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

Example 6 with RbmObservable

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

the class SpeciesPatternRoundShape method paintCompartment.

public void paintCompartment(Graphics g) {
    Color structureColor = Color.black;
    Structure structure = null;
    if (owner instanceof ReactionRule && !speciesShapes.isEmpty()) {
        ReactionRule rr = (ReactionRule) owner;
        ReactantPattern rp = rr.getReactantPattern(sp);
        ProductPattern pp = rr.getProductPattern(sp);
        if (rp != null) {
            structure = rp.getStructure();
        } else if (pp != null) {
            structure = pp.getStructure();
        } else {
            structure = ((ReactionRule) owner).getStructure();
        }
    } else if (owner instanceof SpeciesContext && ((SpeciesContext) owner).hasSpeciesPattern()) {
        structure = ((SpeciesContext) owner).getStructure();
        structureColor = Color.gray;
    } else if (owner instanceof RbmObservable && !speciesShapes.isEmpty()) {
        structure = ((RbmObservable) owner).getStructure();
    } else {
        // other things don't have structure
        return;
    }
    if (structure == null) {
        return;
    }
    // don't have a real structure, so we show them structureless (for now)
    if (structure.getName() == null) {
        return;
    }
    Graphics2D g2 = (Graphics2D) g;
    Color colorOld = g2.getColor();
    Paint paintOld = g2.getPaint();
    Font fontOld = g2.getFont();
    Font font;
    // width of compartment shape, adjusted continuously based on zoom factor
    int w;
    String name = structure.getName();
    int z = shapePanel.getZoomFactor();
    if (z > -3) {
        font = fontOld.deriveFont(Font.BOLD);
        g.setFont(font);
        w = 46 + 3 * z;
        name = buildCompartmentName(g, name, "..", w);
    } else if (z < LargeShapeCanvas.SmallestZoomFactorWithText) {
        font = fontOld.deriveFont(fontOld.getSize2D() * 0.8f);
        g.setFont(font);
        w = 20;
        name = buildCompartmentName(g, name, ".", w);
    } else {
        font = fontOld;
        g.setFont(font);
        w = 44 + 3 * z;
        name = buildCompartmentName(g, name, "..", w);
    }
    // a bit darker for border
    Color darker = Color.gray;
    Rectangle2D border = new Rectangle2D.Double(xPos - 9, yPos - 4, w, 58);
    g2.setColor(darker);
    g2.draw(border);
    Color lighter = new Color(224, 224, 224);
    Rectangle2D filling = new Rectangle2D.Double(xPos - 9, yPos - 3, w, 57);
    g2.setPaint(lighter);
    g2.fill(filling);
    g.setColor(structureColor);
    g2.drawString(name, xPos - 4, yPos + 48);
    g2.setFont(fontOld);
    g2.setPaint(paintOld);
    g2.setColor(colorOld);
}

Example 7 with RbmObservable

use of cbit.vcell.model.RbmObservable 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 8 with RbmObservable

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

the class ObservablePropertiesPanel method onSelectedObjectsChange.

@Override
protected void onSelectedObjectsChange(Object[] selectedObjects) {
    RbmObservable observable = null;
    if (selectedObjects.length == 1 && selectedObjects[0] instanceof RbmObservable) {
        observable = (RbmObservable) selectedObjects[0];
    }
    setObservable(observable);
    updateSequence();
}

Example 9 with RbmObservable

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

the class ObservableTableModel method computeData.

@Override
protected List<RbmObservable> computeData() {
    if (getModel() == null) {
        return new ArrayList<RbmObservable>();
    }
    List<RbmObservable> oList;
    if (searchText == null || searchText.length() == 0) {
        oList = new ArrayList<RbmObservable>(getModel().getRbmModelContainer().getObservableList());
    } else {
        oList = new ArrayList<RbmObservable>();
        String lowerCaseSearchText = searchText.toLowerCase();
        for (RbmObservable o : getModel().getRbmModelContainer().getObservableList()) {
            String name = o.getName();
            String struct = o.getStructure().getName();
            String type = o.getType().name();
            if (name != null && name.toLowerCase().contains(lowerCaseSearchText)) {
                oList.add(o);
            } else if (struct != null && struct.toLowerCase().contains(lowerCaseSearchText)) {
                oList.add(o);
            } else if (type != null && type.toLowerCase().contains(lowerCaseSearchText)) {
                oList.add(o);
            } else {
                String expression = "";
                for (SpeciesPattern sp : o.getSpeciesPatternList()) {
                    expression += sp.toString() + " ";
                }
                if (expression.toLowerCase().contains(lowerCaseSearchText)) {
                    oList.add(o);
                }
            }
        }
    }
    return oList;
}

Example 10 with RbmObservable

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

the class ObservableTableModel method getComparator.

@Override
protected Comparator<RbmObservable> getComparator(final int columnIndex, final boolean ascending) {
    return new Comparator<RbmObservable>() {

        int scale = ascending ? 1 : -1;

        Column col = Column.values()[columnIndex];

        public int compare(RbmObservable o1, RbmObservable o2) {
            switch(col) {
                case name:
                    return scale * o1.getName().compareToIgnoreCase(o2.getName());
                case structure:
                    return scale * o1.getStructure().getName().compareToIgnoreCase(o2.getStructure().getName());
                case species_pattern:
                    return scale * RbmUtils.toBnglString(o1.getSpeciesPattern(0), null, CompartmentMode.hide, 0).compareToIgnoreCase(RbmUtils.toBnglString(o2.getSpeciesPattern(0), null, CompartmentMode.hide, 0));
                case type:
                    return scale * o1.getType().name().compareToIgnoreCase(o2.getType().name());
                case depiction:
                    // the sp list is always allocated even though it may be empty
                    Integer s1 = o1.getSpeciesPatternList().size();
                    Integer s2 = o2.getSpeciesPatternList().size();
                    if (s1 != s2) {
                        // different number of species patterns, sort by number of patterns
                        return scale * s1.compareTo(s2);
                    // this includes the case when one list is empty
                    }
                    if (s1 > 1 && s2 > 1) {
                        // same number of species patterns, more than one - we don't bother to sort
                        return 0;
                    // TODO: add functionality to sort by total number of molecules / sites
                    }
                    // one pattern each, sort by number of molecules, if that equal sort by total number of sites
                    if (s1 == 1 && s2 == 1) {
                        Integer i1 = o1.getSpeciesPattern(0).getMolecularTypePatterns().size();
                        Integer i2 = o2.getSpeciesPattern(0).getMolecularTypePatterns().size();
                        if (scale * i1.compareTo(i2) == 0) {
                            // if same number of molecule we try to sort by number of sites of the mt
                            i1 = 0;
                            i2 = 0;
                            for (MolecularTypePattern mtp : o1.getSpeciesPattern(0).getMolecularTypePatterns()) {
                                i1 += mtp.getMolecularType().getComponentList().size();
                            }
                            for (MolecularTypePattern mtp : o2.getSpeciesPattern(0).getMolecularTypePatterns()) {
                                i2 += mtp.getMolecularType().getComponentList().size();
                            }
                            return scale * i1.compareTo(i2);
                        } else {
                            return scale * i1.compareTo(i2);
                        }
                    }
                    return 0;
                default:
                    return 0;
            }
        }
    };
}