src/org/gel/mauve/chado/ChadoFeatureLoader.java

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package org.gel.mauve.chado;

import java.sql.*;

public class ChadoFeatureLoader {
        
        // type_id -> cvterm 
        
        // join 
        
        private Connection conn;
        
        public ChadoFeatureLoader (Connection chado_conn){
                conn = chado_conn;
        }
        
        public void getFeatures(String genus, String species /*...and coming soon, String strain !!!! */) throws SQLException{
                String query = "SELECT organism_id FROM organism WHERE " +
                                                        "genus = "+genus+" AND species = "+species+";";
                Statement st = conn.createStatement();
                ResultSet rs = st.executeQuery(query);
                String org_id = rs.getString("organism_id");
                st = conn.createStatement();
                query = "SELECT * FROM feature WHERE organism_id = "+org_id;
                query = "SELECT * FROM feature INNER JOIN annotations WHERE feature.unique_name = annotations.organism_id = "+org_id;
                rs = st.executeQuery(query);
                int left = -1;
                int right = -1;
                int strand = 0;
                String type = null;
                while(rs.next()){
                        left = rs.getInt("fmin");
                        right = rs.getInt("fmax");
                        strand = rs.getInt("strand");
                        type = rs.getString("name");
                        
                } 
        }
        
        private static String QUERY = 
        "SELECT featureprop.feature_id, cvterm.name, featureprop.value, featureloc.fmin, featureloc.fmax, featureloc.strand, feature.name, db.name, dbxref.accession, feature.dbxref_id, feature_dbxref.dbxref_id, dbxref.dbxref_id "+
        "FROM featureprop, cvterm, featureloc, feature, feature_dbxref, dbxref, db "+ 
        "WHERE organism_id = ? " +
                        "(featureprop.type_id = cvterm.cvterm_id) AND " +
                        "(featureprop.feature_id = featureloc.feature_id) AND "+ 
                "(featureprop.feature_id = feature.feature_id)  AND " +
                "(featureprop.feature_id = feature_dbxref.feature_id) AND "+
                "(feature_dbxref.dbxref_id = dbxref.dbxref_id) AND "+
                "(dbxref.db_id = db.db_id) "+
                "LIMIT 100 OFFSET 0";

}

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