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

Example 6 with DBFormalSpecies

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

the class SpeciesQueryPanel method createDBSpecies.

/**
 * Comment
 */
private void createDBSpecies(javax.swing.event.ListSelectionEvent listSelectionEvent) {
    if (bIgnoreSelection) {
        return;
    }
    if (getDocumentManager() != null) {
        if (!listSelectionEvent.getValueIsAdjusting()) {
            if (!((javax.swing.ListSelectionModel) listSelectionEvent.getSource()).isSelectionEmpty()) {
                try {
                    javax.swing.JList selectionJList = null;
                    if (getCompoundJList().getSelectionModel() == listSelectionEvent.getSource()) {
                        selectionJList = getCompoundJList();
                    } else if (getEnzymeJList().getSelectionModel() == listSelectionEvent.getSource()) {
                        selectionJList = getEnzymeJList();
                    } else if (getProteinJList().getSelectionModel() == listSelectionEvent.getSource()) {
                        selectionJList = getProteinJList();
                    } else {
                        throw new RuntimeException("Unknown ListSelectionModel");
                    }
                    int[] selection = new int[1];
                    selection[0] = selectionJList.getSelectedIndex();
                    DBFormalSpecies[] dbFormalSpecies = jlistData.get(selectionJList);
                    String query = jlistQuery.get(selectionJList);
                    ButtonModel scope = jlistScope.get(selectionJList);
                    boolean bBound = (scope != getDictionaryJRadioButton().getModel());
                    boolean bOnlyUser = (scope == getMyModelJRadioButton().getModel());
                    DictionaryQueryResults dqr = null;
                    if (bBound) {
                        if (getDocumentManager().getUser() == null) {
                            throw new RuntimeException("Query results for 'My Model' can't be bound to null user");
                        }
                        org.vcell.util.document.User user = (bOnlyUser ? getDocumentManager().getUser() : null);
                        dqr = new DictionaryQueryResults(query, user, (DBSpecies[]) dbFormalSpecies, selection);
                    } else {
                        dqr = new DictionaryQueryResults(query, dbFormalSpecies, selection);
                    }
                    setDictionaryQueryResults(dqr);
                    // Clear other selections
                    bIgnoreSelection = true;
                    if (getCompoundJList() != selectionJList) {
                        getCompoundJList().clearSelection();
                    }
                    if (getEnzymeJList() != selectionJList) {
                        getEnzymeJList().clearSelection();
                    }
                    if (getProteinJList() != selectionJList) {
                        getProteinJList().clearSelection();
                    }
                    bIgnoreSelection = false;
                } catch (Exception e) {
                    e.printStackTrace();
                    PopupGenerator.showErrorDialog(this, "Error:\n" + e.getMessage(), e);
                }
            } else {
                setDictionaryQueryResults(null);
            }
        }
    }
}

Example 7 with DBFormalSpecies

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

the class DBReactionWizardPanel method showSpeciesBrowser.

/**
 * Comment
 */
private DBFormalSpecies showSpeciesBrowser() {
    SpeciesQueryDialog sqd = new SpeciesQueryDialog((java.awt.Frame) null, true);
    sqd.setSearchableTypes(SpeciesQueryPanel.SEARCHABLE_ENZYME | SpeciesQueryPanel.SEARCHABLE_COMPOUND | (getSearchUserJRadioButton().isSelected() ? SpeciesQueryPanel.SEARCHABLE_PROTEIN : 0x00L));
    // boolean isDictSearch = getJTabbedPane1().getTitleAt(getJTabbedPane1().getSelectedIndex()).equals("Dictionary");
    // if(getSearchDictionaryJRadioButton().isSelected()){
    // if(getAnyJRadioButton().isSelected()){
    // sqd.setSearchableTypes(SpeciesQueryPanel.SEARCHABLE_ENZYME | SpeciesQueryPanel.SEARCHABLE_COMPOUND);
    // }else{
    // sqd.setSearchableTypes((getCatalystJRadioButton().isSelected()?SpeciesQueryPanel.SEARCHABLE_ENZYME:SpeciesQueryPanel.SEARCHABLE_COMPOUND));
    // }
    // }
    sqd.setDocumentManager(getDocumentManager());
    sqd.setSize(550, 500);
    BeanUtils.centerOnScreen(sqd);
    DialogUtils.showModalJDialogOnTop(sqd, this);
    // sqd.setVisible(true);
    DBFormalSpecies dbfs = null;
    DictionaryQueryResults dqr = sqd.getDictionaryQueryResults();
    if (dqr != null && dqr.getSelection() != null) {
        dbfs = dqr.getDBFormalSpecies()[dqr.getSelection()[0]];
    }
    if (dbfs != null) {
        setCurrentDBFormalSpecies(dbfs);
    }
    return dbfs;
}

