[Biojava-l] SymbolTokenization patch
Thomas Down
td2@sanger.ac.uk
Tue, 16 Oct 2001 15:11:35 +0100
Here's a list of files which got changed in the patch.
This includes new files, and old files which have been
deleted. Note that in many cases, the changes are rather
small, so don't worry too much if you see your favourite
class has changed...
Thomas.
diff -urN biojava-live/src biojava-symtoke/src | grep "^+++" | grep -v "CVS"
+++ biojava-symtoke/src/org/biojava/bio/dp/FlatModel.java Tue Oct 16 12:55:38 2001
+++ biojava-symtoke/src/org/biojava/bio/dp/XmlMarkovModel.java Tue Oct 16 12:55:38 2001
+++ biojava-symtoke/src/org/biojava/bio/gui/StackedLogoPainter.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/gui/TextBlock.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/gui/TextLogoPainter.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/gui/sequence/FilteringRenderer.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/gui/sequence/PaddingRenderer.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/gui/sequence/SequencePanel.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/gui/sequence/SymbolSequenceRenderer.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/program/Meme.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/program/das/DASGFFParser.old Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/program/das/DASRawSymbolList.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/program/das/FeatureFetcher.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/program/das/FeatureRequestManager.old Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/program/phred/PhredFormat.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/program/phred/PhredTools.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/program/search/FastaSearchBuilder.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/program/ssbind/BlastLikeHomologyBuilder.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/program/ssbind/BlastLikeSearchBuilder.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/proteomics/Digest.java Tue Oct 16 12:55:41 2001
+++ biojava-symtoke/src/org/biojava/bio/proteomics/MassCalc.java Tue Oct 16 12:55:41 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/CircularSequence.java Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/CircularView.java Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/DNATools.java Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/ProjectedComponentFeatureWrapper.java.old Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/ProteinTools.java Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/RNATools.java Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/db/EmblCDROMIndexStore.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/db/IndexStore.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/db/IndexedSequenceDB.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/db/TabIndexStore.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/impl/AssembledSymbolList.java Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/CharacterTokenization.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/ChunkedSymbolListBuilder.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/CrossProductSymbolNameParser.java Thu Jan 1 01:00:00 1970
+++ biojava-symtoke/src/org/biojava/bio/seq/io/CrossProductTokenization.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/DefaultDescriptionReader.java.old Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/DoubleTokenization.java Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/EmblFileFormer.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/EmblFormat.java.old Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/EmblLikeFormat.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/FastaDescriptionReader.java.old Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/FastaFormat.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/FastaFormat.java.old Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/FeatureBuilder.java.old Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/FixedWidthParser.java Thu Jan 1 01:00:00 1970
+++ biojava-symtoke/src/org/biojava/bio/seq/io/GenbankFileFormer.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/GenbankFormat.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/IntegerParser.java Thu Jan 1 01:00:00 1970
+++ biojava-symtoke/src/org/biojava/bio/seq/io/IntegerTokenization.java Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/MSFAlignmentFormat.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/NameParser.java Thu Jan 1 01:00:00 1970
+++ biojava-symtoke/src/org/biojava/bio/seq/io/NameTokenization.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/ProteinRefSeqFileFormer.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/SeqIOTools.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/SequenceFormat.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/SimpleFeatureBuilder.java.old Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/StreamReader.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/SwissprotFileFormer.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/SymbolParser.java Thu Jan 1 01:00:00 1970
+++ biojava-symtoke/src/org/biojava/bio/seq/io/SymbolTokenization.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/TokenParser.java Thu Jan 1 01:00:00 1970
+++ biojava-symtoke/src/org/biojava/bio/seq/io/WordTokenization.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/io/game/GAMEResiduesPropHandler.java Tue Oct 16 12:55:39 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/ragbag/RagbagEmblParser.java Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/seq/ragbag/RagbagGenbankParser.java Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/symbol/AbstractAlphabet.java Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/symbol/AbstractSymbolList.java Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/symbol/AllTokensAlphabet.java Thu Jan 1 01:00:00 1970
+++ biojava-symtoke/src/org/biojava/bio/symbol/Alphabet.java Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/symbol/AlphabetIndex.html Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/symbol/AlphabetManager.java Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/symbol/DoubleAlphabet.java Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/symbol/EmptyAlphabet.java Tue Oct 16 12:55:41 2001
+++ biojava-symtoke/src/org/biojava/bio/symbol/IndexCrossProductAlphabet.java,.devel Tue Oct 16 12:55:41 2001
+++ biojava-symtoke/src/org/biojava/bio/symbol/InfiniteCrossProductAlphabet.java Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/symbol/IntegerAlphabet.java Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/symbol/SimpleAlphabet.java Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/symbol/SimpleCrossProductAlphabet.java Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/symbol/SimpleSymbolList.java Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/symbol/SingletonAlphabet.java Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/symbol/SparseCrossProductAlphabet.java Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/bio/symbol/Symbol.java Tue Oct 16 12:55:40 2001
+++ biojava-symtoke/src/org/biojava/utils/ActivityListener.java Tue Oct 16 12:55:42 2001
+++ biojava-symtoke/src/org/biojava/utils/ChangeType.java.old Tue Oct 16 12:55:41 2001
+++ biojava-symtoke/src/org/biojava/utils/stax/StAXContentHandler.java Tue Oct 16 12:55:41 2001