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

Example 41 with Structure

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

the class DBReactionWizardPanel method setStructure.

/**
 * Sets the structure property (cbit.vcell.model.Structure) value.
 * @param structure The new value for the property.
 * @see #getStructure
 */
public void setStructure(Structure structure) {
    Structure oldValue = fieldStructure;
    fieldStructure = structure;
    firePropertyChange("structure", oldValue, structure);
}

Example 42 with Structure

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

the class DBReactionWizardPanel method setupRX.

/**
 * Insert the method's description here.
 * Creation date: (8/5/2003 2:50:56 PM)
 * @param dbfr cbit.vcell.dictionary.ReactionDescription
 */
private void setupRX(ReactionDescription dbfr) {
    resolvedReaction = dbfr;
    if (resolvedReaction != null) {
        if (speciesAssignmentJCB != null) {
            for (int i = 0; i < speciesAssignmentJCB.length; i += 1) {
                speciesAssignmentJCB[i].removeActionListener(this);
            }
        }
        if (structureAssignmentJCB != null) {
            for (int i = 0; i < structureAssignmentJCB.length; i += 1) {
                structureAssignmentJCB[i].removeActionListener(this);
            }
        }
        getReactionCanvas1().setReactionCanvasDisplaySpec(resolvedReaction.toReactionCanvasDisplaySpec());
        getRXParticipantsJPanel().removeAll();
        // java.awt.Insets zeroInsets = new java.awt.Insets(0,0,0,0);
        java.awt.Insets fourInsets = new java.awt.Insets(4, 4, 4, 4);
        java.awt.GridBagConstraints gbc = new java.awt.GridBagConstraints();
        gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
        gbc.insets = fourInsets;
        gbc.gridx = 0;
        gbc.gridy = 0;
        javax.swing.JLabel rxjlabel = new javax.swing.JLabel("RX Elements");
        // rxjlabel.setForeground(java.awt.Color.white);
        // rxjlabel.setOpaque(true);
        // rxjlabel.setBackground(java.awt.Color.white);
        getRXParticipantsJPanel().add(rxjlabel, gbc);
        // gbc.insets = zeroInsets;
        for (int i = 0; i < resolvedReaction.elementCount(); i += 1) {
            gbc.gridy = i + 1;
            javax.swing.JLabel jlabel = new javax.swing.JLabel(resolvedReaction.getReactionElement(i).getPreferredName() + (resolvedReaction.isFluxReaction() && resolvedReaction.getFluxIndexOutside() == i ? " (Outside)" : "") + (resolvedReaction.isFluxReaction() && resolvedReaction.getFluxIndexInside() == i ? " (Inside)" : ""));
            // jlabel.setOpaque(true);
            // jlabel.setBackground(java.awt.Color.white);
            // jlabel.setForeground(java.awt.Color.black);
            getRXParticipantsJPanel().add(jlabel, gbc);
        }
        // gbc.insets = fourInsets;
        gbc.gridx = 1;
        gbc.gridy = 0;
        speciesAssignmentJCB = new javax.swing.JComboBox[resolvedReaction.elementCount()];
        DefaultListCellRenderer speciesListCellRenderer = new DefaultListCellRenderer() {