Example 8 with DBFormalSpecies

use of cbit.vcell.model.DBFormalSpecies 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;
}

Example 9 with DBFormalSpecies

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

the class EnzymeReactionTable method getSQLReactionQuery.

/**
 * Insert the method's description here.
 * Creation date: (4/18/2003 10:29:26 AM)
 */
public String getSQLReactionQuery(cbit.vcell.model.ReactionQuerySpec rqs) {
    DBFormalSpecies reactantsCompoundRef = rqs.getReactantBoundSpecies();
    DBFormalSpecies enzymeRef = rqs.getCatalystBoundSpecies();
    DBFormalSpecies productsCompoundRef = rqs.getProductBoundSpecies();
    String reactantWildCard = rqs.getReactantLikeString();
    String enzymeWildCard = rqs.getCatalystLikeString();
    String productWildCard = rqs.getProductLikeString();
    String repWildCard = rqs.getAnyReactionParticipantLikeString();
    DBFormalSpecies typeWildCardDBFS = rqs.getAnyReactionParticipantBoundSpecies();
    String typeWildCard = (typeWildCardDBFS != null ? typeWildCardDBFS.getDBFormalSpeciesKey().toString() : null);
    // 
    if ((repWildCard != null || typeWildCard != null) && ((reactantWildCard != null) || (enzymeWildCard != null) || (productWildCard != null) || (reactantsCompoundRef != null) || (enzymeRef != null) || (productsCompoundRef != null))) {
        throw new IllegalArgumentException("Illegal arguments to getSQLReactionQuery");
    }
    String nameConditionWild = null;
    String nameConditionR = null;
    String nameConditionP = null;
    String nameConditionE = null;
    String typeConditionWild = null;
    String typeConditionR = null;
    String typeConditionP = null;
    String typeConditionE = null;
    String rpNameCondition = " SELECT DISTINCT " + EnzymeReactionTable.table.reactionId.getQualifiedColName() + " FROM " + EnzymeReactionTable.table.getTableName() + "," + CompoundTable.table.getTableName() + "," + CompoundAliasTable.table.getTableName() + " WHERE " + EnzymeReactionTable.table.compoundRef.getQualifiedColName() + "=" + CompoundTable.table.id.getQualifiedColName() + " AND " + CompoundAliasTable.table.compoundRef.getQualifiedColName() + "=" + CompoundTable.table.id.getQualifiedColName() + " AND " + CompoundAliasTable.table.preferred.getQualifiedColName() + "=" + "'T'";
    // 
    if (repWildCard == null) {
        if (reactantWildCard != null) {
            nameConditionR = rpNameCondition + " AND " + "LOWER(" + CompoundAliasTable.table.name.getQualifiedColName() + ") LIKE LOWER('" + reactantWildCard + "')" + " AND " + EnzymeReactionTable.table.type.getQualifiedColName() + "=" + "'" + REACANT_TYPE_REACTANT + "'";
        } else if (productWildCard != null) {
            nameConditionP = rpNameCondition + " AND " + "LOWER(" + CompoundAliasTable.table.name.getQualifiedColName() + ") LIKE LOWER('" + productWildCard + "')" + " AND " + EnzymeReactionTable.table.type.getQualifiedColName() + "=" + "'" + REACANT_TYPE_PRODUCT + "'";
        }
    }
    // 
    if (typeWildCard == null) {
        if (reactantsCompoundRef != null) {
            typeConditionR = createRPTypeSearchCondition(REACANT_TYPE_REACTANT, new String[] { reactantsCompoundRef.getDBFormalSpeciesKey().toString() });
        } else if (productsCompoundRef != null) {
            typeConditionP = createRPTypeSearchCondition(REACANT_TYPE_PRODUCT, new String[] { productsCompoundRef.getDBFormalSpeciesKey().toString() });
        }
    }
    // 
    if (repWildCard != null || enzymeWildCard != null) {
