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

Example 46 with MolecularComponentPattern

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

the class ObservableTableModel method propertyChange.

@Override
public void propertyChange(PropertyChangeEvent evt) {
    super.propertyChange(evt);
    Object source = evt.getSource();
    // if (source == getModel().getRbmModelContainer()) {
    if (source == getModel()) {
        if (evt.getPropertyName().equals(RbmModelContainer.PROPERTY_NAME_OBSERVABLE_LIST)) {
            refreshData();
            List<RbmObservable> oldValue = (List<RbmObservable>) evt.getOldValue();
            if (oldValue != null) {
                for (RbmObservable observable : oldValue) {
                    observable.removePropertyChangeListener(this);
                    SpeciesPattern speciesPattern = observable.getSpeciesPattern(0);
                    RbmUtils.removePropertyChangeListener(speciesPattern, this);
                }
            }
            List<RbmObservable> newValue = (List<RbmObservable>) evt.getNewValue();
            if (newValue != null) {
                for (RbmObservable observable : newValue) {
                    observable.addPropertyChangeListener(this);
                    SpeciesPattern speciesPattern = observable.getSpeciesPattern(0);
                    RbmUtils.addPropertyChangeListener(speciesPattern, this);
                }
            }
        } else if (evt.getPropertyName().equals(RbmModelContainer.PROPERTY_NAME_MOLECULAR_TYPE_LIST)) {
            // we need this?
            refreshData();
        }
    } else if (source instanceof RbmObservable) {
        RbmObservable mt = (RbmObservable) source;
        int changeRow = getRowIndex(mt);
        if (changeRow >= 0) {
            fireTableRowsUpdated(changeRow, changeRow);
        }
    // if (evt.getPropertyName().equals(RbmObservable.PROPERTY_NAME_SPECIES_PATTERN_LIST)) {
    // SpeciesPattern oldValue = (SpeciesPattern) evt.getOldValue();
    // if (oldValue != null) {
    // RbmUtils.removePropertyChangeListener(oldValue, this);
    // }
    // SpeciesPattern newValue = (SpeciesPattern) evt.getNewValue();
    // if (newValue != null) {
    // RbmUtils.addPropertyChangeListener(newValue, this);
    // }
    // }
    } else if (source instanceof SpeciesPattern) {
        fireTableRowsUpdated(0, getRowCount() - 1);
        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) {
        fireTableRowsUpdated(0, getRowCount() - 1);
        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) {
        fireTableRowsUpdated(0, getRowCount() - 1);
        if (source.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);
            }
        }
    } else if (evt.getSource() instanceof MolecularComponent) {
        fireTableRowsUpdated(0, getRowCount() - 1);
    } else if (evt.getSource() instanceof ComponentStateDefinition) {
        fireTableRowsUpdated(0, getRowCount() - 1);
    }
// updateStructureComboBox();
}

Example 47 with MolecularComponentPattern

use of org.vcell.model.rbm.MolecularComponentPattern 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 48 with MolecularComponentPattern

use of org.vcell.model.rbm.MolecularComponentPattern 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 49 with MolecularComponentPattern

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

the class RbmObservable method checkComponentStateConsistency.

public void checkComponentStateConsistency(IssueContext issueContext, List<Issue> issueList, MolecularTypePattern mtpThis) {
    if (issueList == null) {
        // this may be called during parsing before the model is consistent
        return;
    }
    MolecularType mtThat = mtpThis.getMolecularType();
    for (MolecularComponentPattern mcpThis : mtpThis.getComponentPatternList()) {
        if (mcpThis.isImplied()) {
        // continue;
        }
        ComponentStatePattern cspThis = mcpThis.getComponentStatePattern();
        String mcNameThis = mcpThis.getMolecularComponent().getName();
        if (cspThis == null && mcpThis.getMolecularComponent().getComponentStateDefinitions().size() > 0) {
            // String msg = "Component pattern " + mcNameThis + " is in no State while the component has possible States defined.";
            String msg = "One of the possible States must be chosen for " + MolecularComponentPattern.typeName + " " + mcNameThis + ".";
            issueList.add(new Issue(this, mcpThis, issueContext, IssueCategory.Identifiers, msg, null, Issue.SEVERITY_WARNING));
        }
        MolecularComponent[] mcThatList = mtThat.getMolecularComponents(mcNameThis);
        if (mcThatList.length == 0) {
            System.out.println("we already fired an issue about component missing");
            // nothing to do here, we already fired an issue about component missing
            continue;
        } else if (mcThatList.length > 1) {
            String msg = "Multiple " + MolecularComponent.typeName + "s with the same name are not yet supported.";
            issueList.add(new Issue(this, mcpThis, issueContext, IssueCategory.Identifiers, msg, null, Issue.SEVERITY_ERROR));
        } else {
            // found exactly 1 component
            MolecularComponent mcThat = mcThatList[0];
            List<ComponentStateDefinition> csdListThat = mcThat.getComponentStateDefinitions();
            if (csdListThat.size() == 0) {
                // component has no states, we check if mcpThis has any states... it shouldn't
                if (cspThis == null) {
                    // all is well
                    continue;
                }
                if (!cspThis.isAny() || (cspThis.getComponentStateDefinition() != null)) {
                    String msg = MolecularComponentPattern.typeName + " " + mcNameThis + " is in an invalid State.";
                    issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.SEVERITY_WARNING));
                }
            } else {
                // we check if mcpThis has any of these states... it should!
                if ((cspThis == null) || cspThis.isAny() || (cspThis.getComponentStateDefinition() == null)) {
                // String msg = "Component pattern " + mcNameThis + " must be in an explicit State.";
                // issueList.add(new Issue(this, IssueCategory.Identifiers, msg, Issue.SEVERITY_WARNING));
                } else {
                    String csdNameThis = cspThis.getComponentStateDefinition().getName();
                    if (csdNameThis.isEmpty() || (mcThat.getComponentStateDefinition(csdNameThis) == null)) {
                        String msg = "Invalid State " + csdNameThis + " " + MolecularComponentPattern.typeName + " " + mcNameThis;
                        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.SEVERITY_WARNING));
                    }
                }
            }
        }
    }
}

Example 50 with MolecularComponentPattern

use of org.vcell.model.rbm.MolecularComponentPattern 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;
}