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main(String[]) - Static method in class org.cellmicrocosmos.cm2.Start
Entry Point.
MAIN_FRAME_SCALE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.GUI_SETTINGS_AND_CONTROLS
 
MainGui - Class in org.cellmicrocosmos.cm2.gui
Builds up a Gui Framework with multiple Dockable Frames.
MainGui() - Constructor for class org.cellmicrocosmos.cm2.gui.MainGui
 
MainGui.TabComponentNoBorder - Class in org.cellmicrocosmos.cm2.gui
This class prevents borders from being painted.
makeToolbarsFloatable(boolean) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
makeToolbarsFloatable(boolean) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
Make toolbars floatable.
makeToolbarsFloatable(boolean) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
makeUpdate(int) - Static method in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPEUpdater
Performs an update of the pdbtm.mif and other files.
ManageTitleSectionDialog - Class in org.cellmicrocosmos.cm2.gui.dialogs
The dialog that lets the user enter his text for the title section of the membrane
ManageTitleSectionDialog() - Constructor for class org.cellmicrocosmos.cm2.gui.dialogs.ManageTitleSectionDialog
 
MANAGING_MODE - Static variable in class org.cellmicrocosmos.cm2.gui.dialogs.AlgorithmWizzard
 
manuallyUpdateStatistics() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Forces the statistics to update on current values.
massValue - Variable in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
 
MASTER_EPSILON - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.MyDefaults
 
MASTER_SIGMA - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.MyDefaults
 
masterEpsilon - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Energies
 
masterSigma - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Energies
 
matchFound(Vector<String>) - Method in interface org.cellmicrocosmos.cm2.interfaces.SearchListener
 
matrixUpdated(Matrix3f, float) - Method in interface org.cellmicrocosmos.cm2.interfaces.CM2AdditionalListener
 
MAX_ATOMS_FOR_PROPER_SECONDARY_STRUCTURE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.MEMBRANE_SIZES
 
MAX_PDB_SEARCH_HISTORY_SIZE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.GUI_SETTINGS_AND_CONTROLS
the max numbers of previous selections that remain in the combobox in the pdb search dialog
MAX_QUICKLOAD_HISTORY_SIZE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.GUI_SETTINGS_AND_CONTROLS
the max numbers of previous selections that remain in the combobox for quickload
MAX_SIZE_OF_MEMBRANE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.MEMBRANE_SIZES
 
MAX_Y_TRANSLATION - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.MEMBRANE_SIZES
 
MAX_Y_TRANSLATION - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Application_Constants
The maximal y-translation that is allowed
maxAtomRadius - Variable in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
maximizeView(int) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
maximizes the specified view
mayGenerate() - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
MembersUpdated(Atom[]) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.EnergyFunction
Gets called everytime when any atoms have been added, or removed from the model during runtime
Membrane3D - Class in org.cellmicrocosmos.cm2.functionality3d
This is the component that displays the Membrane in 3D.
Membrane3D() - Constructor for class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
Initializes the 3d classes
Membrane_Image2D_Generator() - Constructor for class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit.Membrane_Image2D_Generator
 
MEMBRANE_SIZES() - Constructor for class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.MEMBRANE_SIZES
 
MembraneHasAnyExtracellularLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Deprecated.
use hasMembraneAnyExtracellularLipids instead!
MembraneHasAnyIntracellularLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Deprecated.
use hasMembraneAnyIntracellularLipids instead!
MembraneMetaInfo - Class in org.cellmicrocosmos.cm2.io
A small sheet that is used to transfer some Membrane Data
MembraneMetaInfo() - Constructor for class org.cellmicrocosmos.cm2.io.MembraneMetaInfo
 
MembraneModel - Class in org.cellmicrocosmos.cm2.dataobjects
/** This class represents the Membrane that all parts of the Application need to work with.
MembraneModel() - Constructor for class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Constructs a new Membrane Model.
membraneOperations - Variable in class org.cellmicrocosmos.cm2.engine.Engine
 
MembraneOperations() - Constructor for class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
MembranePackingAlgorithm - Class in org.cellmicrocosmos.cm2.membranepackingalgorithm
This is the required superclass for all Membrane Algorithms that can be used by the membrane editor! Membrane calculating algorithms need to extend this class and to implement all of the methods from the MembranePackingAlgorithmInterface which this class implements.
MembranePackingAlgorithm() - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
 