        nameConditionE = " SELECT DISTINCT " + EnzymeReactionTable.table.reactionId.getQualifiedColName() + " FROM " + EnzymeReactionTable.table.getTableName() + "," + EnzymeTable.table.getTableName() + "," + EnzymeAliasTable.table.getTableName() + " WHERE " + EnzymeReactionTable.table.enzymeRef.getQualifiedColName() + " IS NOT NULL" + " AND " + EnzymeReactionTable.table.enzymeRef.getQualifiedColName() + "=" + EnzymeTable.table.id.getQualifiedColName() + " AND " + EnzymeAliasTable.table.enzymeRef.getQualifiedColName() + "=" + EnzymeTable.table.id.getQualifiedColName() + " AND " + EnzymeAliasTable.table.preferred.getQualifiedColName() + "=" + "'T'" + " AND " + "LOWER(" + EnzymeAliasTable.table.name.getQualifiedColName() + ") LIKE LOWER('" + (repWildCard != null ? repWildCard : enzymeWildCard) + "')";
    }
    if (enzymeRef != null || typeWildCard != null) {
        typeConditionE = " SELECT DISTINCT " + EnzymeReactionTable.table.reactionId.getQualifiedColName() + " FROM " + EnzymeReactionTable.table.getTableName() + " WHERE " + EnzymeReactionTable.table.enzymeRef.getQualifiedColName() + " IS NOT NULL" + " AND " + EnzymeReactionTable.table.enzymeRef.getQualifiedColName() + "=" + (typeWildCard != null ? typeWildCard : enzymeRef.getDBFormalSpeciesKey().toString());
    }
    // 
    if (repWildCard != null) {
        nameConditionWild = rpNameCondition + " AND " + "LOWER(" + CompoundAliasTable.table.name.getQualifiedColName() + ") LIKE LOWER('" + repWildCard + "')" + " UNION " + nameConditionE;
    }
    if (typeWildCard != null) {
        typeConditionWild = "SELECT DISTINCT " + EnzymeReactionTable.table.reactionId.getQualifiedColName() + " FROM " + EnzymeReactionTable.table.getTableName() + " WHERE " + EnzymeReactionTable.table.compoundRef.getQualifiedColName() + "=" + typeWildCard + " OR " + EnzymeReactionTable.table.enzymeRef.getQualifiedColName() + "=" + typeWildCard;
    }
    // 
    String nameConditions = "";
    nameConditions = nameConditions + (nameConditionWild != null ? nameConditionWild + " " : "");
    nameConditions = nameConditions + (nameConditionR != null ? nameConditionR + " " : "");
    nameConditions = nameConditions + (nameConditionP != null ? (nameConditions.length() > 0 ? " INTERSECT " : "") + nameConditionP + " " : "");
    nameConditions = nameConditions + (nameConditionE != null && nameConditionWild == null ? (nameConditions.length() > 0 ? " INTERSECT " : "") + nameConditionE + " " : "");
    String typeConditions = "";
    typeConditions = typeConditions + (typeConditionWild != null ? typeConditionWild + " " : "");
    typeConditions = typeConditions + (typeConditionR != null ? typeConditionR + " " : "");
    typeConditions = typeConditions + (typeConditionP != null ? (typeConditions.length() > 0 ? " INTERSECT " : "") + typeConditionP + " " : "");
    typeConditions = typeConditions + (typeConditionE != null && typeWildCard == null ? (typeConditions.length() > 0 ? " INTERSECT " : "") + typeConditionE + " " : "");
    String conditions = null;
    if (nameConditions.length() > 0 && typeConditions.length() > 0) {
        conditions = "(" + nameConditions + ") UNION (" + typeConditions + ")";
    } else if (nameConditions.length() > 0) {
        conditions = nameConditions;
    } else if (typeConditions.length() > 0) {
        conditions = typeConditions;
    }
    // 
