Examples with ComponentStateDefinition org.vcell.model.rbm.ComponentStateDefinition used on opensource projects

Example 16 with ComponentStateDefinition

use of org.vcell.model.rbm.ComponentStateDefinition in project vcell by virtualcell.

the class XmlReader method getRbmMolecularComponentPattern.

private MolecularComponentPattern getRbmMolecularComponentPattern(Element e, MolecularTypePattern mtp, MolecularType mt, Model newModel) {
    RbmModelContainer mc = newModel.getRbmModelContainer();
    String s = e.getAttributeValue(XMLTags.RbmMolecularComponentTag);
    if (s == null || s.isEmpty()) {
        System.out.println("XMLReader: getRbmMolecularComponentPattern: MolecularComponent name is missing.");
        return null;
    }
    MolecularComponent c = mt.getMolecularComponent(s);
    if (c == null) {
        System.out.println("XMLReader: getRbmMolecularComponentPattern: encountered reference " + s + " to non-existing MolecularComponent.");
        return null;
    }
    ComponentStatePattern csp = new ComponentStatePattern();
    MolecularComponentPattern mcp = new MolecularComponentPattern(c);
    s = e.getAttributeValue(XMLTags.RbmMolecularComponentStatePatternTag);
    if (s != null && !s.isEmpty()) {
        // state may be missing, we set it only if is present
        ComponentStateDefinition cs = c.getComponentStateDefinition(s);
        if (cs == null) {
            System.out.println("XMLReader: getRbmMolecularComponentPattern: encountered reference " + s + " to non-existing MolecularComponentState.");
            return null;
        }
        csp = new ComponentStatePattern(cs);
        mcp.setComponentStatePattern(csp);
    }
    // s = e.getAttributeValue(XMLTags.RbmMolecularTypeAnyTag);
    // if(s!=null && !s.isEmpty()) {
    // boolean any = Boolean.parseBoolean(s);
    // csp.setAny(any);
    // }
    s = e.getAttributeValue(XMLTags.RbmBondTypeAttrTag);
    BondType bondType = BondType.fromSymbol(s);
    if (bondType == BondType.Specified) {
        int bondId = Integer.parseInt(s);
        mcp.setBondId(bondId);
    }
    mcp.setBondType(bondType);
    // sanity check, we only read the names here and make sure they make sense
    Element bondElement = e.getChild(XMLTags.RbmBondTag, vcNamespace);
    if (bondElement != null) {
        // it's actually the name of the MolecularType inside this pattern
        String molecularTypeName = bondElement.getAttributeValue(XMLTags.RbmMolecularTypePatternTag);
        String molecularComponentName = bondElement.getAttributeValue(XMLTags.RbmMolecularComponentPatternTag);
        if (molecularTypeName == null || molecularTypeName.isEmpty()) {
            System.out.println("XMLReader: getRbmMolecularComponentPattern: Bond Attribute molecularTypeName missing.");
            return mcp;
        }
        if (molecularComponentName == null || molecularComponentName.isEmpty()) {
            System.out.println("XMLReader: getRbmMolecularComponentPattern: Bond Attribute molecularComponentName missing.");
            return mcp;
        }
        // we'll have a bond here, it will be properly initialized during RbmObservable.resolveBonds() call  !!!
        Bond bond = new Bond();
        mcp.setBond(bond);
    }
    return mcp;
}

Example 17 with ComponentStateDefinition

use of org.vcell.model.rbm.ComponentStateDefinition in project vcell by virtualcell.

the class XmlReader method getRbmComponentStateDefinition.

private ComponentStateDefinition getRbmComponentStateDefinition(Element e, Model newModel) {
    String s = e.getAttributeValue(XMLTags.NameAttrTag);
    if (s == null || s.isEmpty()) {
        System.out.println("XMLReader: getRbmComponentState: name is missing.");
        return null;
    }
    ComponentStateDefinition cs = new ComponentStateDefinition(s);
    // }
    return cs;
}