MembranePackingAlgorithmGUI - Class in org.cellmicrocosmos.cm2.membranepackingalgorithm
This class can be used in order to show your algorithm-GUI to the user
MembranePackingAlgorithmGUI() - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithmGUI
 
MembranePackingAlgorithmInterface - Interface in org.cellmicrocosmos.cm2.membranepackingalgorithm
Indicates Methods relevant for the MembranePackingAlgorithm.
MembraneShifter - Class in org.cellmicrocosmos.cm2.membranepackingalgorithms
This tool algorihtm can be used to shift all membrane components of one type (lipids of the inner and/or outer layer and/or proteins) at once.
MembraneShifter() - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithms.MembraneShifter
 
membraneUniverseCanvas - Static variable in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
membraneUniverseCanvasRight - Static variable in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
membraneview - Variable in class org.cellmicrocosmos.cm2.engine.Engine
 
MembraneView - Class in org.cellmicrocosmos.cm2.gui.elements
The MembraneView Class.
MembraneView() - Constructor for class org.cellmicrocosmos.cm2.gui.elements.MembraneView
constructor MembraneView
MembraneView.IntersectionPanel - Class in org.cellmicrocosmos.cm2.gui.elements
 
MembraneViewListener - Interface in org.cellmicrocosmos.cm2.interfaces
Listener used by the MembraneView
membraneViewListener - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
 
MembraneXmlReader - Class in org.cellmicrocosmos.cm2.io
The Reader for our Membranes; Reads in a File, creates a new Membrane Model which gets set up with the Data.
MembraneXmlReader() - Constructor for class org.cellmicrocosmos.cm2.io.MembraneXmlReader
Plain Constructor
MembraneXmlReader(StatusDialog) - Constructor for class org.cellmicrocosmos.cm2.io.MembraneXmlReader
Contructor with the StatusDialog that will be updated each step
MembraneXmlWriter - Class in org.cellmicrocosmos.cm2.io
The Writer for the MembraneModel
MembraneXmlWriter(File) - Constructor for class org.cellmicrocosmos.cm2.io.MembraneXmlWriter
 
MicroDomain - Class in org.cellmicrocosmos.cm2.membranepackingalgorithm
This class represents a microdomain in the membrane.
MicroDomain(MicroDomain_3D, MembranePackingAlgorithm) - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithm.MicroDomain
Contructs a new MicroDomain object ! NOT MEANT TO BE USED BY PLUGIN DEVELOPERS !
MicroDomain_3D - Class in org.cellmicrocosmos.cm2.dataobjects
This class represents the microdomains/lipid rafts objects.
MicroDomain_3D() - Constructor for class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
MicroDomainManager - Class in org.cellmicrocosmos.cm2.functionality3d
Manages the microdomains of a membrane.
MicroDomainManager(Canvas3D, BranchGroup, PickNDragManager, MicroDomain_3D) - Constructor for class org.cellmicrocosmos.cm2.functionality3d.MicroDomainManager
 
microDomains - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
 
MIDDLE_BUTTON_MODIFIER - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.GUI_SETTINGS_AND_CONTROLS
modifiers for the middle Mouse Button for Systems that only have one button (like Mac)
MIF_FILENAME_OPM - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.IO
 
MIF_FILENAME_PDBTM - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.IO
 
MIFHandler - Class in org.cellmicrocosmos.cm2.io.ppe.toolbox
The MIFHandler reads in a MIFile and generates a Hashmap with the required transformation matrixes.
MIFHandler() - Constructor for class org.cellmicrocosmos.cm2.io.ppe.toolbox.MIFHandler
Constructs a new MIFHandler.
MIFILE() - Constructor for class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.MIFILE
 
MIN_SIZE_OF_MEMBRANE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.MEMBRANE_SIZES
 
MIN_Y_TRANSLATION - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.MEMBRANE_SIZES
 
MIN_Y_TRANSLATION - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Application_Constants
The minimal y-translation that is allowed
minatomdistance - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
 
minprecision - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
 
MinRadius(Object[]) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Property which sets the minimum radius for the OrbitBehavior.
MISC() - Constructor for class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.MISC
 
mode - Variable in class org.cellmicrocosmos.cm2.functionality3d.Hud
 
mode - Variable in class org.cellmicrocosmos.cm2.functionality3d.SelectionBox
 
MODE_ATOMS - Static variable in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit.Membrane_Image2D_Generator
 