            @Override
            public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
                // TODO Auto-generated method stub
                return super.getListCellRendererComponent(list, (value instanceof Species ? "Existing " + ((Species) value).getCommonName() : value), index, isSelected, cellHasFocus);
            }
        };
        javax.swing.JLabel rspjlabel = new javax.swing.JLabel("Assign to Model Species");
        // rspjlabel.setForeground(java.awt.Color.white);
        // rspjlabel.setOpaque(true);
        // rspjlabel.setBackground(java.awt.Color.white);
        getRXParticipantsJPanel().add(rspjlabel, gbc);
        // getRXParticipantsJPanel().add(new javax.swing.JLabel("Resolve to Model Species"),gbc);
        speciesOrder = new Species[getModel().getSpecies().length + 1];
        speciesOrder[0] = null;
        for (int j = 0; j < getModel().getSpecies().length; j += 1) {
            speciesOrder[j + 1] = getModel().getSpecies(j);
        }
        for (int i = 0; i < resolvedReaction.elementCount(); i += 1) {
            javax.swing.JComboBox jcb = new javax.swing.JComboBox();
            jcb.setRenderer(speciesListCellRenderer);
            speciesAssignmentJCB[i] = jcb;
            jcb.addItem("New Species");
            for (int j = 1; j < speciesOrder.length; j += 1) {
                jcb.addItem(/*"Existing "+*/
                speciesOrder[j]);
            }
            gbc.gridy = i + 1;
            getRXParticipantsJPanel().add(jcb, gbc);
            jcb.setEnabled(false);
        }
        gbc.gridx = 2;
        gbc.gridy = 0;
        structureAssignmentJCB = new javax.swing.JComboBox[resolvedReaction.elementCount()];
        DefaultListCellRenderer structureListCellRenderer = new DefaultListCellRenderer() {

            @Override
            public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
                // TODO Auto-generated method stub
                return super.getListCellRendererComponent(list, (value instanceof Structure ? ((Structure) value).getName() : value), index, isSelected, cellHasFocus);
            }
        };
        javax.swing.JLabel rstjlabel = new javax.swing.JLabel("Assign to Model Compartment");
        // rstjlabel.setForeground(java.awt.Color.white);
        // rstjlabel.setOpaque(true);
        // rstjlabel.setBackground(java.awt.Color.white);
        getRXParticipantsJPanel().add(rstjlabel, gbc);
        // getRXParticipantsJPanel().add(new javax.swing.JLabel("Resolve to Model Compartment"),gbc);
        StructureTopology structTopology = getModel().getStructureTopology();
        for (int i = 0; i < resolvedReaction.elementCount(); i += 1) {
            javax.swing.JComboBox jcb = new javax.swing.JComboBox();
            jcb.setRenderer(structureListCellRenderer);
            structureAssignmentJCB[i] = jcb;
            if (resolvedReaction.isFluxReaction() && resolvedReaction.isFlux(i) && resolvedReaction.getFluxIndexOutside() == i) {
                jcb.addItem(structTopology.getOutsideFeature((Membrane) getStructure()));
                jcb.setEnabled(false);
            } else if (resolvedReaction.isFluxReaction() && resolvedReaction.isFlux(i) && resolvedReaction.getFluxIndexInside() == i) {
                jcb.addItem((structTopology).getInsideFeature((Membrane) getStructure()));
                jcb.setEnabled(false);
            } else {
                jcb.addItem(getStructure());
                if (getStructure() instanceof Membrane) {
                    jcb.addItem(structTopology.getOutsideFeature((Membrane) getStructure()));
                    jcb.addItem(structTopology.getInsideFeature((Membrane) getStructure()));
                } else {
                    jcb.setEnabled(false);
                }
            }
            gbc.gridy = i + 1;
            getRXParticipantsJPanel().add(jcb, gbc);
        }
        for (int i = 0; i < resolvedReaction.elementCount(); i += 1) {
            speciesAssignmentJCB[i].addActionListener(this);
            structureAssignmentJCB[i].addActionListener(this);
        }
    }
}

Example 43 with Structure

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

the class DBReactionWizardPanel method applySelectedReactionElements.

