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Closeable and
sending any error to the logger but not forcing any explicit catching of
stream errors.
SequenceMixin#countCompounds(org.biojava3.core.sequence.template.Sequence, C[])
Integer.
BitSequenceReader.BitArrayWorker.generateCompoundsToIndex()
returns i.e. if the Compound C returns 1 from compoundsToIndex then we
should find that compound here in position 1
Sequence at given index.
List containing the individual Sequences of this alignment.
Frame.values()
SequenceMixin.toList(org.biojava3.core.sequence.template.Sequence)
Compound elements of the original Sequences at the given column.
CompoundSet of all Sequences
SequenceMixin.getComposition(Sequence) but returns the
distribution of that Compound over the given sequence.
IOUtils.getList(BufferedReader) by wrapping the InputStream
in a valid reader.
IOUtils.getList(InputStream) by wrapping the File
in a valid stream.
Location.getSubLocations() which returns sub-locations
of sub-locations; this will continue until it runs out of those locations.
AbstractSequence.getInverse() for the reverse complement
SequenceMixin.toList(org.biojava3.core.sequence.template.Sequence)
SequenceProxyView for the given coordinates
Float.floatToIntBits(float) which allows
the encoding of a float as an int.
o is a possibly-null object field, and possibly an
array.
IOUtils#processReader(String).SequenceMixin.SequenceIterator
ReversedSequenceView and passing it into
SequenceMixin.indexOf(Sequence, Compound).
LocationHelper.location(java.util.List, java.lang.String)
method to bring the given location list together as a join (the default
type)
BitSequenceReader.BitArrayWorker.setCompoundAt(Compound, int)
BitSequenceReader.BitArrayWorker.setCompoundAt(char, int)
Sequence of NucleotideCompound which should
represent an RNA sequence (RNASequence is good for this) and returns
a list of Sequence which hold AminoAcidCompound.hashCode, to which we add
contributions from fields.
ThreadPoolExecutor to allow use of an alternative execution style.
Sequence into a List, applying
Collections.shuffle(List) and then returning the shuffled
elements in a new instance of SequenceBackingStore which behaves
as a Sequence.
IUPACTable even
though this is the only implementing class for the interface.IUPACParser to find instances of
IUPACParser.IUPACTables by ID.
IUPACParser to find instances of
IUPACParser.IUPACTables by its String name
NucleotideCompounds, its
corresponding AminoAcidCompound and if it is a start or stop codon.Sequence this will return a List filled with
the Compounds of that Sequence.
SequenceMixin.toStringBuilder(org.biojava3.core.sequence.template.Sequence)
which calls toString() on the resulting object.
StringBuilder object
filled with the results of Compound#toString().
TranslationEngine.Sequence because they do not fit how this works.RnaSequenceView as a
ProxySequenceReader.
OutputStream.
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