Examples with KineticsDescription cbit.vcell.model.KineticsDescription used on opensource projects

Example 1 with KineticsDescription

use of cbit.vcell.model.KineticsDescription in project vcell by virtualcell.

the class KineticsTypeTemplatePanel method getKineticsTypeComboBox.

private javax.swing.JComboBox getKineticsTypeComboBox() {
    if (kineticsTypeComboBox == null) {
        try {
            kineticsTypeComboBox = new javax.swing.JComboBox();
            kineticsTypeComboBox.setName("JComboBox1");
            kineticsTypeComboBox.setRenderer(new DefaultListCellRenderer() {

                private static final String MU = "\u03BC";

                private static final String MICROMOLAR = MU + "M";

                private static final String SQUARED = "\u00B2";

                private static final String SQUAREMICRON = MU + "m" + SQUARED;

                public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
                    java.awt.Component component = super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
                    if (value instanceof KineticsDescription) {
                        KineticsDescription kineticsDescription = (KineticsDescription) value;
                        if (getKinetics() != null && getKinetics().getReactionStep() != null) {
                            if (getKinetics().getReactionStep().getStructure() instanceof Feature) {
                                if (kineticsDescription.equals(KineticsDescription.General)) {
                                    setText("General [" + MICROMOLAR + "/s]");
                                } else if (kineticsDescription.equals(KineticsDescription.MassAction)) {
                                    setText("Mass Action [" + MICROMOLAR + "/s] (recommended for stochastic application)");
                                } else if (kineticsDescription.equals(KineticsDescription.GeneralLumped)) {
                                    setText("General [molecules/s]");
                                } else if (kineticsDescription.equals(KineticsDescription.HMM_irreversible)) {
                                    setText("Henri-Michaelis-Menten (Irreversible) [" + MICROMOLAR + "/s]");
                                } else if (kineticsDescription.equals(KineticsDescription.HMM_reversible)) {
                                    setText("Henri-Michaelis-Menten (Reversible) [" + MICROMOLAR + "/s]");
                                } else {
                                    setText(kineticsDescription.getDescription());
                                }
                            } else if (getKinetics().getReactionStep().getStructure() instanceof Membrane) {
                                if (kineticsDescription.equals(KineticsDescription.General)) {
                                    setText("General [molecules/(" + SQUAREMICRON + " s)]");
                                } else if (kineticsDescription.equals(KineticsDescription.MassAction)) {
                                    setText("Mass Action [molecules/(" + SQUAREMICRON + " s)]");
                                } else if (kineticsDescription.equals(KineticsDescription.GeneralLumped)) {
                                    setText("General [molecules/s)]");
                                } else if (kineticsDescription.equals(KineticsDescription.HMM_irreversible)) {
                                    setText("Henri-Michaelis-Menten (Irreversible) [molecules/(" + SQUAREMICRON + " s)]");
                                } else if (kineticsDescription.equals(KineticsDescription.HMM_reversible)) {
                                    setText("Henri-Michaelis-Menten (Reversible) [molecules/(" + SQUAREMICRON + " s)]");
                                } else if (kineticsDescription.equals(KineticsDescription.Macroscopic_irreversible)) {
                                    setText("Macroscopic (Irreversible) [molecules/(" + SQUAREMICRON + " s)]");
                                } else if (kineticsDescription.equals(KineticsDescription.Microscopic_irreversible)) {
                                    setText("Microscopic (Irreversible) [molecules/(" + SQUAREMICRON + " s)]");
                                } else {
                                    setText(kineticsDescription.getDescription());
                                }
                            }
                        } else {
                            setText(kineticsDescription.getDescription());
                        }
                    }
                    return component;
                }
            });
        // user code begin {1}
        // user code end
        } catch (java.lang.Throwable ivjExc) {
            // user code begin {2}
            // user code end
            handleException(ivjExc);
        }
    }
    return kineticsTypeComboBox;
}

Example 2 with KineticsDescription

use of cbit.vcell.model.KineticsDescription in project vcell by virtualcell.

the class KineticsTypeTemplatePanel method initKineticChoices.