/**
 * Comment
 */
private void applySelectedReactionElements() {
    AsynchClientTask getRXSourceModelTask = new AsynchClientTask("Get RX source model", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // Get the complete original model the user selected reaction is from
            Model fromModel = getDocumentManager().getBioModel(resolvedReaction.getVCellBioModelID()).getModel();
            // find the user selected ReactionStep in the original model
            ReactionStep fromRXStep = null;
            ReactionStep[] rxArr = fromModel.getReactionSteps();
            for (int i = 0; i < rxArr.length; i++) {
                if (rxArr[i].getKey().equals(resolvedReaction.getVCellRXID())) {
                    fromRXStep = rxArr[i];
                    break;
                }
            }
            // Create user assignment preferences
            BioCartoonTool.UserResolvedRxElements userResolvedRxElements = new BioCartoonTool.UserResolvedRxElements();
            userResolvedRxElements.fromSpeciesContextArr = new SpeciesContext[resolvedReaction.elementCount()];
            userResolvedRxElements.toSpeciesArr = new Species[resolvedReaction.elementCount()];
            userResolvedRxElements.toStructureArr = new Structure[resolvedReaction.elementCount()];
            StringBuffer warningsSB = new StringBuffer();
            for (int i = 0; i < resolvedReaction.elementCount(); i++) {
                System.out.println(resolvedReaction.getOrigSpeciesContextName(i));
                userResolvedRxElements.fromSpeciesContextArr[i] = fromModel.getSpeciesContext(resolvedReaction.getOrigSpeciesContextName(i));
                userResolvedRxElements.toSpeciesArr[i] = (speciesAssignmentJCB[i].getSelectedItem() instanceof Species ? (Species) speciesAssignmentJCB[i].getSelectedItem() : null);
                userResolvedRxElements.toStructureArr[i] = (Structure) structureAssignmentJCB[i].getSelectedItem();
                if (userResolvedRxElements.toSpeciesArr[i] != null) {
                    SpeciesContext fromSpeciesContext = userResolvedRxElements.fromSpeciesContextArr[i];
                    Species toSpecies = userResolvedRxElements.toSpeciesArr[i];
                    if (fromSpeciesContext.getSpecies().getDBSpecies() != null && !Compare.isEqualOrNull(toSpecies.getDBSpecies(), fromSpeciesContext.getSpecies().getDBSpecies())) {
                        warningsSB.append((warningsSB.length() > 0 ? "\n" : "") + "'" + fromSpeciesContext.getSpecies().getCommonName() + "' formal(" + (fromSpeciesContext.getSpecies().getDBSpecies() != null ? fromSpeciesContext.getSpecies().getDBSpecies().getPreferredName() : "null") + ")" + "\nwill be re-assigned to\n" + "'" + toSpecies.getCommonName() + "' formal(" + (toSpecies.getDBSpecies() != null ? toSpecies.getDBSpecies().getPreferredName() : "null") + ")");
                    }
                }
            }
            if (warningsSB.length() > 0) {
                final String proceed = "Add reaction anyway";
                final String cancel = "Cancel";
                String result = DialogUtils.showWarningDialog(DBReactionWizardPanel.this, "A user choice selected under 'Assign to Model species' will force re-assignment of " + "the formal reference for one of the species in the reaction.\n" + warningsSB, new String[] { proceed, cancel }, cancel);
                if (result.equals(cancel)) {
                    throw UserCancelException.CANCEL_GENERIC;
                }
            }
            hashTable.put("fromRXStep", fromRXStep);
            hashTable.put("userResolvedRxElements", userResolvedRxElements);
        }
    };
    AsynchClientTask pasteReactionTask = new AsynchClientTask("Paste reaction", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // TODO Auto-generated method stub
            Model pasteToModel = DBReactionWizardPanel.this.getModel();
            Structure pasteToStructure = DBReactionWizardPanel.this.getStructure();
            BioCartoonTool.pasteReactionSteps(DBReactionWizardPanel.this, new ReactionStep[] { (ReactionStep) hashTable.get("fromRXStep") }, pasteToModel, pasteToStructure, false, (UserResolvedRxElements) hashTable.get("userResolvedRxElements"), rxPasteInterface);
            closeParent();
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { getRXSourceModelTask, pasteReactionTask }, false, false, null, true);
}

