmentBlock
```
- Class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel extends JPrintPanel implements Serializable
  
  serialVersionUID:
  
  -6892229111166263764L
  - Serialized Fields
    - multAln
```
MultipleAlignment multAln
```
    - alnSeq
```
java.util.List<E> alnSeq
```
    - mapSeqToStruct
```
java.util.List<E> mapSeqToStruct
```
    - size
```
int size
```
    - length
```
int length
```
    - seqFont
```
java.awt.Font seqFont
```
    - eqFont
```
java.awt.Font eqFont
```
    - jmol
```
AbstractAlignmentJmol jmol
```
    - mouseMoLi
```
MultipleAligPanelMouseMotionListener mouseMoLi
```
    - coordManager
```
MultipleAlignmentCoordManager coordManager
```
    - selection
```
java.util.BitSet selection
```
    - selectionLocked
```
boolean selectionLocked
```
    - colorBySimilarity
```
boolean colorBySimilarity
```
    - colorByAlignmentBlock
```
boolean colorByAlignmentBlock
```
- Class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay extends javax.swing.JTextField implements Serializable
  
  serialVersionUID:
  
  6939947266417830429L
  - Serialized Fields
    - panel
```
MultipleAligPanel panel
```
- Class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay extends javax.swing.JTextField implements Serializable
  
  serialVersionUID:
  
  6939947266417830429L
  - Serialized Fields
    - afpChain
```
AFPChain afpChain
```
    - ca1
```
Atom[] ca1
```
    - ca2
```
Atom[] ca2
```
Package org.biojava.nbio.structure.align.gui.autosuggest
- Class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest extends javax.swing.JTextField implements Serializable
  
  serialVersionUID:
  
  8591734727984365156L
  - Serialized Fields
    - defaultText
```
java.lang.String defaultText
```
    - dialog
```
javax.swing.JDialog dialog
```
    - location
```
java.awt.Point location
```
    - list
```
javax.swing.JList<E> list
```
    - suggestions
```
java.util.Vector<E> suggestions
```
    - lastWord
```
java.lang.String lastWord
```
      last word that was entered by user
    - autoSuggestProvider
```
AutoSuggestProvider autoSuggestProvider
```
    - regular
```
java.awt.Font regular
```
    - busy
```
java.awt.Font busy
```
    - matcher
```
org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest.SuggestionFetcher matcher
```
Package org.biojava.nbio.structure.align.gui.jmol
- Class org.biojava.nbio.structure.align.gui.jmol.JmolPanel extends JPrintPanel implements Serializable
  
  serialVersionUID:
  
  -3661941083797644242L
  - Serialized Fields
    - viewer
```
org.jmol.api.JmolViewer viewer
```
    - adapter
```
org.jmol.api.JmolAdapter adapter
```
    - statusListener
```
org.jmol.api.JmolStatusListener statusListener
```
    - currentSize
```
java.awt.Dimension currentSize
```
    - rectClip
```
java.awt.Rectangle rectClip
```
    - structure
```
Structure structure
```
Package org.biojava.nbio.structure.gui
- Class org.biojava.nbio.structure.gui.JMatrixPanel extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  -1720879395453257846L
  - Serialized Fields
    - _bufImage
```
java.awt.image.BufferedImage _bufImage
```
    - matrix
```
Matrix matrix
```
    - cellColor
```
ContinuousColorMapper cellColor
```
    - scale
```
float scale
```
    - fragmentPairs
```
FragmentPair[] fragmentPairs
```
    - aligs
```
AlternativeAlignment[] aligs
```
    - selectedAlignmentPos
```
int selectedAlignmentPos
```
    - params
```
StrucAligParameters params
```
- Class org.biojava.nbio.structure.gui.ScaleableMatrixPanel extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  -8082261434322968652L
  - Serialized Fields
    - mPanel
```
JMatrixPanel mPanel
```
    - slider
```
javax.swing.JSlider slider
```
    - scroll
```
javax.swing.JScrollPane scroll
```
    - coloring
```
javax.swing.JComboBox<E> coloring
```
    - gradients
```
java.util.Map<K,V> gradients
```
- Class org.biojava.nbio.structure.gui.ScaleableMatrixPanel.GradientRenderer extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  -2000575579184232365L
  - Serialized Fields
    - min
```
int min
```
    - max
```
int max
```
    - title
```
javax.swing.JLabel title
```
    - gradientContainer
```
javax.swing.JPanel gradientContainer
```
- Class org.biojava.nbio.structure.gui.SequenceDisplay extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  -1829252532712454236L
  - Serialized Fields
    - structure1
```
Structure structure1
```
    - structure2
```
Structure structure2
```
    - alig
```
AlternativeAlignment alig
```
    - structurePairAligner
```
StructurePairAligner structurePairAligner
```
    - panel1
```
SequenceScalePanel panel1
```
    - panel2
```
SequenceScalePanel panel2
```
    - residueSizeSlider
```
javax.swing.JSlider residueSizeSlider
```
    - percentageDisplay
```
javax.swing.JLabel percentageDisplay
```
    - idx1
```
int[] idx1
```
    - idx2
```
int[] idx2
```
    - apos
```
java.util.List<E> apos
```
    - scale
```
float scale
```
    - mouseListener1
```
SequenceMouseListener mouseListener1
```
    - mouseListener2
```
SequenceMouseListener mouseListener2
```
    - label1
```
javax.swing.JLabel label1
```
    - label2
```
javax.swing.JLabel label2
```
- Class org.biojava.nbio.structure.gui.WrapLayout extends java.awt.FlowLayout implements Serializable
