ControlPanel.TitledPanel tp1
javax.swing.JPanel tp2
ControlPanel.TitledPanel tp3
javax.swing.JButton undoBtn
javax.swing.JButton resetInitialBtn
javax.swing.JButton defaultBtn
javax.swing.JButton cam1Btn
javax.swing.JButton cam2Btn
javax.swing.JButton cam3Btn
javax.swing.JPanel componentPanel
javax.swing.JLabel logArea
javax.swing.JPanel logPanel
javax.swing.JPanel headerpanel
javax.swing.JLabel headerTitle
javax.swing.JLabel headerText
MoleculeEditor editor
ControlPanel.TitledPanel tp1
ControlPanel.TitledPanel tp2
ControlPanel.TitledPanel tp3
ParticlePropertiesPanel ppp
javax.swing.JButton combine
javax.swing.JButton restore
javax.swing.JButton editMembers
javax.swing.JButton editPropsBtn
javax.swing.JButton test
javax.swing.JButton membersOkBtn
javax.swing.JButton membersCancelBtn
javax.swing.JButton saveAsBtn
javax.swing.JButton applyBtn
javax.swing.JButton exitBtn
javax.swing.JComboBox<E> combo
MoleculeEditor editor
javax.swing.JComponent comp1
javax.swing.JComponent comp2
javax.swing.JComponent comp3
javax.swing.JPanel p1
javax.swing.JPanel p2
javax.swing.JLabel l1
javax.swing.JLabel l2
javax.swing.JLabel l3
javax.swing.DefaultComboBoxModel<E> model1
javax.swing.DefaultComboBoxModel<E> model2
javax.swing.DefaultComboBoxModel<E> model3
javax.swing.JButton cBtn
com.sun.j3d.utils.universe.ConfiguredUniverse membraneConfiguredUniverse
CameraMode cameraMode
IntersectManager intersector
PickNDragManager PNDmanager
MicroDomainManager MDmanager
Hud hud
javax.media.j3d.BranchGroup mainBranchGroup
javax.media.j3d.BranchGroup basementBranchGroup
javax.media.j3d.BranchGroup publicBranchGroup
CoordinateBar coordinateBar
Raster raster
com.sun.j3d.utils.picking.PickCanvas MyPick
boolean axisVisible
boolean rasterVisible
javax.media.j3d.PointLight light1
javax.media.j3d.PointLight light2
javax.media.j3d.PointLight light3
javax.media.j3d.AmbientLight ambientLight
javax.media.j3d.Background background
javax.media.j3d.ImageComponent2D ic
MembraneViewListener listener
boolean isQuadBufferedStereoAvailable
int stereoViewMode
int stereoViewScalingMode
int stereoViewAutoFocusMode
MyGradientBufferedImage BIdark
MyGradientBufferedImage BIbright
MyGradientBufferedImage BIbright_Wet
MyGradientBufferedImage BIdark_Wet
MyGradientBufferedImage BIdarkUni
MyGradientBufferedImage BIbrightUni
MyGradientBufferedImage BIbrightUni_Wet
MyGradientBufferedImage BIdarkUni_Wet
boolean notWet
MicroDomain_3D defaultArea
Compatibility[] comps
javax.swing.ImageIcon green
javax.swing.ImageIcon warning
java.awt.Dimension DIRECTHELPBUTTONSIZE
int mode
java.lang.String[] str1
java.lang.String[] str2
java.lang.String header
java.awt.Color originalbackground
java.lang.String size
javax.swing.JFileChooser chooser
int mode
boolean isRollingOver
java.awt.Image img
javax.swing.JPanel main
org.cellmicrocosmos.cm2.gui.MylFCAccessoryForGenerating.WritePanel wp
org.cellmicrocosmos.cm2.gui.MylFCAccessoryForGenerating.MyCompatibilityPanel cpanel
javax.swing.JPanel right
javax.swing.JPanel top
javax.swing.JPanel middle
javax.swing.JPanel bottom
javax.swing.JPanel space
javax.swing.JLabel jump
javax.swing.JScrollPane scroll
javax.swing.JTextArea tp
javax.swing.JButton close
java.lang.String[] tags
