- 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
-