  - Serialized Fields
    - preferredLayoutSize
```
java.awt.Dimension preferredLayoutSize
```
Package org.biojava.nbio.structure.gui.util
- Class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame extends javax.swing.JFrame implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - aligs
```
AlternativeAlignment[] aligs
```
    - panel
```
javax.swing.JPanel panel
```
    - structure1
```
Structure structure1
```
    - structure2
```
Structure structure2
```
    - structurePairAligner
```
StructurePairAligner structurePairAligner
```
- Class org.biojava.nbio.structure.gui.util.PDBDirPanel extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  -5682120627824627408L
  - Serialized Fields
    - debug
```
boolean debug
```
    - pdbDir
```
javax.swing.JTextField pdbDir
```
    - f1
```
javax.swing.JTextField f1
```
    - f2
```
javax.swing.JTextField f2
```
    - c1
```
javax.swing.JTextField c1
```
    - c2
```
javax.swing.JTextField c2
```
- Class org.biojava.nbio.structure.gui.util.PDBServerPanel extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  -5682120627824627408L
  - Serialized Fields
    - debug
```
boolean debug
```
    - pdbDir
```
javax.swing.JTextField pdbDir
```
    - f1
```
javax.swing.JTextField f1
```
    - f2
```
javax.swing.JTextField f2
```
    - c1
```
javax.swing.JTextField c1
```
    - c2
```
javax.swing.JTextField c2
```
- Class org.biojava.nbio.structure.gui.util.PDBUploadPanel extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - fileType
```
javax.swing.JComboBox<E> fileType
```
    - filePath1
```
javax.swing.JTextField filePath1
```
    - filePath2
```
javax.swing.JTextField filePath2
```
    - chain1
```
javax.swing.JTextField chain1
```
    - chain2
```
javax.swing.JTextField chain2
```
- Class org.biojava.nbio.structure.gui.util.ScopSelectPanel extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  757947454156959178L
  - Serialized Fields
    - dom1
```
JAutoSuggest dom1
```
    - dom2
```
JAutoSuggest dom2
```
- Class org.biojava.nbio.structure.gui.util.SelectMultiplePanel extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  757947454156959178L
  - Serialized Fields
    - input
```
javax.swing.JTextField input
```
- Class org.biojava.nbio.structure.gui.util.SequenceScalePanel extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  7893248902423L
  - Serialized Fields
    - chain
```
Chain chain
```
    - chainLength
```
int chainLength
```
    - scale
```
float scale
```
    - seqArr
```
java.lang.Character[] seqArr
```
    - coordManager
```
CoordManager coordManager
```
    - position
```
int position
```
    - apos
```
java.util.List<E> apos
```
Package org.biojava.nbio.structure.gui.util.color
- Class org.biojava.nbio.structure.gui.util.color.GradientPanel extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  -6387922432121206731L
  - Serialized Fields
    - mapper
```
ContinuousColorMapper mapper
```
    - min
```
double min
```
    - max
```
double max
```
- Class org.biojava.nbio.structure.gui.util.color.HSVColorSpace extends java.awt.color.ColorSpace implements Serializable
  
  serialVersionUID:
  
  8324413992279510075L

Package org.biojava.nbio.structure.symmetry.gui

Class org.biojava.nbio.structure.symmetry.gui.SymmetryGui extends javax.swing.JFrame implements Serializable

serialVersionUID:: 0L

Serialized Fields

params
```
CESymmParameters params
```
abortB
```
javax.swing.JButton abortB
```
tab1
```
SelectPDBPanel tab1
```
tab2
```
PDBUploadPanel tab2
```
tab3
```
ScopSelectPanel tab3
```
thread
```
java.lang.Thread thread
```
alicalc
```
AlignmentCalculationRunnable alicalc
```
masterPane
```
javax.swing.JTabbedPane masterPane
```
tabPane
```
javax.swing.JTabbedPane tabPane
```
progress
```
javax.swing.JProgressBar progress
```

Serialized Form

Package demo

Class demo.GetColorGradient extends javax.swing.JPanel implements Serializable

Serialized Fields

colors

Package org.biojava.nbio.structure.align.gui

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

Serialized Fields

algorithm

abortB

tab1

tab2

tab3

thread

alicalc

masterPane

tabPane

progress

dbsearch

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

Serialized Fields

tp

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

Serialized Fields

textField

config

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

Serialized Fields

fromFtp

fileType

pdbDir

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

Serialized Fields

algorithm

tab1

tabPane

tab2

tab3

listPane

abortB

alicalc

progress

drawer

outFileLocation

useDomainSplit

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

Class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener extends javax.swing.JPanel implements Serializable

Serialized Fields

alignmentsProcessed

progressBar

taskOutput

stopButton

farmJob

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

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

Serialized Fields

surf

controls

doControls

tf

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

Serialized Fields

thread

sleepAmount

w

h

bimg

big

font

r

columnInc

pts

ptNum

ascent

descent

graphOutlineRect

mfRect

muRect

graphLine

graphColor