MODE_CONFORMATION - Static variable in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
 
MODE_GRANULARITY - Static variable in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
 
MODE_HYBRID - Static variable in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit.Membrane_Image2D_Generator
 
MODE_POLYGON - Static variable in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit.Membrane_Image2D_Generator
 
model - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.ParameterMatrixPanel
 
ModelByFile - Static variable in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
 
MODELCHANGE - Static variable in class org.cellmicrocosmos.cm2.functionality3d.Hud
 
mol - Variable in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeProfile
 
Molecule - Class in org.cellmicrocosmos.cm2.membranepackingalgorithm
This class is a wrapper class for the Molecule_3D class.
Molecule(Molecule_3D, MembranePackingAlgorithm) - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
Creates a new wrapper object of the given Molecule_3D ! NOT MEANT TO BE USED BY PLUGIN DEVELOPERS !
Molecule_3D - Class in org.cellmicrocosmos.cm2.dataobjects
This parent class represents the molecules used in the model.
Molecule_3D() - Constructor for class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Creates a new molecule with a default matrix and all nessecary capabilities set
MOLECULE_DEFAULTS() - Constructor for class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.MOLECULE_DEFAULTS
 
Molecule_Profile_IO - Class in org.cellmicrocosmos.cm2.coarsegrainsupport
Manages all Input / Output operations for Molecule Profiles and is generely responsible for their creation
Molecule_Profile_IO() - Constructor for class org.cellmicrocosmos.cm2.coarsegrainsupport.Molecule_Profile_IO
 
MOLECULE_PROFILES_DIR - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
 
MoleculeEditor - Class in org.cellmicrocosmos.cm2.coarsegrainsupport
This is the base class of the Molecule Editor.
MoleculeEditor(Molecule_3D, boolean, Engine, String, Double) - Constructor for class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
 
MoleculeEditorToolbar - Class in org.cellmicrocosmos.cm2.coarsegrainsupport
This class describes the toolbar of the MoleculeEditor
MoleculeEditorToolbar(MoleculeEditor) - Constructor for class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditorToolbar
 
MoleculeProfile - Class in org.cellmicrocosmos.cm2.coarsegrainsupport
Used as a sheet that contains all relevant data of a molecule profile.
MoleculeProfile() - Constructor for class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeProfile
 
moleculeSources - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool
 
moleculesPdbFiles - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool
 
MONTHS - Static variable in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
 
MOUSE_SENSITIVITY - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
mouseClicked(MouseEvent) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
 
mouseClicked(MouseEvent) - Method in class org.cellmicrocosmos.cm2.functionality3d.MicroDomainManager
 
mouseClicked(MouseEvent) - Method in class org.cellmicrocosmos.cm2.functionality3d.PickNDragManager
 
mouseClicked(MouseEvent) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
mouseClicked(MouseEvent) - Method in class org.cellmicrocosmos.cm2.gui.MyJRadioButton
 
mouseDragged(MouseEvent) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
 
mouseDragged(MouseEvent) - Method in class org.cellmicrocosmos.cm2.functionality3d.MicroDomainManager
 
mouseDragged(MouseEvent) - Method in class org.cellmicrocosmos.cm2.functionality3d.PickNDragManager
 
mouseDragged(MouseEvent) - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
 
mouseDragged(MouseEvent) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
mouseEntered(MouseEvent) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
 
mouseEntered(MouseEvent) - Method in class org.cellmicrocosmos.cm2.functionality3d.MicroDomainManager
 
mouseEntered(MouseEvent) - Method in class org.cellmicrocosmos.cm2.functionality3d.PickNDragManager
 
mouseEntered(MouseEvent) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
mouseEntered(MouseEvent) - Method in class org.cellmicrocosmos.cm2.gui.MyJRadioButton
 
mouseExited(MouseEvent) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
 
mouseExited(MouseEvent) - Method in class org.cellmicrocosmos.cm2.functionality3d.MicroDomainManager
 
mouseExited(MouseEvent) - Method in class org.cellmicrocosmos.cm2.functionality3d.PickNDragManager
 
