Examples with UniProtBoxImp org.vcell.sybil.util.http.uniprot.box.imp.UniProtBoxImp used on opensource projects

Example 1 with UniProtBoxImp

use of org.vcell.sybil.util.http.uniprot.box.imp.UniProtBoxImp in project vcell by virtualcell.

the class UniProtConstants method getNameFromID.

public static String getNameFromID(String urnStr) {
    // extract id of entry from urnStr : urn string is of the form "urn:miriam:uniprot:XXXX" ; we need to extract 'XXXX'
    if (!urnStr.toLowerCase().contains("uniprot")) {
        throw new RuntimeException("Resource '" + urnStr + "' is not a UniProt entry");
    }
    String entryId = urnStr.substring(urnStr.lastIndexOf(":") + 1);
    System.out.println("EntryId from urn : " + entryId);
    UniProtBox box = new UniProtBoxImp();
    getInfoForID(box, entryId);
    String recommendedName = null;
    for (UniProtBox.Entry entry : box.entries()) {
        // System.out.println("UniProt ID :  : " + entry.id() + (entry.isObsolete() ? " is obsolete" : ""));
        if (entry.isObsolete()) {
            UniProtBox box2 = new UniProtBoxImp();
            for (UniProtBox.Entry entryReplacing : entry.replacingEntries()) {
                // System.out.println("  replaced by " + entryReplacing.id());
                getInfoForID(box2, entryReplacing.id());
                for (UniProtBox.Entry entry1 : box2.entries()) {
                    if (!entry1.isObsolete() && recommendedName == null) {
                        recommendedName = entry1.recommendedName();
                    }
                }
                if (recommendedName != null) {
                    break;
                }
            }
            if (recommendedName != null) {
                break;
            }
        } else {
            recommendedName = entry.recommendedName();
        }
    }
    return recommendedName;
}

Example 2 with UniProtBoxImp

use of org.vcell.sybil.util.http.uniprot.box.imp.UniProtBoxImp in project vcell by virtualcell.

the class UniProtExtractor method extractBox.

public UniProtBox extractBox() {
    UniProtBoxImp box = new UniProtBoxImp();
    Iterator<Statement> stmtIter1 = model.match(null, UniProtConstants.replaces, null);
    while (stmtIter1.hasNext()) {
        Statement statement = stmtIter1.next();
        Resource subject = statement.getSubject();
        Value object = statement.getObject();
        if (subject instanceof URI && object instanceof URI) {
            String idSubject = id((URI) subject);
            String idObject = id((URI) object);
            if (StringUtil.notEmpty(idSubject) && StringUtil.notEmpty(idObject)) {
                UniProtBox.Entry entrySubject = box.entry(idSubject);
                UniProtBox.Entry entryObject = box.entry(idObject);
                box.setReplaces(entrySubject, entryObject);
            }
        }
    }
    Iterator<Statement> stmtIter2 = model.match(null, UniProtConstants.replacedBy, null);
    while (stmtIter2.hasNext()) {
        Statement statement = stmtIter2.next();
        Resource subject = statement.getSubject();
        Value object = statement.getObject();
        if (subject instanceof URI && object instanceof URI) {
            String idSubject = id((URI) subject);
            String idObject = id((URI) object);
            if (StringUtil.notEmpty(idSubject) && StringUtil.notEmpty(idObject)) {
                UniProtBox.Entry entrySubject = box.entry(idSubject);
                UniProtBox.Entry entryObject = box.entry(idObject);
                box.setReplaces(entryObject, entrySubject);
            }
        }
    }
    Iterator<Statement> stmtIter3 = model.match(null, UniProtConstants.recommendedName, null);
    if (stmtIter3.hasNext()) {
        while (stmtIter3.hasNext()) {
            Statement statement = stmtIter3.next();
            Resource entryNode = statement.getSubject();
            Value nameNode = statement.getObject();
            if (nameNode instanceof Resource) {
                Resource nameResource = (Resource) nameNode;
                Iterator<Statement> stmtIter4 = model.match(nameResource, UniProtConstants.fullName, null);
                // System.out.println("hello world");
                while (stmtIter4.hasNext()) {
                    Statement statement2 = stmtIter4.next();
                    Value objectNode = statement2.getObject();
                    // System.out.println("hello moon");
                    if (entryNode instanceof URI && objectNode instanceof Literal) {
                        String name = ((Literal) objectNode).stringValue();
                        UniProtBox.Entry entry = box.entry(UniProtConstants.idFromResource((URI) entryNode));
                        System.out.println("UniProtExtractor: name: " + name + "\tid: " + entry.id());
                        entry.setRecommendedName(name);
                    }
                }
            }
        }
    } else {
        // sometimes, recommended name is not present for an uniprot id : check the full name
        stmtIter3 = model.match(null, UniProtConstants.fullName, null);
        while (stmtIter3.hasNext()) {
            Statement statement2 = stmtIter3.next();
            Resource entryNode = statement2.getSubject();
            Value objectNode = statement2.getObject();
            if (entryNode instanceof URI && objectNode instanceof Literal) {
                String name = ((Literal) objectNode).stringValue();
                UniProtBox.Entry entry = box.entry(UniProtConstants.idFromResource((URI) entryNode));
                entry.setRecommendedName(name);
                System.out.println("UniProtExtractor: name: " + name + "\tid: " + entry.id());
            }
        }
    }
    return box;
}