SeqAlignment.java

package org.seqcode.data.seqdata;


import java.sql.*;
import java.util.*;

import org.seqcode.data.core.AlignType;
import org.seqcode.data.core.MetadataLoader;
import org.seqcode.genome.Genome;
import org.seqcode.gseutils.NotFoundException;

/**
 * @author tdanford
 * @author mahony
 *
 * Represents a row from the seqalignment table, in the *seqdata schemas.
 * 
	create table seqalignment (
		id int(10) not null auto_increment,
		expt int(10) not null,
		name varchar(200) not null,
		genome int(10) not null,
		permissions varchar(500) not null,
		aligntype int(10) not null,
		numhits int(15),
		totalweight float(17,2),
		numtype2hits int(15),
		totaltype2weight float(17,2),
		numpairs int(15),
		totalpairweight float(17,2),
		aligndir varchar(400),
		alignfile varchar(500),
		idxfile varchar(400),
		collabalignid varchar(200),
		foreign key fk_seqalignment_expt (expt) references seqexpt(id),
		index(name, genome),
		unique(id),
		primary key(id)
	)Type=InnoDB;
 */
public class SeqAlignment {
	
	private int dbid;
	private SeqExpt expt;
	private String name;
	private Genome genome;
	private List<String> permissions;
	private AlignType atype;
	private int numHits;
	private double totalWeight;
	private int numType2Hits;
	private double totalType2Weight;
	private int numPairs;
	private double totalPairWeight;
	private String alignDir, alignFile, idxFile, collabAlignID;
	
	public SeqAlignment(ResultSet rs, SeqDataLoader loader) throws SQLException, NotFoundException { 
		dbid = rs.getInt(1);
		int exptID = rs.getInt(2);
		name = rs.getString(3);
		int genomeID = rs.getInt(4);
		int atypeID =  rs.getInt(6);
		MetadataLoader mloader= loader==null ? new MetadataLoader() : loader.getMetadataLoader();
		try {
			expt = loader.loadExperiment(exptID);
			genome = Genome.findGenome(genomeID);
			atype = mloader.loadAlignType(atypeID, false);
			permissions = Arrays.asList(rs.getString(5).split(";"));
			numHits = rs.getInt(7);
			totalWeight = rs.getFloat(8);
			numType2Hits = rs.getInt(9);
			totalType2Weight = rs.getFloat(10);
			numPairs = rs.getInt(11);
			totalPairWeight = rs.getFloat(12);
			alignDir = rs.getString(13);
			alignFile = rs.getString(14);
			idxFile = rs.getString(15);
			collabAlignID = rs.getString(16);
		} catch (NotFoundException e) {
			e.printStackTrace();
		}
	}
	
	public SeqAlignment(ResultSet rs, SeqExpt ex, AlignType a) throws SQLException { 
		dbid = rs.getInt(1);
		expt = ex;  // exptID is still in position #2, we just don't need it.
		name = rs.getString(3);
		int genomeID = rs.getInt(4);
		atype =  a; 
		try {
			genome = Genome.findGenome(genomeID);
		} catch (NotFoundException e) {
			e.printStackTrace();
		}
		permissions = Arrays.asList(rs.getString(5).split(";"));
		numHits = rs.getInt(7);
		totalWeight = rs.getFloat(8);
		numType2Hits = rs.getInt(9);
		totalType2Weight = rs.getFloat(10);
		numPairs = rs.getInt(11);
		totalPairWeight = rs.getFloat(12);
		alignDir = rs.getString(13);
		alignFile = rs.getString(14);
		idxFile = rs.getString(15);
		collabAlignID = rs.getString(16);
	}
	
	public int getDBID() { return dbid; }
	public String getName() { return name; }
	public SeqExpt getExpt() { return expt; }
	public AlignType getAlignType() {return atype;}
	public Genome getGenome() { return genome; }
	public List<String> getPermissions() { return permissions; }
	public int getNumHits() {return numHits;}
	public double getTotalWeight() {return totalWeight;}
	public int getNumType2Hits() {return numType2Hits;}
	public double getTotalType2Weight() {return totalType2Weight;}
	public int getNumPairs() {return numPairs;}
	public double getTotalPairWeight() {return totalPairWeight;}
	public String getAlignDir() {return alignDir;}
	public String getAlignFile() {return alignFile;}
	public String getIDXFile() {return idxFile;}
	public String getCollabAlignID() {return collabAlignID;}
	
	
	public int hashCode() { 
		int code = 17;
		code += dbid; code *= 37;
		return code;
	}
	
	public String toString() { 
		return String.format("\"%s\" %s -> %s", name, expt.getName(), genome.getVersion());
	}
	
