Examples with DBFormalSpecies cbit.vcell.model.DBFormalSpecies used on opensource projects

Example 1 with DBFormalSpecies

use of cbit.vcell.model.DBFormalSpecies in project vcell by virtualcell.

the class DictionaryDbDriver method getCompoundFromKeggID.

/**
 * Returns the compound referenced by the keggID
 * @return Compound
 * @param con Connection
 * @param dbLink DBLink
 */
public FormalCompound getCompoundFromKeggID(Connection con, String keggID) throws SQLException {
    FormalCompound result = null;
    DBFormalSpecies[] dbfsArr = getDatabaseSpecies(con, null, keggID, false, FormalSpeciesType.compound, FormalSpeciesType.COMPOUND_KEGGID, -1, false);
    if (dbfsArr != null && dbfsArr.length == 1) {
        result = (FormalCompound) dbfsArr[0];
    } else {
        throw new RuntimeException("Expecting only 1 result");
    }
    return result;
}

Example 2 with DBFormalSpecies

use of cbit.vcell.model.DBFormalSpecies in project vcell by virtualcell.

the class DictionaryDbDriver method getBoundSpecies.

/**
 * Insert the method's description here.
 * Creation date: (2/26/2003 1:38:19 PM)
 * @return cbit.vcell.dictionary.DBSpecies
 * @param dbfs cbit.vcell.dictionary.DBFormalSpecies
 */
public DBSpecies getBoundSpecies(Connection con, DBFormalSpecies dbfs) throws SQLException {
    // Check if this is already a DBSpecies
    if (dbfs instanceof DBSpecies) {
        return (DBSpecies) dbfs;
    }
    int restrictsearch = 0;
    if (dbfs.getFormalSpeciesType().equals(FormalSpeciesType.compound)) {
        restrictsearch = FormalSpeciesType.COMPOUND_KEGGID;
    } else if (dbfs.getFormalSpeciesType().equals(FormalSpeciesType.enzyme)) {
        restrictsearch = FormalSpeciesType.ENZYME_ECNUMBER;
    } else if (dbfs.getFormalSpeciesType().equals(FormalSpeciesType.protein)) {
        restrictsearch = FormalSpeciesType.PROTEIN_SWISSPROTID;
    } else {
        throw new IllegalArgumentException("DictionaryDbDriver.getBoundSpecies: Unsupported FormalSpeciesType");
    }
    // Check if binding already exists in database
    DBFormalSpecies[] dbfsBound = getDatabaseSpecies(con, null, dbfs.getFormalSpeciesInfo().getFormalID(), true, dbfs.getFormalSpeciesType(), restrictsearch, -1, false);
    if (dbfsBound != null) {
        if (dbfsBound.length == 1) {
            return (DBSpecies) dbfsBound[0];
        } else {
            throw new RuntimeException("Expecting only 1 result");
        }
    }
    // Create new binding
    // Add entry to binding table
    KeyValue newKey = keyFactory.getNewKey(con);
    String sql = "INSERT INTO " + DBSpeciesTable.table.getTableName() + " VALUES " + DBSpeciesTable.table.getSQLValueList(newKey, dbfs);
    DbDriver.updateCleanSQL(con, sql);
    // Get new DBSpecies
    dbfsBound = getDatabaseSpecies(con, null, dbfs.getFormalSpeciesInfo().getFormalID(), true, dbfs.getFormalSpeciesType(), restrictsearch, -1, false);
    if (dbfsBound != null) {
        if (dbfsBound.length == 1) {
            return (DBSpecies) dbfsBound[0];
        } else {
            throw new RuntimeException("Expecting only 1 result");
        }
    }
    throw new RuntimeException("Couldn't Get New DBSpecies");
}

Example 3 with DBFormalSpecies

use of cbit.vcell.model.DBFormalSpecies in project vcell by virtualcell.

the class CompoundTable method getCompounds.