Example 44 with Structure

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

the class IssueTableModel method getSourceObjectPathDescription.

private String getSourceObjectPathDescription(VCDocument vcDocument, Issue issue) {
    VCAssert.assertValid(issue);
    Object source = issue.getSource();
    {
        IssueOrigin io = BeanUtils.downcast(IssueOrigin.class, source);
        if (io != null) {
            return io.getDescription();
        }
    }
    if (vcDocument instanceof BioModel) {
        BioModel bioModel = (BioModel) vcDocument;
        String description = "";
        if (source instanceof SymbolTableEntry) {
            if (source instanceof SpeciesContext) {
                description = "Model / Species";
            } else if (source instanceof RbmObservable) {
                description = "Model / Observables";
            } else {
                description = ((SymbolTableEntry) source).getNameScope().getPathDescription();
            }
        } else if (source instanceof MolecularType) {
            description = "Model / Molecules";
        } else if (source instanceof ReactionStep) {
            ReactionStep reactionStep = (ReactionStep) source;
            description = ((ReactionNameScope) reactionStep.getNameScope()).getPathDescription();
        } else if (source instanceof ReactionRule) {
            ReactionRule reactionRule = (ReactionRule) source;
            description = ((ReactionRuleNameScope) reactionRule.getNameScope()).getPathDescription();
        } else if (source instanceof SpeciesPattern) {
            // if (issue.getIssueContext().hasContextType(ContextType.SpeciesContext)){
            // description = "Model / Species";
            // }else if(issue.getIssueContext().hasContextType(ContextType.ReactionRule)) {
            // ReactionRule thing = (ReactionRule)issue.getIssueContext().getContextObject(ContextType.ReactionRule);
            // description = ((ReactionRuleNameScope)thing.getNameScope()).getPathDescription();
            // }else if(issue.getIssueContext().hasContextType(ContextType.RbmObservable)) {
            // description = "Model / Observables";
            // } else {
            System.err.println("Bad issue context for " + ((SpeciesPattern) source).toString());
            description = ((SpeciesPattern) source).toString();
        // }
        } else if (source instanceof Structure) {
            Structure structure = (Structure) source;
            description = "Model / " + structure.getTypeName() + "(" + structure.getName() + ")";
        } else if (source instanceof StructureMapping) {
            StructureMapping structureMapping = (StructureMapping) source;
            description = ((StructureMappingNameScope) structureMapping.getNameScope()).getPathDescription();
        } else if (source instanceof OutputFunctionIssueSource) {
            SimulationContext simulationContext = (SimulationContext) ((OutputFunctionIssueSource) source).getOutputFunctionContext().getSimulationOwner();
            description = "App(" + simulationContext.getName() + ") / " + "Simulations" + " / " + "Output Functions";
        } else if (source instanceof Simulation) {
            Simulation simulation = (Simulation) source;
            try {
                SimulationContext simulationContext = bioModel.getSimulationContext(simulation);
                description = "App(" + simulationContext.getName() + ") / Simulations";
            } catch (ObjectNotFoundException e) {
                e.printStackTrace();
                description = "App(" + "unknown" + ") / Simulations";
            }
        } else if (source instanceof UnmappedGeometryClass) {
            UnmappedGeometryClass unmappedGC = (UnmappedGeometryClass) source;
