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AboutPane - Class in org.cellmicrocosmos.cm2.gui.dialogs
A small frame that shows the "About" information of this application retrieved from the constant class
AboutPane() - Constructor for class org.cellmicrocosmos.cm2.gui.dialogs.AboutPane
 
actionPerformed(ActionEvent) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.ConformationPanel
 
actionPerformed(ActionEvent) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.GranularityPanel
 
actionPerformed(ActionEvent) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditorToolbar
 
actionPerformed(ActionEvent) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.ParticlePropertiesPanel
 
actionPerformed(ActionEvent) - Method in class org.cellmicrocosmos.cm2.gui.dialogs.AlgorithmWizzard
 
actionPerformed(ActionEvent) - Method in class org.cellmicrocosmos.cm2.gui.dialogs.ChangeSizeDialog
 
actionPerformed(ActionEvent) - Method in class org.cellmicrocosmos.cm2.gui.dialogs.EditDBEntryDialog
Actions for the 3 Buttons in the Toolbar
actionPerformed(ActionEvent) - Method in class org.cellmicrocosmos.cm2.gui.dialogs.EnterMatrixDialog
Values from the textFields are passed to the Interface
actionPerformed(ActionEvent) - Method in class org.cellmicrocosmos.cm2.gui.dialogs.J3DSettingsDialog
 
actionPerformed(ActionEvent) - Method in class org.cellmicrocosmos.cm2.gui.dialogs.ManageTitleSectionDialog
 
actionPerformed(ActionEvent) - Method in class org.cellmicrocosmos.cm2.gui.dialogs.NewMembraneDialog
Actions for the 3 Buttons in the Toolbar
actionPerformed(ActionEvent) - Method in class org.cellmicrocosmos.cm2.gui.dialogs.PdbSettingsWindow
 
actionPerformed(ActionEvent) - Method in class org.cellmicrocosmos.cm2.gui.dialogs.SetUpConnectionsDialog
 
actionPerformed(ActionEvent) - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
Possible clicks on one of the 4 DB-Toolbar Buttons are handled here
actionPerformed(ActionEvent) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
ActionPerformed method for the ComboBox and the Buttons
actionPerformed(ActionEvent) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView.IntersectionPanel
 
actionPerformed(ActionEvent) - Method in class org.cellmicrocosmos.cm2.gui.GlobalDatabaseBrowser
Catches ButtonClicks
actionPerformed(ActionEvent) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
the common implementation, where actionEvents are handled
actionPerformed(ActionEvent) - Method in class org.cellmicrocosmos.cm2.gui.PDBFileBrowser
 
actionPerformed(ActionEvent) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Gui
 
actionPerformed(ActionEvent) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
action performed method.
activate(String, String, int) - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.DNDBridge
Creates or copies a new Protein Instance to use
activate(Lipid_3D) - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.DNDBridge
 
activateAddOptions(boolean) - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
Turn the Options to add an Entry to the Membrane on or off
activateQuickloadLinks(boolean) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
(De)Activates all quickload links.
addAlgorithmStringRepresentation(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
addANewProteinAtRandomPosition(String, String, int, int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
addANewProteinAtRandomPosition(String, String, int, int) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
Tries to add the passed Protein to the Membrane.
addANewProteinAtRandomPosition(String, String, int, int) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
addBalls(Molecule_3D, Atom_3D[], boolean, Color, int, boolean) - Static method in class org.cellmicrocosmos.cm2.functionality3d.Atom_Creator_3D
 
addDatabaseViewListener(DatabaseViewListener) - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
Sets the listener to invoke Actions for Parent Classes
addDatabaseViewListener(DatabaseViewListener) - Method in class org.cellmicrocosmos.cm2.gui.elements.PropertiesView
 
addEntry(String, Exception) - Method in exception org.cellmicrocosmos.cm2.io.InvalidEntriesException
makes an Entry in the Errorlist
addEntryToDB(File) - Method in class org.cellmicrocosmos.cm2.engine.Engine.DatabaseOperations
 
