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

Example 46 with Structure

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

the class BioModel method getVCID.

public VCID getVCID(Identifiable identifiable) {
    String localName;
    String className;
    if (identifiable instanceof SpeciesContext) {
        localName = ((SpeciesContext) identifiable).getName();
        className = "SpeciesContext";
    } else if (identifiable instanceof Species) {
        localName = ((Species) identifiable).getCommonName();
        className = VCID.CLASS_SPECIES;
    } else if (identifiable instanceof Structure) {
        localName = ((Structure) identifiable).getName();
        className = "Structure";
    } else if (identifiable instanceof ReactionStep) {
        localName = ((ReactionStep) identifiable).getName();
        className = VCID.CLASS_REACTION_STEP;
    } else if (identifiable instanceof BioModel) {
        localName = ((BioModel) identifiable).getName();
        className = VCID.CLASS_BIOMODEL;
    // }else if (identifiable instanceof SimulationContext){
    // localName = ((SimulationContext)identifiable).getName();
    // className = "Application";
    } else if (identifiable instanceof BioPaxObject) {
        localName = ((BioPaxObject) identifiable).getID();
        className = "BioPaxObject";
    } else if (identifiable instanceof MolecularType) {
        localName = ((MolecularType) identifiable).getName();
        className = "MolecularType";
    } else if (identifiable instanceof ReactionRule) {
        localName = ((ReactionRule) identifiable).getName();
        className = "ReactionRule";
    } else if (identifiable instanceof RbmObservable) {
        localName = ((RbmObservable) identifiable).getName();
        className = "RbmObservable";
    } else {
        throw new RuntimeException("unsupported Identifiable class");
    }
    localName = TokenMangler.mangleVCId(localName);
    VCID vcid;
    try {
        vcid = VCID.fromString(className + "(" + localName + ")");
    } catch (VCID.InvalidVCIDException e) {
        e.printStackTrace();
        throw new RuntimeException(e.getMessage());
    }
    return vcid;
}

Example 47 with Structure

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

the class SbmlExtensionFilter method askUser.