            description = "App(" + unmappedGC.getSimulationContext().getName() + ") / Subdomain(" + unmappedGC.getGeometryClass().getName() + ")";
        } else if (source instanceof GeometryContext) {
            description = "App(" + ((GeometryContext) source).getSimulationContext().getName() + ")";
        } else if (source instanceof ModelOptimizationSpec) {
            description = "App(" + ((ModelOptimizationSpec) source).getSimulationContext().getName() + ") / Parameter Estimation";
        } else if (source instanceof MicroscopeMeasurement) {
            description = "App(" + ((MicroscopeMeasurement) source).getSimulationContext().getName() + ") / Microscope Measurements";
        } else if (source instanceof SpatialObject) {
            description = "App(" + ((SpatialObject) source).getSimulationContext().getName() + ") / Spatial Objects";
        } else if (source instanceof SpatialProcess) {
            description = "App(" + ((SpatialProcess) source).getSimulationContext().getName() + ") / Spatial Processes";
        } else if (source instanceof SpeciesContextSpec) {
            SpeciesContextSpec scs = (SpeciesContextSpec) source;
            description = "App(" + scs.getSimulationContext().getName() + ") / Specifications / Species";
        } else if (source instanceof ReactionCombo) {
            ReactionCombo rc = (ReactionCombo) source;
            description = "App(" + rc.getReactionContext().getSimulationContext().getName() + ") / Specifications / Reactions";
        } else if (source instanceof RbmModelContainer) {
            IssueCategory ic = issue.getCategory();
            switch(ic) {
                case RbmMolecularTypesTableBad:
                    description = "Model / " + MolecularType.typeName + "s";
                    break;
                case RbmReactionRulesTableBad:
                    description = "Model / Reactions";
                    break;
                case RbmObservablesTableBad:
                    description = "Model / Observables";
                    break;
                case RbmNetworkConstraintsBad:
                    description = "Network Constrains";
                    break;
                default:
                    description = "Model";
                    break;
            }
        } else if (source instanceof SimulationContext) {
            SimulationContext sc = (SimulationContext) source;
            IssueCategory ic = issue.getCategory();
            switch(ic) {
                case RbmNetworkConstraintsBad:
                    description = "Specifications / Network";
                    break;
                default:
                    description = "Application";
                    break;
            }
        } else if (source instanceof Model) {
            description = "Model";
        } else if (source instanceof BioEvent) {
            return "Protocols / Events";
        } else if (source instanceof MathDescription) {
            return "Math Description";
        } else {
            System.err.println("unknown source type in IssueTableModel.getSourceObjectPathDescription(): " + source.getClass());
        }
        return description;
    } else if (vcDocument instanceof MathModel) {
        if (source instanceof Geometry) {
            return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_GEOMETRY;
        } else if (source instanceof OutputFunctionIssueSource) {
            return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_OUTPUTFUNCTIONS;
        } else if (source instanceof Simulation) {
            return "Simulation(" + ((Simulation) source).getName() + ")";
        } else {
            return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_VCML;
        }
    } else {
        System.err.println("unknown document type in IssueTableModel.getSourceObjectPathDescription()");
        return "";
    }
}