/**
 * returns a Compound object from the ResultSet
 * @return cbit.vcell.dictionary.Compound
 * @param rset java.sql.ResultSet
 */
public DBFormalSpecies[] getCompounds(java.sql.ResultSet rset, boolean createBound) throws java.sql.SQLException {
    Vector compounds = new Vector();
    Vector aliasNames = new Vector();
    String currentAliasName = null;
    String currentCASID = null;
    String currentFormula = null;
    String currentKeggID = null;
    String currentPreferred = null;
    org.vcell.util.document.KeyValue currentCompoundID = null;
    org.vcell.util.document.KeyValue currentDBSpeciesID = null;
    while (rset.next() || rset.isAfterLast()) {
        KeyValue compoundID = null;
        if (!rset.isAfterLast()) {
            compoundID = new KeyValue(rset.getBigDecimal(CompoundTable.table.id.toString()));
        }
        if (!rset.isFirst() && (!currentCompoundID.equals(compoundID))) {
            if (currentCompoundID != null) {
                if (aliasNames.size() > 0) {
                    String[] aliasNamesArr = new String[aliasNames.size()];
                    aliasNames.copyInto(aliasNamesArr);
                    CompoundInfo compoundInfo = new CompoundInfo(currentKeggID, aliasNamesArr, currentFormula, currentCASID, null);
                    FormalCompound formalCompound = new FormalCompound(currentCompoundID, compoundInfo);
                    Object compound = formalCompound;
                    if (createBound) {
                        BoundCompound boundCompound = new BoundCompound(currentDBSpeciesID, formalCompound);
                        compound = boundCompound;
                    }
                    compounds.add(compound);
                }
            }
            aliasNames.clear();
            if (rset.isAfterLast()) {
                break;
            }
        }
        if (aliasNames.size() == 0) {
            currentCompoundID = compoundID;
            currentKeggID = rset.getString(CompoundTable.table.keggID.toString());
            currentCASID = rset.getString(CompoundTable.table.casID.toString());
            currentFormula = rset.getString(CompoundTable.table.formula.toString());
            currentFormula = (currentFormula != null ? org.vcell.util.TokenMangler.getSQLRestoredString(currentFormula) : null);
            if (createBound) {
                currentDBSpeciesID = new KeyValue(rset.getBigDecimal("dbspecies_id"));
            }
        }
        currentPreferred = rset.getString(CompoundAliasTable.table.preferred.toString());
        currentAliasName = org.vcell.util.TokenMangler.getSQLRestoredString(rset.getString(CompoundAliasTable.table.name.toString()));
        if (currentPreferred.compareToIgnoreCase("T") == 0) {
            aliasNames.add(0, currentAliasName);
        } else {
            aliasNames.add(currentAliasName);
        }
    }
    DBFormalSpecies[] compoundsArr = null;
    if (compounds.size() > 0) {
        if (createBound) {
            BoundCompound[] boundCompoundsArr = null;
            boundCompoundsArr = new BoundCompound[compounds.size()];
            compounds.copyInto(boundCompoundsArr);
            compoundsArr = boundCompoundsArr;
        } else {
            FormalCompound[] formalCompoundsArr = null;
            formalCompoundsArr = new FormalCompound[compounds.size()];
            compounds.copyInto(formalCompoundsArr);
            compoundsArr = formalCompoundsArr;
        }
    }
    return compoundsArr;
}

Example 4 with DBFormalSpecies

use of cbit.vcell.model.DBFormalSpecies in project vcell by virtualcell.

the class ProteinTable method getProteins.