    String selectSQL_NotNull = "SELECT DISTINCT " + EnzymeReactionTable.table.reactionId.getQualifiedColName() + "," + EnzymeTable.table.ecNumber.getQualifiedColName() + " " + RXQ_ENZYMEFID_ALIAS + "," + EnzymeTable.table.id.getQualifiedColName() + " " + RXQ_ENZYMEID_ALIAS + "," + EnzymeAliasTable.table.name.getQualifiedColName() + " " + RXQ_ENZYMENAME_ALIAS + "," + EnzymeReactionTable.table.type.getQualifiedColName() + "," + EnzymeReactionTable.table.stoich.getQualifiedColName() + "," + CompoundTable.table.keggID.getQualifiedColName() + "," + CompoundTable.table.id.getQualifiedColName() + " " + RXQ_CMPNDID_ALIAS + "," + CompoundAliasTable.table.name.getQualifiedColName() + " " + RXQ_CMPDNDNAME_ALIAS;
    String selectSQL_Null = "SELECT DISTINCT " + EnzymeReactionTable.table.reactionId.getQualifiedColName() + "," + EnzymeReactionTable.table.parsedECNumber.getQualifiedColName() + " " + RXQ_ENZYMEFID_ALIAS + "," + "TO_NUMBER(NULL)" + " " + RXQ_ENZYMEID_ALIAS + "," + "TO_CHAR(NULL)" + " " + RXQ_ENZYMENAME_ALIAS + "," + EnzymeReactionTable.table.type.getQualifiedColName() + "," + EnzymeReactionTable.table.stoich.getQualifiedColName() + "," + CompoundTable.table.keggID.getQualifiedColName() + "," + CompoundTable.table.id.getQualifiedColName() + " " + RXQ_CMPNDID_ALIAS + "," + CompoundAliasTable.table.name.getQualifiedColName() + " " + RXQ_CMPDNDNAME_ALIAS;
    String fromSQL_NotNull = " FROM " + EnzymeReactionTable.table.getTableName() + "," + CompoundTable.table.getTableName() + "," + CompoundAliasTable.table.getTableName() + "," + EnzymeTable.table.getTableName() + "," + EnzymeAliasTable.table.getTableName();
    String fromSQL_Null = " FROM " + EnzymeReactionTable.table.getTableName() + "," + CompoundTable.table.getTableName() + "," + CompoundAliasTable.table.getTableName();
    String joinSQL_NotNull = EnzymeReactionTable.table.enzymeRef.getQualifiedColName() + " IS NOT NULL " + " AND " + EnzymeReactionTable.table.compoundRef.getQualifiedColName() + "=" + CompoundTable.table.id.getQualifiedColName() + " AND " + CompoundAliasTable.table.compoundRef.getQualifiedColName() + "=" + CompoundTable.table.id.getQualifiedColName() + " AND " + CompoundAliasTable.table.preferred.getQualifiedColName() + "=" + "'T'" + " AND " + EnzymeReactionTable.table.enzymeRef.getQualifiedColName() + "=" + EnzymeTable.table.id.getQualifiedColName() + " AND " + EnzymeAliasTable.table.enzymeRef.getQualifiedColName() + "=" + EnzymeTable.table.id.getQualifiedColName() + " AND " + EnzymeAliasTable.table.preferred.getQualifiedColName() + "=" + "'T'";
    String joinSQL_Null = EnzymeReactionTable.table.enzymeRef.getQualifiedColName() + " IS NULL " + " AND " + EnzymeReactionTable.table.compoundRef.getQualifiedColName() + "=" + CompoundTable.table.id.getQualifiedColName() + " AND " + CompoundAliasTable.table.compoundRef.getQualifiedColName() + "=" + CompoundTable.table.id.getQualifiedColName() + " AND " + CompoundAliasTable.table.preferred.getQualifiedColName() + "=" + "'T'";
    String orderBy = " ORDER BY " + EnzymeReactionTable.table.reactionId.getUnqualifiedColName() + "," + RXQ_ENZYMEFID_ALIAS + "," + EnzymeReactionTable.table.type.getUnqualifiedColName() + " DESC";
    String sqlNonNull = selectSQL_NotNull + " " + fromSQL_NotNull + " WHERE " + EnzymeReactionTable.table.reactionId.getQualifiedColName() + " IN " + "(" + conditions + ")" + " AND " + joinSQL_NotNull;
    String sqlNull = selectSQL_Null + " " + fromSQL_Null + " WHERE " + EnzymeReactionTable.table.reactionId.getQualifiedColName() + " IN " + "(" + conditions + ")" + " AND " + joinSQL_Null;
    String sql = sqlNonNull + " UNION " + sqlNull + orderBy;
    // System.out.println(sqlNonNull+"\n"+sqlNull+"\n"+sql);
    return sql;
}