private void initKineticChoices() {
    KineticsDescription[] kineticTypes = reactionStep == null || reactionStep instanceof SimpleReaction ? Simple_Reaction_Kinetic_Types : Flux_Reaction_KineticTypes;
    javax.swing.DefaultComboBoxModel model = new DefaultComboBoxModel();
    for (int i = 0; i < kineticTypes.length; i++) {
        model.addElement(kineticTypes[i]);
    }
    getKineticsTypeComboBox().setModel(model);
    return;
}

Example 3 with KineticsDescription

use of cbit.vcell.model.KineticsDescription in project vcell by virtualcell.

the class ReactionPropertiesPanel method getKineticsTypeComboBox.

private javax.swing.JComboBox getKineticsTypeComboBox() {
    if (kineticsTypeComboBox == null) {
        try {
            kineticsTypeComboBox = new javax.swing.JComboBox();
            kineticsTypeComboBox.setName("JComboBox1");
            kineticsTypeComboBox.setRenderer(new DefaultListCellRenderer() {

                private static final String MU = "\u03BC";

                private static final String MICROMOLAR = MU + "M";

                private static final String SQUARED = "\u00B2";

                private static final String SQUAREMICRON = MU + "m" + SQUARED;

                private static final String MICRON = MU + "m";

                public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
                    java.awt.Component component = super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
                    if (value instanceof KineticsDescription) {
                        KineticsDescription kineticsDescription = (KineticsDescription) value;
                        setText(kineticsDescription.getDescription());
                        if (reactionStep != null) {
                            if (reactionStep instanceof SimpleReaction) {
                                if (reactionStep.getStructure() instanceof Feature) {
                                    if (kineticsDescription.equals(KineticsDescription.General)) {
                                        setText("General [" + MICROMOLAR + "/s]");
                                    } else if (kineticsDescription.equals(KineticsDescription.MassAction)) {
                                        setText("Mass Action [" + MICROMOLAR + "/s] (recommended for stochastic application)");
                                    } else if (kineticsDescription.equals(KineticsDescription.GeneralLumped)) {
                                        setText("General [molecules/s]");
                                    } else if (kineticsDescription.equals(KineticsDescription.HMM_irreversible)) {
                                        setText("Henri-Michaelis-Menten (Irreversible) [" + MICROMOLAR + "/s]");
                                    } else if (kineticsDescription.equals(KineticsDescription.HMM_reversible)) {
                                        setText("Henri-Michaelis-Menten (Reversible) [" + MICROMOLAR + "/s]");
                                    } else {
                                        setText(kineticsDescription.getDescription());
                                    }
                                } else if (reactionStep.getStructure() instanceof Membrane) {
                                    if (kineticsDescription.equals(KineticsDescription.General)) {
                                        setText("General [molecules/(" + SQUAREMICRON + " s)]");
                                    } else if (kineticsDescription.equals(KineticsDescription.MassAction)) {
                                        setText("Mass Action [molecules/(" + SQUAREMICRON + " s)]");
                                    } else if (kineticsDescription.equals(KineticsDescription.GeneralLumped)) {
                                        setText("General [molecules/s)]");
                                    } else if (kineticsDescription.equals(KineticsDescription.HMM_irreversible)) {
                                        setText("Henri-Michaelis-Menten (Irreversible) [molecules/(" + SQUAREMICRON + " s)]");
                                    } else if (kineticsDescription.equals(KineticsDescription.HMM_reversible)) {
                                        setText("Henri-Michaelis-Menten (Reversible) [molecules/(" + SQUAREMICRON + " s)]");
                                    } else if (kineticsDescription.equals(KineticsDescription.Macroscopic_irreversible)) {
                                        setText("Macroscopic (Irreversible) [molecules/(" + SQUAREMICRON + " s)]");
                                    } else if (kineticsDescription.equals(KineticsDescription.Microscopic_irreversible)) {
                                        setText("Microscopic (Irreversible) [molecules/(" + SQUAREMICRON + " s)]");
                                    }
                                }
                            } else if (reactionStep instanceof FluxReaction) {
                                if (kineticsDescription.equals(KineticsDescription.General)) {
                                    setText("General Flux Density (" + MICROMOLAR + "-" + MICRON + "/s)");
                                } else if (kineticsDescription.equals(KineticsDescription.GeneralLumped)) {
                                    setText("General Flux (molecules/s)");
                                } else if (kineticsDescription.equals(KineticsDescription.GeneralCurrent)) {
                                    setText("General Current Density (pA/" + SQUAREMICRON + ")");
                                } else if (kineticsDescription.equals(KineticsDescription.GeneralCurrentLumped)) {
                                    setText("General Current (pA)");
                                } else if (kineticsDescription.equals(KineticsDescription.GHK)) {
                                    setText("Goldman-Hodgkin-Katz Current Density (pA/" + SQUAREMICRON + ") - permeability in " + MICRON + "/s");
                                } else if (kineticsDescription.equals(KineticsDescription.Nernst)) {
                                    setText("Nernst Current Density (pA/" + SQUAREMICRON + ") - conductance in nS/" + SQUAREMICRON);
                                } else if (kineticsDescription.equals(KineticsDescription.GeneralPermeability)) {
                                    setText("General Permeability (" + MICROMOLAR + "-" + MICRON + "/s) - permeability in " + MICRON + "/s");
                                }
                            }
                        }
                    }
                    return component;
                }
            });
        // user code begin {1}
        // user code end
        } catch (java.lang.Throwable ivjExc) {
            // user code begin {2}
            // user code end
            handleException(ivjExc);
        }
    }
    return kineticsTypeComboBox;
}