int textlength
int mode
MembraneViewListener listener
javax.swing.JButton runBtn
javax.swing.JButton closeBtn
javax.swing.JButton addBtn
javax.swing.JButton restoreBtn
javax.swing.JButton removeBtn
javax.swing.JButton refreshBtn
org.cellmicrocosmos.cm2.gui.dialogs.AlgorithmWizzard.MyTable table
javax.swing.table.DefaultTableModel model
javax.swing.JPanel mainpanel
javax.swing.JPanel left
javax.swing.JPanel right
javax.swing.JPanel infopanel
javax.swing.JPanel namepanel
javax.swing.JPanel typepanel
javax.swing.JPanel pathpanel
javax.swing.JPanel textfieldpanel
javax.swing.JLabel namelabel
javax.swing.JLabel typelabel
javax.swing.JTextField pathlabel
javax.swing.JPanel leftBtnbar
javax.swing.JPanel rightBtnbarUpper
javax.swing.JPanel rightBtnbarBottom
javax.swing.JPanel leftinnerBtnbar
javax.swing.JLabel ta
javax.swing.JScrollPane scroll
javax.swing.JScrollPane scroll2
javax.swing.JCheckBox chkStartInBackground
javax.swing.JCheckBox chkShowProtocol
javax.swing.JCheckBox chkUniqueRandom
javax.swing.JSpinner jspUniqueRandomSeed
javax.swing.ImageIcon yesIcon
javax.swing.ImageIcon noIcon
PluginManager pluginmanager
int CANCEL
int out
javax.swing.JButton cancelBtn
javax.swing.JButton okBtn
javax.swing.JPanel buttonbar
javax.swing.JPanel header1
javax.swing.JPanel header2
javax.swing.JPanel header3
javax.swing.JLabel lx
javax.swing.JLabel lz
javax.swing.JLabel lTransX
javax.swing.JLabel lTransZ
javax.swing.JSpinner tfx
javax.swing.JSpinner tfz
javax.swing.JSpinner tfTransX
javax.swing.JSpinner tfTransZ
javax.swing.JPanel groundxy
javax.swing.JPanel groundTransxy
javax.swing.JLabel h1
java.awt.Point location
Engine engine
javax.vecmath.Point3f[] oldPositions
java.awt.Shape[] oldMDGeometries
java.awt.Dimension oldSize
int APPROVE
int CANCEL
java.util.Vector<E> rowdata
int out
javax.swing.JScrollPane scroll
javax.swing.JButton cancelBtn
javax.swing.JButton okBtn
javax.swing.JButton choose
javax.swing.JPanel buttonbar
javax.swing.JLabel tf1
javax.swing.JLabel tf2
javax.swing.JLabel tf3
javax.swing.JLabel tf4
javax.swing.JTextArea tf5
javax.swing.JLabel tf6
javax.swing.JLabel message
javax.swing.JLabel message2
javax.swing.JPanel ground1
javax.swing.JPanel ground2
javax.swing.JPanel ground3
javax.swing.JPanel ground4
javax.swing.JPanel ground5
javax.swing.JPanel ground6
javax.swing.JPanel ground7
javax.swing.JPanel mground1
javax.swing.JPanel mground2
javax.swing.JPanel superground
javax.swing.JPanel radioPanel
EditDBEntryDialogListener listener
javax.swing.JRadioButton radio1
javax.swing.JRadioButton radio2
java.lang.String selectedcode
javax.swing.JPanel ground2
javax.swing.JButton ok
javax.swing.JButton cancel
javax.swing.JButton pdbdefault
javax.swing.JButton axisAngleToMatrix
javax.swing.JPanel panelMatrix
javax.swing.JPanel panelAxisAngle
javax.swing.JTextField[] tfMatrix
javax.swing.JTextField[] tfTranslation
javax.swing.JTextField[] tfAxisAngle
javax.swing.JPanel panelTranslation
javax.vecmath.Matrix3f retmatrix
float rettranslation
javax.swing.JTextField tfinfo
Molecule_3D currentMolecule
javax.swing.JPanel main
javax.swing.JTabbedPane tab
javax.swing.JPanel main2
javax.swing.JPanel main3
javax.swing.JPanel main4
javax.swing.JPanel header
