[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