Examples with NameMap gov.sandia.n2a.backend.neuroml.PartMap.NameMap used on opensource projects

Example 6 with NameMap

use of gov.sandia.n2a.backend.neuroml.PartMap.NameMap in project n2a by frothga.

the class ImportJob method q10.

public void q10(Node node, MNode container) {
    String id = "Q10Parameters";
    int suffix = 2;
    // This seems pointless, but the NeuroML XSD says the number of elements is unbounded.
    while (container.child(id) != null) id = "Q10Parameters" + suffix++;
    MNode part = container.set(id, "");
    // This isn't the correct name for use with ion channel, but it will still work.
    NameMap nameMap = partMap.importMap("baseQ10Settings");
    String inherit = nameMap.internal;
    part.set("$inherit", "\"" + inherit + "\"");
    addDependency(part, inherit);
    NamedNodeMap attributes = node.getAttributes();
    int count = attributes.getLength();
    for (int i = 0; i < count; i++) {
        Node a = attributes.item(i);
        String name = a.getNodeName();
        // probably switches between fixed and exponential, but there is no example/guidance on its use
        if (name.equals("type"))
            continue;
        String value = biophysicalUnits(a.getNodeValue());
        if (name.equals("fixedQ10"))
            value = "*" + value;
        name = nameMap.importName(name);
        part.set(name, value);
    }
}

Example 7 with NameMap

use of gov.sandia.n2a.backend.neuroml.PartMap.NameMap in project n2a by frothga.

the class ImportJob method rate.

public void rate(Node node, MNode container, boolean KS, boolean instantaneous) {
    String name = node.getNodeName();
    String inherit = getAttribute(node, "type");
    MNode part = container.set(name, "");
    NameMap nameMap = partMap.importMap(inherit);
    inherit = nameMap.internal;
    part.set("$inherit", "\"" + inherit + "\"");
    addDependency(part, inherit);
    addAttributes(node, part, nameMap, "type");
    // add appropriate "$up.var=x" statement
    String up = "";
    if (name.equals("forwardRate")) {
        if (KS)
            up = "$up.forward";
        else
            up = "$up.α";
    } else if (name.equals("reverseRate")) {
        if (KS)
            up = "$up.reverse";
        else
            up = "$up.β";
    } else if (name.equals("steadyState")) {
        if (// Because the Gate model is written so that inf only initializes q once, while "instantaneous" requires continually changing q.
        instantaneous)
            // Because the Gate model is written so that inf only initializes q once, while "instantaneous" requires continually changing q.
            up = "$up.q";
        else
            up = "$up.inf";
    } else if (name.equals("timeCourse")) {
        up = "$up.τUnscaled";
    }
    if (!up.isEmpty())
        part.set(up, "x");
}

Example 8 with NameMap

use of gov.sandia.n2a.backend.neuroml.PartMap.NameMap in project n2a by frothga.

the class ImportJob method genericPart.