javax.swing.JPanel btnbar
javax.swing.JButton close
Engine.J3DOperations j3d
javax.swing.JSlider precslider
javax.swing.JSlider minprecslider
javax.swing.JSlider verticesslider
javax.swing.JSlider ambientslider
javax.swing.JCheckBox light1check
javax.swing.JCheckBox light2check
javax.swing.JSlider shinprotslider
javax.swing.JSlider shinlipslider
javax.swing.JRadioButton filledradio
javax.swing.JRadioButton wireframeradio
javax.swing.JButton defaultBtn
javax.swing.JSlider mousesen
javax.swing.JCheckBox shapesCollisions
javax.swing.JSpinner atomDistances
javax.swing.JCheckBox atomDistancesAbsolute
javax.swing.JSlider leaveOutAtomsFactor
javax.swing.JCheckBox atomsCollisions
javax.swing.JRadioButton rbDetail1
javax.swing.JRadioButton rbDetail2
javax.swing.JPanel main1
javax.swing.JCheckBox disableDragging
javax.swing.JCheckBox enablePPEAutomatic
javax.swing.JCheckBox enableFastTransitions
javax.swing.JCheckBox enableAtomPerformanceMode
javax.swing.JCheckBox antialiasing
javax.swing.JCheckBox parallelProjection
javax.swing.JCheckBox showAllMultilayers
javax.swing.JCheckBox uniformBackground
int limit
javax.swing.text.JTextComponent c
javax.swing.JButton cancelBtn
javax.swing.JButton okBtn
javax.swing.JPanel buttonbar
javax.swing.JPanel header1
javax.swing.JTextField tf1
javax.swing.JTextField tf2
javax.swing.JTextField tf3
MembraneModel model
javax.swing.JLabel h1
javax.swing.JPanel ground1
javax.swing.JPanel ground2
javax.swing.JPanel ground3
javax.swing.JPanel ground4
javax.swing.JPanel ground
javax.swing.JButton dateBtn
javax.swing.JTabbedPane tab
javax.swing.ImageIcon warningIcon
int width
org.cellmicrocosmos.cm2.gui.dialogs.ManageTitleSectionDialog.EditPane title
org.cellmicrocosmos.cm2.gui.dialogs.ManageTitleSectionDialog.EditPane source
org.cellmicrocosmos.cm2.gui.dialogs.ManageTitleSectionDialog.EditPane keywds
org.cellmicrocosmos.cm2.gui.dialogs.ManageTitleSectionDialog.EditPane expdta
org.cellmicrocosmos.cm2.gui.dialogs.ManageTitleSectionDialog.EditPane author
org.cellmicrocosmos.cm2.gui.dialogs.ManageTitleSectionDialog.EditPane jrnl
org.cellmicrocosmos.cm2.gui.dialogs.ManageTitleSectionDialog.EditPane remark
int out
javax.swing.JButton cancelBtn
javax.swing.JButton okBtn
javax.swing.JPanel buttonbar
javax.swing.JTextField tf1
javax.swing.JTextField tf2
javax.swing.JPanel header1
javax.swing.JPanel header2
javax.swing.JLabel lx
javax.swing.JLabel lz
javax.swing.JSpinner tfx
javax.swing.JSpinner tfz
javax.swing.JPanel ground1
javax.swing.JPanel ground2
javax.swing.JPanel groundxz
javax.swing.JLabel h1
javax.swing.JLabel h2
MembraneModel model
Engine.MembraneOperations operations
javax.swing.JButton ok
javax.swing.JButton cancel
org.cellmicrocosmos.cm2.gui.dialogs.PdbSettingsWindow.NumberingPanel npanel
org.cellmicrocosmos.cm2.gui.dialogs.PdbSettingsWindow.TransformationsPanel tpanel
org.cellmicrocosmos.cm2.gui.dialogs.PdbSettingsWindow.MyCompatibilityPanel cpanel
javax.swing.JRadioButton radio1
javax.swing.JRadioButton radio2
javax.swing.JButton okBtn
javax.swing.JButton cancelBtn
javax.swing.JButton testBtn
javax.swing.JTextField tflogin
javax.swing.JPasswordField tfpassword
javax.swing.JTextField tfhttpport
javax.swing.JTextField tfftpport