@Override
public void askUser(ChooseContext c) throws UserCancelException {
    BioModel bioModel = c.chosenContext.getBioModel();
    JFrame currentWindow = c.currentWindow;
    selectedSimWOSBE = null;
    selectedSimContext = c.chosenContext;
    // get user choice of structure and its size and computes absolute sizes of compartments using the StructureSizeSolver.
    Structure[] structures = bioModel.getModel().getStructures();
    // get the nonspatial simulationContexts corresponding to names in applicableAppNameList
    // This is needed in ApplnSelectionAndStructureSizeInputPanel
    String strucName = null;
    double structSize = 1.0;
    int structSelection = -1;
    int option = JOptionPane.CANCEL_OPTION;
    ApplnSelectionAndStructureSizeInputPanel applnStructInputPanel = null;
    while (structSelection < 0) {
        applnStructInputPanel = new ApplnSelectionAndStructureSizeInputPanel();
        applnStructInputPanel.setSimContext(c.chosenContext);
        applnStructInputPanel.setStructures(structures);
        if (applnStructInputPanel.isNeedStructureSizes()) {
            applnStructInputPanel.setPreferredSize(new java.awt.Dimension(350, 400));
            applnStructInputPanel.setMaximumSize(new java.awt.Dimension(350, 400));
            option = DialogUtils.showComponentOKCancelDialog(currentWindow, applnStructInputPanel, "Specify Structure Size to Export:");
            structSelection = applnStructInputPanel.getStructSelectionIndex();
            if (option == JOptionPane.CANCEL_OPTION || option == JOptionPane.CLOSED_OPTION) {
                break;
            } else if (option == JOptionPane.OK_OPTION && structSelection < 0) {
                DialogUtils.showErrorDialog(currentWindow, "Please select a structure and set its size");
            }
        } else {
            // adapt to legacy logic ...
            structSelection = 0;
            option = JOptionPane.OK_OPTION;
        }
    }
    if (option == JOptionPane.OK_OPTION) {
        applnStructInputPanel.applyStructureNameAndSizeValues();
        strucName = applnStructInputPanel.getSelectedStructureName();
        selectedSimContext = applnStructInputPanel.getSelectedSimContext();
        GeometryContext geoContext = selectedSimContext.getGeometryContext();
        if (!isSpatial) {
            // calculate structure Sizes only if appln is not spatial
            structSize = applnStructInputPanel.getStructureSize();
            // Invoke StructureSizeEvaluator to compute absolute sizes of compartments if all sizes are not set
            if ((geoContext.isAllSizeSpecifiedNull() && geoContext.isAllVolFracAndSurfVolSpecifiedNull()) || ((strucName == null || structSize <= 0.0) && (geoContext.isAllSizeSpecifiedNull() && geoContext.isAllVolFracAndSurfVolSpecified())) || (!geoContext.isAllSizeSpecifiedPositive() && geoContext.isAllVolFracAndSurfVolSpecifiedNull()) || (!geoContext.isAllSizeSpecifiedPositive() && !geoContext.isAllVolFracAndSurfVolSpecified()) || (geoContext.isAllSizeSpecifiedNull() && !geoContext.isAllVolFracAndSurfVolSpecified())) {
                DialogUtils.showErrorDialog(currentWindow, "Cannot export to SBML without compartment sizes being set. This can be automatically " + " computed if the absolute size of at least one compartment and the relative sizes (Surface-to-volume-ratio/Volume-fraction) " + " of all compartments are known. Sufficient information is not available to perform this computation." + "\n\nThis can be fixed by going back to the application '" + selectedSimContext.getName() + "' and setting structure sizes in the 'StructureMapping' tab.");
                throw UserCancelException.CANCEL_XML_TRANSLATION;
            }
            if (!geoContext.isAllSizeSpecifiedPositive() && geoContext.isAllVolFracAndSurfVolSpecified()) {
                Structure chosenStructure = selectedSimContext.getModel().getStructure(strucName);
                StructureMapping chosenStructMapping = selectedSimContext.getGeometryContext().getStructureMapping(chosenStructure);
                try {
                    StructureSizeSolver.updateAbsoluteStructureSizes(selectedSimContext, chosenStructure, structSize, chosenStructMapping.getSizeParameter().getUnitDefinition());
                } catch (Exception e) {
                    throw new ProgrammingException("exception updating sizes", e);
                }
            }
        } else {
            if (!geoContext.isAllUnitSizeParameterSetForSpatial()) {
                DialogUtils.showErrorDialog(currentWindow, "Cannot export to SBML without compartment size ratios being set." + "\n\nThis can be fixed by going back to the application '" + selectedSimContext.getName() + "' and setting structure" + " size ratios in the 'StructureMapping' tab.");
                throw UserCancelException.CANCEL_XML_TRANSLATION;
            }
        }
        // Select simulation whose overrides need to be exported
        // If simContext doesn't have simulations, don't pop up simulationSelectionPanel
        Simulation[] sims = bioModel.getSimulations(selectedSimContext);
        // display only those simulations that have overrides in the simulationSelectionPanel.
        Vector<Simulation> orSims = new Vector<Simulation>();
        for (int s = 0; (sims != null) && (s < sims.length); s++) {
            if (sims[s].getMathOverrides().hasOverrides()) {
                orSims.addElement(sims[s]);
            }
        }
        Simulation[] overriddenSims = orSims.toArray(new Simulation[orSims.size()]);
        if (overriddenSims.length > 0) {
            SimulationSelectionPanel simSelectionPanel = new SimulationSelectionPanel();
            simSelectionPanel.setPreferredSize(new java.awt.Dimension(600, 400));
            simSelectionPanel.setMaximumSize(new java.awt.Dimension(600, 400));
            simSelectionPanel.setSimulations(overriddenSims);
            int simOption = DialogUtils.showComponentOKCancelDialog(currentWindow, simSelectionPanel, "Select Simulation whose overrides should be exported:");
            if (simOption == JOptionPane.OK_OPTION) {
                selectedSimWOSBE = simSelectionPanel.getSelectedSimulation();
            // if (chosenSimulation != null) {
            // CARRY						hashTable.put("selectedSimulation", chosenSimulation);
            // }
            } else if (simOption == JOptionPane.CANCEL_OPTION || simOption == JOptionPane.CLOSED_OPTION) {
                // Hence canceling the entire export to SBML operation.
                throw UserCancelException.CANCEL_XML_TRANSLATION;
            }
        }
    } else if (option == JOptionPane.CANCEL_OPTION || option == JOptionPane.CLOSED_OPTION) {
        // Hence canceling the entire export to SBML operation.
        throw UserCancelException.CANCEL_XML_TRANSLATION;
    }
    if (selectedSimWOSBE != null) {
        String selectedFileName = c.filename;
        // rename file to contain exported simulation.
        String ext = FilenameUtils.getExtension(selectedFileName);
        String base = FilenameUtils.getBaseName(selectedFileName);
        String path = FilenameUtils.getPath(selectedFileName);
        base += "_" + TokenMangler.mangleToSName(selectedSimWOSBE.getName());
        selectedFileName = path + base + ext;
        c.selectedFile.renameTo(new File(selectedFileName));
    }
}

