Examples with BoundEnzyme cbit.vcell.dictionary.BoundEnzyme used on opensource projects

Example 1 with BoundEnzyme

use of cbit.vcell.dictionary.BoundEnzyme in project vcell by virtualcell.

the class XmlReader method getDBSpecies.

/**
 * This method reads a DBSpecies from a XML representation.
 * Creation date: (6/3/2003 8:20:54 PM)
 * @return cbit.vcell.dictionary.DBSpecies
 * @param dbSpeciesElement org.jdom.Element
 */
private DBSpecies getDBSpecies(Element dbSpeciesElement) throws XmlParseException {
    // Read the key
    String keystring = dbSpeciesElement.getAttributeValue(XMLTags.KeyValueAttrTag);
    KeyValue key = new KeyValue(keystring);
    DBSpecies dbSpecies = null;
    // read the type
    String type = dbSpeciesElement.getAttributeValue(XMLTags.TypeAttrTag);
    // Read the DBFormalSpecies
    org.jdom.Element formalSpeciesElement = dbSpeciesElement.getChild(XMLTags.DBFormalSpeciesTag, vcNamespace);
    if (type.equalsIgnoreCase(XMLTags.CompoundTypeTag)) {
        // Create a BoundCompound
        dbSpecies = new BoundCompound(key, (FormalCompound) getDBFormalSpecies(formalSpeciesElement));
    } else if (type.equalsIgnoreCase(XMLTags.EnzymeTypeTag)) {
        // Create a BoundEnzyme
        dbSpecies = new BoundEnzyme(key, (FormalEnzyme) getDBFormalSpecies(formalSpeciesElement));
    } else if (type.equalsIgnoreCase(XMLTags.ProteinTypeTag)) {
        // Create a BoundProtein
        dbSpecies = new BoundProtein(key, (FormalProtein) getDBFormalSpecies(formalSpeciesElement));
    } else {
        throw new XmlParseException("DBSpecies type: " + type + ", not supported yet!");
    }
    return dbSpecies;
}

Example 2 with BoundEnzyme

use of cbit.vcell.dictionary.BoundEnzyme in project vcell by virtualcell.

the class Xmlproducer method getXML.

/**
 * This method returns the XML representation of a DBSpecies.
 * Creation date: (6/3/2003 4:36:40 PM)
 * @return Element
 * @param dbSpecies cbit.vcell.dictionary.DBSpecies
 */
private Element getXML(DBSpecies dbSpecies) throws XmlParseException {
    // create xml node
    Element dbSpeciesElement = new Element(XMLTags.DBSpeciesTag);
    if (this.printKeysFlag) {
        // add the DBSpecieKey (IT ALWAYS NEED THE KEY!)
        dbSpeciesElement.setAttribute(XMLTags.KeyValueAttrTag, dbSpecies.getDBSpeciesKey().toString());
    }
    // detect the type of DBSpecie
    if (dbSpecies instanceof BoundCompound) {
        // add type
        dbSpeciesElement.setAttribute(XMLTags.TypeAttrTag, XMLTags.CompoundTypeTag);
        // add FormalCompound
        dbSpeciesElement.addContent(getXML(((BoundCompound) dbSpecies).getFormalCompound()));
    } else if (dbSpecies instanceof BoundEnzyme) {
        // add type
        dbSpeciesElement.setAttribute(XMLTags.TypeAttrTag, XMLTags.EnzymeTypeTag);
        // add FormalEnzyme
        dbSpeciesElement.addContent(getXML(((BoundEnzyme) dbSpecies).getFormalEnzyme()));
    } else if (dbSpecies instanceof BoundProtein) {
        // add type
        dbSpeciesElement.setAttribute(XMLTags.TypeAttrTag, XMLTags.ProteinTypeTag);
        // add FormalProtein
        dbSpeciesElement.addContent(getXML(((BoundProtein) dbSpecies).getProteinEnzyme()));
    } else {
        throw new XmlParseException("DBSpecies type " + dbSpecies.getClass().getName() + " not supported yet!");
    }
    return dbSpeciesElement;
}

Example 3 with BoundEnzyme

use of cbit.vcell.dictionary.BoundEnzyme in project vcell by virtualcell.

the class EnzymeTable method getEnzymes.