javax.swing.JTextField tfhttp
javax.swing.JTextField tfftp
javax.swing.JLabel l1
javax.swing.JLabel l2
javax.swing.JLabel l3
javax.swing.JLabel l4
javax.swing.JLabel l5
javax.swing.JLabel l6
javax.swing.JPanel headerpanel
javax.swing.JPanel p2
javax.swing.JPanel p3
javax.swing.JPanel btnbar
javax.swing.JPanel p21
javax.swing.JPanel p22
javax.swing.JPanel p31
javax.swing.JPanel p32
javax.swing.JPanel p33
javax.swing.JLabel header
javax.swing.JPanel p01
javax.swing.JPanel p02
javax.swing.JPanel main1
javax.swing.JPanel main2
javax.swing.JTabbedPane tab
javax.swing.JTextArea ta
javax.swing.JPanel linkp1
javax.swing.JPanel linkp2
javax.swing.JPanel linkp3
javax.swing.JPanel linkp4
javax.swing.JPanel linkp5
javax.swing.JPanel linkp6
javax.swing.JPanel linkp7
javax.swing.JButton defaultBtn
javax.swing.JTextField linktf1
javax.swing.JTextField linktf2
javax.swing.JTextField linktf3
javax.swing.JTextField linktf4
javax.swing.JTextField linktf5
javax.swing.JTextField linktf6
javax.swing.JLabel linkl1
javax.swing.JLabel linkl2
javax.swing.JLabel linkl3
javax.swing.JLabel linkl4
javax.swing.JLabel linkl5
javax.swing.JLabel linkl6
GuiListener listener
javax.swing.JProgressBar bar
int mode
boolean showBar
boolean paintStringOnImage
boolean stringwithbackground
java.lang.String string
java.awt.Color startupcolor
javax.swing.JPanel ground
boolean closePressed
javax.swing.JLabel label
MembraneViewListener listener
javax.swing.JCheckBox syncEcIc
javax.swing.JCheckBox absolutevalues
javax.swing.JCheckBox autosetpercent
javax.swing.JCheckBox promptdelete
javax.swing.SpinnerNumberModel spinnerModel
javax.swing.JSpinner decimalplaces
int oldDecimalPlaces
javax.swing.JLabel overallPercentage
org.cellmicrocosmos.cm2.gui.elements.ComponentView.DomainPanel domainPanel
javax.swing.JTabbedPane tab
javax.swing.JToolBar Btnbar
javax.swing.JButton popUpBtn
org.cellmicrocosmos.cm2.gui.elements.ComponentView.MicroPanel selectedPanel
int lastindex
java.util.Vector<E> lists
boolean updating
boolean initing
org.cellmicrocosmos.cm2.gui.elements.ComponentView.DNDThread dndThread
java.io.File currentFile
java.lang.String[] headers
java.lang.String[] relevantContents
java.awt.Color alreadyinTextColor
java.awt.Color invalidTextColor
int VALIDROW
int EMPTYFILENAME
int FILEDOESNOTEXIST
int FILEISNOTVALID
boolean sortAscending
DatabaseViewListener listener
javax.swing.JToolBar controlpanel
javax.swing.JTable table1
javax.swing.JTable table2
javax.swing.JButton btn1
javax.swing.JButton btn2
javax.swing.JPopupMenu pop
javax.swing.JMenuItem item1
javax.swing.JMenuItem item3
javax.swing.JMenuItem item4
javax.swing.JMenuItem item6
javax.swing.JMenuItem item7
javax.swing.JMenuItem item8
javax.swing.JMenuItem item9
javax.swing.JMenuItem item10
javax.swing.JButton b1
javax.swing.JButton b3
javax.swing.JButton b4
javax.swing.JButton b6
javax.swing.JButton b7
javax.swing.JButton b8
javax.swing.JButton b9
javax.swing.JButton b10
javax.swing.table.DefaultTableModel tablemodel1
javax.swing.table.DefaultTableModel tablemodel2
boolean activateAddOptions
javax.swing.JLabel namelabel
javax.swing.JRadioButton radio1
javax.swing.JRadioButton radio2
javax.swing.ButtonGroup bg
javax.swing.JScrollPane scr1