mouseExited(MouseEvent) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
mouseExited(MouseEvent) - Method in class org.cellmicrocosmos.cm2.gui.MyJRadioButton
 
mouseFactor - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
 
mouseMoved(MouseEvent) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
 
mouseMoved(MouseEvent) - Method in class org.cellmicrocosmos.cm2.functionality3d.MicroDomainManager
 
mouseMoved(MouseEvent) - Method in class org.cellmicrocosmos.cm2.functionality3d.PickNDragManager
 
mouseMoved(MouseEvent) - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
 
mouseMoved(MouseEvent) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
mousePressed(MouseEvent) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
 
mousePressed(MouseEvent) - Method in class org.cellmicrocosmos.cm2.functionality3d.MicroDomainManager
 
mousePressed(MouseEvent) - Method in class org.cellmicrocosmos.cm2.functionality3d.PickNDragManager
 
mousePressed(MouseEvent) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
mousePressed(MouseEvent) - Method in class org.cellmicrocosmos.cm2.gui.MyJRadioButton
 
mouseReleased(MouseEvent) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
 
mouseReleased(MouseEvent) - Method in class org.cellmicrocosmos.cm2.functionality3d.MicroDomainManager
 
mouseReleased(MouseEvent) - Method in class org.cellmicrocosmos.cm2.functionality3d.PickNDragManager
 
mouseReleased(MouseEvent) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
mouseReleased(MouseEvent) - Method in class org.cellmicrocosmos.cm2.gui.MyJRadioButton
 
move() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
moveDNDObject(Molecule_3D, Point) - Method in class org.cellmicrocosmos.cm2.functionality3d.PickNDragManager
Moves the passed Object to the passed mouse location on canvas (this time while Drag and drop is active)
moveMolecule(Lipid, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
Moves the molecule to a new position.
moveY(float) - Method in class org.cellmicrocosmos.cm2.functionality3d.CameraMode
 
MRNA - Class in org.cellmicrocosmos.cmX.mrna
The messengerRNA: The abstract class for external calls to the MembraneEditor.
MRNA() - Constructor for class org.cellmicrocosmos.cmX.mrna.MRNA
 
MyBounds - Class in org.cellmicrocosmos.cm2.dataobjects
This class is needed to compute the bounds of molecules by using its atoms.
MyBounds() - Constructor for class org.cellmicrocosmos.cm2.dataobjects.MyBounds
 
MyBounds(Point3f[]) - Constructor for class org.cellmicrocosmos.cm2.dataobjects.MyBounds
 
MyBounds(Atom_3D[]) - Constructor for class org.cellmicrocosmos.cm2.dataobjects.MyBounds
 
MyBounds(Vector<Atom_3D>) - Constructor for class org.cellmicrocosmos.cm2.dataobjects.MyBounds
 
MyData - Class in org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer
This class stores most of the current values, members and settings of the Algorithm
MyData() - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.MyData
 
MyDefaults - Class in org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer
This class is used to create default values for the Lennard-Jones-parameter.
MyDefaults() - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.MyDefaults
 
MyFCAccessory - Class in org.cellmicrocosmos.cm2.gui
A Component that gets added to the filechoosers.
MyFCAccessory(JFileChooser, int, String) - Constructor for class org.cellmicrocosmos.cm2.gui.MyFCAccessory
 
MyGradientBufferedImage - Class in org.cellmicrocosmos.cm2.gui
This class is needed to create color gradient backgrounds in the cell universe.
MyGradientBufferedImage(Color, Color, int) - Constructor for class org.cellmicrocosmos.cm2.gui.MyGradientBufferedImage
 
MyJRadioButton - Class in org.cellmicrocosmos.cm2.gui
Class for the 3 buttons that control the camera mode.
MyJRadioButton(int) - Constructor for class org.cellmicrocosmos.cm2.gui.MyJRadioButton
 
MylFCAccessoryForGenerating - Class in org.cellmicrocosmos.cm2.gui
The component that appears in the filechooser before generating a Membrane.
MylFCAccessoryForGenerating() - Constructor for class org.cellmicrocosmos.cm2.gui.MylFCAccessoryForGenerating
 
MyNumberTextField - Class in org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer
This is an extended textfield, used as the number input fields in the options dialog
MyNumberTextField(double, double, int, Double, boolean) - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.MyNumberTextField
 
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