Package ubic.gemma.persistence.util

Class SequenceBinUtils

java.lang.Object

ubic.gemma.persistence.util.SequenceBinUtils

public class SequenceBinUtils
extends Object

Used to assign a bin to a chromosome location, identify bins for a range, or to generate SQL to add to a query on a GoldenPath database. Directly ported from Jim Kent's binRange.c and hdb.c.

Author:

pavlidis

Constructor Summary

Constructors

Constructor	Description
SequenceBinUtils()

Method Summary

Modifier and Type	Method	Description
static String	addBinToQuery(String table, Long start, Long end)	Directly ported from jksrc binRange.c and hdb.c From the binRange.c comments: There's a bin for each 128k segment, for each 1M segment, for each 8M segment, for each 64M segment, and for each chromosome (which is assumed to be less than 512M.) A range goes into the smallest bin it will fit in.
static int	binFromRange(int start, int end)	return bin that this start-end segment is in

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SequenceBinUtils

public SequenceBinUtils()

Method Detail

addBinToQuery

public static String addBinToQuery(String table,
                                   Long start,
                                   Long end)

Directly ported from jksrc binRange.c and hdb.c From the binRange.c comments: There's a bin for each 128k segment, for each 1M segment, for each 8M segment, for each 64M segment, and for each chromosome (which is assumed to be less than 512M.) A range goes into the smallest bin it will fit in.

Parameters:

table - The alias of the table (SQL) or class (HQL)

start - start

end - end

Returns:

clause that will restrict to relevant bins to query. This should be ANDed into your WHERE clause.

binFromRange

public static int binFromRange(int start,
                               int end)

return bin that this start-end segment is in

Parameters:

start - start

end - end

Returns:

bin