Example 48 with Structure

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

the class GraphContainerLayoutReactions method getPreferedSizeReactionContainerShape.

public Dimension getPreferedSizeReactionContainerShape(ReactionContainerShape shape, Graphics2D g) {
    // get size when empty
    Font origFont = g.getFont();
    g.setFont(shape.getLabelFont(g));
    try {
        Dimension preferredSize = shape.getPreferedSizeSelf(g);
        // make larger than empty size so that children fit
        for (Shape child : shape.getChildren()) {
            if (child instanceof ReactionStepShape || child instanceof SpeciesContextShape || child instanceof RuleParticipantSignatureFullDiagramShape || child instanceof RuleParticipantSignatureShortDiagramShape || child instanceof ReactionRuleDiagramShape) {
                preferredSize.width = Math.max(preferredSize.width, child.getSpaceManager().getRelPos().x + child.getSpaceManager().getSize().width);
                preferredSize.height = Math.max(preferredSize.height, child.getSpaceManager().getRelPos().y + child.getSpaceManager().getSize().height);
            }
        }
        preferredSize.width = preferredSize.width + WIDTH_PADDING;
        preferredSize.height = preferredSize.height + HEIGHT_PADDING;
        Structure structure = shape.getStructure();
        int minWidthSum = 0;
        for (Structure structure2 : shape.getStructureSuite().getStructures()) {
            if (structure2 instanceof Feature) {
                minWidthSum += FEATURE_MIN_WIDTH;
            } else {
                minWidthSum += MEMBRANE_MIN_WIDTH;
            }
        }
        int compartmentMinWidth = 0;
        if (structure instanceof Feature) {
            compartmentMinWidth = FEATURE_MIN_WIDTH;
        } else {
            compartmentMinWidth = MEMBRANE_MIN_WIDTH;
        }
        int apportionedWidth = compartmentMinWidth * TOTAL_MIN_WIDTH / minWidthSum;
        if (preferredSize.width < compartmentMinWidth) {
            preferredSize.width = compartmentMinWidth;
        }
        if (preferredSize.width < apportionedWidth) {
            preferredSize.width = apportionedWidth;
        }
        if (preferredSize.height < MIN_HEIGHT) {
            preferredSize.height = MIN_HEIGHT;
        }
        return preferredSize;
    } finally {
        g.setFont(origFont);
    }
}

Example 49 with Structure

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

the class MolecularTypeLargeShape method getAnchorsHTML.

// ----------------------------------------------------------------------------------------
public String getAnchorsHTML() {
    String str = "";
    if (mt != null && !mt.isAnchorAll() && mt.getAnchors().size() > 0) {
        str += "<html>";
        boolean first = true;
        for (Structure s : mt.getAnchors()) {
            if (!first) {
                str += "<br>";
            }
            first = false;
            str += s.getName();
        }
        str += "</html>";
    }
    return str;
}

Example 50 with Structure

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

the class MolecularTypeLargeShape method paintNarrowCompartmentRight.

public void paintNarrowCompartmentRight(Graphics g) {
    Graphics2D g2 = (Graphics2D) g;
    Color colorOld = g2.getColor();
    Paint paintOld = g2.getPaint();
    int z = shapePanel.getZoomFactor();
    Rectangle r = getAnchorRectangleRight();
    Rectangle2D border = new Rectangle2D.Double(r.x, r.y, r.width, r.height);
    // a bit darker for border
    Color darker = getDefaultColor(Color.gray);
    g2.setColor(darker);
    g2.draw(border);
    Color lighter;
    if (owner instanceof MolecularType) {
        if (mt.getAnchors().size() == 0) {
            lighter = MolecularComponentLargeShape.componentBad;
        } else {
            // molecules may be anchored to multiple structures,
            // so we leave it white since it may be a mix of membranes and compartments
            lighter = Color.white;
        }
    } else {
        // non molecular type, we make sure before calling this that structure is not null
        boolean found = false;
        for (Structure struct : mt.getAnchors()) {
            if (structure.getName().equals(struct.getName())) {
                found = true;
                break;
            }
        }
        if (!found) {
            // molecule can't be in the structure where the species pattern is
            lighter = MolecularComponentLargeShape.componentBad;
        } else {
            if (structure.getTypeName().equals(Structure.TYPE_NAME_MEMBRANE)) {
                // 192	208
                lighter = new Color(192, 192, 192);
            } else {
                // 244
                lighter = new Color(240, 240, 240);
            }
        }
    }
    Rectangle2D filling = new Rectangle2D.Double(r.x, r.y + 1, r.width, r.height - 1);
    g2.setPaint(lighter);
    g2.fill(filling);
    g2.setPaint(paintOld);
    g2.setColor(colorOld);
}