asivache 9ec96414c7 git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@114 348d0f76-0448-11de-a6fe-93d51630548a		2009-03-20 15:54:29 +00:00
..
DiscardingPileReceiver.java	a trivial interface and even more trivial implementations that do nothing (ignore the data they receive)	2009-03-20 05:08:15 +00:00
DiscardingReceiver.java	a trivial interface and even more trivial implementations that do nothing (ignore the data they receive)	2009-03-20 05:08:15 +00:00
Indel.java	Indel also implements Interval interface but has its quirks	2009-03-20 05:11:17 +00:00
IndelInspector.java	git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@114 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-20 15:54:29 +00:00
IndelRecordPileCollector.java	git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@114 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-20 15:54:29 +00:00
IndexedSequence.java	Sequence bundled with its Kmer-based lookup index (same thing as old lookup table)	2009-03-16 21:52:57 +00:00
IntervalComparator.java	comparator for interval objects	2009-03-20 05:15:13 +00:00
KmerCodeIterator.java	Walks along the sequence and emits a sequence of subsequent, encoded Kmers (uses short int, so currently it's up to K=8)	2009-03-16 21:54:45 +00:00
Matrix.java	just a square matrix of arbitrary stuff; the stuff must be full fledged Java type, however, not a primitive type. Hooray Java!	2009-03-16 21:56:45 +00:00
MultipleAlignment.java	removed unnecessary import that produced a warning. where did it come from in the first place??	2009-03-17 15:46:27 +00:00
PairwiseAlignment.java	this class really computes (and keeps) a gapless pairwise alignment between the two sequences, ILT-style	2009-03-16 21:59:26 +00:00
PileBuilder.java	git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@114 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-20 15:54:29 +00:00
RecordPileReceiver.java	a trivial interface and even more trivial implementations that do nothing (ignore the data they receive)	2009-03-20 05:08:15 +00:00
RecordReceiver.java	a trivial interface and even more trivial implementations that do nothing (ignore the data they receive)	2009-03-20 05:08:15 +00:00
StrictlyUpperTriangularMatrix.java	matrix as the name suggests; utilizes special property (zeros at diagonal and below) to use less memory at the expense of slower access; this one is built directly on primitive data type (double) so it should not have any overhead associated with java classes	2009-03-16 22:01:53 +00:00