com.act.lcms.db.model.PlateWell.java Source code

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Here is the source code for com.act.lcms.db.model.PlateWell.java

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/*************************************************************************
*                                                                        *
*  This file is part of the 20n/act project.                             *
*  20n/act enables DNA prediction for synthetic biology/bioengineering.  *
*  Copyright (C) 2017 20n Labs, Inc.                                     *
*                                                                        *
*  Please direct all queries to act@20n.com.                             *
*                                                                        *
*  This program is free software: you can redistribute it and/or modify  *
*  it under the terms of the GNU General Public License as published by  *
*  the Free Software Foundation, either version 3 of the License, or     *
*  (at your option) any later version.                                   *
*                                                                        *
*  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 General Public License for more details.                          *
*                                                                        *
*  You should have received a copy of the GNU General Public License     *
*  along with this program.  If not, see <http://www.gnu.org/licenses/>. *
*                                                                        *
*************************************************************************/

package com.act.lcms.db.model;

import com.act.lcms.db.io.DB;
import org.apache.commons.lang3.StringUtils;

import java.io.IOException;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.List;

public abstract class PlateWell<T extends PlateWell> extends BaseDBModel<T> {
    protected String makeGetByPlateIDQuery() {
        return StringUtils.join(new String[] { "SELECT", StringUtils.join(this.getAllFields(), ','), "from",
                this.getTableName(), "where plate_id = ?", "order by plate_row asc, plate_column asc" }, " ");
    }

    protected abstract String getGetByPlateIDQuery();

    public List<T> getByPlateId(DB db, Integer plateId) throws SQLException, IOException, ClassNotFoundException {
        try (PreparedStatement stmt = db.getConn().prepareStatement(getGetByPlateIDQuery())) {
            stmt.setInt(1, plateId);
            try (ResultSet resultSet = stmt.executeQuery()) {
                return fromResultSet(resultSet);
            }
        }
    }

    protected T insert(DB db, T toInsert) throws SQLException, IOException {
        return insert(db, toInsert, String.format("could not retrieve autogenerated key for well at %d @ %d x %d",
                plateId, plateRow, plateColumn));
    }

    /* Use protected rather than private, as this class represents common attributes of all plate wells.  Extending
     * classes can/should have access to its fields, as its existence is simply an organizational convenience. */
    protected Integer plateId;
    protected Integer plateRow;
    protected Integer plateColumn;

    public Integer getPlateId() {
        return plateId;
    }

    public void setPlateId(Integer plateId) {
        this.plateId = plateId;
    }

    public Integer getPlateRow() {
        return plateRow;
    }

    public void setPlateRow(Integer plateRow) {
        this.plateRow = plateRow;
    }

    public Integer getPlateColumn() {
        return plateColumn;
    }

    public void setPlateColumn(Integer plateColumn) {
        this.plateColumn = plateColumn;
    }

    public String getCoordinatesString() {
        if (plateRow == null || plateColumn == null) {
            return "(unknown)";
        }
        return String.format("%s%d", Character.valueOf((char) (this.getPlateRow() + 'A')).toString(),
                this.getPlateColumn() + 1);
    }
}