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

Example 76 with SpeciesPattern

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

the class ObservableTreeModel method populateTree.

public void populateTree() {
    if (observable == null || bioModel == null) {
        return;
    }
    rootNode.setUserObject(observable);
    rootNode.removeAllChildren();
    int count = 0;
    for (SpeciesPattern sp : observable.getSpeciesPatternList()) {
        BioModelNode spNode = new BioModelNode(new SpeciesPatternLocal(sp, ++count));
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            BioModelNode node = createMolecularTypePatternNode(mtp);
            spNode.add(node);
        }
        rootNode.add(spNode);
    }
    nodeStructureChanged(rootNode);
    // GuiUtils.treeExpandAll(ownerTree, rootNode, true);
    GuiUtils.treeExpandAllRows(ownerTree);
    observable.firePropertyChange("entityChange", null, "bbb");
}

Example 77 with SpeciesPattern

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

the class ObservableTreeModel method setObservable.

public void setObservable(RbmObservable newValue) {
    if (newValue == observable) {
        return;
    }
    RbmObservable oldValue = observable;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(this);
        for (SpeciesPattern speciesPattern : oldValue.getSpeciesPatternList()) {
            RbmUtils.removePropertyChangeListener(speciesPattern, this);
        }
    }
    observable = newValue;
    if (newValue != null) {
        newValue.addPropertyChangeListener(this);
        for (SpeciesPattern speciesPattern : newValue.getSpeciesPatternList()) {
            RbmUtils.addPropertyChangeListener(speciesPattern, this);
        }
    }
    populateTree();
}

Example 78 with SpeciesPattern

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

the class ObservableTreeModel method propertyChange.

public void propertyChange(PropertyChangeEvent evt) {
    if (evt.getPropertyName().equals(PropertyConstants.PROPERTY_NAME_NAME)) {
        nodeChanged(rootNode);
    } else if (evt.getSource() == observable && evt.getPropertyName().equals(RbmObservable.PROPERTY_NAME_TYPE)) {
        nodeChanged(rootNode);
    } else if (evt.getPropertyName().equals("entityChange")) {
        nodeChanged(rootNode);
    } else {
        populateTree();
        Object source = evt.getSource();
        if (source == observable) {
            if (evt.getPropertyName().equals(RbmObservable.PROPERTY_NAME_SPECIES_PATTERN_LIST)) {
                List<SpeciesPattern> oldValue = (List<SpeciesPattern>) evt.getOldValue();
                if (oldValue != null) {
                    for (SpeciesPattern sp : oldValue) {
                        RbmUtils.removePropertyChangeListener(sp, this);
                    }
                }
                List<SpeciesPattern> newValue = (List<SpeciesPattern>) evt.getNewValue();
                if (newValue != null) {
                    for (SpeciesPattern sp : newValue) {
                        RbmUtils.addPropertyChangeListener(sp, this);
                    }
                }
            } else if (evt.getPropertyName().equals(RbmObservable.PROPERTY_NAME_SPECIES_PATTERN)) {
                SpeciesPattern newValue = (SpeciesPattern) evt.getNewValue();
                if (newValue != null) {
                    RbmUtils.addPropertyChangeListener(newValue, this);
                }
            }
        } else if (source instanceof SpeciesPattern) {
            if (evt.getPropertyName().equals(SpeciesPattern.PROPERTY_NAME_MOLECULAR_TYPE_PATTERNS)) {
                List<MolecularTypePattern> oldValue = (List<MolecularTypePattern>) evt.getOldValue();
                if (oldValue != null) {
                    for (MolecularTypePattern mtp : oldValue) {
                        RbmUtils.removePropertyChangeListener(mtp, this);
                    }
                }
                List<MolecularTypePattern> newValue = (List<MolecularTypePattern>) evt.getNewValue();
                if (newValue != null) {
                    for (MolecularTypePattern mtp : newValue) {
                        RbmUtils.addPropertyChangeListener(mtp, this);
                    }
                }
            }
        } else if (source instanceof MolecularTypePattern) {
            if (evt.getPropertyName().equals(MolecularTypePattern.PROPERTY_NAME_COMPONENT_PATTERN_LIST)) {
                List<MolecularComponentPattern> oldValue = (List<MolecularComponentPattern>) evt.getOldValue();
                if (oldValue != null) {
                    for (MolecularComponentPattern mcp : oldValue) {
                        RbmUtils.removePropertyChangeListener(mcp, this);
                    }
                }
                List<MolecularComponentPattern> newValue = (List<MolecularComponentPattern>) evt.getNewValue();
                if (newValue != null) {
                    for (MolecularComponentPattern mcp : newValue) {
                        RbmUtils.addPropertyChangeListener(mcp, this);
                    }
                }
            }
        } else if (source instanceof MolecularComponentPattern) {
            if (evt.getSource().equals(MolecularComponentPattern.PROPERTY_NAME_COMPONENT_STATE)) {
                ComponentStateDefinition oldValue = (ComponentStateDefinition) evt.getOldValue();
                if (oldValue != null) {
                    oldValue.removePropertyChangeListener(this);
                }
                ComponentStateDefinition newValue = (ComponentStateDefinition) evt.getNewValue();
                if (newValue != null) {
                    newValue.addPropertyChangeListener(this);
                }
            }
        }
    }
}

Example 79 with SpeciesPattern

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

the class RbmObservable method gatherIssues.