	public boolean equals(Object o) { 
		if(!(o instanceof SeqAlignment)) { return false; }
		SeqAlignment a = (SeqAlignment)o;
		if(dbid != a.dbid) { return false; }
		return true;
	}

	public static PreparedStatement createLoadByIDStatement(java.sql.Connection c) throws SQLException { 
		String query = "select id, expt, name, genome, permissions, aligntype, numhits, totalweight, numtype2hits, totaltype2weight, numpairs, totalpairweight, aligndir, alignfile, idxfile, collabalignid from seqalignment where id=?";
		return c.prepareStatement(query);
	}
	
	public static PreparedStatement createLoadByNameAndExptStatement(java.sql.Connection c) throws SQLException { 
		String query = "select id, expt, name, genome, permissions, aligntype, numhits, totalweight, numtype2hits, totaltype2weight, numpairs, totalpairweight, aligndir, alignfile, idxfile, collabalignid from seqalignment where name=? and expt=?";
		return c.prepareStatement(query);
	}

	public static PreparedStatement createLoadAllStatement(java.sql.Connection c) throws SQLException { 
		String query = "select id, expt, name, genome, permissions, aligntype, numhits, totalweight, numtype2hits, totaltype2weight, numpairs, totalpairweight, aligndir, alignfile, idxfile, collabalignid from seqalignment";
		return c.prepareStatement(query);
	}
	public static PreparedStatement createLoadAllByExptStatement(java.sql.Connection c) throws SQLException { 
		String query = "select id, expt, name, genome, permissions, aligntype, numhits, totalweight, numtype2hits, totaltype2weight, numpairs, totalpairweight, aligndir, alignfile, idxfile, collabalignid from seqalignment where expt=?";
		return c.prepareStatement(query);
	}

	public static PreparedStatement createLoadAllByGenomeStatement(java.sql.Connection c) throws SQLException { 
		String query = "select id, expt, name, genome, permissions, aligntype, numhits, totalweight, numtype2hits, totaltype2weight, numpairs, totalpairweight, aligndir, alignfile, idxfile, collabalignid from seqalignment where genome=?";
		return c.prepareStatement(query);
	}

	public static PreparedStatement createLoadAllByExptAndGenomeStatement(java.sql.Connection c) throws SQLException { 
		String query = "select id, expt, name, genome, permissions, aligntype, numhits, totalweight, numtype2hits, totaltype2weight, numpairs, totalpairweight, aligndir, alignfile, idxfile, collabalignid from seqalignment where expt=? and genome=?";
		return c.prepareStatement(query);
	}
	
	public static PreparedStatement createInsertStatement(java.sql.Connection c) throws SQLException { 
		String query = String.format(
				"insert into seqalignment (expt, name, genome, permissions, aligntype, numhits, totalweight, numtype2hits, totaltype2weight, numpairs, totalpairweight, aligndir, alignfile, idxfile, collabalignid) " +
				"values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)");
		return c.prepareStatement(query);
	}
	
	public static PreparedStatement createInsertStatementWithID(java.sql.Connection c) throws SQLException { 
		String query = String.format(
				"insert into seqalignment (id, expt, name, genome, permissions, aligntype, numhits, totalweight, numtype2hits, totaltype2weight, numpairs, totalpairweight, aligndir, alignfile, idxfile, collabalignid) " +
				"values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)");
		return c.prepareStatement(query);
	}
	
	public static PreparedStatement createUpdateStatementWithID(java.sql.Connection c) throws SQLException { 
		String query = String.format(
				"update seqalignment set expt=?, name=?, genome=?, permissions=?, aligntype=?, numhits=?, totalweight=?, numpairs=?,  numtype2hits=?, totaltype2weight=?, totalpairweight=?, aligndir=?, alignfile=?, idxfile=?, collabalignid=? " +
				" where id=?");
		return c.prepareStatement(query);
	}
	
	public static PreparedStatement createUpdatePermissions(java.sql.Connection c) throws SQLException { 
		String query = "update seqalignment set permissions=? where id=?";
		return c.prepareStatement(query);
	}
	
	public static PreparedStatement createUpdatePermissionsByExpt(java.sql.Connection c) throws SQLException { 
		String query = "update seqalignment set permissions=? where expt=?";
		return c.prepareStatement(query);
	}
	
	public static PreparedStatement createUpdateHitsAndWeights(java.sql.Connection c) throws SQLException { 
		String query = "update seqalignment set numhits=?, totalweight=?,  numtype2hits=?, totaltype2weight=?, numpairs=?, totalpairweight=? where id=?";
		return c.prepareStatement(query);
	}
	
	public static PreparedStatement createDeleteByIDStatement(java.sql.Connection c) throws SQLException { 
		String query = "delete from seqalignment where id=?";
		return c.prepareStatement(query);
	}
	
}