- T - Variable in class org.cellmicrocosmos.cm2.pluginmanager.CalculationManager
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- tab - Variable in class org.cellmicrocosmos.cm2.gui.dialogs.J3DSettingsDialog
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- TabComponentNoBorder() - Constructor for class org.cellmicrocosmos.cm2.gui.MainGui.TabComponentNoBorder
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- table - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.ParameterMatrixPanel
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- TAGNAMES_MEMBRANE - Static variable in class org.cellmicrocosmos.cm2.io.MembraneXmlReader
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- TEMP_APLVORO_FILE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
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- TEMP_DIRECTORY - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
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- TEMP_MEMBRANE_FILE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
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- tempFactor - Variable in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
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- teporaryMolecule - Variable in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
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- terCount - Variable in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
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- TestArea - Class in org.cellmicrocosmos.cm2.engine
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A class that allows to execute code any time the user pressed the testbutton.
- TestArea() - Constructor for class org.cellmicrocosmos.cm2.engine.TestArea
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- testForBetterPositionInFirstState(Lipid, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
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Tests if a new Random Position is better then the old Position.
- Tetris - Class in org.cellmicrocosmos.cm2.membranepackingalgorithms
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See algorithm description...
- Tetris() - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithms.Tetris
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- TheWandererRookie - Class in org.cellmicrocosmos.cm2.membranepackingalgorithms
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The Wanderer is an algorithm looking for an opportunity to rest.
- TheWandererRookie() - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithms.TheWandererRookie
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- THREADS() - Constructor for class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.THREADS
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- TitledPanel(String) - Constructor for class org.cellmicrocosmos.cm2.coarsegrainsupport.ControlPanel.TitledPanel
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- toc_file - Variable in class org.cellmicrocosmos.cm2.gui.dialogs.HelpDialog
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- toggleAllTitlesAndBorders(boolean) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
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Hide or show all titles and borders.
- toggleOPMLayersButton - Variable in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
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- ToolkitMembranePackingAlgorithm() - Constructor for class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit.ToolkitMembranePackingAlgorithm
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- toString() - Method in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
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Returns a String for Debugging
- toString() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
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Returns a string representation of this object for debugging
- toSystemTray() - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
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- totalEnergy(Atom) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Energies
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- totalInternalEnergy(Atom) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Energies
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- TransFactors(Object[]) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
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Property which sets the translation x and y factors.
- TRANSFORM_BOTTOM - Static variable in class org.cellmicrocosmos.cm2.io.Compatibility
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- TRANSFORM_NONE - Static variable in class org.cellmicrocosmos.cm2.io.Compatibility
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- TRANSFORM_PHYSICAL - Static variable in class org.cellmicrocosmos.cm2.io.Compatibility
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- transformToNewPoint(Matrix3f, Point3f) - Static method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.RotationToolkit
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Rotates a point according to the passed matrix.
- transformToNewPoint(Matrix3f, Point3f) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
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Rotates a point according to the passed matrix.
- translateAllMolecules(float, boolean, boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
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- TranslateEnable(Object[]) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
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Property which enables or disables translate.
- TransXFactor(Object[]) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
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Property which sets the translation x factor.
- TransYFactor(Object[]) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
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Property which sets the translation y factor.
- treatCurrent(boolean, boolean) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
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- treeClicked(TreeSelectionEvent) - Method in class org.cellmicrocosmos.cm2.gui.dialogs.HelpDialog
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Called if an Event gets fired from the JTree.
- type - Variable in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
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