Example 4 with KineticsDescription

use of cbit.vcell.model.KineticsDescription in project vcell by virtualcell.

the class ReactionPropertiesPanel method initKineticChoices.

private void initKineticChoices() {
    KineticsDescription[] kineticTypes = reactionStep == null || reactionStep instanceof SimpleReaction ? Simple_Reaction_Kinetic_Types : Flux_Reaction_KineticTypes;
    javax.swing.DefaultComboBoxModel model = new DefaultComboBoxModel();
    for (int i = 0; i < kineticTypes.length; i++) {
        if (!(kineticTypes[i].equals(KineticsDescription.Macroscopic_irreversible) || kineticTypes[i].equals(KineticsDescription.Microscopic_irreversible))) {
            model.addElement(kineticTypes[i]);
        } else // macroscopic/microscopic irreversible
        {
            // reactions on membrane in a 3D geometry
            if (reactionStep != null && reactionStep.getStructure() != null && reactionStep.getStructure() instanceof Membrane) {
                // check if reactants are all on membrane and calculate sum of reactants' stoichiometry
                ReactionParticipant[] rps = reactionStep.getReactionParticipants();
                int order = 0;
                boolean bAllMembraneReactants = true;
                for (ReactionParticipant rp : rps) {
                    if (rp instanceof Reactant) {
                        if (!(rp.getStructure() instanceof Membrane)) {
                            bAllMembraneReactants = false;
                            break;
                        }
                        order += rp.getStoichiometry();
                    }
                }
                // add only if 2nd order membrane reaction
                if (order == 2 && bAllMembraneReactants && !reactionStep.hasCatalyst()) {
                    model.addElement(kineticTypes[i]);
                }
            }
        }
    }
    getKineticsTypeComboBox().setModel(model);
    return;
}

Example 5 with KineticsDescription

use of cbit.vcell.model.KineticsDescription in project vcell by virtualcell.

the class ReactionPropertiesPanel method updateKineticChoice.

private void updateKineticChoice() {
    KineticsDescription newKineticChoice = (KineticsDescription) getKineticsTypeComboBox().getSelectedItem();
    // 
    if (reactionStep == null || reactionStep.getKinetics().getKineticsDescription().equals(newKineticChoice)) {
        return;
    }
    boolean bFoundKineticType = false;
    KineticsDescription[] kineticTypes = reactionStep instanceof SimpleReaction ? Simple_Reaction_Kinetic_Types : Flux_Reaction_KineticTypes;
    for (int i = 0; i < kineticTypes.length; i++) {
        if (kineticTypes[i].equals(newKineticChoice)) {
            bFoundKineticType = true;
            break;
        }
    }
    if (!bFoundKineticType) {
        return;
    }
    try {
        reactionStep.setKinetics(newKineticChoice.createKinetics(reactionStep));
    } catch (Exception exc) {
        handleException(exc);
    }
}