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

Example 56 with MolecularTypePattern

use of org.vcell.model.rbm.MolecularTypePattern 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 57 with MolecularTypePattern

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

Example 58 with MolecularTypePattern

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

the class RbmObservable method findComponentUsage.

public void findComponentUsage(MolecularType mt, MolecularComponent mc, Map<String, Pair<Displayable, SpeciesPattern>> usedHere) {
    for (SpeciesPattern sp : getSpeciesPatternList()) {
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            if (mtp.getMolecularType() == mt) {
                List<MolecularComponentPattern> componentPatterns = mtp.getComponentPatternList();
                for (MolecularComponentPattern mcp : componentPatterns) {
                    if (mcp.isImplied()) {
                        // we don't care about these
                        continue;
                    }
                    if (mcp.getMolecularComponent() == mc) {
                        // found mc in use
                        String key = sp.getDisplayName();
                        key = getDisplayType() + getDisplayName() + key;
                        usedHere.put(key, new Pair<Displayable, SpeciesPattern>(this, sp));
                    }
                }
            }
        }
    }
}

Example 59 with MolecularTypePattern

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

the class ReactionRule method findComponentUsage.

// TODO: almost identical to findStateUsage() below - pay attention to keep both in sync
public void findComponentUsage(MolecularType mt, MolecularComponent mc, Map<String, Pair<Displayable, SpeciesPattern>> usedHere) {
    for (ProductPattern pp : getProductPatterns()) {
        SpeciesPattern sp = pp.getSpeciesPattern();
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            if (mtp.getMolecularType() == mt) {
                List<MolecularComponentPattern> componentPatterns = mtp.getComponentPatternList();
                for (MolecularComponentPattern mcp : componentPatterns) {
                    if (mcp.isImplied()) {
                        // we don't care about these
                        continue;
                    }
                    if (mcp.getMolecularComponent() == mc) {
                        // found mc in use
                        String key = getDisplayType() + getDisplayName() + sp.getDisplayName();
                        usedHere.put(key, new Pair<Displayable, SpeciesPattern>(this, sp));
                    }
                }
            }
        }
    }
    for (ReactantPattern rp : getReactantPatterns()) {
        SpeciesPattern sp = rp.getSpeciesPattern();
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            if (mtp.getMolecularType() == mt) {
                List<MolecularComponentPattern> componentPatterns = mtp.getComponentPatternList();
                for (MolecularComponentPattern mcp : componentPatterns) {
                    if (mcp.isImplied()) {
                        continue;
                    }
                    if (mcp.getMolecularComponent() == mc) {
                        String key = getDisplayType() + getDisplayName() + sp.getDisplayName();
                        usedHere.put(key, new Pair<Displayable, SpeciesPattern>(this, sp));
                    }
                }
            }
        }
    }
}

Example 60 with MolecularTypePattern

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

the class ReactionRule method checkReactantPatterns.

public void checkReactantPatterns(IssueContext issueContext, List<Issue> issueList) {
    issueContext = issueContext.newChildContext(ContextType.ReactionRule, this);
    int cnt = 0;
    // StringBuilder warning = new StringBuilder();
    for (ReactantPattern rp : reactantPatterns) {
        ++cnt;
        if (rp.getSpeciesPattern().getMolecularTypePatterns().size() == 0) {
            String msg = "Reactant " + cnt + " does not have any molecules.\n";
            // warning.append(msg);
            if (issueList != null) {
                issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.Severity.ERROR));
            }
        } else {
            rp.getSpeciesPattern().checkSpeciesPattern(issueContext, issueList);
            for (MolecularTypePattern mtpThis : rp.getSpeciesPattern().getMolecularTypePatterns()) {
                checkComponentStateConsistency(issueContext, issueList, mtpThis);
            }
        }
    }
// setReactantWarning(warning.length() == 0 ? null : warning.toString());
}