javax.swing.JScrollPane scr2
org.cellmicrocosmos.cm2.gui.elements.DatabaseView.RBRenderer rbrenderer
org.cellmicrocosmos.cm2.gui.elements.DatabaseView.RBEditor rbeditor
org.cellmicrocosmos.cm2.gui.elements.DatabaseView.RBRenderer rbrenderer2
org.cellmicrocosmos.cm2.gui.elements.DatabaseView.RBEditor rbeditor2
java.awt.Font defaultTableFont
org.cellmicrocosmos.cm2.gui.elements.DatabaseView.DNDThread dndThread
java.awt.Point lastPoint
MembraneViewListener listener
Membrane3D m3d
javax.swing.JToolBar toolbar2
javax.swing.JToolBar toolbar
org.cellmicrocosmos.cm2.gui.elements.MembraneView.MyAlignButtonBar toolbar3
javax.swing.JPanel calcuPanel
javax.swing.JButton calcu
javax.swing.JButton clearLip
javax.swing.JButton clearAll
javax.swing.JButton align
javax.swing.JButton alignPlus
javax.swing.JButton remove
javax.swing.JButton detailBtn
MyJRadioButton intraBtn
MyJRadioButton extraBtn
MyJRadioButton freelookBtn
javax.swing.JCheckBox showAxis
javax.swing.JCheckBox showRaster
javax.swing.JCheckBox toggleOPMLayersButton
javax.swing.JLabel opmLabel
javax.swing.JComboBox<E> comboRender
javax.swing.JToolBar bilayerinfo
MembraneView.IntersectionPanel intersectPanel
org.cellmicrocosmos.cm2.gui.elements.MembraneView.AtomCountPanel atomcountpanel
int EXTRA
int INTRA
int FREE
javax.swing.JPopupMenu popcanvas
javax.swing.JMenuItem alPopItem
javax.swing.JMenuItem alPopPlusItem
javax.swing.JMenuItem rmPopItem
javax.swing.JMenuItem cmPopItem
javax.swing.JMenuItem bfPopItem
javax.swing.JPanel popPanel
javax.swing.JLabel popLabel
IntersectionsDisplayer intersectionsDisplayer
org.cellmicrocosmos.cm2.gui.elements.MembraneView.AlgorithmInfo ainfo
java.util.Vector<E> otherProteins
java.util.Vector<E> oldMatrices
java.util.Vector<E> oldYTranslations
javax.swing.JPanel placeholder
org.cellmicrocosmos.cm2.gui.elements.MembraneView.MultiLayerPanel multilayerpanel
java.util.Vector<E> invalidones
org.cellmicrocosmos.cm2.gui.elements.MembraneView.PaintDomainDialog paintDomainDialog
Molecule_3D currentMoleculeAligning
java.awt.Point oldCursor
double translating_Distance
int oldModel
boolean haveToReInsert
java.util.Vector<E> comps
javax.swing.JLabel label
javax.swing.JLabel nonelabel
javax.swing.JCheckBox showBtn
javax.swing.JButton lipidsBtn
Molecule_3D[] currentMolecules
boolean isMembraneAttrsShowing
int MINFO
int ENTRYP
int ENTRYL
int SSELECT
int MSELECT
int LIPID
int ERR
int OFF
int NEUTRAL
java.awt.Font font1
java.awt.Font font2
java.awt.Font fontheader
org.cellmicrocosmos.cm2.gui.elements.PropertiesView.HeaderPanel headerpanel
org.cellmicrocosmos.cm2.gui.elements.PropertiesView.Panel P
javax.swing.JScrollPane scroll
int mode
org.cellmicrocosmos.cm2.gui.elements.PropertiesView.StringWrapper[] wrappers
float xcoord
float zcoord
float ytrans
javax.vecmath.Matrix3f matrix
long filesizesingle
int lipidcountExtra
int lipidcountIntra
long filesizemulti
int borderL
int rowspace
java.awt.image.BufferedImage image1
java.awt.image.BufferedImage image1w
java.awt.image.BufferedImage image2
java.awt.image.BufferedImage image2w
java.awt.image.BufferedImage image3
java.awt.image.BufferedImage image3w
java.awt.image.BufferedImage image4
java.awt.image.BufferedImage image4w