/**
 * returns a protein object from the ResultSet
 * @return cbit.vcell.dictionary.protein
 * @param rset java.sql.ResultSet
 */
public DBFormalSpecies[] getProteins(java.sql.ResultSet rset, boolean createBound) throws java.sql.SQLException {
    Vector proteins = new Vector();
    Vector aliasNames = new Vector();
    String currentAliasName = null;
    String currentKeywords = null;
    String currentSwissProtId = null;
    String currentAccession = null;
    String currentOrganism = null;
    String currentPreferred = null;
    String currentDescription = null;
    double currentMolWeight = ProteinInfo.UNKNOWN_MW;
    org.vcell.util.document.KeyValue currentProteinID = null;
    org.vcell.util.document.KeyValue currentDBSpeciesID = null;
    while (rset.next() || rset.isAfterLast()) {
        KeyValue proteinID = null;
        if (!rset.isAfterLast()) {
            proteinID = new KeyValue(rset.getBigDecimal(ProteinTable.table.id.toString()));
        }
        if (!rset.isFirst() && (!currentProteinID.equals(proteinID))) {
            if (currentProteinID != null) {
                if (aliasNames.size() > 0) {
                    String[] aliasNamesArr = new String[aliasNames.size()];
                    aliasNames.copyInto(aliasNamesArr);
                    String[] keywordsArr = null;
                    ProteinInfo proteinInfo = new ProteinInfo(currentSwissProtId, aliasNamesArr, currentOrganism, currentAccession, currentKeywords, currentDescription, currentMolWeight);
                    FormalProtein formalProtein = new FormalProtein(currentProteinID, proteinInfo);
                    Object protein = formalProtein;
                    if (createBound) {
                        BoundProtein boundProtein = new BoundProtein(currentDBSpeciesID, formalProtein);
                        protein = boundProtein;
                    }
                    proteins.add(protein);
                }
            }
            aliasNames.clear();
            if (rset.isAfterLast()) {
                break;
            }
        }
        if (aliasNames.size() == 0) {
            currentProteinID = proteinID;
            currentSwissProtId = rset.getString(ProteinTable.table.swissProtEntryName.toString());
            currentAccession = rset.getString(ProteinTable.table.accessionNumber.toString());
            currentOrganism = rset.getString(ProteinTable.table.organism.toString());
            currentOrganism = (currentOrganism != null ? org.vcell.util.TokenMangler.getSQLRestoredString(currentOrganism) : null);
            currentKeywords = rset.getString(ProteinTable.table.keywords.toString());
            currentKeywords = (currentKeywords != null ? org.vcell.util.TokenMangler.getSQLRestoredString(currentKeywords) : null);
            currentDescription = rset.getString(ProteinTable.table.description.toString());
            currentDescription = (currentDescription != null ? org.vcell.util.TokenMangler.getSQLRestoredString(currentDescription) : null);
            currentMolWeight = rset.getDouble(ProteinTable.table.molWeight.toString());
            if (rset.wasNull()) {
                currentMolWeight = ProteinInfo.UNKNOWN_MW;
            }
            if (createBound) {
                currentDBSpeciesID = new KeyValue(rset.getBigDecimal("dbspecies_id"));
            }
        }
        currentAliasName = org.vcell.util.TokenMangler.getSQLRestoredString(rset.getString(ProteinAliasTable.table.name.toString()));
        if (!aliasNames.contains(currentAliasName)) {
            currentPreferred = rset.getString(ProteinAliasTable.table.preferred.toString());
            if (currentPreferred.compareToIgnoreCase("true") == 0) {
                aliasNames.add(0, currentAliasName);
            } else {
                aliasNames.add(currentAliasName);
            }
        }
    }
    DBFormalSpecies[] proteinsArr = null;
    if (proteins.size() > 0) {
        if (createBound) {
            BoundProtein[] boundProteinsArr = null;
            boundProteinsArr = new BoundProtein[proteins.size()];
            proteins.copyInto(boundProteinsArr);
            proteinsArr = boundProteinsArr;
        } else {
            FormalProtein[] formalProteinsArr = null;
            formalProteinsArr = new FormalProtein[proteins.size()];
            proteins.copyInto(formalProteinsArr);
            proteinsArr = formalProteinsArr;
        }
    }
    return proteinsArr;
}

Example 5 with DBFormalSpecies

use of cbit.vcell.model.DBFormalSpecies in project vcell by virtualcell.

the class XmlReader method getDBFormalSpecies.

/**
 * This method returns a DBFormalSpecies from a XML representation.
 * Creation date: (6/3/2003 8:46:44 PM)
 * @return cbit.vcell.dictionary.DBFormalSpecies
 * @param formalSpeciesElement org.jdom.Element
 */
private DBFormalSpecies getDBFormalSpecies(Element formalSpeciesElement) throws XmlParseException {
    // read key
    String keystring = formalSpeciesElement.getAttributeValue(XMLTags.KeyValueAttrTag);
    KeyValue key = new KeyValue(keystring);
    // read type
    String typestring = formalSpeciesElement.getAttributeValue(XMLTags.TypeAttrTag);
    // read the FormalSpeciesInfo
    Element speciesInfoElement = formalSpeciesElement.getChild(XMLTags.FormalSpeciesInfoTag, vcNamespace);
    // create the DBFormalSpecies upon the type
    DBFormalSpecies formalSpecies = null;
    if (typestring.equalsIgnoreCase(XMLTags.CompoundTypeTag)) {
        formalSpecies = new FormalCompound(key, (CompoundInfo) getFormalSpeciesInfo(speciesInfoElement));
    } else if (typestring.equalsIgnoreCase(XMLTags.EnzymeTypeTag)) {
        formalSpecies = new FormalEnzyme(key, (EnzymeInfo) getFormalSpeciesInfo(speciesInfoElement));
    } else if (typestring.equalsIgnoreCase(XMLTags.ProteinTypeTag)) {
        formalSpecies = new FormalProtein(key, (ProteinInfo) getFormalSpeciesInfo(speciesInfoElement));
    } else {
        throw new XmlParseException("DBFormalSpecies type:" + typestring + ", not supported yet!");
    }
    return formalSpecies;
}