/**
 * returns a enzyme object from the ResultSet
 * @return cbit.vcell.dictionary.enzyme
 * @param rset java.sql.ResultSet
 */
public DBFormalSpecies[] getEnzymes(java.sql.ResultSet rset, boolean createBound) throws java.sql.SQLException {
    Vector enzymes = new Vector();
    Vector aliasNames = new Vector();
    String currentAliasName = null;
    String currentECNumber = null;
    String currentSysname = null;
    String currentReaction = null;
    String currentPreferred = null;
    String currentCasID = null;
    org.vcell.util.document.KeyValue currentEnzymeID = null;
    org.vcell.util.document.KeyValue currentDBSpeciesID = null;
    while (rset.next() || rset.isAfterLast()) {
        KeyValue enzymeID = null;
        if (!rset.isAfterLast()) {
            enzymeID = new KeyValue(rset.getBigDecimal(EnzymeTable.table.id.toString()));
        }
        if (!rset.isFirst() && (!currentEnzymeID.equals(enzymeID))) {
            if (currentEnzymeID != null) {
                if (aliasNames.size() > 0) {
                    String[] aliasNamesArr = new String[aliasNames.size()];
                    aliasNames.copyInto(aliasNamesArr);
                    EnzymeInfo enzymeInfo = new EnzymeInfo(currentECNumber, aliasNamesArr, currentReaction, currentSysname, currentCasID);
                    FormalEnzyme formalEnzyme = new FormalEnzyme(currentEnzymeID, enzymeInfo);
                    Object enzyme = formalEnzyme;
                    if (createBound) {
                        BoundEnzyme boundEnzyme = new BoundEnzyme(currentDBSpeciesID, formalEnzyme);
                        enzyme = boundEnzyme;
                    }
                    enzymes.add(enzyme);
                }
            }
            aliasNames.clear();
            if (rset.isAfterLast()) {
                break;
            }
        }
        if (aliasNames.size() == 0) {
            currentEnzymeID = enzymeID;
            currentECNumber = rset.getString(EnzymeTable.table.ecNumber.toString());
            currentSysname = rset.getString(EnzymeTable.table.sysname.toString());
            currentSysname = (currentSysname != null ? org.vcell.util.TokenMangler.getSQLRestoredString(currentSysname) : null);
            currentReaction = rset.getString(EnzymeTable.table.reaction.toString());
            currentReaction = (currentReaction != null ? org.vcell.util.TokenMangler.getSQLRestoredString(currentReaction) : null);
            currentCasID = rset.getString(EnzymeTable.table.casID.toString());
            currentCasID = (currentCasID != null ? org.vcell.util.TokenMangler.getSQLRestoredString(currentCasID) : null);
            if (createBound) {
                currentDBSpeciesID = new KeyValue(rset.getBigDecimal("dbspecies_id"));
            }
        }
        currentPreferred = rset.getString(EnzymeAliasTable.table.preferred.toString());
        currentAliasName = org.vcell.util.TokenMangler.getSQLRestoredString(rset.getString(EnzymeAliasTable.table.name.toString()));
        if (currentPreferred.compareToIgnoreCase("T") == 0) {
            aliasNames.add(0, currentAliasName);
        } else {
            aliasNames.add(currentAliasName);
        }
    }
    DBFormalSpecies[] enzymesArr = null;
    if (enzymes.size() > 0) {
        if (createBound) {
            BoundEnzyme[] boundEnzymesArr = null;
            boundEnzymesArr = new BoundEnzyme[enzymes.size()];
            enzymes.copyInto(boundEnzymesArr);
            enzymesArr = boundEnzymesArr;
        } else {
            FormalEnzyme[] formalEnzymesArr = null;
            formalEnzymesArr = new FormalEnzyme[enzymes.size()];
            enzymes.copyInto(formalEnzymesArr);
            enzymesArr = formalEnzymesArr;
        }
    }
    return enzymesArr;
}