Example 45 with Structure

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

the class IssueTableModel method getSourceObjectDescription.

private String getSourceObjectDescription(VCDocument vcDocument, Issue issue) {
    if (vcDocument instanceof BioModel) {
        Object object = issue.getSource();
        {
            DecoratedIssueSource dis = BeanUtils.downcast(DecoratedIssueSource.class, object);
            if (dis != null) {
                return dis.getSourcePath();
            }
        }
        String description = "";
        if (object instanceof SymbolTableEntry) {
            description = ((SymbolTableEntry) object).getName();
        } else if (object instanceof ReactionStep) {
            description = ((ReactionStep) object).getName();
        } else if (object instanceof ReactionRule) {
            description = ((ReactionRule) object).getName();
        } else if (object instanceof SpeciesPattern) {
            // Object parent = issue.getIssueContext().getContextObject();
            // if (parent instanceof SpeciesContext){
            // description = ((SpeciesContext)parent).getName();
            // }
            // if (issue.getIssueContext().hasContextType(ContextType.SpeciesContext)){
            // SpeciesContext thing = (SpeciesContext)issue.getIssueContext().getContextObject(ContextType.SpeciesContext);
            // description = thing.getName();
            // }else if(issue.getIssueContext().hasContextType(ContextType.ReactionRule)) {
            // ReactionRule thing = (ReactionRule)issue.getIssueContext().getContextObject(ContextType.ReactionRule);
            // description = thing.getName();
            // }else if(issue.getIssueContext().hasContextType(ContextType.RbmObservable)) {
            // RbmObservable thing = (RbmObservable)issue.getIssueContext().getContextObject(ContextType.RbmObservable);
            // description = thing.getName();
            // } else {
            System.err.println("Bad issue context for " + ((SpeciesPattern) object).toString());
            description = ((SpeciesPattern) object).toString();
        // }
        } else if (object instanceof MolecularType) {
            description = ((MolecularType) object).getName();
        } else if (object instanceof MolecularComponent) {
            description = ((MolecularComponent) object).getName();
        } else if (object instanceof ComponentStateDefinition) {
            description = ((ComponentStateDefinition) object).getName();
        } else if (object instanceof Structure) {
            description = ((Structure) object).getName();
        } else if (object instanceof SubDomain) {
            description = ((SubDomain) object).getName();
        } else if (object instanceof Geometry) {
            description = ((Geometry) object).getName();
        } else if (object instanceof StructureMapping) {
            description = ((StructureMapping) object).getStructure().getName();
        } else if (object instanceof OutputFunctionIssueSource) {
            description = ((OutputFunctionIssueSource) object).getAnnotatedFunction().getName();
        } else if (object instanceof UnmappedGeometryClass) {
            description = ((UnmappedGeometryClass) object).getGeometryClass().getName();
        } else if (object instanceof MicroscopeMeasurement) {
            description = ((MicroscopeMeasurement) object).getName();
        } else if (object instanceof SpatialObject) {
            description = ((SpatialObject) object).getName();
        } else if (object instanceof SpatialProcess) {
            description = ((SpatialProcess) object).getName();
        } else if (object instanceof GeometryContext) {
            description = "Geometry";
        } else if (object instanceof ModelOptimizationSpec) {
            description = ((ModelOptimizationSpec) object).getParameterEstimationTask().getName();
        } else if (object instanceof Simulation) {
            description = ((Simulation) object).getName();
        } else if (object instanceof SpeciesContextSpec) {
            SpeciesContextSpec scs = (SpeciesContextSpec) object;
            description = scs.getSpeciesContext().getName();
        } else if (object instanceof ReactionCombo) {
            ReactionSpec rs = ((ReactionCombo) object).getReactionSpec();
            description = rs.getReactionStep().getName();
        } else if (object instanceof RbmModelContainer) {
            // RbmModelContainer mc = (RbmModelContainer)object;
            description = "Rules validator";
        } else if (object instanceof SimulationContext) {
            SimulationContext sc = (SimulationContext) object;
            description = sc.getName();
        } else if (object instanceof Model) {
            Model m = (Model) object;
            description = m.getName();
        } else if (object instanceof BioEvent) {
            return ((BioEvent) object).getName() + "";
        } else if (object instanceof MathDescription) {
            return ((MathDescription) object).getName() + "";
        } else {
            System.err.println("unknown object type in IssueTableModel.getSourceObjectDescription(): " + object.getClass());
        }
        return description;
    } else if (vcDocument instanceof MathModel) {
        Object object = issue.getSource();
        String description = "";
        if (object instanceof Variable) {
            description = ((Variable) object).getName();
        } else if (object instanceof SubDomain) {
            description = ((SubDomain) object).getName();
        } else if (object instanceof Geometry) {
            description = "Geometry";
        } else if (object instanceof OutputFunctionIssueSource) {
            description = ((OutputFunctionIssueSource) object).getAnnotatedFunction().getName();
        } else if (object instanceof MathDescription) {
            return "math";
        } else if (object instanceof Simulation) {
            return "Simulation " + ((Simulation) object).getName() + "";
        }
        return description;
    } else {
        System.err.println("unknown document type in IssueTableModel.getSourceObjectDescription()");
        return "";
    }
}