Serialized Form (biojava-structure-gui 6.0.0 API)

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

Serialized Form

Package demo

Class demo.GetColorGradient extends JPanel implements Serializable

Serialized Fields

colors

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

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

Serialized Fields

abortB

algorithm

alicalc

masterPane

progress

tab1

tab2

tab3

tabPane

thread

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

Serialized Fields

tp

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

Serialized Fields

config

textField

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

Serialized Fields

fileType

fromFtp

pdbDir

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

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

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

Serialized Fields

controls

doControls

surf

tf

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

Serialized Fields

ascent

big

bimg

columnInc

descent

font

graphColor

graphLine

graphOutlineRect

h

mfColor

mfRect

muRect

ptNum

pts

r

sleepAmount

thread

usedStr

w

Class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI extends JFrame implements Serializable

Serialized Fields

abortB

alicalc

multiple

pairwise

progress

tab

tabPane

thread

Class org.biojava.nbio.structure.align.gui.ParameterGUI extends JFrame implements Serializable

Serialized Fields

params

textFields

Class org.biojava.nbio.structure.align.gui.SelectPDBPanel extends JPanel implements Serializable

Serialized Fields

c1

c2

config

configPane