Example 10 with DBFormalSpecies

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

the class DictionaryDbDriver method getDatabaseSpecies.

/**
 * Insert the method's description here.
 * Creation date: (2/15/2003 10:12:24 PM)
 * @return cbit.vcell.dictionary.DBSpecies[]
 * @param con java.sql.Connection
 * @param user cbit.vcell.server.User
 * @param bOnlyUser boolean
 */
public DBFormalSpecies[] getDatabaseSpecies(Connection con, User user, String likeString, boolean isBound, FormalSpeciesType speciesType, int restrictSearch, int rowLimit, boolean bOnlyUser) throws SQLException {
    if (speciesType != null && speciesType.equals(FormalSpeciesType.speciesMatchSearch)) {
        FormalSpeciesType.MatchSearchFormalSpeciesType matchSearchFormalSpeciesType = (FormalSpeciesType.MatchSearchFormalSpeciesType) speciesType;
        if (matchSearchFormalSpeciesType.getMatchCriterias() == null || matchSearchFormalSpeciesType.getMatchCriterias().length == 0) {
            return null;
        }
        ArrayList<VCDocumentInfo> matchedVCDocumentInfos = new ArrayList<VCDocumentInfo>();
        Statement stmt = null;
        // OR condition
        // String sql =
        // "SELECT UNIQUE "  +BioModelTable.table.id.getQualifiedColName() +
        // " FROM "  + BioModelTable.table.getTableName() + "," + SpeciesContextModelTable.table.getTableName() +
        // " WHERE " + BioModelTable.table.modelRef.getQualifiedColName() + " = "+ SpeciesContextModelTable.table.modelRef.getQualifiedColName() +
        // " AND (";
        // for (int i = 0; i < matchSearchFormalSpeciesType.getMatchCriterias().length; i++) {
        // sql+=
        // (i>0?" OR ":"") +
        // " LOWER("+SpeciesContextModelTable.table.name.getQualifiedColName()+") LIKE " + "'" + matchSearchFormalSpeciesType.getMatchCriterias()[i] + "'" + " ESCAPE '"+BeanUtils.SQL_ESCAPE_CHARACTER+"'";
        // }
        // sql+=")";
        // AND condition
        String sql = "";
        for (int i = 0; i < matchSearchFormalSpeciesType.getMatchCriterias().length; i++) {
            sql += (i > 0 ? " INTERSECT " : "") + "SELECT UNIQUE " + BioModelTable.table.id.getQualifiedColName() + " FROM " + BioModelTable.table.getTableName() + "," + SpeciesContextModelTable.table.getTableName() + " WHERE " + BioModelTable.table.modelRef.getQualifiedColName() + " = " + SpeciesContextModelTable.table.modelRef.getQualifiedColName() + " AND " + " LOWER(" + SpeciesContextModelTable.table.name.getQualifiedColName() + ") LIKE " + "'" + matchSearchFormalSpeciesType.getMatchCriterias()[i] + "'" + " ESCAPE '" + BeanUtils.SQL_ESCAPE_CHARACTER + "'";
        }
        try {
            stmt = con.createStatement();
            ResultSet rset = stmt.executeQuery(sql);
            while (rset.next()) {
                BigDecimal versionKey = rset.getBigDecimal(1);
                Version version = new Version(new KeyValue(versionKey), null, null, null, null, null, null, null, null);
                matchedVCDocumentInfos.add(new BioModelInfo(version, null, (BioModelChildSummary) null, null));
            }
        } finally {
            if (stmt != null) {
                stmt.close();
            }
        }
        if (matchedVCDocumentInfos.size() == 0) {
            return null;
        }
        return new DBFormalSpecies[] { new MatchedVCDocumentsFromSearch(matchedVCDocumentInfos) };
    }