addEntryToDB(File, int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.DatabaseOperations
 
addEntryToDB(File) - Method in interface org.cellmicrocosmos.cm2.interfaces.DatabaseViewListener
 
addEntryToDB(File, int) - Method in interface org.cellmicrocosmos.cm2.interfaces.DatabaseViewListener
 
addEntryToDB(File, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Add a PDB file to the local database.
addExampleLipidExtra(Lipid_3D, int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Adds an sample lipid to the membrane
addExampleLipidIntra(Lipid_3D, int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Adds an sample lipid to the membrane
addExtracellularLipid(Lipid) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
adds the given extracellular lipid to the extracellular side of the membrane.
addFromRSCB(File, int) - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
Add a protein or lipid to the database.
addFromRSCB(File) - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
Add a protein to the database.
addGuiListener(GuiListener) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
Adds the GuiListener, that is needed to invoke Actions in the parent class of this gui
addIntracellularLipid(Lipid) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Adds the given intracellular lipid to the intracellular side of the membrane.
additionalAtomInfoTG - Variable in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
addLayer(Layer) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
addLipidExtra(Lipid_3D, int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
adds a Lipid to the Model
addLipidExtra(Lipid_3D) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
addLipidExtra(Lipid_3D) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
addLipidIntra(Lipid_3D, int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
adds a Lipid to the Model
addLipidIntra(Lipid_3D) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
addLipidIntra(Lipid_3D) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
addLipids(int, boolean) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
Tries to add new lipids to the membrane.
addMembraneListener(Engine.MembraneOperations) - Method in class org.cellmicrocosmos.cm2.gui.elements.PropertiesView
 
addMembraneViewListener(MembraneViewListener) - Method in class org.cellmicrocosmos.cm2.functionality3d.CameraMode
 
addMembraneViewListener(MembraneViewListener) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
Establishes access to major functionalities for the 3d classes
addMembraneViewListener(MembraneViewListener) - Method in class org.cellmicrocosmos.cm2.functionality3d.PickNDragManager
 
addMembraneViewListener(MembraneViewListener) - Method in class org.cellmicrocosmos.cm2.gui.elements.ComponentView
 
addMembraneViewListener(MembraneViewListener) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
MembranViewListener
addMembraneViewListener(MembraneViewListener) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
adds the MembraneViewListener, that is needed to invoke Actions in the parent class of this gui
addMicroDomain(MicroDomain_3D) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
addMolecule(Molecule_3D, boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
adds a Molecule to the 3d view if the boolean is set, the axis of the 3D modell will be repainted.
addMultilayerPressed() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
 
addMultilayerPressed() - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
 
addNewLipid(Lipid, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.TheWandererRookie
Add the given lipid to the membrane.
addProtein(Protein_3D, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
adds a single Protein into the Model
addQuickloadLink(File) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
Adds a quickloadlink to the filemenu.
addRow(Vector, int) - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
adds a row of data to a table
addSearchListener(SearchListener) - Method in class org.cellmicrocosmos.cm2.gui.Searcher
Adds a searchListener to inform about events
addValue(String, String) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.ConfigIO
Here, a user can add his Value(s) under his specified key.
addValue(String, String) - Static method in class org.cellmicrocosmos.cm2.misc.ConfigParser
Here, a user can add his Value(s) under his specified key.
addView(String, JComponent) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
Adds a JComponent to the Gui
addView(String, ImageIcon, JComponent) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
* Adds a JComponent to the Gui
adoptTitleSections - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.LimitationSettings
 
adoptTitleSections() - Method in class org.cellmicrocosmos.cm2.io.Compatibility
 
AdvancedRandomPlacing - Class in org.cellmicrocosmos.cm2.membranepackingalgorithms
This algorithm places lipids at randomly picked positions.
AdvancedRandomPlacing() - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithms.AdvancedRandomPlacing
 
ALGORITHM_SETTINGS - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
 
ALGORITHMS() - Constructor for class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.ALGORITHMS
 
