DBInterface.java

/*
*   EuroCarbDB, a framework for carbohydrate bioinformatics
*
*   Copyright (c) 2006-2009, Eurocarb project, or third-party contributors as
*   indicated by the @author tags or express copyright attribution
*   statements applied by the authors.  
*
*   This copyrighted material is made available to anyone wishing to use, modify,
*   copy, or redistribute it subject to the terms and conditions of the GNU
*   Lesser General Public License, as published by the Free Software Foundation.
*   A copy of this license accompanies this distribution in the file LICENSE.txt.
*
*   This program is distributed in the hope that it will be useful,
*   but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
*   or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
*   for more details.
*
*   Last commit: $Rev: 1210 $ by $Author: glycoslave $ on $Date:: 2009-06-12 #$  
*/
/**
* 
*/
package org.eurocarbdb.applications.ms.glycopeakfinder.calculation.xmlfiles;

import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;

/**
* @author Logan
*
*/
public class DBInterface
{
    private Connection m_objDB;
    private String m_strSchema = "glycopeakfinder";

    public DBInterface() throws ClassNotFoundException, SQLException 
    {
        String t_database_ip = "193.174.61.146";
        String t_database_driver = "jdbc:postgresql";
        String t_database_user = "postgres";
        String t_database_pw = "postgres";
        String t_database_name = "glycopeakfinder";
        String t_database_port = "5432";
        
        t_database_ip = "127.0.0.1";
        
        this.m_strSchema = "glycopeakfinder";
        
        Class.forName("org.postgresql.Driver");
        
        String t_strURL = t_database_driver + "://" + t_database_ip + ":"
        + t_database_port + "/" + t_database_name;
        // open database connection
        this.m_objDB = DriverManager.getConnection(t_strURL, t_database_user,
                t_database_pw);
    }

    /**
     * @return
     */
    public ResultSet getFragmentsAX() throws SQLException 
    {
        String t_strQuery = "SELECT gf.* , gr.abbr FROM " + this.m_strSchema + ".fragment_ax as gf LEFT JOIN " 
                + this.m_strSchema + ".residue as gr ON gf.residue_id=gr.residue_id ORDER BY fragment_ax_id";
        PreparedStatement t_objStatement = this.m_objDB.prepareStatement( t_strQuery) ;
        return t_objStatement.executeQuery();
    }

    /**
     * @return
     */
    public ResultSet getFragmentsOther() throws SQLException
    {
        String t_strQuery = "SELECT gf.* , gr.abbr FROM " + this.m_strSchema + ".fragment_other as gf LEFT JOIN " 
                + this.m_strSchema + ".residue as gr ON gf.residue_id=gr.residue_id ORDER BY fragment_other_id";
        PreparedStatement t_objStatement = this.m_objDB.prepareStatement( t_strQuery) ;
        return t_objStatement.executeQuery();
    }

    /**
     * @return
     */
    public ResultSet getResidues() throws SQLException
    {
        String t_strQuery = "SELECT * FROM " + this.m_strSchema + ".residue ORDER BY residue_id";
        PreparedStatement t_objStatement = this.m_objDB.prepareStatement( t_strQuery) ;
        return t_objStatement.executeQuery();
    }

    /**
     * @return
     */
    public ResultSet getPersubstitution() throws SQLException 
    {
        String t_strQuery = "SELECT * FROM " + this.m_strSchema + ".persubstitution ORDER BY persubstitution_id";
        PreparedStatement t_objStatement = this.m_objDB.prepareStatement( t_strQuery) ;
        return t_objStatement.executeQuery();
    }

    /**
     * @return
     */
    public ResultSet getIons() throws SQLException 
    {
        String t_strQuery = "SELECT * FROM " + this.m_strSchema + ".ions ORDER BY \"order\"";
        PreparedStatement t_objStatement = this.m_objDB.prepareStatement( t_strQuery) ;
        return t_objStatement.executeQuery();
    }

    /**
     * @return
     */
    public ResultSet getDerivatisations() throws SQLException
    {
        String t_strQuery = "SELECT * FROM " + this.m_strSchema + ".derivates ORDER BY derivates_id";
        PreparedStatement t_objStatement = this.m_objDB.prepareStatement( t_strQuery) ;
        return t_objStatement.executeQuery();
    }

    /**
     * @return
     */
    public ResultSet getMolecules() throws SQLException
    {
        String t_strQuery = "SELECT * FROM " + this.m_strSchema + ".small_molecules ORDER BY \"order\"";
        PreparedStatement t_objStatement = this.m_objDB.prepareStatement( t_strQuery) ;
        return t_objStatement.executeQuery();
    }
}