    if (!speciesType.bValidProperties(restrictSearch)) {
        throw new IllegalArgumentException("Improper properties in restrictSearch");
    }
    if (bOnlyUser && isBound == false) {
        throw new IllegalArgumentException("user not null expects isBound = true");
    }
    if (!((rowLimit == -1) || (rowLimit > 0))) {
        throw new IllegalArgumentException("rowLimit must be -1(Unlimited) or greater than 0");
    }
    if ((((restrictSearch & FormalSpeciesType.COMPOUND_ID) != 0) && (restrictSearch != FormalSpeciesType.COMPOUND_ID)) || (((restrictSearch & FormalSpeciesType.ENZYME_ID) != 0) && (restrictSearch != FormalSpeciesType.ENZYME_ID)) || (((restrictSearch & FormalSpeciesType.PROTEIN_ID) != 0) && (restrictSearch != FormalSpeciesType.PROTEIN_ID))) {
        throw new RuntimeException("Incompatible search properties together");
    }
    likeString = likeString.toUpperCase();
    // Columns always needed
    String columns = (speciesType.equals(FormalSpeciesType.compound) ? CompoundTable.table.getTableName() + ".*" + "," + CompoundAliasTable.table.name.getQualifiedColName() + "," + CompoundAliasTable.table.preferred.getQualifiedColName() : "") + (speciesType.equals(FormalSpeciesType.enzyme) ? EnzymeTable.table.getTableName() + ".*" + "," + EnzymeAliasTable.table.name.getQualifiedColName() + "," + EnzymeAliasTable.table.preferred.getQualifiedColName() : "") + (speciesType.equals(FormalSpeciesType.protein) ? ProteinTable.table.getTableName() + ".*" + "," + ProteinAliasTable.table.name.getQualifiedColName() + "," + ProteinAliasTable.table.preferred.getQualifiedColName() : "");
    // Columns if Bound (aliased because id in other tables)
    String dbSpeciesTable_id_alias = "dbspecies_id";
    if (isBound) {
        columns = columns + "," + DBSpeciesTable.table.id.getQualifiedColName() + " " + dbSpeciesTable_id_alias;
    }
    // Tables always needed
    String tables = (speciesType.equals(FormalSpeciesType.compound) ? CompoundTable.table.getTableName() + "," + CompoundAliasTable.table.getTableName() : "") + (speciesType.equals(FormalSpeciesType.enzyme) ? EnzymeTable.table.getTableName() + "," + EnzymeAliasTable.table.getTableName() : "") + (speciesType.equals(FormalSpeciesType.protein) ? ProteinTable.table.getTableName() + "," + ProteinAliasTable.table.getTableName() : "");
    // Tables if Bound
    if (isBound) {
        tables = tables + "," + DBSpeciesTable.table.getTableName();
        if (bOnlyUser) {
            tables = tables + "," + SpeciesContextModelTable.table.getTableName() + "," + SpeciesTable.table.getTableName() + "," + ModelTable.table.getTableName();
        }
    }
    String condition = "";
    // Conditions always needed
    condition = condition + (speciesType.equals(FormalSpeciesType.compound) ? CompoundTable.table.id.getQualifiedColName() + "=" + CompoundAliasTable.table.compoundRef.getQualifiedColName() : "") + (speciesType.equals(FormalSpeciesType.enzyme) ? EnzymeTable.table.id.getQualifiedColName() + "=" + EnzymeAliasTable.table.enzymeRef.getQualifiedColName() : "") + (speciesType.equals(FormalSpeciesType.protein) ? ProteinTable.table.id.getQualifiedColName() + "=" + ProteinAliasTable.table.proteinRef.getQualifiedColName() : "");
    java.util.Vector<String> likeConditions = new java.util.Vector<String>();
    if (speciesType.equals(FormalSpeciesType.compound)) {
