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 _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