java.awt.image.BufferedImage image5
java.awt.image.BufferedImage image5w
java.awt.image.BufferedImage image6
java.awt.image.BufferedImage image6w
DatabaseViewListener dblistener
Engine.MembraneOperations melistener
javax.swing.JTabbedPane massTabPane
javax.swing.JTabbedPane massAbsTabPane
javax.swing.JTabbedPane numberTabPane
javax.swing.JTabbedPane numberAbsTabPane
javax.swing.JTabbedPane tab
org.jfree.data.category.DefaultCategoryDataset barDatasetICMass
org.jfree.data.category.DefaultCategoryDataset barDatasetECMass
org.jfree.data.category.DefaultCategoryDataset barDatasetICMassAbs
org.jfree.data.category.DefaultCategoryDataset barDatasetECMassAbs
org.jfree.data.category.DefaultCategoryDataset barDatasetICNumb
org.jfree.data.category.DefaultCategoryDataset barDatasetECNumb
org.jfree.data.category.DefaultCategoryDataset barDatasetICNumbAbs
org.jfree.data.category.DefaultCategoryDataset barDatasetECNumbAbs
org.jfree.data.category.DefaultCategoryDataset barDatasetAllMass
org.jfree.data.category.DefaultCategoryDataset barDatasetAllMassAbs
org.jfree.data.category.DefaultCategoryDataset barDatasetAllNumb
org.jfree.data.category.DefaultCategoryDataset barDatasetAllNumbAbs
org.jfree.chart.plot.CategoryPlot bPlotInMass
org.jfree.chart.plot.CategoryPlot bPlotExMass
org.jfree.chart.plot.CategoryPlot bPlotAllMass
org.jfree.chart.plot.CategoryPlot bPlotInMassAbs
org.jfree.chart.plot.CategoryPlot bPlotExMassAbs
org.jfree.chart.plot.CategoryPlot bPlotAllMassAbs
org.jfree.chart.plot.CategoryPlot bPlotInNumb
org.jfree.chart.plot.CategoryPlot bPlotExNumb
org.jfree.chart.plot.CategoryPlot bPlotAllNumb
org.jfree.chart.plot.CategoryPlot bPlotInNumbAbs
org.jfree.chart.plot.CategoryPlot bPlotExNumbAbs
org.jfree.chart.plot.CategoryPlot bPlotAllNumbAbs
org.jfree.chart.JFreeChart bChartInMass
org.jfree.chart.JFreeChart bChartExMass
org.jfree.chart.JFreeChart bChartAllMass
org.jfree.chart.JFreeChart bChartInMassAbs
org.jfree.chart.JFreeChart bChartExMassAbs
org.jfree.chart.JFreeChart bChartAllMassAbs
org.jfree.chart.JFreeChart bChartInNumb
org.jfree.chart.JFreeChart bChartExNumb
org.jfree.chart.JFreeChart bChartAllNumb
org.jfree.chart.JFreeChart bChartInNumbAbs
org.jfree.chart.JFreeChart bChartExNumbAbs
org.jfree.chart.JFreeChart bChartAllNumbAbs
java.util.Vector<E> errorlist
org.jfree.data.xy.XYSeriesCollection dataset
org.jfree.chart.ChartPanel chartPanel
org.jfree.chart.JFreeChart chart
org.jfree.chart.plot.XYPlot plot
javax.swing.JTable table
javax.swing.table.DefaultTableModel model
javax.swing.table.TableColumnModel columnModel
java.lang.String[] headers
java.util.Random rand
long seed
java.util.Random rand
javax.swing.JCheckBox controlsBtn
javax.swing.JCheckBox parametersBtn
javax.swing.JCheckBox graphBtn
javax.swing.JButton startBtn
org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Gui.MyGraphPanel graphPanel
org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Gui.ControlPanel controlPanel
org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Gui.ParameterPanel paraPanel
Atom_Level_Minimizer algo
int guiMode
javax.swing.JFrame dialog
float lastGood
double min
double max
int mode
java.lang.Double defaultValue
boolean mayBeEmpty
boolean isValid