        if ((restrictSearch & FormalSpeciesType.COMPOUND_ID) != 0) {
            likeConditions.add(" UPPER(" + CompoundTable.table.id.getQualifiedColName() + ") = " + likeString);
        }
        if ((restrictSearch & FormalSpeciesType.COMPOUND_ALIAS) != 0) {
            likeConditions.add(" UPPER(" + CompoundAliasTable.table.name.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        if ((restrictSearch & FormalSpeciesType.COMPOUND_KEGGID) != 0) {
            likeConditions.add(" UPPER(" + CompoundTable.table.keggID.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        if ((restrictSearch & FormalSpeciesType.COMPOUND_CASID) != 0) {
            likeConditions.add(" UPPER(" + CompoundTable.table.casID.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        if ((restrictSearch & FormalSpeciesType.COMPOUND_FORMULA) != 0) {
            likeConditions.add(" UPPER(" + CompoundTable.table.formula.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
    } else if (speciesType.equals(FormalSpeciesType.enzyme)) {
        if ((restrictSearch & FormalSpeciesType.ENZYME_ID) != 0) {
            likeConditions.add(" UPPER(" + EnzymeTable.table.id.getQualifiedColName() + ") = " + likeString);
        }
        if ((restrictSearch & FormalSpeciesType.ENZYME_ALIAS) != 0) {
            likeConditions.add(" UPPER(" + EnzymeAliasTable.table.name.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        if ((restrictSearch & FormalSpeciesType.ENZYME_SYSNAME) != 0) {
            likeConditions.add(" UPPER(" + EnzymeTable.table.sysname.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        if ((restrictSearch & FormalSpeciesType.ENZYME_ECNUMBER) != 0) {
            likeConditions.add(" UPPER(" + EnzymeTable.table.ecNumber.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        // if((restrictSearch & FormalSpeciesType.ENZYME_ECNUMBER) != 0){likeConditions.add(" UPPER("+EnzymeTable.table.ecNumber.getQualifiedColName() + ") LIKE " + "'EC "+likeString+"'");}
        if ((restrictSearch & FormalSpeciesType.ENZYME_REACTION) != 0) {
            likeConditions.add(" UPPER(" + EnzymeTable.table.reaction.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        if ((restrictSearch & FormalSpeciesType.ENZYME_CASID) != 0) {
            likeConditions.add(" UPPER(" + EnzymeTable.table.casID.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
    } else if (speciesType.equals(FormalSpeciesType.protein)) {
        if ((restrictSearch & FormalSpeciesType.PROTEIN_ID) != 0) {
            likeConditions.add(" UPPER(" + ProteinTable.table.id.getQualifiedColName() + ") = " + likeString);
        }
        if ((restrictSearch & FormalSpeciesType.PROTEIN_ALIAS) != 0) {
            likeConditions.add(" UPPER(" + ProteinAliasTable.table.name.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        if ((restrictSearch & FormalSpeciesType.PROTEIN_ACCESSION) != 0) {
            likeConditions.add(" UPPER(" + ProteinTable.table.accessionNumber.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        if ((restrictSearch & FormalSpeciesType.PROTEIN_SWISSPROTID) != 0) {
            likeConditions.add(" UPPER(" + ProteinTable.table.swissProtEntryName.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        if ((restrictSearch & FormalSpeciesType.PROTEIN_ORGANISM) != 0) {