AlgorithmSettings() - Constructor for class org.cellmicrocosmos.cm2.engine.DataPool.AlgorithmSettings
 
AlgorithmWizzard - Class in org.cellmicrocosmos.cm2.gui.dialogs
The Calculation Wizzard helps the user to start the calculation.
AlgorithmWizzard(PluginManager, MembraneViewListener) - Constructor for class org.cellmicrocosmos.cm2.gui.dialogs.AlgorithmWizzard
 
ALIGN - Static variable in class org.cellmicrocosmos.cm2.functionality3d.Hud
 
alignExampleLipid(Lipid_3D, int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
alignExampleLipid(Lipid_3D, int) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
ALIGNLIPID - Static variable in class org.cellmicrocosmos.cm2.functionality3d.Hud
 
alignSingleProtein(Molecule_3D) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
alignSingleProtein(Molecule_3D) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
alignSingleProteinPlus(Molecule_3D) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
alignSingleProteinPlus(Molecule_3D) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
all99999 - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.LimitationSettings
 
allAtomsSorted - Variable in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
ALLOW_ATOM_MODE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.MISC
 
ALLOW_MULTIPLE_ENTRIES_IN_DB - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.MISC
 
allowDragging(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.PickNDragManager
En-or disables dragging
allVectors - Variable in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
ALT_TEXT_COLOR - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.GUI_SETTINGS_AND_CONTROLS
Alternative Text Color to use
ambientlight - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
 
amIRunningOnWebstart() - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
This is a dirty approach, i know
antialiasing - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
 
anyChanges() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Gui
 
anyCurrentIntersections(boolean, StatusDialog) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
aplVoroExecutionLink - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.APLVoroSettings
 
APLVoroSettings() - Constructor for class org.cellmicrocosmos.cm2.engine.DataPool.APLVoroSettings
 
Application_Constants - Class in org.cellmicrocosmos.cm2.membranepackingalgorithm
A class that provides constant values of the membrane editor.
Application_Constants() - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithm.Application_Constants
 
applyAble - Variable in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
 
applyAtomPosition(int, Point3f) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Assigns a new Position to the Atom at the specified index.
applyCurrent() - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
 
applyOPMAlignmentTo(Molecule_3D) - Method in class org.cellmicrocosmos.cm2.io.ppe.toolbox.MIFHandler
This methods adjust the rotation and the position of the given Protein to the actual membrane which it is placed into.
applyProfile(Molecule_3D[], MoleculeProfile) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
 
applyProfile(MoleculeProfile) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
APPROVE - Static variable in class org.cellmicrocosmos.cm2.gui.dialogs.ChangeSizeDialog
 
APPROVE - Variable in class org.cellmicrocosmos.cm2.gui.dialogs.EditDBEntryDialog
 
APPROVE - Static variable in class org.cellmicrocosmos.cm2.gui.dialogs.NewMembraneDialog
 
areaContainsMolecules(int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
areAxisVisible() - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
areAxisVisible() - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
Returns if the axis are visible currently
areAxisVisible() - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
areLipidAbsoluteValuesOk() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Test, wheter the current absolute value settings have at least one lipid per side.
areLipidPercentagesOk() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Test, wheter the current percentage settings of the lipids on both sides have an overall of 100%
askForInput(Particle, String, String, String, Color) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.GranularityPanel
 
askForWorkspace() - Static method in class org.cellmicrocosmos.cm2.io.FileIOHandler
 
askForYHeight(Double) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
askParameters(Vector) - Method in class org.cellmicrocosmos.cm2.gui.dialogs.EditDBEntryDialog
Pop up this Dialog and the user can edit the passed rowdata
askPDBFile(File) - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
Pops up a Filechooser where the User may select a PDB File.
askPDBFile(File) - Method in interface org.cellmicrocosmos.cm2.interfaces.EditDBEntryDialogListener
 
