/************************************************************************* * * * 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); } }