public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
    issueContext = issueContext.newChildContext(ContextType.RbmObservable, this);
    if (name == null) {
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, "Name of Observable is null", Issue.SEVERITY_ERROR));
    } else if (name.equals("")) {
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, "Name of Observable is empty", Issue.SEVERITY_WARNING));
    } else {
        if (speciesPatternList == null) {
            issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, "Observable '" + name + "' Species Pattern List is null", Issue.SEVERITY_ERROR));
        } else if (speciesPatternList.isEmpty()) {
            issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, "Observable '" + name + "' Species Pattern List is empty", Issue.SEVERITY_WARNING));
        } else {
            for (SpeciesPattern sp : speciesPatternList) {
                sp.checkSpeciesPattern(issueContext, issueList);
                sp.gatherIssues(issueContext, issueList);
                for (MolecularTypePattern mtpThis : sp.getMolecularTypePatterns()) {
                    checkComponentStateConsistency(issueContext, issueList, mtpThis);
                }
            }
        }
        if (type == null) {
            issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, "Observable '" + name + "' Type is null", Issue.SEVERITY_ERROR));
        }
    }
    for (SpeciesPattern sp : speciesPatternList) {
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            String name = mtp.getMolecularType().getDisplayName().toLowerCase();
            if (name.equals("trash")) {
                String message = "'Trash' is a reserved NFSim keyword and it cannot be used as an observable.";
                issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, message, Issue.Severity.WARNING));
            }
        }
    }
    // ---------------------------------------- polymer notation restrictions
    // polymer notation may only contain one species pattern and one type of molecule
    boolean polymerAllowedSingle = true;
    // ---------------,,---------------- molecules in trivial state (question marks for bonds and states)
    boolean polymerAllowedSimple = true;
    if (speciesPatternList.size() > 1) {
        polymerAllowedSingle = false;
    }
    if (speciesPatternList.size() > 0) {
        SpeciesPattern sp = speciesPatternList.get(0);
        if (sp != null && !sp.getMolecularTypePatterns().isEmpty()) {
            if (sp.getMolecularTypePatterns().size() > 1) {
                polymerAllowedSingle = false;
            } else {
                MolecularTypePattern mtp = sp.getMolecularTypePatterns().get(0);
                if (mtp != null) {
                    for (MolecularComponentPattern mcp : mtp.getComponentPatternList()) {
                        if (mcp.isbVisible()) {
                            polymerAllowedSimple = false;
                            break;
                        }
                    }
                }
            }
        }
    }
    if (!polymerAllowedSingle && sequence != Sequence.Multimolecular) {
        String message = "Polymer may only be specified for Observable containing a single Molecule.";
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, message, Issue.Severity.ERROR));
    } else if (!polymerAllowedSimple && sequence != Sequence.Multimolecular) {
        String message = "Polymer may only be specified for Observable with all bonds set to 'Possible' and all States set to 'Any'";
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, message, Issue.Severity.ERROR));
    }
    if (sequence != Sequence.Multimolecular && type == ObservableType.Molecules) {
        String message = "The Polymer Observable must be of type 'Species'.";
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, message, Issue.Severity.ERROR));
    }
    if (name.equalsIgnoreCase("Rg3")) {
        System.out.println(name);
    }
    for (SpeciesPattern sp : speciesPatternList) {
        // we look for species patterns where the polymer notation would be more suitable
        Set<String> moleculeNames = new HashSet<>();
        boolean isTrivial = true;
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            moleculeNames.add(mtp.getMolecularType().getDisplayName());
            for (MolecularComponentPattern mcp : mtp.getComponentPatternList()) {
                if (mcp.isbVisible()) {
                    isTrivial = false;
                    // we may have more than 1 sp in the observable, check them all
                    continue;
                }
            }
        }
        if (isTrivial && sp.getMolecularTypePatterns().size() > 1 && moleculeNames.size() == 1) {
            String message = "Please use the Polymer notation (i.e. " + moleculeNames.toArray()[0] + "()>" + (sp.getMolecularTypePatterns().size() - 1) + " ) ";
            message += "instead of " + sp.toString();
            issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, message, Issue.Severity.WARNING));
            // if we find one sp that is suitable for polymer notation we stop here and don't check other sp
            break;
        }
    }
}

Example 80 with SpeciesPattern

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

the class RbmObservable method deleteStateFromPatterns.

public boolean deleteStateFromPatterns(MolecularType mt, MolecularComponent mc, ComponentStateDefinition csd) {
    for (SpeciesPattern sp : getSpeciesPatternList()) {
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            if (mtp.getMolecularType() == mt) {
                List<MolecularComponentPattern> componentPatterns = mtp.getComponentPatternList();
                for (MolecularComponentPattern mcp : componentPatterns) {
                    if (!(mcp.getMolecularComponent() == mc)) {
                        continue;
                    }
                    ComponentStatePattern csp = mcp.getComponentStatePattern();
                    if (csp == null) {
                        continue;
                    }
                    if (csp.isAny()) {
                        if (mc.getComponentStateDefinitions().size() == 1) {
                            mcp.setComponentStatePattern(null);
                        }
                        continue;
                    }
                    if (csp.getComponentStateDefinition() == csd) {
                        if (mc.getComponentStateDefinitions().size() == 1) {
                            // we are about to delete the last possible state, so we set the ComponentStatePattern to null
                            mcp.setComponentStatePattern(null);
                        } else {
                            // some other state is still available, we set the ComponentStatePattern to Any and let the user deal with it
                            csp = new ComponentStatePattern();
                            mcp.setComponentStatePattern(csp);
                        }
                    }
                }
            }
        }
    }
    return true;
}