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## Package org.biojava.bio.program.ssaha

SSAHA sequence searching API.

See:
Description

Interface Summary
DataStore | A repository that can be searched with a sequence.
DataStoreFactory | Builder for a data store.
SearchListener | The interface used to inform interested parties that some sequence has been searched and something found.
SequenceStreamer |

Class Summary
CompactedDataStore | An implementation of DataStore that will map onto a file using the NIO constructs.
CompactedDataStoreFactory | Builder for a data store that is backed by a java.nio.MappedByteBuffer.
HitMerger | A listener that merges overlapping hits and culls all hits under a given length.
MappedDataStoreFactory | Builder for a data store that is backed by a java.nio.MappedByteBuffer.
NIODataStoreFactory | Builder for a datastore that has no practical file size limit.
SearchListener.Echo | A SearchListener that prints events out to a PrintStream.
SearchListener.FilterByLength | A simple listener that filters out all hits that are too short.
SearchListener.Tee | A SearchListener that passes events on to two delegate listeners.
SearchListener.Wrapper | A simple wrapper implementation.
SequenceStreamer.FileStreamer |
SequenceStreamer.SequenceDBStreamer |

Exception Summary
SearchException | There has been some failure that prevents a search from completing.

## Package org.biojava.bio.program.ssaha Description

SSAHA sequence searching API.

## Overview

SSAHA is Sequence Searching Algorithm by Hashing. The idea is to take a sequence database, such as EMBL, walk over all of the sequences using a window size and step size, represent each of these same-sized fragments as a bit-string, and use the bit-string as an index into a hash-table. The hash-table is used to store the location of every window (sequence and position). Search sequences are encoded as bit-patterns in the same manner, and then this is used as an index into the table to fetch all hits. Finaly, these hits are sorted and potentialy merged to produce HSPs.

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