            likeConditions.add(" UPPER(" + ProteinTable.table.organism.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        if ((restrictSearch & FormalSpeciesType.PROTEIN_KEYWORD) != 0) {
            likeConditions.add(" UPPER(" + ProteinTable.table.keywords.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        if ((restrictSearch & FormalSpeciesType.PROTEIN_DESCR) != 0) {
            likeConditions.add(" UPPER(" + ProteinTable.table.description.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
    } else {
        throw new RuntimeException(speciesType.getName() + " Unsupported");
    }
    if (likeConditions.size() > 0) {
        condition = condition + " AND ( ";
        for (int i = 0; i < likeConditions.size(); i += 1) {
            String newCondition = (String) likeConditions.get(i);
            if (i != 0) {
                condition = condition + " OR ";
            }
            condition = condition + newCondition;
        }
        condition = condition + ")";
    }
    if (isBound) {
        condition = condition + " AND " + (speciesType.equals(FormalSpeciesType.compound) ? CompoundTable.table.id.getQualifiedColName() + "=" + DBSpeciesTable.table.compoundRef.getQualifiedColName() : "") + (speciesType.equals(FormalSpeciesType.enzyme) ? EnzymeTable.table.id.getQualifiedColName() + "=" + DBSpeciesTable.table.enzymeRef.getQualifiedColName() : "") + (speciesType.equals(FormalSpeciesType.protein) ? ProteinTable.table.id.getQualifiedColName() + "=" + DBSpeciesTable.table.proteinRef.getQualifiedColName() : "");
        if (bOnlyUser) {
            condition = condition + " AND " + SpeciesContextModelTable.table.speciesRef.getQualifiedColName() + " = " + SpeciesTable.table.id.getQualifiedColName() + " AND " + SpeciesTable.table.dbSpeciesRef.getQualifiedColName() + " = " + DBSpeciesTable.table.id.getQualifiedColName() + " AND " + SpeciesContextModelTable.table.modelRef.getQualifiedColName() + " = " + ModelTable.table.id.getQualifiedColName() + " AND " + ModelTable.table.ownerRef.getQualifiedColName() + " = " + user.getID();
        }
    }
    // ORDER BY 'id' must not be changed, used to collect multiple aliasnames into same info object
    String orderBy = (speciesType.equals(FormalSpeciesType.compound) ? CompoundTable.table.id.getQualifiedColName() : "") + (speciesType.equals(FormalSpeciesType.enzyme) ? EnzymeTable.table.id.getQualifiedColName() : "") + (speciesType.equals(FormalSpeciesType.protein) ? ProteinTable.table.id.getQualifiedColName() : "");
    String sql = "SELECT " + columns + " FROM " + tables + " WHERE " + condition + " ORDER BY " + orderBy;
    DBFormalSpecies[] databaseSpecies = null;
    Statement stmt = con.createStatement();
    if (rowLimit > 0) {
        stmt.setMaxRows(rowLimit);
    }
    try {
        ResultSet rset = stmt.executeQuery(sql);
        if (speciesType.equals(FormalSpeciesType.compound)) {
            databaseSpecies = CompoundTable.table.getCompounds(rset, isBound);
        } else if (speciesType.equals(FormalSpeciesType.enzyme)) {
            databaseSpecies = EnzymeTable.table.getEnzymes(rset, isBound);
        } else if (speciesType.equals(FormalSpeciesType.protein)) {
            databaseSpecies = ProteinTable.table.getProteins(rset, isBound);
        } else {
            throw new RuntimeException("FormalSpeciesType=" + speciesType.getName() + " Unsupported");
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    // 
    return databaseSpecies;
}