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.
Interface Summary Interface Description DataStoreA repository that can be searched with a sequence. DataStoreFactoryBuilder for a data store. SearchListenerThe interface used to inform interested parties that some sequence has been searched and something found. SequenceStreamer
Class Summary Class Description CompactedDataStoreAn implementation of DataStore that will map onto a file using the NIO constructs. CompactedDataStoreFactoryBuilder for a data store that is backed by a java.nio.MappedByteBuffer. HitMergerA listener that merges overlapping hits and culls all hits under a given length. MappedDataStoreFactoryBuilder for a data store that is backed by a java.nio.MappedByteBuffer. NIODataStoreFactoryBuilder for a datastore that has no practical file size limit. SearchListener.EchoA SearchListener that prints events out to a PrintStream. SearchListener.FilterByLengthA simple listener that filters out all hits that are too short. SearchListener.TeeA SearchListener that passes events on to two delegate listeners. SearchListener.WrapperA simple wrapper implementation. SequenceStreamer.FileStreamer SequenceStreamer.SequenceDBStreamer
Exception Summary Exception Description SearchExceptionThere has been some failure that prevents a search from completing.