/**
 *        Handles elements in a generic manner, including metadata elements.
 *        Generic elements get processed into parts under the given container.
 *        Metadata elements get added to the $metadata node of the given container.
 */
public MNode genericPart(Node node, MNode container) {
    String nodeName = node.getNodeName();
    if (nodeName.equals("notes")) {
        container.set("$metadata", "notes", getText(node));
        return container.child("$metadata", "notes");
    }
    if (nodeName.equals("property")) {
        String tag = getAttribute(node, "tag");
        String value = getAttribute(node, "value");
        container.set("$metadata", tag, value);
        return container.child("$metadata", tag);
    }
    // TODO: process annotations
    if (nodeName.equals("annotation"))
        return null;
    String id = getAttribute(node, "id", nodeName);
    String stem = id;
    int suffix = 2;
    while (container.child(id) != null) id = stem + suffix++;
    MNode part = container.childOrCreate(id);
    nodeName = getAttribute(node, "type", nodeName);
    List<MNode> parents = collectParents(container);
    String inherit = typeFor(nodeName, parents);
    NameMap nameMap;
    if (inherit.isEmpty()) {
        nameMap = partMap.importMap(nodeName);
        inherit = nameMap.internal;
    } else {
        // Because typeFor() finds internal names, we need to retrieve a map from the opposite direction.
        // It will still map parameter names correctly for import.
        nameMap = partMap.exportMap(inherit);
    }
    part.set("$inherit", "\"" + inherit + "\"");
    addDependency(part, inherit);
    // Now we follow our own inheritance chain, not our container's.
    parents = collectParents(part);
    NamedNodeMap attributes = node.getAttributes();
    int count = attributes.getLength();
    for (int i = 0; i < count; i++) {
        Node a = attributes.item(i);
        String name = a.getNodeName();
        String value = a.getNodeValue();
        if (name.equals("id"))
            continue;
        if (name.equals("type"))
            continue;
        if (name.equals("neuroLexId")) {
            part.set("$metadata", "neuroLexID", value);
            continue;
        }
        name = nameMap.importName(name);
        if (isPart(name, parents)) {
            inherit = value;
            part.set(name, "$inherit", "\"" + inherit + "\"");
            addDependency(part.child(name), inherit);
            addAlias(inherit, name);
        } else {
            String defaultUnit = nameMap.defaultUnit(name);
            part.set(name, biophysicalUnits(value, defaultUnit));
        }
    }
    // Thus, we add hacks here to detect these special cases and do the extra processing.
    if (nodeName.startsWith("channel"))
        channel(node, part, true);
    for (Node child = node.getFirstChild(); child != null; child = child.getNextSibling()) {
        if (child.getNodeType() == Node.ELEMENT_NODE)
            genericPart(child, part);
    }
    return part;
}

Example 9 with NameMap

use of gov.sandia.n2a.backend.neuroml.PartMap.NameMap in project n2a by frothga.

the class ImportJob method blockingPlasticSynapse.

public void blockingPlasticSynapse(Node node) {
    String id = getAttribute(node, "id");
    MNode part = models.childOrCreate(modelName, id);
    NameMap nameMap = partMap.importMap(node.getNodeName());
    part.set("$inherit", "\"" + nameMap.internal + "\"");
    addAttributes(node, part, nameMap, "id");
    for (Node child = node.getFirstChild(); child != null; child = child.getNextSibling()) {
        if (child.getNodeType() != Node.ELEMENT_NODE)
            continue;
        MNode c = genericPart(child, part);
        String name = child.getNodeName();
        if (// This handles both block and plasticity mechanisms.
        name.endsWith("Mechanism")) {
            String species = c.get("species");
            c.clear("species");
            if (!species.isEmpty())
                c.set("$metadata", "species", species);
        }
    }
}

Example 10 with NameMap

use of gov.sandia.n2a.backend.neuroml.PartMap.NameMap in project n2a by frothga.

the class ImportJob method gate.

public void gate(Node node, MNode container) {
    String id = getAttribute(node, "id");
    String type = getAttribute(node, "type");
    boolean instantaneous = type.contains("Instantaneous");
    String inherit;
    if (type.isEmpty())
        inherit = node.getNodeName();
    else
        inherit = type;
    NameMap nameMap = partMap.importMap(inherit);
    inherit = nameMap.internal;
    MNode part = container.set(id, "");
    part.set("$inherit", "\"" + inherit + "\"");
    addDependency(part, inherit);
    addAttributes(node, part, nameMap, "id", "type");
    for (Node child = node.getFirstChild(); child != null; child = child.getNextSibling()) {
        if (child.getNodeType() != Node.ELEMENT_NODE)
            continue;
        String name = child.getNodeName();
        switch(name) {
            case "subGate":
                gate(child, part);
                break;
            case "notes":
                part.set("$metadata", "notes", getText(child));
                break;
            case "q10Settings":
                q10(child, part);
                break;
            case "openState":
            case "closedState":
                id = getAttribute(child, "id");
                part.set(id, "$inherit", "\"Kinetic State\"");
                part.set(id, "relativeConductance", name.equals("openState") ? "1" : "0");
                break;
            case "forwardTransition":
            case "reverseTransition":
            case "tauInfTransition":
            case "vHalfTransition":
                transition(child, part);
                break;
            default:
                rate(child, part, false, instantaneous);
        }
    }
}