Example 18 with ComponentStateDefinition

use of org.vcell.model.rbm.ComponentStateDefinition in project vcell by virtualcell.

the class MolecularTypePropertiesPanel method addNewFromTree.

public void addNewFromTree() {
    Object obj = molecularTypeTree.getLastSelectedPathComponent();
    if (obj == null || !(obj instanceof BioModelNode)) {
        return;
    }
    BioModelNode selectedNode = (BioModelNode) obj;
    Object selectedUserObject = selectedNode.getUserObject();
    if (selectedUserObject == molecularType) {
        MolecularComponent molecularComponent = molecularType.createMolecularComponent();
        molecularType.addMolecularComponent(molecularComponent);
        bioModel.getModel().getRbmModelContainer().adjustSpeciesContextPatterns(molecularType, molecularComponent);
        bioModel.getModel().getRbmModelContainer().adjustObservablesPatterns(molecularType, molecularComponent);
        bioModel.getModel().getRbmModelContainer().adjustRulesPatterns(molecularType, molecularComponent);
        molecularTypeTree.startEditingAtPath(molecularTypeTreeModel.findObjectPath(null, molecularComponent));
    } else if (selectedUserObject instanceof MolecularComponent) {
        MolecularComponent molecularComponent = (MolecularComponent) selectedUserObject;
        ComponentStateDefinition componentStateDefinition = molecularComponent.createComponentStateDefinition();
        molecularComponent.addComponentStateDefinition(componentStateDefinition);
        bioModel.getModel().getRbmModelContainer().adjustObservablesPatterns(molecularType, molecularComponent, componentStateDefinition);
        molecularTypeTree.startEditingAtPath(molecularTypeTreeModel.findObjectPath(null, componentStateDefinition));
    }
}

Example 19 with ComponentStateDefinition

use of org.vcell.model.rbm.ComponentStateDefinition in project vcell by virtualcell.

the class MolecularTypePropertiesPanel method deleteFromTree.

