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Commits on Jan 24, 2013
Adding a plain fasta header parser for atypical data header formats
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aalhossary
Commits on Nov 19, 2012
Typo and format
Show description for 69dca43committedaalhossaryTypo and format
Show description for ebabdbecommittedaalhossaryfixing a warning, by closing InputStream
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Commits on Nov 13, 2012
keeping a Deprecated stub to getConsituents() in order not t break old codes
Show description for 8f03b3fcommittedaalhossaryTypo correction
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Commits on Apr 30, 2012
default color is green not black
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Commits on Mar 27, 2012
Adding CasePreservingProteinSequenceCreator, which stores the case of the input string in the ProteinSequence user collection
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Commits on Feb 27, 2012
added another method to QualityFeature; also some javadoc
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Commits on Feb 26, 2012
fixed a typo in QualityFeature
Show description for 9e72740committedbrandstaetteradded a QualityFeature to hold quality information in DNASequences
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Commits on Feb 11, 2012
NCBIQBlastService replaced with the new implementation.
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Commits on Feb 8, 2012
adding patch from Hannes
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Commits on Jan 16, 2012
Simplified boolean expressions.
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Commits on Jan 11, 2012
Removed the case where length= at the end of a header would get parsed out. Requested by Hannes Brandstätter-Müller <biojava@hannes.oib.com>
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Commits on Jan 10, 2012
Changed instances of String concatenation in StringBuffer to use append.
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Commits on Dec 15, 2011
replacing < and > with < and > in order not to break HTML and enable generating .CHM files using http://jan.baresovi.cz/dr/en/javadoc-chm
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Commits on Oct 12, 2011
Fix Bug #3305 for not closing open file
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Commits on Oct 8, 2011
Added some documentation to functions that take 1-based indices, although there are definitely more which need documentation.
Show description for 4a202f6committedblivensAdded the ability to fetch AminoAcidCompounds by 3 letter names
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Commits on Sep 21, 2011
moving from test section to main section
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Commits on Sep 19, 2011
moving StringManipulationTestsHelper to org.biojava3.core.util
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Commits on Aug 31, 2011
cleaning up some javadoc warnings
Show description for 236454ecommittedandreascleaning up some javadoc
Show description for 3b20d0dcommittedandreascleaning up some javadoc
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Commits on Aug 16, 2011
Improved Exception documentation in FastaReader
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Commits on Apr 21, 2011
Clearing up something which has been wrong for some time. The code changed an init met even without looking at if the codon was an initiator
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Commits on Mar 31, 2011
Put BufferedOutputStream at FastaWriterHelper and made FastaWriter generic.
Show description for 144da15committedhwillisAdded handling of BufferedOutputStream in FastaWriter. If the outputstream passed in is not Buffered then create one use it and then flush.
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Commits on Mar 30, 2011
Added handling of BufferedOutputStream in FastaWriter. If the outputstream passed in is not Buffered then create one use it and the close it.
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Commits on Mar 11, 2011
Equality now added to backing stores & compounds. SequenceMixin now has a method for assessing sequence equality
Show description for 778ee18committedayatesBugzilla 3180 applied. Frame parameter was ignored by code
Show description for 9a43d7ecommittedayatesBug fix for dealing with X amino acids during translation. Submitted by Brad Chapman. Patch available at https://gist.github.com/864088. Many thanks.
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Commits on Mar 1, 2011
Added setLineSeperator(String line) to FastaWriter to allow user to set CRLF or LF. Currently using operating system line.separator
Show description for 5c21f09committedhwillis