askPDBFileForExternalPreview() - Method in class org.cellmicrocosmos.cm2.io.FileIOHandler
Pops up a Filechooser where the User may select a PDB File.
askPDBFileForRestoring() - Method in class org.cellmicrocosmos.cm2.io.FileIOHandler
 
assignResSeqNumbers - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.LimitationSettings
 
assignResSeqNumbers() - Method in class org.cellmicrocosmos.cm2.io.Compatibility
 
Atom - Class in org.cellmicrocosmos.cm2.membranepackingalgorithm
This class is a wrapper for an Atom that is contained by a molecule.
Atom(Atom_3D, Molecule, int, MembranePackingAlgorithm) - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
!NOT MEANT TO BE USED BY ALGORITHM DEVELOPERS!
Atom_3D - Class in org.cellmicrocosmos.cm2.dataobjects
A class that represents an Atom, very similar to a line in the coordinate section of a pdb file.
Atom_3D() - Constructor for class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
Creates an empty instance
Atom_3D(String) - Constructor for class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
Creates an instance using the passed atom entry string of a pdb file in order to set up the varialbles.
Atom_Creator_3D - Class in org.cellmicrocosmos.cm2.functionality3d
This class creates and attaches the visuals for Atomic representation of a molecule
Atom_Creator_3D() - Constructor for class org.cellmicrocosmos.cm2.functionality3d.Atom_Creator_3D
 
Atom_Level_Minimizer - Class in org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer
This is the base-class of the Atom-Level-Minimizer, described by my Diploma-Thesis.
Atom_Level_Minimizer() - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Atom_Level_Minimizer
 
ATOM_PERFORMANCE_MODE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
atomA - Variable in class org.cellmicrocosmos.cm2.dataobjects.Constraint_3D
 
atomB - Variable in class org.cellmicrocosmos.cm2.dataobjects.Constraint_3D
 
atomCollisionCheck - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
 
atomDistanceAbsolute - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
 
atomPassedOverByCursor(int) - Method in interface org.cellmicrocosmos.cm2.interfaces.CM2AdditionalListener
 
atoms - Variable in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
atomserials - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.LimitationSettings
 
atomserials_All99999() - Method in class org.cellmicrocosmos.cm2.io.Compatibility
 
ATOMSERIALS_BOTH - Static variable in class org.cellmicrocosmos.cm2.io.Compatibility
 
ATOMSERIALS_NONE - Static variable in class org.cellmicrocosmos.cm2.io.Compatibility
 
ATOMSERIALS_PROTSONLY - Static variable in class org.cellmicrocosmos.cm2.io.Compatibility
 
atomserials_RestartNumberingWith0() - Method in class org.cellmicrocosmos.cm2.io.Compatibility
 
ATOMVALUES() - Constructor for class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.ATOMVALUES
 
AtomValues() - Constructor for class org.cellmicrocosmos.cm2.engine.DataPool.AtomValues
 
author - Variable in class org.cellmicrocosmos.cm2.io.MembraneMetaInfo
 
authorizeDiscargingOfCurrentMembrane() - Method in class org.cellmicrocosmos.cm2.io.FileIOHandler
Ask if the currently opened Membrane may be discarged.
authorizeSaving(File) - Method in class org.cellmicrocosmos.cm2.io.FileIOHandler
Asks if the given File may be written.
AutoBox - Class in org.cellmicrocosmos.cm2.membranepackingalgorithm
The represents a box around the passed scatter-plot.
AutoBox() - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithm.AutoBox
Creates a clear instance only
AutoBox(Point3f[]) - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithm.AutoBox
Creates an AutoBox around the passed scatter-plot
AutoBox(Atom[]) - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithm.AutoBox
Creates an AutoBox around the passed scatter-plot by the coordinates of atoms
autofill() - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
 
automaticDetailSettings - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
 
autorotateUpwards(Lipid_3D) - Static method in class org.cellmicrocosmos.cm2.io.PdbReader_3D
Tries to autorotate the passed lipid, so that its head faces upwards
axisVisible - Variable in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
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