public void deleteFromTree() {
    Object obj = molecularTypeTree.getLastSelectedPathComponent();
    if (obj == null || !(obj instanceof BioModelNode)) {
        return;
    }
    BioModelNode selectedNode = (BioModelNode) obj;
    TreeNode parent = selectedNode.getParent();
    if (!(parent instanceof BioModelNode)) {
        return;
    }
    BioModelNode parentNode = (BioModelNode) parent;
    Object selectedUserObject = selectedNode.getUserObject();
    if (selectedUserObject instanceof MolecularComponent) {
        MolecularComponent mc = (MolecularComponent) selectedUserObject;
        Object userObject = parentNode.getUserObject();
        if (userObject instanceof MolecularType) {
            MolecularType mt = (MolecularType) userObject;
            // detailed verifications will be done there, to see if they are being used in reactions, species, observables
            if (!mc.getComponentStateDefinitions().isEmpty()) {
                String[] options = { "OK" };
                String errMsg = mc.getDisplayType() + " '<b>" + mc.getDisplayName() + "</b>' cannot be deleted because it contains explicit States.";
                errMsg += "<br>Please delete each individual State first.";
                errMsg += "<br><br>Detailed usage information will be provided at that time to help you decide.";
                errMsg = "<html>" + errMsg + "</html>";
                JOptionPane.showOptionDialog(this.getParent().getParent(), errMsg, "Delete " + mc.getDisplayType(), JOptionPane.NO_OPTION, JOptionPane.WARNING_MESSAGE, null, options, options[0]);
                return;
            }
            // we find and display component usage information to help the user decide
            Map<String, Pair<Displayable, SpeciesPattern>> usedHere = new LinkedHashMap<String, Pair<Displayable, SpeciesPattern>>();
            bioModel.getModel().getRbmModelContainer().findComponentUsage(mt, mc, usedHere);
            if (!usedHere.isEmpty()) {
                String errMsg = mc.dependenciesToHtml(usedHere);
                errMsg += "<br><br>Delete anyway?";
                errMsg = "<html>" + errMsg + "</html>";
                int dialogButton = JOptionPane.YES_NO_OPTION;
                int returnCode = JOptionPane.showConfirmDialog(this.getParent().getParent(), errMsg, "Delete " + mc.getDisplayType(), dialogButton);
                if (returnCode == JOptionPane.YES_OPTION) {
                    // keep this code in sync with MolecularTypeTableModel.setValueAt
                    if (bioModel.getModel().getRbmModelContainer().delete(mt, mc) == true) {
                        mt.removeMolecularComponent(mc);
                    }
                } else {
                    return;
                }
            } else {
                if (bioModel.getModel().getRbmModelContainer().delete(mt, mc) == true) {
                    mt.removeMolecularComponent(mc);
                }
            }
        }
    } else if (selectedUserObject instanceof ComponentStateDefinition) {
        ComponentStateDefinition csd = (ComponentStateDefinition) selectedUserObject;
        Object userObject = parentNode.getUserObject();
        if (!(userObject instanceof MolecularComponent)) {
            System.out.println("Unexpected parent in tree hierarchy for " + ComponentStateDefinition.typeName + " " + csd.getDisplayName() + "!");
            return;
        }
        MolecularComponent mc = (MolecularComponent) userObject;
        TreeNode grandParent = parentNode.getParent();
        BioModelNode grandParentNode = (BioModelNode) grandParent;
        userObject = grandParentNode.getUserObject();
        if (!(userObject instanceof MolecularType)) {
            System.out.println("Unexpected parent in tree hierarchy for " + mc.getDisplayType() + " " + mc.getDisplayName() + "!");
            return;
        }
        MolecularType mt = (MolecularType) userObject;
        Map<String, Pair<Displayable, SpeciesPattern>> usedHere = new LinkedHashMap<String, Pair<Displayable, SpeciesPattern>>();
        bioModel.getModel().getRbmModelContainer().findStateUsage(mt, mc, csd, usedHere);
        if (!usedHere.isEmpty()) {
            String errMsg = csd.dependenciesToHtml(usedHere);
            errMsg += "<br><br>Delete anyway?";
            errMsg = "<html>" + errMsg + "</html>";
            int dialogButton = JOptionPane.YES_NO_OPTION;
            int returnCode = JOptionPane.showConfirmDialog(this.getParent().getParent(), errMsg, "Delete " + ComponentStateDefinition.typeName, dialogButton);
            if (returnCode == JOptionPane.YES_OPTION) {
                // keep this code in sync with MolecularTypeTableModel.setValueAt
                if (bioModel.getModel().getRbmModelContainer().delete(mt, mc, csd) == true) {
                    // this stays
                    mc.deleteComponentStateDefinition(csd);
                }
            } else {
                return;
            }
        } else {
            if (bioModel.getModel().getRbmModelContainer().delete(mt, mc, csd) == true) {
                // this stays
                mc.deleteComponentStateDefinition(csd);
            }
        }
    // mc.deleteComponentStateDefinition(csd);
    }
}

Example 20 with ComponentStateDefinition

use of org.vcell.model.rbm.ComponentStateDefinition in project vcell by virtualcell.

the class MolecularTypeTableModel method pattern.

private String pattern(MolecularType molecularType) {
    String str = molecularType.getName() + "(";
    List<MolecularComponent> mcl = molecularType.getComponentList();
    for (int i = 0; i < mcl.size(); i++) {
        MolecularComponent mc = mcl.get(i);
        str += mc.getName();
        List<ComponentStateDefinition> csdl = mc.getComponentStateDefinitions();
        for (int j = 0; j < csdl.size(); j++) {
            ComponentStateDefinition cs = csdl.get(j);
            str += "~" + cs.getName();
        }
        if (i < mcl.size() - 1) {
            str += ",";
        }
    }
    str += ")";
    return str;
}